gebhart/patrepeval huggingface dataset:
Inertia-Controlled Ambipolar Diffusion (1962)

The general nonlinear ambipolar-flow equations are derived and discussed. The important non-linearities are caused by the inertia of the ions and by the heat-conduction mechanism. It is shown that all essential effects associated with these nonlinearities can be demonstrated in the plane-parallel case. The influence of the nonlinearity caused by the inertia is discussed in detail for the plane-parallel case and it is shown that this flow is analogous to the flow of a fluid with friction through a contracting nozzle. The limiting velocity—the isothermal or the adiabatic sound velocity—which is found in the exit of a nozzle is also found at the boundary in the case of inertia-controlled diffusion, provided this boundary acts like a perfect sink. Bohm's criterion—the ion drift velocity less than or equal to the sound velocity of the electron-ion gas in front of the boundary or the wall sheath—appears as an integral part of the inertia-controlled-diffusion theory. In the inertia-controlled-diffusion theory are incorporated, as integral parts, all the assumptions that necessarily must be added to the linear-diffusion theory in order to make it realistic. The isothermal and inertia-controlled diffusion leads always to wall-stabilized plasma configurations which directly correspond to the fundamental mode solution in the linear-diffusion theory.
Exercise-induced muscle damage (1995)

The purpose of this study was to determine the effect of downhill and level running on circulating leukocyte and lymphocyte subsets and T lymphocyte activation. Using a random cross-over design, 10 runners completed two trials of 60 min of level running (0% grade; LR) and downhill running (-10% grade; DHR) at 70% of level VO2max. Blood samples were obtained preexercise and immediately postexercise (POST) and at 1.5, 12, 24, and 48 h of recovery. Creatine kinase activity peaked at 12 h of recovery from DHR and was not significantly altered following LR. The number of total T, CD16+, CD3+CD56+ cells were significantly higher POST DHR compared with LR. Leukocyte and neutrophil counts were significantly higher at 1.5 and 12 h of recovery from DHR compared with LR. The number of activated CD8+ cells (CD25+ CD8+) was significantly higher at 12 h of DHR compared to LR. Total T cells were significantly reduced at various time points during the 48 h of recovery from LR and DHR. In summary, DHR relative to LR resulted in a greater mobilization of lymphocytes (post), neutrophils (1.5-12 h of recovery) and activation of CD8+ cells at 12 h of recovery. In addition, reductions in circulating T lymphocyte subsets occurred following both conditions.
THE EFFECT OF RENAL DENERVATION ON THE LEVEL OF ARTERIAL BLOOD PRESSURE AND RENAL FUNCTION IN ESSENTIAL HYPERTENSION (1935)

Hypertension is one of the most frequent com- plications of renal disease, both acute and chronic. The fact that in nephritis renal influences, nervous or other, apparently produce hypertension sug- gests the possibility that the unknown cause of essential hypertension may lie in nervous im- pulses from the kidney, even though the kidneys themselves appear to be entirely normal at the onset of the hypertension.
2‐Hydroxyglutaryl‐CoA dehydratase from Clostridium symbiosum (1999)

Component D (HgdAB) of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum was purified to homogeneity. It is able to use component A from Acidaminococcus fermentans (HgdC) to initiate catalysis together with ATP, Mg2+ and a strong reducing agent such as Ti(III)citrate. Component D from C. symbiosum has a 6 x higher specific activity compared with that from A. fermentans and contains a second [4Fe-4S] cluster but the same amount of riboflavin 5'-phosphate (1.0 per heterodimeric enzyme, m = 100 kDa). Mössbauer spectroscopy revealed symmetric cube-type structures of the two [4Fe-4S]2+ clusters. EPR spectroscopy showed the resistance of the clusters to reducing agents, but detected a sharp signal at g = 2. 004 probably due to a stabilized flavin semiquinone. Three genes from C. symbiosum coding for components D (hgdA and hgdB) and A (hgdC) were cloned and sequenced. Primer extension experiments indicated that the genes are transcribed in the order hgdCAB from an operon only half the size of that from A. fermentans. Sequence comparisons detected a close relationship to the dehydratase system from A. fermentans and HgdA from Fusobacterium nucleatum, as well as to putative proteins of unknown function from Archaeoglobus fulgidus. Lower, but significant, identities were found with putative enzymes from several methanogenic Archaea and Escherichia coli, as well as with the mechanistically related benzoyl-CoA reductases from the Proteobacteria Rhodopseudomonas palustris and Thauera aromatica.
Spatial organization of cardiac gap junctions can affect access resistance (1995)

