gebhart/patrepeval huggingface dataset:
Cathepsin B inhibitors as potential anti-metastatic agents (1998)

Classical cancer treatments have focused on the use of cytotoxic agents and/or radiation therapy that target both tumour and normal cells. Consequently, current cancer treatments with chemotherapeutic agents are subject to limitations associated with high toxicity and resistance. There is a need to develop new agents and therapies that will permit long-term administration without compromising the patient. The individual steps of angiogenesis and metastasis during cancer progression are now well understood and present new targets for chemotherapy. The cysteine protease cathepsin B has been linked to the invasive steps during the metastatic process and provides a new target for drug development. Cathepsin B has also been implicated in other disease states with aberrant protein turnover such as muscular dystrophy, inflammatory airway diseases, bone and joint disorders and pancreatitis. Examination of the x-ray crystal structure of cathepsin B reveals the presence of an insertion loop extending for 18 residues that obstructs part of the active-site cleft. This ‘occluding loop’ is a unique feature that can be targeted for the development of specific inhibitors of cathepsin B as potential therapeutic agents. Inhibitors can be classified as to whether they act in a reversible or irreversible manner. This review details members of both of these classes of inhibitors and their therapeutic applications.
Fluctuations, Gravity, and the Quantum Potential (2005)

Abstract. We show how the quantum potential arises in various ways and trace its connection to quantum fluctuations and Fisher information along with its realization in terms of Weyl curvature. It represents a genuine quantization factor for certain classical systems as well as an expression for quantum matter in gravity theories of Weyl-Dirac type. Many of the facts and examples are extracted from the literature (with references cited) and we mainly provide connections and interpretation, with a few new observations. We deliberately avoid ontological and epistemological discussion and resort to a collection of contexts where the quantum potential plays a visibly significant role. In particular we sketch some recent results of F. and A. Shojai on Dirac-Weyl action and Bohmian mechanics which connects quantum mass to the Weyl geometry. Connections à la Santamato of the quantum potential with Weyl curvature arising from a stochastic geometry, are also indicated for the Schrödinger equation (SE) and Klein-Gordon (KG) equation. Quantum fluctuations and quantum geometry are linked with the quantum potential via Fisher information. Derivations of SE and KG from Nottale’s scale relativity are sketched along with a variety of approaches to the KG equation. Finally
Crystallization on Confined Engineered Surfaces:  A Method to Control Crystal Size and Generate Different Polymorphs (2005)

Patterned glycine crystals nucleated on functionalized metallic square islands. This approach can be used to fabricate particles with micron dimensions and screen solid forms under different conditions. The size of the glycine crystals is controlled by the dimensions of the islands. High energy metastable beta-glycine crystallizes on small metallic islands, whereas for large islands, the polymorphic outcome becomes biased toward the alpha-form.
Formation of Single-Phase Microemulsions in Toluene/Water/Nonionic Surfactant Systems (2008)

Mixtures of toluene and water from 5 to 50% oil fraction and 5 to 25% surfactant by weight were studied. Winsor Type IV microemulsions were formed in numerous cases. Review of partial ternary phase diagrams for these systems indicated the area of single-phase microemulsion with toluene could be maximized at an hydrophilic-lipophilic balance (HLB) of approximately 14.5. Select single-phase samples were further analyzed by surface tension and dynamic light scattering techniques, which allowed a detailed characterization of the solution equilibrium thermodynamics and size stability. Particle sizes averaged approximately 5 nm and were nearly constant over a wide variety of conditions and for 6-18 months. When benzyl alcohol was used instead of toluene, the optimum HLB for the formation of single-phase systems was found to have a lower limit of 17. Particle sizes in these systems were <30 nm but showed greater variability. The decrease in particle size as surfactant concentration increased was determined to be associated with changes in ethlyene oxide chain conformation. The increase in particle size due to swelling with increased oil concentration was used to determine the surfactant surface area in the oil phase. A detailed comparison of alkylamine ethoxylate to octyl- and nonylphenol ethoxylate surfactants in terms of micelle thermodynamics, size, and stability indicate that the alkylamine-based surfactants are potential candidates for the replacement of nonylphenol-based surfactants in some systems with a more polar oil phase like benzyl alcohol.
Inhibition of fibroblast growth factor-2-induced vascular tumor formation by the acyclic nucleoside phosphonate cidofovir. (2001)

