gebhart/patrepeval huggingface dataset:
Action of rolipram on specific PDE4 cAMP phosphodiesterase isoforms and on the phosphorylation of cAMP-response-element-binding protein (CREB) and p38 mitogen-activated protein (MAP) kinase in U937 monocytic cells (2000)

U937 monocytic cells are shown here to express a range of PDE4, cAMP-specific phosphodiesterase (PDE) isoenzymes: the long isoenzymes, PDE4A4, PDE4D5 and PDE4D3, plus the short isoenzyme, PDE4B2. These isoenzymes provide around 76% of the total cAMP PDE activity of U937 cells. The specific activities of the total PDE4A, PDE4B and PDE4D activities were 0.63+/-0.09, 8.8+/-0.2 and 34.4+/-2.9 pmol/min per mg of protein respectively. The PDE4 selective inhibitor, rolipram, inhibited immunopurified PDE4B and PDE4D activities similarly, with IC(50) values of approx. 130 nM and 240 nM respectively. In contrast, rolipram inhibited immunopurified PDE4A activity with a dramatically lower IC(50) value of around 3 nM. Rolipram increased phosphorylation of cAMP-response-element-binding protein (CREB) in U937 cells in a dose-dependent fashion, which implied the presence of both high affinity (IC(50) value approx. 1 nM) and low affinity (IC(50) value approx. 120 nM) components. Rolipram dose-dependently inhibited the interferon-gamma (IFN-gamma)-stimulated phosphorylation of p38 mitogen-activated protein (MAP) kinase in a simple monotonic fashion with an IC(50) value of approx. 290 nM. On this basis, it is suggested that rolipram inhibition of PDE4A4 is involved in regulating CREB phosphorylation but not IFN-gamma-stimulated p38 MAP kinase phosphorylation. PDE4A4 was also selectively activated by challenge of U937 cells with either bacterial lipopolysaccharide (LPS) or IFN-gamma through a process which was attenuated by both wortmannin and rapamycin. It is proposed that the PDE4A4 isoform is involved in compartmentalized cAMP signalling responses in U937 monocytes.
Reversion of the neoplastic phenotype of human glioblastoma cells by connexin 43 (cx43). (1998)

Connexins (cx), structural components of gap junction, are believed to play a role in the regulation of cell proliferation and suppression of the neoplastic phenotype. We used human brain glioblastoma tumor cells as a model system to test this hypothesis. Western blot and reverse transcription-PCR analysis indicate that the expression levels of the gap junction protein connexin 43 (cx43) are profoundly decreased in several human brain tumor cell lines examined. Transfection of human cx43 into human glioblastoma cell lines U251 and T98G profoundly reduces cell proliferation in monolayer culture, in soft agar, and in athymic nude mice. Surprisingly, these effects are not associated with the establishment of gap junction communication in cx43 transfected cells. We conclude that the loss of cx43 expression may play a role in the development of human gliomas and that cx43 acts as a tumor suppressor gene to human glioblastoma.
Application of the Circulating Moving Bed Process for CO2 Recovery from the Flue Gas of Coal-Thermal Power Plants. (2002)

石炭の燃焼排ガスからのCO2回収技術として，石炭火力発電所構内に50m3/hのテストプラントを設置して，物理吸着法・移動床循環再生方式の適応性を評価した．移動床循環再生方式は排ガスを，吸着材が充填されている吸着塔に連続的に通気してCO2を回収するシステムである．吸着材は再生塔に移動して加熱，減圧により再生されて，循環する．本プロセスの特徴はCO2回収のエネルギーが少なく，容易に高純度の回収CO2が得られることである．テストプラントの延運転時間は約8,500時間を達成している．また，520時間の連続運転を行った．その結果，長時間にわたりCO2回収率90%，回収CO2純度99%以上を確認し，本プロセスによるCO2回収は技術的には可能であるとの見通しを得た．CO2回収の消費エネルギーは電力消費量が263kWh/t-CO2，熱消費量が3.66× 106kJ/t-CO2であった．電力量は冷凍機，排ガスブロワー，熱量は再生塔加熱蒸気の消費量が多かった．なお，本プロセスは乾式であるため装置材料の腐食対策が不要で耐久性，保守性に優れ，かつ吸着材（ゼオライト）の安全性も高く，環境保全性が高い．
Genetics Underlying Atypical Parkinsonism and Related Neurodegenerative Disorders (2015)

