gebhart/patrepeval huggingface dataset:
miR-2909-mediated regulation of KLF4: a novel molecular mechanism for differentiating between B-cell and T-cell pediatric acute lymphoblastic leukemias (2014)

This study identified a novel miR-2909-KLF4 molecular axis able to differentiate between the pathogeneses of pediatric B- and T-cell ALLs, and which may represent a new diagnostic/prognostic marker.
Top-Down Reservoir Modelling (2004)

Abstract Over the last twenty or more years of reservoir performance prediction through simulation there have been only two fundamental changes. First was the evolutionary increase in computing speed that has allowed larger, more detailed reservoir models to be built. Second was the revolutionary change in approach that involved the entire subsurface community in building integrated reservoir descriptions. The next big change may in time prove to be BP's Top-Down Reservoir Modelling (TDRM). This is a new pragmatic approach to fully incorporate reservoir uncertainty in model construction and performance prediction. TDRM is proprietary technology that has been developed in BP through extensive R&amp;D, and consists of a philosophy and tools that enable a faster and more robust exploration of uncertainty than has hitherto been possible. The philosophy is to start investigations with the simplest possible model and simulator appropriate to the business decision. Detail is added later as required. The approach overcomes the problems of the conventional "bottom-up" process, which uses detailed models that are too slow and cumbersome to fully explore uncertainty and identify critical issues. Highly detailed models cannot overcome an underlying absence of information, and can have the negative effect of creating a false sense of understanding. The TDRM tools have been designed to minimise manual iterations by creating a semi automated, flexible workflow for case management, assisted history matching, depletion planning optimisation and post-analysis. TDRM has been successfully applied to eighteen oil and gas reservoirs that range from development appraisal stage to mature fields, and has resulted in up to 20% increase in estimated net present value for the projects.
The impact of inrush currents on the mechanical stress of high voltage power transformer coils (2002)

From failure experience on power transformers, it was very often suspected that inrush currents, occurring when energizing unloaded transformers, were reason for damage. In this paper, it was investigated how mechanical forces within the transformer coils build up under inrush compared to those occurring at short circuit. Two-dimensional and three-dimensional computer modeling for a real 268 MVA, 525/17.75 kV three-legged step up transformer was employed. The results show that inrush current peaks of 70% of the rated short circuit current cause local forces in the same order of magnitude as those at short circuit. The resulting force summed up over the high voltage coil is even three times higher. Although inrush currents normally are smaller, the forces can have similar amplitudes as those at short circuit however with longer exposure time. Therefore, care has to be taken to avoid such high inrush currents. Today controlled switching offers an elegant and practical solution.
Meiotic Recombination Break Points Resolve at High Rates at the 5' End of a Maize Coding Sequence (1995)

Xiaojie Xu, An-Ping Hsia, Lei Zhang, Basil J. Nikolau, Patrick S. Schnable, Meiotic Recombination Break Points Resolve at High Rates at the 5′ End of a Maize Coding Sequence, The Plant Cell, Vol. 7, No. 12 (Dec., 1995), pp. 2151-2161
Synthesis and Evaluation of 4-Bromo-1-(3-[18F]fluoropropyl)-2-nitroimidazole with a Low Energy LUMO Orbital Designed as Brain Hypoxia-Targeting Imaging Agent. (2002)

In order to develop new imaging markers for brain hypoxia, 4-bromo-1-(3-fluoropropyl)-2-nitroimidazole (4-BrFPN) was designed based on molecular orbital calculations, synthesized and labeled with fluorine-18 as a lipophilic nitroimidazole analog with a lower energy LUMO orbital than those for fluoromisonidazole (FMISO) and 1-(3-fluoropropyl)-2-nitroimidazole (FPN). In an in vitro radiosensitization study, the sensitizer enhancement ratio for 4-BrFPN was found to be 1.65 at a I mM concentration, in comparison to 1.81 for FMISO. The preparation of 18F-labeled 4-BrFPN (4-Br18FPN) was achieved by [18F]fluoride ion displacement reaction of the tosylate precursor, in a reasonable radiochemical yield (33%, not corrected for decay). Metabolites in tumor and muscle extracts from methylcholanthrene-induced fibrosarcoma mice, as well as the tissue distribution of 4-Br18FPN in normal rats, were studied. The initial uptake into rat brain of 4-Br18FPN was significantly higher relative to 18F-labeled FMISO (18FMISO), followed by a rapid washout from the brain. The tumor uptake of 4-Br18FPN was somewhat enhanced compared to those obtained with 18FMISO and 18F-labeled FPN (18FPN), but with lower tumor localization than 18FMISO. Analyses of tumor and muscle extracts showed metabolites remaining base line on the radio-TLC plates, and they were produced to a greater extent in tumor than muscle. The use of two drugs which increase hypoxic cell fraction in tumor, hydralazine or nitro-L-arginine, produced a significant increase in tumor levels of 4-Br18FPN, suggestive of a hypoxic mechanism of accumulation. The results imply that lowering of the LUMO energy of a molecule alone is not sufficient to improve its biodistribution properties for better imaging of regions of hypoxia.
Newcastle Disease Virus V Protein Is Associated with Viral Pathogenesis and Functions as an Alpha Interferon Antagonist (2003)