In the heart, gap junctions electrically couple myocytes together. Electron- and light-microscope-based analyses have revealed that cardiac gap junctions show a variety of organizational patterns. At the level of gap-junctional channel aggregates, freeze fracture has demonstrated diverse channel packing arrangements in the membranes of different myocardial tissues. Ultrastructural and immunohistochemical studies have shown variation and specialization in the 3-dimensional spatial distribution of gap junctional contacts between different types of myocardial cells. Here, we estimate the access resistance of various configurations of gap junctions using physical principles and explore how certain of these specializations in gap-junctional organization may influence access resistance, a potentially important determinant of electrical conductance between coupled myocardial cells.
The gastric H+,K+‐ATPase (1990)

Mammalian extramitochondrial pumps can be divided into two different classes: the vacuolar H(+)-ATPases, which are responsible for acidification of intracellular compartments, and the E1E2-type of ATPases, which are represented by the Na+,K(+)-ATPase, the Ca2(+)-ATPase and the gastric H+,K(+)-ATPase. The latter enzyme is confined to the tubulovesicles and to the secretory membranes of the parietal cell and has been shown to be the proton pump of the gastric mucosa. The H+,K(+)-ATPase carries out the electroneutral exchange of H+ and K+ and thereby generates a pH of less than 1 in the secretory canaliculus. For this process to occur, the enzyme must be activated by extracytosolic potassium ions. These ions reach the parietal cell luminal space by a secretagogue-induced stimulation of a KCl pathway in the secretory membrane of the parietal cell. Kinetic studies in isolated ion-tight and ion-permeable gastric vesicles have shown that intravesicular K+ stimulates the ATPase activity and accelerates the breakdown of the phosphorylenzyme intermediate formed during the catalytic cycle of the H+,K(+)-ATPase. Thus the stimulation of the ATPase activity by K+ is due to an increased rate of hydrolysis of phosphoenzyme. When the ATPase activity was analysed in permeable vesicles and at high K+ concentrations, the ATPase activity was inhibited. In contrast, when the overall ATPase activity was analysed in ion-tight vesicles, which developed an intravesicular positive potential in the presence of valinomycin, no inhibition of the ATPase activity was observed.(ABSTRACT TRUNCATED AT 250 WORDS)
Juvenile Hormone: Activity of Aromatic Terpenoid Ethers (1969)

Several aromatic terpenoid ethers possess a high degree of morpho-genetic activity when assayed on the yellow mealworm Tenebrio molitor L. and the milkweed bug Oncopeltus fasciatus (Dallas). The most active compounds were the 3,4-methylenedioxy-phenyl ethers of 6,7-epoxygeraniol and the corresponding ethyl-branched homologs.
The Inhibitory Effect of Calumenin on the Vitamin K-dependent γ-Carboxylation System (2004)

The vitamin K-dependent gamma-carboxylation system is responsible for post-translational modification of vitamin K-dependent proteins, converting them to Gla-containing proteins. The system consists of integral membrane proteins located in the endoplasmic reticulum membrane and includes the gamma-carboxylase and the warfarin-sensitive enzyme vitamin K(1) 2,3-epoxide reductase (VKOR), which provides gamma-carboxylase with reduced vitamin K(1) cofactor. In this work, an in vitro gamma-carboxylation system was designed and used to understand how VKOR and gamma-carboxylase work together as a system and to identify factors that can regulate the activity of the system. Results are presented that demonstrate that the endoplasmic reticulum chaperone protein calumenin is associated with gamma-carboxylase and inhibits its activity. Silencing of the calumenin gene with siRNA resulted in a 5-fold increase in gamma-carboxylase activity. The results provide the first identification of a protein that can regulate the activity of the gamma-carboxylation system. The propeptides of vitamin K-dependent proteins stimulate gamma-carboxylase activity. Here we show that the factor X and prothrombin propeptides do not increase reduced vitamin K(1) cofactor production by VKOR in the system where VKOR is the rate-limiting step for gamma-carboxylation. These findings put calumenin in a central position concerning regulation of gamma-carboxylation of vitamin K-dependent proteins. Reduced vitamin K(1) cofactor transfer between VKOR and gamma-carboxylase is shown to be significantly impaired in the in vitro gamma-carboxylation system prepared from warfarin-resistant rats. Furthermore, the sequence of the 18-kDa subunit 1 of the VKOR enzyme complex was found to be identical in the two rat strains. This finding supports the notion that different forms of genetic warfarin resistance exist.
The SH2 Domain-containing Tyrosine Phosphatase PTP1D Is Required for Interferon α/β-induced Gene Expression (1996)

