gebhart/patrepeval huggingface dataset:
An electrorotation technique for measuring the dielectric properties of cells with simultaneous use of negative quadrupolar dielectrophoresis and electrorotation (2013)

This paper presents an effective electrorotation technique for measuring the dielectric properties of cells using a superposed electrical signal, which can simultaneously generate negative quadrupolar dielectrophoretic (nQDEP) force and electrorotational (ROT) torque. The proposed technique involves a three-dimensional (3D) octode, which includes four electrodes arranged in a crisscross pattern on the top and bottom of a microchannel, respectively. A single cell was trapped in the center of the 3D octode by the nQDEP force and simultaneously rotated by the ROT torque. Using the proposed electrorotation technique, ROT spectra of human leukocyte subpopulations (T and B lymphocytes, granulocytes, and monocytes) and metastatic human breast (SkBr3) and lung (A549) cancer cell lines were accurately measured without any disturbance. Torque on the cells generated by the ROT signal was analyzed theoretically based on the single-shell dielectric model for the cells. Furthermore, the dielectric properties of the cells, such as area-specific membrane capacitance and cytoplasm conductivity, were extracted using the measured ROT spectra and the analyzed torque.
A Water-Soluble, Small Molecular Fluorescent Sensor with Femtomolar Sensitivity for Zinc Ion (2007)

A water-soluble fluorescent sensor, 1, based on the quinoline platform, demonstrates femtomolar sensitivity for zinc ion with a 14-fold enhanced quantum yield upon chelation to zinc ion and also exhibits high selectivity to zinc ion over other physiological relevant divalent metals in the presence of EDTA. X-ray crystal structure of zinc complex reveals that an acetic carboxylic group participates in coordination, which significantly enhances the affinity of 1 for zinc ion.
Polymeric Particulates to Improve Oral Bioavailability of Peptide Drugs (2005)

Oral administration remains the most convenient way of delivering drugs. Recent advances in biotechnology have produced highly potent new molecules such as peptides, proteins and nucleic acids. Due to their sensitivity to chemical and enzymatic hydrolysis as well as a poor cellular uptake, their oral bioavailability remains very low. Despite sophisticated new delivery systems, the development of a satisfactory oral formulation remains a challenge. Among the possible strategies to improve the absorption of drugs, micro- and nanoparticles represent an exciting approach to enhance the uptake and transport of orally administered molecules. Increasing attention has been paid to their potential use as carriers for peptide drugs for oral administration. This article reviews the most common manufacturing methods for polymeric particles and the physiology of particle absorption from the gastrointestinal (GI) tract. In a second part, the use of polymeric particulate systems to improve the oral absorption of insulin is discussed.
[Effect of the novel dipeptide nootropic agent noopept and its metabolite cyclo-L-prolylglycine on the transcallosal evoked potential in the rat brain]. (2002)

The effect of new nootropic dipeptides--noopept (N-phenylacetyl-L-prolylglycine, GVS-111) and its metabolite (cyclo-L-prolylglycine)--and a standard nootrope piracetam on the transcallosal evoked potential (TEP) in rat brain was studied. In the dose range from 150 to 300 mg/kg, piracetam increased the TEP amplitude, which exhibited a maximum after 1.5-2 h and then gradually decreased. Both noopept and cyclo-L-prolylglycine also increased the TEP amplitude, which attained a plateau and retained this level over the entire observation time (above 3.5 h). All the nootropes studied increased both components of the evoked potential. Piracetam and cyclo-L-prolylglycine led to an approximately equal increase in both waves, while noopept induced a somewhat greater increase in the negative TEP wave amplitude. It is suggested that the positive effect of noopept and cyclo-L-prolylglycine upon the interhemispheric signal transfer (indicated by the improved transcallosal response) can be considered as a potential neurophysiological basis for a positive drug influence on the behavioral level.
Effects of metabolic modulation by trimetazidine on left ventricular function and phosphocreatine/adenosine triphosphate ratio in patients with heart failure (2006)