Cidofovir [(S)-HPMPC; (S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine] is an antiviral drug that has been approved for the treatment of cytomegalovirus retinitis in AIDS patients. Cidofovir also possesses potent inhibitory activity against various human papillomavirus-induced tumors in animal models and patients. In addition, cidofovir inhibits the development of murine polyomavirus-induced hemangiomas in rats by an as-yet-uncharacterized, antivirus-independent mechanism. Here we report the inhibitory effect of cidofovir on the development of virus-independent vascular tumors originated by basic fibroblast growth factor (FGF2)-overexpressing endothelial cells (FGF2-T-MAE cells). In vitro, cidofovir was cytostatic to FGF2-T-MAE cells at a 50% cytostatic concentration of 6.7 microg/ml. Cidofovir concentrations >25 microg/ml resulted in cytotoxicity because of induction of apoptosis. Cidofovir did not affect FGF2-T-MAE cell sprouting in three-dimensional fibrin gel and morphogenesis on Matrigel at noncytotoxic concentrations. In vivo, cidofovir (100 microg/egg) completely suppressed hemangioma formation on the chick chorioallantoic membrane (CAM) induced by intra-allantoic injection of FGF2-T-MAE cells, without affecting the formation of normal CAM vessels. Accordingly, cidofovir applied locally at 200 microg/disc, reduced neovascularization on the CAM by only 35%. Intratumoral or systemic administration of cidofovir caused a significant inhibition of the growth of s.c., i.p., or intracerebral FGF2-T-MAE xenografts in nude mice and severe combined immunodeficient mice. Drug-induced apoptosis was observed in FGF2-T-MAE tumors as soon as 2 days after the beginning of treatment. In conclusion, cidofovir appears to inhibit the growth of endothelium-derived tumors via induction of apoptosis without exerting a direct antiangiogenic activity.
Interleukin-6 stimulates epithelial sodium channels in mouse cortical collecting duct cells (2010)

The aim of this study is to elucidate the effects of interleukin-6 (IL-6) on the expression and activity of the epithelial sodium channel (ENaC), which is one of the key mechanisms underlying tubular sodium reabsorption. M-1 cortical collecting duct cells were treated with IL-6 (100 ng/ml) for 12 h. Real-time polymerase chain reaction and immunoblotting were employed to examine the mRNA and protein abundance. Transepithelial voltage (V(te)) and resistance (R(te)) were measured with an ohm/voltmeter (EVOM, WPI). The equivalent current was calculated as the ratio of V(te) to R(te.) Treatment with IL-6 (n = 5) increased the mRNA abundance of alpha-ENaC by 11 +/- 7% (P = not significant), beta-ENaC by 78 +/- 14% (P = 0.01), gamma-ENaC by 185 +/- 38% (P = 0.02), and prostasin by 29 +/- 5% (P = 0.01), all normalized by beta-actin. Treatment with IL-6 increased the protein expression of alpha-ENaC by 19 +/- 3% (P = 0.001), beta-ENaC by 89 +/- 21% (P = 0.01), gamma-ENaC by 36 +/- 12% (P = 0.02), and prostasin by 33 +/- 6% (P = 0.02). The amiloride-sensitive sodium current increased by 37 +/- 5%, from 6.0 +/- 0.4 to 8.2 +/- 0.3 muA/cm(2) (P < 0.01), in the cells treated with IL-6 compared with controls (P = 0.01). Aprotinin (28 microg/ml), a prostasin inhibitor, reduced the amiloride-sensitive sodium current by 61 +/- 5%, from 6.1 +/- 0.3 to 3.7 +/- 0.2 muA/cm(2) (P = 0.01). The magnitude of the IL-6-induced amiloride-sensitive sodium current in the presence of aprotinin dropped by 57 +/- 2%, from 8.6 +/- 0.2 to 4.9 +/- 0.2 muA/cm(2) (P < 0.01). This study has identified a novel function of IL-6, namely, IL-6 may activate ENaC. Therefore, renal inflammation mediated by IL-6 likely contributes to impaired pressure natriuresis.
Quantitative Assessment of TongueShape and Movement Using Ultrasound Imaging (2008)

In phonological research, it is often important to corroborate assumptions and models with speech data. While acoustic and perceptual evaluations are valuable, the motor basis of speech processes can only be understood fully if information about articulatory movement is included. The tongue is the
Histone deacetylase activity is essential for the expression of HoxA9 and for endothelial commitment of progenitor cells (2005)