Interferons (IFNs) induce early response genes by stimulating Janus family (Jak) tyrosine kinases, leading to tyrosine phosphorylation of Stat (signal transducer and activator of transcription) proteins. Previous studies demonstrated that a protein-tyrosine phosphatase (PTP) is required for activation of the ISGF3 transcription complex by IFNalpha/beta, but the specific PTP responsible remained unidentified. We now show that the SH2 domain containing tyrosine phosphatase PTP1D (also designated as SHPTP2, SHPTP3, PTP2C, or Syp) is constitutively associated with the IFNalpha/beta receptor and becomes tyrosine-phosphorylated in response to ligand. Furthermore, transient expression of a phosphatase-inactive mutant or the COOH-terminal SH2 domain of PTP1D causes a dominant negative effect on IFNalpha/beta-induced early response gene expression. These results provide strong evidence that PTP1D functions as a positive regulator of the IFNalpha/beta-induced Jak/Stat signal transduction pathway.
Recent developments in the anemia of chronic disease. (2003)

The anemia of chronic disease (ACD) is a hypoproliferative anemia defined by a low serum or plasma iron concentration in the presence of adequate reticuloendothelial iron stores. It is been established that ACD results from the effects of cytokines that mediate the immune or inflammatory response. During the past 3 years, the clinical scope of this syndrome has been expanded beyond the traditional chronic infectious, inflammatory, or neoplastic diseases to include other, often acute, syndromes in which the same pathogenetic mechanisms are operating. An improved understanding of the use of the soluble transferrin receptor concentration in clinical medicine has enhanced the ability to diagnose ACD, and further experience with the use of recombinant human erythropoietin in the management of severely affected patients with ACD has provided a basis for rational and effective management. Ongoing studies of the mechanisms contributing to the development of ACD continue to elucidate the pathogenesis of this common and clinically significant syndrome.
Prediction of response to treatment in superficial bladder carcinoma through pattern of interleukin-2 gene expression. (1996)

IL-2 gene expression is essential for mounting an antitumor response in superficial bladder carcinoma. Inducibility of IL-2 mRNA is an independent prognostic parameter and useful predictive indicator of remission versus relapse.
Identification of a Specialized Adenylyl Cyclase That May Mediate Odorant Detection (1990)

The mammalian olfactory system may transduce odorant information via a G protein-mediated adenosine 3',5'-monophosphate (cAMP) cascade. A newly discovered adenylyl cyclase, termed type III, has been cloned, and its expression was localized to olfactory neurons. The type III protein resides in the sensory neuronal cilia, which project into the nasal lumen and are accessible to airborne odorants. The enzymatic activity of the type III adenylyl cyclase appears to differ from nonsensory cyclases. The large difference seen between basal and stimulated activity for the type III enzyme could allow considerable modulation of the intracellular cAMP concentration. This property may represent one mechanism of achieving sensitivity in odorant perception.
Ultrasound thermography in vivo: A new model for calculation of temperature change in the presence of temperature heterogeneity (2013)