Trimetazidine improves functional class and LV function in patients with heart failure. These effects are associated to the observed trimetazidine-induced increase in the PCr/ATP ratio, indicating preservation of the myocardial high-energy phosphate levels.
Conductance-Controlled Point Functionalization of Single-Walled Carbon Nanotubes (2007)

We used covalent attachments to single-walled carbon nanotubes (SWNTs) to fabricate single-molecule electronic devices. The technique does not rely on submicrometer lithography or precision mechanical manipulation, but instead uses circuit conductance to monitor and control covalent attachment to an electrically connected SWNT. Discrete changes in the circuit conductance revealed chemical processes happening in real time and allowed the SWNT sidewalls to be deterministically broken, reformed, and conjugated to target species. By controlling the chemistry through electronically controlled electrochemical potentials, we were able to achieve single chemical attachments. We routinely functionalized pristine, defect-free SWNTs at one, two, or more sites and demonstrated three-terminal devices in which a single attachment controls the electronic response.
Single-Walled Carbon Nanotube Thin Film Transistor Fabricated Using Solution Prepared with 9,9-Dioctyfluorenyl-2,7-diyl–Bipyridine Copolymer (2011)

Performance of thin film transistor (TFT) whose channel is fabricated by using a solution process of single-walled carbon nanotube (SWCNT) has been studied. SWCNT solution is prepared by using 9,9-dioctyfluorenyl-2,7-diyl–bipyridine (PFO–BPy) copolymer as solubilizer. Over 4 decades' on/off ratio is obtained by using drop-coating at room temperature without any further optimization. Other solubilizers are chosen as control groups to measure the on/off ratio of SWCNT TFT to investigate effects of the use of PFO–BPy. Results suggest that thick SWCNT network should be uniformly established at the channel region and the channel is required to be formed with well-separated SWCNTs.
Are Cancer Stem Cells Responsible for Cancer Recurrence? (2012)

Are Cancer Stem Cells Responsible for Cancer Recurrence? Local recurrence or distant organ metastasis are the major causes of cancer mortality. Conventional treatments, including surgery, chemotherapy, and irradiation, do not consistently prevent cancer recurrence. Thus, an alternative therapeutic approach is needed. Recent evidence indicates a specific cell population of cancer stem cells or tumor initiating cells (jointly CSC) exists in various cancers that may be identified by cell surface markers, such as CD133, CD44, aldehyde dehydrogenase 1 (ALDH1) enzyme expression, or side population.
Effects of Botulinum Toxin Type B on Stump Pain and Involuntary Movements of the Stump (2004)

Patients who had previously undergone amputation of the arm (n = 2) or leg (n = 2) were treated with botulinum toxin type B injections at several trigger points of their stump musculature. We administered a total dose of 2500 IU of botulinum toxin type B (Neurobloc, Elan Pharma, Munich, Germany) to the arm amputation stumps, 5000 IU for one amputation of the lower leg, and 2500 IU to the other lower leg amputation of a patient with a very low baseline body weight. Two patients reported that the injection was very painful. All patients experienced a reduction in stump pain, which lasted for many weeks. Other reports included a reduction in the frequency of pain attacks, cessation of "balloon feelings," improvement in stump allodynia, and decreased occurrence of involuntary stump movements. In addition, quality of sleep at night significantly improved in one patient. Botulinum toxin type B can therefore be regarded as a new treatment option for possible improvements in the rehabilitation of amputees.
Recombinant Protein-co-PEG Networks as Cell-Adhesive and Proteolytically Degradable Hydrogel Matrixes. Part I:  Development and Physicochemical Characteristics (2005)