The regulation of acetylation is central for the epigenetic control of lineage-specific gene expression and determines cell fate decisions. We provide evidence that the inhibition of histone deacetylases (HDACs) blocks the endothelial differentiation of adult progenitor cells. To define the mechanisms by which HDAC inhibition prevents endothelial differentiation, we determined the expression of homeobox transcription factors and demonstrated that HoxA9 expression is down-regulated by HDAC inhibitors. The causal involvement of HoxA9 in the endothelial differentiation of adult progenitor cells is supported by the finding that HoxA9 overexpression partially rescued the endothelial differentiation blockade induced by HDAC inhibitors. Knockdown and overexpression studies revealed that HoxA9 acts as a master switch to regulate the expression of prototypical endothelial-committed genes such as endothelial nitric oxide synthase, VEGF-R2, and VE-cadherin, and mediates the shear stress-induced maturation of endothelial cells. Consistently, HoxA9-deficient mice exhibited lower numbers of endothelial progenitor cells and showed an impaired postnatal neovascularization capacity after the induction of ischemia. Thus, HoxA9 is regulated by HDACs and is critical for postnatal neovascularization.
Purification and characterization of major antigens from a Mycobacterium bovis culture filtrate (1991)

Ten major antigens from Mycobacterium bovis culture filtrate of 39, 32, 30, 25, 24, 22 (a and b forms), 19, 15, and 12 kDa have been purified and characterized by classical physicochemical methods. With monoclonal antibodies and/or N-terminal amino acid sequencing data, it was found that the antigens of 32, 30, 24, 22 (a), 19, and 12 kDa are related to M. bovis or M. tuberculosis antigens P32, MPB59, MPB64, MPB70, 19 kDa, and 12 kDa, respectively. The 39-, 25-, 22 (b)-, and 19-kDa antigens showed concanavalin A-binding properties and were positive in a glycan detection test, suggesting that they are glycoproteins. The 25- and 22 (b)-kDa proteins were found to be glycosylated forms of MPB70.
The mechanism of autooxidation of myoglobin. (1993)

Time courses for the autooxidation of native and mutant sperm whale and pig myoglobins were measured at 37 degrees C in the presence of catalase and superoxide dismutase. In sperm whale myoglobin, His64(E7) was replaced with Gln, Gly, Ala, Val, Thr, Leu, and Phe; Val68(E11) was replaced with Ala, Ile, Leu, and Phe; Leu29(B10) was replaced with Ala, Val, and Phe. In pig myoglobin, His64(E7) was replaced with Val; Val68(E11) was replaced with Thr and Ser; Thr67(E10) was replaced with Ala, Val, Glu, and Arg; Lys45(CD3) was replaced with Ser, Glu, His, and Arg. The observed pseudo-first order rate constants varied over 4 orders of magnitude, from 58 h-1 (H64A) to 0.055 h-1 (native) to 0.005 h-1 (L29F) at 37 degrees C, pH 7, in air. The dependences of the observed autooxidation rate constant on oxygen concentration and pH were measured for native and selected mutant myoglobins. In the native proteins and in most mutants still possessing the distal histidine, autooxidation occurs through a combination of two mechanisms. At high [O2], direct dissociation of the neutral superoxide radical (HO2) from oxymyoglobin dominates, and this process is accelerated by decreasing pH. At low [O2], autooxidation occurs by a bimolecular reaction between molecular oxygen and deoxymyoglobin containing a weakly coordinated water molecule. The neutral side chain of the distal histidine (His64) inhibits autooxidation by hydrogen bonding to bound oxygen, preventing both HO2 dissociation and the oxidative bimolecular reaction with deoxymyoglobin. Replacement of His64 by amino acids incapable of hydrogen bonding to the bound ligand markedly increases the rate of autooxidation and causes the superoxide mechanism to predominate. Increasing the polarity of the distal pocket by substitution of Val68 with Ser and Thr accelerates autooxidation, presumably by facilitating protonation of the Fe(II).O2 complex. Increasing the net anionic charge at the protein surface in the vicinity of the heme group also enhances the rate of autooxidation. Decreasing the volume of the distal pocket by replacing small amino acids with larger aliphatic or aromatic residues at positions 68 (E11) and 29 (B10) inhibits autooxidation markedly by decreasing the accessibility of the iron atom to solvent water molecules.
Chondroitin Sulfate Characterized by the E-disaccharide Unit Is a Potent Inhibitor of Herpes Simplex Virus Infectivity and Provides the Virus Binding Sites on gro2C Cells (2005)