Atypical parkinsonism syndromes, such as dementia with Lewy bodies, multiple system atrophy, progressive supranuclear palsy and corticobasal degeneration, are neurodegenerative diseases with complex clinical and pathological features. Heterogeneity in clinical presentations, possible secondary determinants as well as mimic syndromes pose a major challenge to accurately diagnose patients suffering from these devastating conditions. Over the last two decades, significant advancements in genomic technologies have provided us with increasing insights into the molecular pathogenesis of atypical parkinsonism and their intriguing relationships to related neurodegenerative diseases, fueling new hopes to incorporate molecular knowledge into our diagnostic, prognostic and therapeutic approaches towards managing these conditions. In this review article, we summarize the current understanding of genetic mechanisms implicated in atypical parkinsonism syndromes. We further highlight mimic syndromes relevant to differential considerations and possible future directions.
In-Situ Combustion Model (1980)

Abstract This paper describes a numerical model for simulating wet or dry, forward or reverse combustion in one, two, or three dimensions. The formulation is considerably more general than any reported to date. The model allows any number and identities of components. Any component may be distributed in any or all of the four phases (water, oil, gas, and solid or coke). The formulation allows any number of chemical reactions. Any reaction may have any number of reactants, products, and stoichiometry, identified through input data. The energy balance accounts for heat loss and conduction, conversion, and radiation within the reservoir. The model uses no assumptions regarding degree of oxygen consumption. The oxygen concentration is calculated throughout the reservoir in accordance with the calculated fluid flow pattern and reaction kinetics. The model, therefore, simulates the effects of oxygen bypassing caused by kinetic-limited combustion or conformance factors. We believe the implicit model formulation results in maximum efficiency (lowest computing cost), and required computing times are reported in the paper. The paper includes comparisons of model results with reported laboratory adiabatic-tube test results. In addition, the paper includes example field-scale cases, with a sensitivity study showing effects on oil recovery of uncertainties in rock/fluid properties.
Human Mitochondrial Hsp70 (Mortalin): Shedding Light on ATPase Activity, Interaction with Adenosine Nucleotides, Solution Structure and Domain Organization (2015)

The human mitochondrial Hsp70, also called mortalin, is of considerable importance for mitochondria biogenesis and the correct functioning of the cell machinery. In the mitochondrial matrix, mortalin acts in the importing and folding process of nucleus-encoded proteins. The in vivo deregulation of mortalin expression and/or function has been correlated with age-related diseases and certain cancers due to its interaction with the p53 protein. In spite of its critical biological roles, structural and functional studies on mortalin are limited by its insoluble recombinant production. This study provides the first report of the production of folded and soluble recombinant mortalin when co-expressed with the human Hsp70-escort protein 1, but it is still likely prone to self-association. The monomeric fraction of mortalin presented a slightly elongated shape and basal ATPase activity that is higher than that of its cytoplasmic counterpart Hsp70-1A, suggesting that it was obtained in the functional state. Through small angle X-ray scattering, we assessed the low-resolution structural model of monomeric mortalin that is characterized by an elongated shape. This model adequately accommodated high resolution structures of Hsp70 domains indicating its quality. We also observed that mortalin interacts with adenosine nucleotides with high affinity. Thermally induced unfolding experiments indicated that mortalin is formed by at least two domains and that the transition is sensitive to the presence of adenosine nucleotides and that this process is dependent on the presence of Mg2+ ions. Interestingly, the thermal-induced unfolding assays of mortalin suggested the presence of an aggregation/association event, which was not observed for human Hsp70-1A, and this finding may explain its natural tendency for in vivo aggregation. Our study may contribute to the structural understanding of mortalin as well as to contribute for its recombinant production for antitumor compound screenings.
Normal cerebral, renal and abdominal regional oxygen saturations using near-infrared spectroscopy in preterm infants (2010)

Daily baseline rSO(2) in preterm infants changes over the first weeks of life, especially at the abdomen. Evolution in baseline rSO2 over time may indicate regional developmental maturation of physiological oxygen balance.
Structural properties of hypertext (1998)