Toward the development of synthetic bioactive materials to support tissue repair, we present here the design, production, and characterization of genetically engineered protein polymers carrying specific key features of the natural extracellular matrix, as well as cross-linking with functionalized poly(ethylene glycol) (PEG) to form hybrid hydrogel networks. The repeating units of target recombinant protein polymers contain a cell-binding site for ligation of cell-surface integrin receptors and substrates for plasmin and matrix metalloproteinases (MMPs), proteases implicated in wound healing and tissue regeneration. Hydrogels were formed under physiological conditions via Michael-type conjugate addition of vinyl sulfone groups of end-functionalized PEG with thiols of cysteine residues, representing designed chemical cross-linking sites within recombinant proteins. Cross-linking kinetics was shown to increase with the pH of precursor solutions. The elastic moduli (G') and swelling ratios (Q(m)) of the resulting hydrogels could be varied as a function of the stoichiometry of the reacting groups and precursor concentration. Optima of G' and Q(m), maximum and minimum, respectively, were obtained at stoichiometry ratios r slightly in excess of 1 (r = cysteine/vinyl sulfone). The pool of technologies utilized here represents a promising approach for the development of artificial matrixes tailored for specific medical applications.
Human prostate-specific antigen: structural and functional similarity with serine proteases. (1986)

The complete amino acid sequence of the prostate-specific antigen (PA) from human seminal plasma has been determined from analyses of the peptides generated by cyanogen bromide, hydroxylamine, endoproteinases Arg-C and Lys-C. The single polypeptide chain of PA contains 240-amino acid residues and has a calculated Mr of 26,496. An N-linked carbohydrate side chain is predicted at asparagine-45, and O-linked carbohydrate side chains are possibly attached to serine-69, threonine-70, and serine-71. The primary structure of PA shows a high degree of sequence homology with other serine proteases of the kallikrein family. The active site residues of histidine, aspartic acid, and serine comprising the charge-relay system of typical serine proteases were found in similar positions in PA (histidine-41, aspartic acid-96, and serine-192). At pH 7.8, PA hydrolyzed insulin A and B chains, recombinant interleukin 2, and--to a lesser extent--gelatin, myoglobin, ovalbumin, and fibrinogen. The cleavage sites of these proteins by PA were chemically analyzed as the alpha-carboxyl side of some hydrophobic residues, tyrosine, leucine, valine, and phenylalanine, and of basic residues histidine, lysine, and arginine. The chymotrypsin-like activity of PA exhibited with the chromogenic substrate N-succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenylalanine p-nitroanilide yielded a specific activity of 9.21 microM per min per mg of PA and Km and kcat values of 15.3 mM and 0.075s-1, respectively. "Trypsin-like" activity of PA was also detected with N alpha-benzoyl-DL-arginine p-nitroanilide and gave a specific activity of 1.98 microM per min per mg of PA. Protease inhibitors such as phenylmethylsulfonyl fluoride, diisopropyl fluorophosphate, L-1-tosylamido-2-phenylethyl chloromethyl ketone, aprotinin, leupeptin, soybean trypsin inhibitor as well as Zn2+ and spermidine were effective inhibitors of PA enzymatic activity.
Overexpression of Fibroblast Growth Factor 23 Suppresses Osteoblast Differentiation and Matrix Mineralization In Vitro (2008)

These studies suggest that FGF23 overexpression suppresses not only osteoblast differentiation but also matrix mineralization independently of its systemic effects on Pi homeostasis.
Towards Optimal Cyber Defense Remediation in Energy Delivery Systems (2019)

Prioritized cyber defense remediation plan is critical for effective risk management in Energy Delivery System (EDS). Due to the complexity of EDS in terms of heterogeneous nature blending Information Technology (IT) and Operation Technology (OT) and Industrial Control System (ICS), scale and critical processes tasks, prioritized remediations should be applied gradually to protect critical assets. In this work, we propose a methodology for prioritized cyber risk remediation plan by detecting and evaluating paths to critical nodes in EDS. We propose critical nodes characteristics evaluation based on nodes' architectural positions, measure of centrality based on nodes' connectivity and frequency of network traffic, as well as the controlled amount of electrical power. The paper also examines the relationship between cost models of budget allocation for removal of vulnerabilities on critical nodes and its impact on gradual readiness. The proposed cost models were empirically validated in an actual network ICS test-bed computing nodes criticality. Two cost models were examined, and although varied, we concluded the lack of correlation between types of cost models to most damageable attack path and critical nodes readiness.
Immune Response to Herpes Simplex Virus and &#947;134.5 Deleted HSV Vectors (2005)