Newcastle disease virus (NDV) edits its P gene by inserting one or two G residues at the conserved editing site (UUUUUCCC, genome sense) and transcribes the P mRNA (unedited), the V mRNA (with a +1 frameshift), and the W mRNA (with a +2 frameshift). All three proteins are amino coterminal but vary at their carboxyl terminus in length and amino acid composition. Little is known about the role of the V and W proteins in NDV replication and pathogenesis. We have constructed and recovered two recombinant viruses in which the expression of the V or both the V and W proteins has been abolished. Compared to the parental virus, the mutant viruses showed impaired growth in cell cultures, except in Vero cells. However, transient expression of the carboxyl-terminal portion of the V protein enhanced the growth of the mutant viruses. In embryonated chicken eggs, the parental virus grew to high titers in embryos of different gestational ages, whereas the mutant viruses showed an age-dependent phenomenon, growing to lower titer in more-developed embryos. An interferon (IFN) sensitivity assay showed that the parental virus was more resistant to the antiviral effect of IFN than the mutant viruses. Moreover, infection with the parental virus resulted in STAT1 protein degradation, but not with the mutant viruses. These findings indicate that the V protein of NDV possesses the ability to inhibit alpha IFN and that the IFN inhibitory function lies in the carboxyl-terminal domain. Pathogenicity studies showed that the V protein of NDV significantly contributes to the virus virulence.
Tumor targeting and imaging of intraperitoneal tumors by use of antisense oligo-DNA complexed with dendrimers and/or avidin in mice. (2001)

To establish an effective nonviral gene delivery and a corresponding imaging method for i.p.-disseminated tumors, various oligonucleotide-carrier complexes were synthesized, and their in vitro and in vivo properties were examined. The 20-mer multiamino-linked oligonucleotide (oligo), synthesized as antisense against the c-erbB-2 sequence, and the 3'-biotinylated form of the same oligonucleotide (oligo-Bt) were (111)In labeled through a diethylenetriaminepentaacetic acid chelate. (111)In-oligo was mixed with generation 4 polyamidoamine dendrimer (G4) or with biotinylated G4 (G4-Bt), which are positively charged to form electrostatic complexes. (111)In-oligo/G4-Bt and (111)In-oligo-Bt were conjugated to avidin ((111)In-oligo/G4-Av and (111)In-oligo-Av, respectively). (111)In-oligo/G4, (111)In-oligo/G4-Av, (111)In-oligo-Av, and carrier-free (111)In-oligo (2.96 kBq/22.4-45.9 ng of oligo) were examined for internalization in vitro in human ovarian cancer cells (SHIN3). Biodistribution of (111)In-oligo-carrier complexes or (111)In-oligo was examined in normal (n = 4-7) or i.p. SHIN3 tumor-bearing (n = 6-10) mice 2-24 h after i.p. injection (74 kBq/125-300 ng). Scintigraphy of i.p. tumor-bearing and normal mice was performed at various times postinjection of (111)In-oligo-carrier complex or (111)In-oligo (1.85 MBq/2.2 ng). (111)In-oligo-carrier complexes bound to the tumor cells were internalized at a rate of 34-56% at 24 h. In vivo, G4, G4-Av, and Av significantly enhanced tumor delivery of (111)In-oligo [9.1, 14.5, and 24.4% of injected dose per g of tissue (ID/g) at 24 h; P < 0.05, < 0.01, and < 0.0001, respectively] compared with delivery without carrier (0.8% ID/g). Scintigrams of (111)In-oligo delivered to the i.p.-disseminated tumors by the carriers were successfully obtained. In conclusion, G4, G4-Av, and Av can effectively deliver (111)In-oligo to i.p.-disseminated tumors. (111)In-oligo-carrier complexes also have potential as tracers for imaging and monitoring of gene delivery.
Pharmacokinetics of secnidazole in healthy volunteers after single oral dose (2010)