Although cell surface chondroitin sulfate (CS) is regarded as an auxiliary receptor for binding of herpes simplex virus to cells, and purified CS chain types A, B, and C are known to interfere poorly or not at all with the virus infection of cells, we have found that CS type E (CS-E), derived from squid cartilage, exhibited potent antiviral activity. The IC(50) values ranged from 0.06 to 0.2 mug/ml and substantially exceeded the antiviral potency of heparin, the known inhibitor of virus binding to cells. Furthermore, in mutant gro2C cells that express CS but not heparan sulfate, CS-E showed unusually high anti-herpes virus activity with IC(50) values of <1 ng/ml. Enzymatic degradation of CS-E with chondroitinase ABC abolished its antiviral activity. CS-E inhibited the binding to cells of the purified virus attachment protein gC. A direct interaction of gC with immobilized CS-E and inhibition of this binding by CS-E oligosaccharide fragments greater than octasaccharide were demonstrated. Likewise, the gro2C-specific CS chains interfered with the binding of viral gC to these cells and were found to contain a considerable proportion (13%) of the E-disaccharide unit, suggesting that this unit is an essential component of the CS receptor for herpes simplex virus on gro2C cells and that the antiviral activity of CS-E was due to interference with the binding of viral gC to a CS-E-like receptor on the cell surface. Knowledge of the determinants of antiviral properties of CS-E will help in the development of inhibitors of herpes simplex virus infections in humans.
Maternal Plasma Fetal DNA Fractions in Pregnancies with Low and High Risks for Fetal Chromosomal Aneuploidies (2014)

Recently published international guidelines recommend the clinical use of noninvasive prenatal test (NIPT) for aneuploidy screening only among pregnant women whose fetuses are deemed at high risk. The applicability of NIPT to aneuploidy screening among average risk pregnancies requires additional supportive evidence. A key determinant of the reliability of aneuploidy NIPT is the fetal DNA fraction in maternal plasma. In this report, we investigated if differences in fetal DNA fractions existed between different pregnancy risk groups. One hundred and ninety-five singleton pregnancies with male fetuses divided into 3 groups according to first trimester screening parameters were examined for fetal DNA percentage by counting Y chromosome DNA sequences using massively parallel sequencing. Fetal DNA fractions were compared between risk groups and assessed for correlations with first trimester screening parameters. There was no statistically significant difference in fetal DNA fractions across the high, intermediate and low risk groups. Fetal DNA fraction showed a strong negative correlation with maternal weight. Fetal DNA fraction also showed weak but significant correlations with gestational age, crown-rump length, multiple of medians of free b-subunit of human chorionic gonadotropin and pregnancy-associated plasma protein A. Similar fetal DNA fractions in maternal plasma between high, intermediate and low risk pregnant women is a precondition for uniform performance of the aneuploidy NIPTs for the general population. This study thus shows that the aneuploidy screening by NIPT is likely to offer similar analytical reliability without respect to the a priori fetal aneuploidy risk.
A 1φ3 W grid-connection PV power inverter with APF based on nonlinear programming and FZPD algorithm (2003)

This paper presents design and implementation of a single-phase three-wire (1/spl phi/3 W) grid-connection PV power inverter with active power filter which is based on nonlinear programming and fast-zero-phase detection (FZPD) algorithm. The proposed inverter system can not only transmit PV power but can compensate harmonic currents, supply reactive power, and balance power at source side even when the line voltages are highly distorted. Simulated and experimental results have verified the FZPD algorithm and demonstrated that when the voltage sources are highly distorted, the proposed inverter system can yield better power quality over that with zero-crossing detection.
Novel blind carrier frequency offset estimation for OFDM system with multiple antennas (2010)

In this paper, we address the problem of carrier frequency offset (CFO) estimation for Orthogonal Frequency Division Multiplexing (OFDM) systems with multiple antennas. The received signal can be denoted as a trilinear model, then the trilinear decomposition-based CFO estimation algorithm is proposed. Comparing to both ESPRIT method and the cyclostationarity (CS) approach, the algorithm that we presented has improved CFO estimation performance. Furthermore, our proposed algorithm can even work in condition of no virtual carrier. Simulation results illustrate performance of this algorithm.
Novel Stationary Phases for Affinity Chromatography. Nucleobase-Selective Recognition of Nucleosides and Nucleotides on Poly(9-vinyladenine)-Supported Silica Gel (1988)