Herpes simplex virus (HSV) is a large DNA virus with unique properties that can be exploited for in vivo gene therapy. HSV is neurotropic, establishes latency, and has a large transgene capacity. These properties can be utilized in therapy of nervous system diseases. Wild-type HSV and the vectors derived from it induce both innate and acquired immune response. However, HSV is skillful in escaping the host response. It has evoked mechanisms including avoidance of antigen presentation on major histocompatibility (MHC) molecules, inhibition of host interferon response, impairment of the antibody and complement responses, and inhibition of apoptosis in infected cells. One of the molecules affecting the interferon response is ICP34.5, encoded by the so-called neurovirulence gene gamma(1)34.5. The mutants deleted of this gene are non-neurovirulent, having ca 3000-fold decreased ability to replicate in CNS. The HSV vectors based on the gamma(1)34.5 deletion mutants show efficacy against glioma and in other cancer therapies. These mutants provide an interesting platform for developing safe and efficient gene delivery for numerous neurological diseases or brain tumors. The immune response evoked by the HSV vector is central in determining the spread and persistence of the vector, and its transgene expression, and in controlling the innate and adaptive immune response against effective spread of the vector. These questions are key issues of herpesviral gene therapy and cancer therapy at the moment. This review describes the involvement of immune response in HSV infection and in gamma(1)34.5 deletion HSV-based virotherapy. We discuss the challenge of developing vectors with desired immune response benefiting the therapy and maintaining the efficiency.
Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow (2007)

This paper describes an approach to smooth the surface and improve the quality of quadrilateral/hexahedral meshes with feature preserved using geometric flow. For quadrilateral surface meshes, the surface diffusion flow is selected to remove noise by relocating vertices in the normal direction, and the aspect ratio is improved with feature preserved by adjusting vertex positions in the tangent direction. For hexahedral meshes, besides the surface vertex movement in the normal and tangent directions, interior vertices are relocated to improve the aspect ratio. Our method has the properties of noise removal, feature preservation and quality improvement of quadrilateral/hexahedral meshes, and it is especially suitable for biomolecular meshes because the surface diffusion flow preserves sphere accurately if the initial surface is close to a sphere. Several demonstration examples are provided from a wide variety of application domains. Some extracted meshes have been extensively used in finite element simulations.
Disulfide-mediated interactions of the chlamydial major outer membrane protein: role in the differentiation of chlamydiae? (1985)

The effects of exogenous reducing agents on a number of biological properties of purified Chlamydia trachomatis LGV-434 and Chlamydia psittaci meningopneumonitis elementary bodies (EBs) have been examined in an attempt to identify in vitro correlates of early events in the differentiation of the infectious EB to the replicative cell type, the reticulate body (RB). Treatment of EBs with dithiothreitol elicited a number of changes normally associated with differentiation to the RB. EBs in the presence of 10 mM dithiothreitol displayed enhanced rates of [14C]glutamate oxidation, reduced infectivity, and decreased osmotic stability, and their Machiavello staining properties changed to those characteristic of the RB. A true differentiation of EB to RB did not take place under these conditions, since EBs treated in this manner and examined by transmission electron microscopy did not demonstrate increased size or decreased electron density as do isolated RBs. Additional studies were initiated to identify the macromolecules involved in this process. With polyacrylamide gel electrophoresis and immunoblotting procedures with monoclonal and polyclonal monospecific antibodies, the chlamydial major outer membrane protein was found to be the predominant component that varied under reducing versus nonreducing conditions. Furthermore, the extent of disulfide-mediated cross-linking of the major outer membrane protein varied between the infective and replicative forms of the C. trachomatis LGV-434 life cycle. Implications of disulfide interactions in the life cycle of chlamydiae are discussed.
Detection and Molecular Characterization of Ebola Viruses Causing Disease in Human and Nonhuman Primates (1999)