We provide a framework that allows one to study structural properties of hypertext in connection with formal language theory. We model hypertext as a transformation device (an atransducer) that transforms a link-following into a sequence of matched pairs: basic linkable units. Then, we address the following questions: What can hypertext do? What structure is formed when a link-following is done? What structure is built when a virtual document is constructed? We show that the set of all link-followingsin hypertext is a regular set. Then, the set of all possible outputs of link-followings is shown to be context-free, which means that constructing virtual documents is essentially same as generating words of a contextfree language.
An efficient method for identifying the initial position of a PMSM with an incremental encoder (1998)

This letter describes an efficient method for identifying the initial position of a permanent magnet synchronous motor (PMSM) with an incremental encoder, even when a brake and/or a constant load torque is being applied. The authors' method is more efficient in the respects of accuracy and reliability than the conventional method using commutation signals.
Transformation of tracheal epithelium exposed <i>in vitro</i> to N‐methyl‐N′‐nitro‐N‐nitrosoguanidine (MNNG) (1977)

Using an organ culture/cell culture system, we transformed rat tracheal epithelial cells in vitro by exposure to MNNG. Ten tracheal organ cultures per group were exposed twice (at days 3 and 6) to 0,0.001, 1.0 or 10.0 microgram MNNG/ml of medium. Following this exposure, the explants were placed on the bottom of culture dishes to initiate epithelial cell outgrowths and establish primary cultures. Each explant was replanted 8-10 times to produce multiple outgrowths. The number of primary cultures and the number of subsequently established cell lines obtained was carcinogen-dose-dependent. The average number of primary epithelial cell cultures per explant after exposure to 0, 0.001 1.0 and 10.0 microgram MNNG/ml was 1.3, 1.5, 3.3, and 4.6, respectively. The average yield of cell lines per explant in these groups was 0, 0.8, 1.3, and 2.0, respectively. It is apparent that cell lines could only be established from carcinogen-exposed epithelium. These cell lines are currently being tested for tumorigenicity in vivo. To date, of 35 cell lines tested between the 5th and 15th passages, 5 cell lines from the 10 microgram MNNG/ml group and 2 from the 1.0 microgram MNNG/ml group have produced palpable tumors upon injection into immunosuppressed recipients.
The Nonconserved Hinge Region and Distinct Amino-Terminal Domains of the RORα Orphan Nuclear Receptor Isoforms are Required for Proper DNA Bending and RORα-DNA Interactions (1995)

ROR alpha 1 and ROR alpha 2 are two isoforms of a novel member of the steroid-thyroid-retinoid receptor superfamily and are considered orphan receptors since their cognate ligand has yet to be identified. These putative receptors have previously been shown to bind as monomers to a DNA recognition sequence composed of two distinct moieties, a 3' nuclear receptor core half-site AGGTCA preceded by a 5' AT-rich sequence. Recognition of this bipartite hormone response element (RORE) requires both the zinc-binding motifs and a group of amino acid residues located at the carboxy-terminal end of the DNA-binding domain (DBD) which is referred to here as the carboxy-terminal extension. In this report, we show that binding of ROR alpha 1 and ROR alpha 2 to the RORE induces a large DNA bend of approximately 130 degrees which may be important for receptor function. The overall direction of the DNA bend is towards the major groove at the center of the 3' AGGTCA half-site. The presence of the nonconserved hinge region which is located between the DBD and the putative ligand-binding domain (LBD) or ROR alpha is required for maximal DNA bending. Deletion of a large portion of the amino-terminal domain (NTD) of the ROR alpha protein does not alter the DNA bend angle but shifts the DNA bend center 5' relative to the bend induced by intact ROR alpha. Methylation interference studies using the NTD-deleted ROR alpha 1 mutant indicate that some DNA contacts in the 5' AT-rich half of the RORE are also shifted 5', while those in the 3' AGGTCA half-site are unaffected. These results are consistent with a model in which the ROR alpha NTD and the nonconserved hinge region orient the zinc-binding motifs and the carboxy-terminal extension of the ROR alpha DBD relative to each other to achieve proper interactions with the two halves of its recognition site. Transactivation studies suggest that both protein-induced DNA bending and protein-protein interactions are important for receptor function.
A Systematic Approach to Well Surveying Calculations (1971)