Abstract Poly(9-vinyladenine) (PVAd) was immobilized or coated on macroporous silica gel to be used as a stationary phase for HPLAC of nucleosides and nucleotides. The stationary phases showed nucleobase-selective recognition ability for nucleic acid constituents and gave practically useful HPLAC columns. On the basis of the results, the relationships between separation ability and the structure of PVAd are discussed.
Low-leakage germanium-seeded laterally-crystallized single-grain 100-nm TFTs for vertical integration applications (1999)

We report on 100-nm channel-length thin-film transistors (TFTs) that are fabricated using germanium-seeded lateral crystallization of amorphous silicon. Germanium seeding allows the fabrication of devices with control over grain boundary location. Its effectiveness improves with reduced device geometry, allowing "single-grain" device fabrication. In the first application of this technology to deep submicron devices, we report on 100-nm devices having excellent performance compared to conventional TFTs, which have randomly located grains. Devices have on-off ratio >10/sup 6/ and subthreshold slope of 107 mV/decade, attesting to the suitability of germanium-seeding for the fabrication of high-performance TFTs, suitable for use in vertically integrated three-dimensional (3-D) circuits.
Molecular Farming of Recombinant Antibodies in Plants (1999)

'Molecular farming' is the production of recombinant proteins in plants. It is intended to harness the power of agriculture to cultivate and harvest transgenic plants producing recombinant therapeutics. Molecular farming has the potential to provide virtually unlimited quantities of recombinant antibodies for use as diagnostic and therapeutic tools in both health care and the life sciences. Importantly, recombinant antibody expression can be used to modify the inherent properties of plants, for example by using expressed antipathogen antibodies to increase disease resistance. Plant transformation is technically straightforward for model plant species and some cereals, and the functional expression of recombinant proteins can be rapidly analyzed using transient expression systems in intact or virally infected plants. Protein production can then be increased using plant suspension cell production in fermenters, or by the propagation of stably transformed plant lines in the field. Transgenic plants can be exploited to produce organs rich in a recombinant protein for its long-term storage. This demonstrates the promise of using transgenic plants as bioreactors for the 'molecular farming' of recombinant therapeutics, blood substitutes and diagnostics, such as recombinant antibodies.
Growth of Ultrathin Covalently Attached Polymer Films:  Uniform Thin Films for Chemical Microsensors (1998)

A novel approach to covalently attached polymer films by surface functionalization and hydrosilylation reaction with reactive polymers on the surface is reported. Stable, uniform, and highly sensitive thin film sensors can thus be fabricated. The covalent attachment of polymer through a silane linker results in films with high uniformity, stability, and reasonable reproducibility as far as film thickness is concerned. Incorporation of molecular recognition reagents into the sensing film increases the sensor sensitivity dramatically, which is critical for detecting vapors such as certain explosives at parts per thousand or parts per billion levels. The sensors fabricated can detect o-nitrotoluene, a TNT simulant, at parts per billion concentrations.
Optimizing magnetic stimulator design. (1991)

Optimal magnetic stimulation depends on application and design. The best design generates the desired depolarization current in the desired area with acceptable current speed. Power and cooling requirements, electrical and mechanical safety, stimulus rate, reliability, and ease of use are additional considerations. By understanding the interactions among these requirements, suitable choices are made. Magnetic stimulation requires moving enough charge through an electrically sensitive tissue to depolarize it reliably. Usually there is a need to depolarize a delimited volume of tissue and to repeat the depolarization at convenient intervals. A good design achieves the focality and speed needed for the application. Since the applications for magnetic stimulation are varied, however, the designs for the stimulators also will be different, and defining the application (or applications) is, therefore, a requirement for optimization.
Newborn Screening (2009)

Screening newborns for inherited disorders provides an opportunity for pre-symptomatic identification and early intervention to prevent or mitigate morbidity and mortality associated with these conditions. Since the introduction of newborn screening in 1962 to screen for phenylketonuria, technological advances have enabled the screening panel to expand substantially so that it now includes more than 50 disorders. Newborn screening will continue to evolve,, and deployment of improved methodologies and incorporation of additional disorders are expected. This article provides an overview of the current state of newborn screening, and describes the disorders detectable, the methodologies employed, and the challenges involved in analyses of specimens obtained from newborns.