A new derivation of the temperature change estimation based on speckle-tracking estimation of axial echo shifts is presented which accounts for the nonuniform temperature baseline. The new method includes the spatial gradient of the temperature change in the thermal strain equation. In contrast to the previous method where thermal strain was calculated by accumulating the incremental displacement and differentiating along the axial direction, the solution to the new equation is shown to be found by using a differentiation-integration operator along the axial direction. Using a diagnostic probe and a High Intensity Focused Ultrasound (HIFU) transducer in Dual Mode Ultrasound Array (DMUA) setup the displacement data was collected from sub-therapeutic shots on the hind limb of a Copenhagen rat. The results of applying the new method showed a temperature change in a 2 mm axial extend which was consistent with the field scan pattern of the HIFU array.
Placenta Derived Adherent Cells (PDACs) Suppress Tumor Cells of Diverse Origin. (2006)

Abstract The placenta is a readily available and ethically non-controversial source of large amounts of therapeutic stem cells. We isolated adherent cells from the Umbilical Cord (UC) and the Amnion Chorion (AC) of term placentas. These Placenta Derived Adherent Cells (PDACs) displayed a cell surface phenotype of CD29+, CD44+, CD73+, CD90+, CD105+, CD200+, CD34−, and constitutively secreted IL-6, IL-8 and Monocyte Chemoattractant protein-1 (MCP-1). PDACs demonstrated in vitro pluripotency and suppressed T cell proliferation in both the allogeneic mixed leukocyte reaction, and the autologous EBV regression assay. Because progenitor cells have been described to inhibit tumor growth in some systems, the role of PDACs in tumor suppression was investigated. EBV transformed tumor cells were cultured either alone, or with AC or UC PDACs. After 6 days, live (7-AAD− Annexin-V−) tumor cells were counted on a flow cytometer. Free growing tumor cells numbered 40,000. When tumor cells were co-cultured with AC or UC PDACs, the growth was suppressed to 10,000 cells, a suppression of 75%. We designed and tested a panel of tumor cell lines that included retinoblastoma (RB), histiocytic lymphoma (HL), chronic myelogenous leukemia (CML), and colon adenocarcinoma (CAC). The tissue origin of the selected tumor cell lines included neuronal tissue (retinoblastoma), epithelium (carcinomas) and the hematopoietic lineage (lymphomas and CML). Co-culture experiments showed that the growth of all tumor lines was suppressed more than 40%. When a transwell was introduced separating PDACs and tumor cells, contact dependency of suppression was 12% for HL, 22% for CML, 42% for CAC, and 51% for EBV transformed tumor cells. These results indicate that PDACs may have therapeutic value with respect to certain cancers.
Mechanism of antibody reduction in cell culture production processes (2010)

We recently observed a significant disulfide reduction problem during the scale-up of a manufacturing process for a therapeutic antibody using a CHO expression system. Under certain conditions, extensive reduction of inter-chain disulfide bonds of an antibody produced by CHO cell culture may occur during the harvest operations and/or the protein A chromatography step, resulting in the observation of antibody fragments (light chain, heavy chain, and various combination of both) in the protein A pools. Although all conditions leading to disulfide reduction have not been completely identified, an excessive amount of mechanical cell lysis generated at the harvest step appears to be an important requirement for antibody reduction (Trexler-Schmidt et al., 2010). We have been able to determine the mechanism by which the antibody is reduced despite the fact that not all requirements for antibody reduction were identified. Here we present data strongly suggesting that the antibody reduction was caused by a thioredoxin system or other reducing enzymes with thioredoxin-like activity. The intracellular reducing enzymes and their substrates/cofactors apparently were released into the harvest cell culture fluid (HCCF) when cells were exposed to mechanical cell shear during harvest operations. Surprisingly, the reducing activity in the HCCF can last for a long period of time, causing the reduction of inter-chain disulfide bonds in an antibody. Our findings provide a basis for designing methods to prevent the antibody reduction during the manufacturing process.
Modelling electronegative discharges at low pressure (1996)