Abstract The information used in well surveying calculations is studied and formalized. A general, natural, mathematical approach to the problem is presented and four special cases are developed: (1) triangular or trapezoidal, (2) secant, (3) quadratic and (4) minimum curvature. These methods are compared and their properties analyzed for reasonableness. Two of these methods are new and have appeared promising when applied to real and test data. Introduction Several new approaches have been proposed to the problem of performing well surveying calculations, and it has been pointed out that improvements in directional drilling tools and techniques justify a better treatment than the old tangential methods.1,2 However, a systematic analysis of the problem in a standard mathematical form has not been published. This paper will try to cover several of the more useful methods in a natural mathematical framework and to suggest several alternative approaches and directions for improvement.
Characterizing Heterogeneous Bacterial Surface Functional Groups Using Discrete Affinity Spectra for Proton Binding (1999)

Here we report results from a quantitative investigation of the types and densities of proton binding sites on a bacterial surface, Bacillus subtilis, from replicate acid−base titrations on bacteria at two ionic strengths (0.025 and 0.1 M). In contrast to the surface complexation modeling (SCM) approach developed and widely used for mineral, e.g., iron oxides, and more recently bacterial surfaces; we fit the data using the linear programming method (LPM). Our results using LPM indicate five discrete binding sites occurring on the surface of B. subtilis likely corresponding to carboxylic sites at low pKa values, phosphoric sites at near-neutral pKa values, and amine sites at high pKa values. Replicate titrations on subsamples from the same bacterial population indicated less variability than has been suggested for bacterial surfaces. Both the pKa and site density values were found to be dependent on ionic strength. Comparing the pKa values determined here with LPM for B. subtilis to those determined independently by using a fixed three site SCM model shows excellent agreement with the common sites likely corresponding to carboxylic, phosphoryl, and amine groups. However, the LPM approach identifies a further two sites as compared to the SCM approach. These results have an important implication. Surfaces of a given bacterial strain have a quantifiable, characteristic geochemical reactivity reflecting discrete sites that can be traced back in terms of function to the underlying, cell wall structure, a well-characterized phenomenon for most bacteria. However, an important caveat of our findings is that the absolute densities of these sites are highly dependent on a suite of both microbiological and system chemical parameters.
An efficient multipath forwarding method (2002)

We motivate and formally define dynamic multipath routing and present the problem of packet forwarding in the multipath routing context. We demonstrate that for multipath sets that are suffix matched, forwarding can be efficiently implemented with (1) a per packet overhead of a small, fixed-length path identifier, and (2) router space overhead linear in K, the number of alternate paths between a source and a destination. We derive multipath forwarding schemes for suffix matched path sets computed by both de-centralized (link-state) and distributed (distance-vector) routing algorithms. We also prove that (1) distributed multipath routing algorithms compute suffix matched multipath sets, and (2) for the criterion of ranked k-shortest paths, decentralized routing algorithms also yield suffix matched multipath sets.
Bax 2 Family Alternative Splicing Salvages Bax Microsatellite-Frameshift Mutations (2013)

Mutation or aberrant splicing can interrupt gene expression. Tumor suppressor Bax is one of the susceptible genes prone to microsatellite frameshifting mutations in coding regions. As a result, tumors exhibiting microsatellite instability (MSI) often present a “Bax-negative” phenotype. We previously reported that some Bax-negative cells in fact contain a functional Bax isoform (BaxΔ2), generated when unique alternative splicing “salvages” the shifted reading frame introduced by a microsatellite mutation. Here we compared Bax alternative splicing profiles in a range of cell lines and primary tumors with and without Bax microsatellite mutations. We found that MSI tumors exhibit a high Bax alternative splicing frequency, especially in exon 2, and produce a family of alternatively spliced isoforms that retain many important Bax functional domains. Surprisingly, these BaxΔ2 family isoforms can rescue Bax from all common microsatellite frameshift mutations. Production of BaxΔ2 requires specific cis mutations, while trans components are not cell-type specific. Furthermore, all BaxΔ2 family isoforms are more potent cell death inducers than the parental Bax without directly targeting mitochondria. These results indicate that the BaxΔ2 family can potentially salvage Bax tumor suppressor expression otherwise lost to mutation.
Fast Low-to-High Confinement Mode Bifurcation Dynamics in a Tokamak Edge Plasma Gyrokinetic Simulation (2017)