&lt;p&gt;Résumé publié dans : &lt;em&gt;Fundamental &amp;amp; Clinical Pharmacology&lt;/em&gt;, avril 2010, 24(Suppl. 1): p. 55-56. doi:&lt;a href="http://dx.doi.org/10.1111/j.1472-8206.2010.00819.x"&gt;10.1111/j.1472-8206.2010.00819.x&lt;/a&gt;&lt;/p&gt;
Insulin-Like Growth Factor I Has a Direct Effect on Glucose and Protein Metabolism, But No Effect on Lipid Metabolism in Type 1 Diabetes (2004)

There is evidence of a metabolic role for IGF-I in type 1 diabetes, but it is unclear whether IGF-I acts indirectly by reducing GH secretion or has direct effects. Using stable isotopes we have investigated, on three separate occasions, the effect of a pulse of recombinant human GH, a sc injection of recombinant human IGF-I, and a placebo on glucose, lipid, and protein metabolism in subjects with type 1 diabetes during a basal insulin infusion and a hyperinsulinemic euglycemic clamp. Endogenous GH secretion was suppressed with octreotide. IGF-I reduced the hepatic glucose production rate (Ra), increased peripheral glucose uptake, and reduced protein breakdown during the basal insulin infusion (P < 0.05, P < 0.005, and P < 0.05, respectively, vs. placebo) and the hyperinsulinemic euglycemic clamp (P < 0.05, P < 0.005, and P < 0.05, respectively, vs. placebo). IGF-I had no effect on glycerol Ra, an index of lipolysis. GH increased glucose and glycerol Ra during the basal insulin infusion (P < 0.005 vs. placebo study), but the effects were no different from placebo during the clamp. In conclusion, IGF-I had a direct effect on glucose and protein metabolism, which was maintained during the hyperinsulinemic euglycemic clamp. This suggests that IGF-I acts in concert with insulin and may have an important role in maintaining glucose homeostasis and protein metabolism in type 1 diabetes.
MoS 2 nanoflowers and their field-emission properties (2003)

Elegant three-dimensional MoS2 nanoflowers were uniformly formed via heating a MoO2 thin film in a vapor sulfur atmosphere. Tens to hundreds of petals were self-assembled within a single nanoflower. Each petal, 100–300 nm wide and only several nanometers thick, exhibited a hexagonal structure. The number of petal layers gradually decreased towards the edges, resulting in uniquely thin edges, typically less than 3 nm. The MoS2 nanoflowers appeared to be excellent field emitters displaying a current density of 0.01 and 10 mA/cm2 at macroscopic fields of 4.5–5.5 and 7.6–8.6 V/μm, respectively; the electron field emission was consistent with the Fowler–Nordheim theory.
An analysis framework for understanding layered software architectures (2002)

This paper presents the results of an empirical study. The study aims at evaluating the ability to understand the coherence between design documents that describe the layered architecture of large scale systems, and the actual structure of the software source file organization. A clear set of objectives to be addressed for achieving a good understanding of a layered architecture is defined. The objectives are focused on identifying the interfaces between layers, in terms of cross-layer file dependencies. An analysis framework for achieving these objectives is proposed. The framework is applied to analyze the actual software architecture of 6 subsequent releases of a 15MLoc telecommunications product. Results of that experiment show that the framework can provide much insight on the actual implementation of a system with a layered architecture.
Porphyrin Synthesis in Surfactant Solution:  Multicomponent Assembly in Micelles (1996)

A synthesis of meso-substituted porphyrins in anionic sodium dodecyl sulfate micelles has been developed. Polar, functionalized aromatic aldehydes condense reversibly with pyrrole in the micellar phase. Oxidation of the porphyrinogen then provides functionalized porphyrins in yields of 10-48%. Hydrophobic aldehydes condense irreversibly to give low yields at practical substrate concentrations. Synthesis in D(2)O solution results in per-beta-deuterated porphyrins. A two-phase model is used to rationalize the dependence of porphyrin yield on reactant and surfactant concentration. Micelles are viewed as potential wells which promote porphyrinogen assembly by binding products more tightly than reactants.
Inhibition of brush border dipeptidase with cilastatin reduces toxic accumulation of cyclosporin A in kidney proximal tubule epithelial cells (2004)