Ebola (EBO) viruses were detected in specimens obtained during the hemorrhagic fever outbreak among humans in Kikwit, Democratic Republic of the Congo (DRC), in 1995 (subtype Zaire) and during an outbreak of disease in cynomolgus macaques in Alice, Texas, and the Philippines in 1996 (subtype Reston). Reverse transcriptase-polymerase chain reaction assays were developed and proven effective for detecting viral RNA in body fluids and tissues of infected individuals. Little change was seen in the nucleotide or deduced amino acid sequences of the glycoprotein (GP) of these EBO virus subtypes compared with those of their original representatives (i.e., the 1976 Yambuku, DRC, EBO isolate [subtype Zaire] and the 1989 Philippines and Reston, Virginia, isolates [subtype Reston]). The nonstructural secreted GP (SGP), the primary product of the GP gene, was more highly conserved than the structural GP, indicating different functional roles or evolutionary constraints for these proteins. Significant amounts of SGP were detected in acutely infected humans.
Ligands for the Benzodiazepine Binding Site - a Survey (1999)

Gamma-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian Central Nervous System (CNS). GABA participates in the regulation of neuronal excitability through interaction with specific membrane proteins (the GABAA receptors). The binding of GABA to these postsynaptic receptors, results in an opening of a chloride channel integrated in the receptor which allows the entry of Cl- and consequently leads to hyperpolarization of the recipient cell. The action of GABA is allosterically modulated by a wide variety of chemical entities which interact with distinct binding sites at the GABAA receptor complex. One of the most thoroughly investigated modulatory site is the benzodiazepine binding site. The benzodiazepines constitute a well-known class of therapeutics displaying hypnotic, anxiolytic and anticonvulsant effects. Their usefulness, however, is limited by a broad range of side effects comprising sedation, ataxia, amnesia, alcohol and barbiturate potentiation, tolerance development and abuse potential. Consequently, there has been an intensive search for modulatory agents with an improved profile, and a diversity of chemical entities distinct from the benzodiazepines, but with GABA modulatory effects have been identified. The existence of endogenous ligands for the GABAA receptor complex beside GABA has often been described, but their role in the regulation of GABA action is still a matter of controversy. The progress of molecular biology during the last decade has contributed enormously to the understanding of benzodiazepine receptor pharmacology. A total of 14 GABAA receptor subunits have been cloned from mammalian brain and have been expressed/co-expressed in stable cell lines. These transfected cells constitute an important tool in the characterization of subtype selective ligands. In spite of the rapidly expanding knowledge of the molecular and pharmacological mechanisms involved in GABA/benzodiazepine related CNS disorders, the identification of clinically selective acting drugs is still to come.
Effects of caldesmon, calponin, and tropomyosin on the Mg2+-ATPase activities of smooth muscle myosin. (2004)

The results propose that caldesmon, calponin, and tropomyosin are capable of stimulating Mg2+-ATPase activity of smooth muscle myosin in Ca2+-independent manner, since Ca2+ is not obligating for the stimulating effects of the three proteins. The common characteristic of the three proteins is that when myosin activities are low, their activations are relatively strong and this property might be involved in smooth muscle tension keeping.
Improved electro-optical target detection in a natural fractal environment (1993)

Pictures photographed by optical and electro-optical systems often suffer from distortion caused by atmospheric disturbance, electrical noise, and optical aberration introduced by the imaging system. In this paper, we suggest a method to restore pictures of natural scenes, under the assumption that they can be characterized as two-dimensional representations of fractional Brownian Motion (to be called fractal images). In this paper we synthesize fractal images, find ways to characterize their fractal dimension, and develop a new technique to restore the images.
Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene (1986)

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons.
Display of surfaces from volume data (1988)

The application of volume-rendering techniques to the display of surfaces from sampled scalar functions of three spatial dimensions is discussed. It is not necessary to fit geometric primitives to the sampled data; images are formed by directly shading each sample and projecting it onto the picture plane. Surface-shading calculations are performed at every voxel with local gradient vectors serving as surface normals. In a separate step, surface classification operators are applied to compute a partial opacity of every voxel. Operators that detect isovalue contour surfaces and region boundary surfaces are examined. The technique is simple and fast, yet displays surfaces exhibiting smooth silhouettes and few other aliasing artifacts. The use of selective blurring and supersampling to further improve image quality is described. Examples from molecular graphics and medical imaging are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>