In a previous study, a macroscopic analytical model was developed for a plasma discharge with a three-component (electronegative) core and an electropositive edge region. Both regions were treated in the high-pressure approximation of constant mobility for the positive ions. We extend the treatment to low pressures, for which the ion thermal velocity within the electropositive region is much less than the ion flow velocity, by using a variable mobility model with constant mean free path for the positive ions. The density at the interface between the electropositive region and the sheath is determined by generalizing a low-pressure electropositive solution to a finite-flow boundary condition at the interface with the electronegative plasma. The results are also extended to include an additional transition region in which the flow within the electronegative region is not allowed to exceed the local ion sound speed, which can result in an abrupt decrease in negative ion density. The approximation of a parabolic negative ion profile results in algebraic equations which are solved numerically over a range of parameters. Typical cases are compared with particle-in-cell (PIC) Monte Carlo simulations.
Identification of Tuftelin-and Amelogenin-Interacting Proteins Using the Yeast Two-Hybrid System (1998)

Biomineralization of enamel is a complex process that involves the eventual replacement of an extracellular protein matrix by hydroxyapatite crystallites. To date four different enamel matrix proteins have been identified; the amelogenins, tuftelin, enamelin and ameloblastin. Assembly of the enamel extracellular matrix from these component proteins is believed to be critical in producing a matrix competent to undergo mineral replacement. Enamel formation is a complex process and additional proteins are likely to have a role in the assembly of the extracellular matrix. In order to identify additional proteins involved in the assembly process, the yeast two-hybrid system developed by Fields and Song (1989) has been implemented. This system allows for the identification of unknown proteins that interact with proteins of interest. Typically a known protein is used as "bait" to screen a cDNA expression library of interest. In our studies, tuftelin or amelogenin have been used to screen a mouse tooth library produced from one day old pups. A library screening of six million clones with amelogenin as bait resulted in eleven positive clones all of which show high homology to the human leukocyte antigen-B (HLA-B) associated transcript (BAT) family of genes. A library screening of one million clones using tuftelin as the bait identified twenty-one tuftelin-interacting proteins. Ten of these proteins are either keratin K5 or keratin K6, four are constitutively expressed and the remaining seven are novel. Further characterization of the proteins shown to interact with amelogenin or tuftelin may shed additional light on this complex process of enamel matrix assembly.
Stabilization of the Chemically Amplified Resist Process. (1995)

We approached the problem of airborne chemical contamination from the processing side. By applying a very hydrophobic, polyolefinic coating resin, we completely eliminated T-tops. Patterning a resist in a low ammonia concentration also eliminated T-tops and resulted in low line width deviation rates against PED. When we patterned the resist with an ammonia concentration of 0.2 .t g/m3, the deviation of the line width against PED was within the range 0.56 to 0.80 nm/min for line-and-space patterns between 0.30 and 0.35 m. These low deviation rates were considered to be acceptable for manufacturing purposes.
Cell-penetrating peptide conjugates of peptide nucleic acids (PNA) as inhibitors of HIV-1 Tat-dependent trans-activation in cells (2005)

The trans-activation response (TAR) RNA stem-loop that occurs at the 5' end of HIV RNA transcripts is an important antiviral target and is the site of interaction of the HIV-1 Tat protein together with host cellular factors. Oligonucleotides and their analogues targeted to TAR are potential antiviral candidates. We have investigated a range of cell penetrating peptide (CPP) conjugates of a 16mer peptide nucleic acid (PNA) analogue targeted to the apical stem-loop of TAR and show that disulfide-linked PNA conjugates of two types of CPP (Transportan or a novel chimeric peptide R6-Penetratin) exhibit dose-dependent inhibition of Tat-dependent trans-activation in a HeLa cell assay when incubated for 24 h. Activity is reached within 6 h if the lysosomotropic reagent chloroquine is co-administered. Fluorescein-labelled stably-linked conjugates of Tat, Transportan or Transportan TP10 with PNA were inactive when delivered alone, but attained trans-activation inhibition in the presence of chloroquine. Confocal microscopy showed that such fluorescently labelled CPP-PNA conjugates were sequestered in endosomal or membrane-bound compartments of HeLa cells, which varied in appearance depending on the CPP type. Co-administration of chloroquine was seen in some cases to release fluorescence from such compartments into the nucleus, but with different patterns depending on the CPP. The results show that CPP-PNA conjugates of different types can inhibit Tat-dependent trans-activation in HeLa cells and have potential for development as antiviral agents. Endosomal or membrane release is a major factor limiting nuclear delivery and trans-activation inhibition.