Prevention of CyA-induced reduction of cell membrane fluidity and inhibition of CyA transport are features of cilastatin's direct effects on PTECs. Unaltered distribution of MBCRs in the presence of cilastatin suggests that cilastatin binding to raft-bound dipeptidases, rather than MBCR modifications, causes interference with CyA transport. These results provide additional insight into the mechanisms and scope of cilastatin nephroprotection.
Oxygen permeation through thin mixed‐conducting solid oxide membranes (1994)

Abstract A new approach for developing fundamental equations of oxygen permeation through thin mixed‐conducting oxide ceramic is presented considering both surface reactions on membrane‐gas interfaces and the diffusion of charged species in the bulk oxide. The essence of this work is the coupling of surface reactions with the bulk diffusion using a novel approach which differs from the conventional Wagner. Theory applicable only to limited cases. With this approach, fundamental equations based on various permeation mechanisms can be derived for oxygen permeation through thin mixed‐conducting oxide membranes, which is impossible using conventional approach. In general, the final results are a complex implicit equation correlating the oxygen permeation flux to the driving force, membrane thickness, and rate constants with physical significance in each step. Somewhat simpler theoretical oxygen permeation equations are obtained for some special cases (mixed‐conducting membranes with a rate‐limiting step, ionic‐conducting membranes, ionic‐conducting membranes with a reducing agent in permeate side). Theoretical results derived using this new approach agree excellently with the experimental oxygen permeation data. It is theoretically and experimentally shown that for ionic conductors, the surface permeation parameter measured by the dynamic permeation method is directly related to the oxygen isotope exchange rate constant measured under equilibrium conditions.
Activity of in vivo canine ventricular neurons (1990)

The spontaneous activity of 113 neurons located in the ganglionated plexus in the epicardial fat overlying the cranial portion of the ventral intraventricular groove and the origin of the circumflex coronary artery was recorded in ten anesthetized dogs. Ganglia that contained varying numbers of neurons, some with two or more nucleoli, were subsequently identified anatomically in the vicinity of the recording sites. Spontaneous activity was correlated with the cardiac cycle in 81% and with the respiratory cycle in 17% of the identified neurons. The spontaneous cardiovascular-related activity occurred in relation to specific phases of the cardiac cycle when arterial pressure was between approximately 80 and 175 mmHg. When systolic pressures fell below approximately 80 mmHg or increased above approximately 175 mmHg, neurons displaying cardiovascular-related activity were inactive. The activity of 62% of all identified neurons was altered when discrete regions of the heart or pulmonary tissue were mechanically distorted by gentle touch. In many instances mechanical distortions of tissues were still able to alter neuronal activity following acute decentralization. Single stimuli or trains of stimuli delivered to the vagosympathetic complexes, stellate ganglia, or cardiopulmonary nerves generated bursts of activity in ganglionic neurons. Spontaneous activity occurred whether the ganglia were connected to the central nervous system or acutely decentralized. It is concluded that some neurons located on the canine ventricle display spontaneous activity that is related to cardiovascular or respiratory dynamics. The results also demonstrate that ventricular neurons can be influenced by sympathetic or parasympathetic efferent axons as well as cardiac mechanoreceptors.
Losartan Metabolite EXP3179 Activates Akt and Endothelial Nitric Oxide Synthase via Vascular Endothelial Growth Factor Receptor-2 in Endothelial Cells (2005)

The losartan metabolite EXP3179 stimulates eNOS phosphorylation and suppresses tumor necrosis factor alpha-induced EC apoptosis by activating the VEGFR2/PI3K/Akt pathway.
Security Requirements and Protocols for a Broadcast Scenario (1981)

Previous work (e.g., [1], [2]) has characterized communication security requirements in connection-oriented (virtual circuit) environments supporting applications such as interactive communication and file transfer. This work has developed protocols to achieve these requirements using conventional ciphers (CC's) such as the NBS data encryption standard (DES) [3]. More recently, several authors [4]-[6] have analyzed key distribution protocols for such environments based on CC's and on public-key ciphers (PKC's) such as the RSA algorithm [7], noting similarities in form, function, and vulnerability. Advances in satellite and packet radio technology [8], [9] and the development of high-speed, local area networks [10] have stimulated interest in broadcast protocols for various applications. This article examines security requirements for a simple broadcast scenario characteristic of some of these applications and develops protocols for achieving these requirements. Two sets of protocols, one based on CC's and the other based on PKC's, are developed and analyzed in terms of functionality and performance.
Insulin Needs after CD3-Antibody Therapy in New-Onset Type 1 Diabetes (2005)