Transport barrier formation and its relation to sheared flows in fluids and plasmas are of fundamental interest in various natural and laboratory observations and of critical importance in achieving an economical energy production in a magnetic fusion device. Here we report the first observation of an edge transport barrier formation event in an electrostatic gyrokinetic simulation carried out in a realistic diverted tokamak edge geometry under strong forcing by a high rate of heat deposition. The results show that turbulent Reynolds-stress-driven sheared E×B flows act in concert with neoclassical orbit loss to quench turbulent transport and form a transport barrier just inside the last closed magnetic flux surface.
Effects of adjuvant, dose and carrier pre-sensitisation on the immunisation efficacy of a GnRH analogue. (1996)

A GnRH-neutralising vaccine, with potential applications in the treatment of human sex hormone-dependent disorders, was developed by conjugating GnRH-glycys to tetanus toxoid. An evaluation of adjuvant, dose and carrier pre-sensitisation was made. Male rats immunised with the conjugate, adsorbed onto alum, showed higher anti-GnRH antibody levels and suppressed testosterone concentrations, compared with animals immunised without adjuvant. Conjugate administration in a four injection regime proved to be the most effective in disrupting fertility, as assessed by the degree of lowered testosterone levels and gonadal atrophy. Pre-sensitisation with tetanus toxoid had an initial marked effect on immunisation, observed following 2 drug doses; the pre-sensitised animals showed a lower antibody response to the conjugate than did the non-primed animals. However, as the number of drug doses increased to 4, there was no significant difference between the primed and non-primed animals.
Interferon beta‐1b inhibits gelatinase secretion and in vitro migration of human T cells: A possible mechanism for treatment efficacy in multiple sclerosis (1996)

Treatment with interferon beta-1b has substantial clinical benefit in the demyelinating disease multiple sclerosis, yet the mechanism of action in the disease remains largely unknown. Gelatinase A (matrix metalloproteinase-2, 72-kd gelatinase) and B (matrix metalloproteinase-9, 92-kd gelatinase) are matrix metalloproteinases capable of enzymatic digestion of subendothelial basement membrane constituents. In human T cells, interleukin-2 induces gelatinase secretion and enhances gelatinase-dependent migration across an artificial basement membrane-like layer in vitro. Pretreatment of T cells with interferon beta-1b for 48 hours decreased interleukin-2-induced gelatinase production and secretion as determined by zymography. In parallel to the downregulation of gelatinase secretion, pretreatment with interferon beta-1b inhibited T-cell migration across the basement membrane in vitro by up to 90%, but had only a minor impact on cell locomotion per se. For both gelatinase secretion and T-cell migration, the inhibitory effect mediated by exposure to interferon beta-1b was dose dependent. Fluorescence-activated cell sorter analysis also showed that interferon beta-1b downregulates the interleukin-2 receptor alpha-chain and lowered the affinity of interleukin-2 to the cell surface by 30%, which may represent an additional mechanism for the observed effects of interferon beta-1b. The dramatic effects of interferon beta-1b on gelatinase expression and migration raise the possibility that its beneficial effects in multiple sclerosis may result from interference with the capacity of activated T cells to traverse the basement membrane and migrate to the central nervous system.
A Vortex Contactor for Carbon Dioxide Separations (2001)

Many analysts 1,2,3 identify carbon dioxide (CO2) capture and separation as a major roadblock in efforts to cost effectively mitigate greenhouse gas emissions via sequestration. An assessment 4 conducted by the International Energy Agency (IEA) Greenhouse Gas Research and Development Programme cited separation costs from $35
A Group Signature Scheme Based on an RSA-Variant (1998)

The concept of group signatures allows a group member to sign messages anonymously on behalf of the group. However, in the case of a dispute, the identity of a signature’s originator can be revealed by a designated entity. In this paper we propose a new group signature scheme that is well suited for large groups, i.e., the length of the group’s public key and of signatures do not<br />depend on the size of the group. Our scheme is based on a variation of the RSA problem called strong RSA assumption. It is also more efficient than previous ones satisfying these requirements.