Short-term treatment with CD3 antibody preserves residual beta-cell function for at least 18 months in patients with recent-onset type 1 diabetes.
Systemic Treatment with Tetra-O-Methyl Nordihydroguaiaretic Acid Suppresses the Growth of Human Xenograft Tumors (2005)

These preclinical studies establish that when given systemically, M4N can safely and effectively inhibit the growth of human tumors in nude mice.
Targeting a genetically engineered elastin-like polypeptide to solid tumors by local hyperthermia. (2001)

Elastin-like polypeptides (ELPs) are biopolymers of the pentapeptide repeat Val-Pro-Gly-Xaa-Gly that undergo an inverse temperature phase transition. They are soluble in aqueous solutions below their transition temperature (T1) but hydrophobically collapse and aggregate at temperatures greater than T1. We hypothesized that ELPs conjugated to drugs would enable thermally targeted drug delivery to solid tumors if their T1 were between body temperature and the temperature in a locally heated region. To test this hypothesis, we synthesized a thermally responsive ELP with a T1 of 41 degrees C and a thermally unresponsive control ELP in Escherichia coli using recombinant DNA techniques. In vivo fluorescence videomicroscopy and radiolabel distribution studies of ELP delivery to human tumors (SKOV-3 ovarian carcinoma and D-54MG glioma) implanted in nude mice demonstrated that hyperthermic targeting of the thermally responsive ELP for 1 h provides a approximately 2-fold increase in tumor localization compared to the same polypeptide without hyperthermia. We observed aggregates of the thermally responsive ELP by fluorescence videomicroscopy within the heated tumor microvasculature but not in control experiments, which demonstrates that the phase transition of the thermally responsive ELP carrier can be engineered to occur in vivo at a specified temperature. By exploiting the phase transition-induced aggregation of these polypeptides, this method provides a new way to thermally target polymer-drug conjugates to solid tumors.
Kinetic study on the anelation of heterocycles. 2. pyrido[2,3‐b]pyrazine and pyrido[3,4‐b]pyrazine derivatives synthesized by the hinsberg reaction (1990)

Abstract The regioselective synthesis of pyrido[2,3‐ b ]‐ and [3,4‐ b ]pyrazine derivatives II by the Hinsberg reaction is reported starting from 2,3 and 3,4‐diaminopyridine and excess of pyruvic acid or ethyl pyruvate as reactants. Good yields (higher than 90%) were obtained for pyrido[2,3‐ b ]pyrazine derivatives at room temperature using anhydrous methanol and chloroform as solvents which promote regioselective reactions to give 2‐methylpyrido[2,3‐ b ]pyrazin‐3(4 H )‐one ( 3a ) and 3‐methylpyrido[2,3‐ b ]pyrazin‐2(1 H )‐one ( 4a ) respectively. On the other hand, when the same procedure was applied to 3,4‐diaminopyridine results were not so encouraging for the formation of 2‐methylpyrido[3,4‐ b ]pyrazin‐3(4 H )‐one ( 3b ) and 3‐methylpyrido[3,4‐ b ]‐pyrazin‐2(1 H )one ( 4b ). Kinetic studies were performed in aqueous buffers ( p H ‐0.89 to 11.5) and different organic solvents trying to improve yields and achieve regioselectivity. The course of the reactions was followed by uv spectrophotometry being those with ethyl pyruvate 2 to 800 times faster than with pyruvic acid. This investigation involves the kinetics and mechanism of this reaction studying its factibility when π‐deficient substrates are used and its regioselectivity according to the position of the pyridine nitrogen atom.
Atomic resolution with an atomic force microscope using piezoresistive detection (1993)

A new detection scheme for atomic force microscopy (AFM) is shown to yield atomic resolution images of conducting and nonconducting layered materials. This detection scheme uses a piezoresistive strain sensor embedded in the AFM cantilever. The cantilever is batch fabricated using standard silicon micromachining techniques. The deflection of the cantilever is measured directly from the resistance of the piezoresistive strain sensor without the need for external deflection sensing elements. Using this cantilever we achieved 0.1 Årms vertical resolution in a 10 Hz–1 kHz bandwidth.
HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies (2018)

Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships. Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs and taxonomy assignment. Compared to standard pipelines, HmmUFOtu more accurately and reliably recapitulates microbial community diversity and composition in simulated and real datasets without relying on heuristics or sacrificing speed or accuracy.