gebhart/patrepeval huggingface dataset:
Targeting the Variable Surface of African Trypanosomes with Variant Surface Glycoprotein-Specific, Serum-Stable RNA Aptamers (2003)

African trypanosomes cause sleeping sickness in humans and Nagana in cattle. The parasites multiply in the blood and escape the immune response of the infected host by antigenic variation. Antigenic variation is characterized by a periodic change of the parasite protein surface, which consists of a variant glycoprotein known as variant surface glycoprotein (VSG). Using a SELEX (systematic evolution of ligands by exponential enrichment) approach, we report the selection of small, serum-stable RNAs, so-called aptamers, that bind to VSGs with subnanomolar affinity. The RNAs are able to recognize different VSG variants and bind to the surface of live trypanosomes. Aptamers tethered to an antigenic side group are capable of directing antibodies to the surface of the parasite in vitro. In this manner, the RNAs might provide a new strategy for a therapeutic intervention to fight sleeping sickness.
Solubilities of l-Cystine, l-Tyrosine, l-Leucine, and Glycine in Aqueous Solutions at Various pHs and NaCl Concentrations (1996)

Solubilities at 25 °C of four amino acids (l-cystine, l-tyrosine, l-leucine, and glycine) in aqueous solutions at various pHs and NaCl concentrations (0, 1, 3 mol dm-3) are reported. The pH was varied from 0 to 13 using HCl or NaOH. The NaCl concentration strongly affects the solubilities of l-cystine, l-tyrosine, and l-leucine. In particular, the addition of NaCl increases the l-cystine solubility but reduces the solubility of l-tyrosine and l-leucine. The NaCl concentration has only a slight effect on the solubility of glycine. Experimental solubilities are correlated with the use of a chemical equilibrium model, good agreement in the pH range 1−12 was found. The analysis confirms the dependence reported in the literature between the solubility of amino acids and the salt concentration. For the amino acids examined, the parameters to calculate their solubilities in solutions with NaCl are also given.
Remote Optical Cardiopulmonary Signal Extraction With Noise Artifact Removal, Multiple Subject Detection & Long-Distance (2018)

Most existing imaging technologies are prone to noise artifact resulting from movement of subjects, movement of the camera, facial expressions, talking, skin tone, and lighting variations. In addition, these technologies have been limited to detecting physiological signs from a single subject at a time. Still, another challenge facing these technologies is that they have only been demonstrated over a limited range to a subject. This paper proposes an efficient remote imaging system with a new, low-complexity method for noise artifact removal to extract the cardiopulmonary signal from a number of subjects (up to six people) and at long-distances (up to 60 m). The experimental results of the proposed system showed a strong agreement, high correlation, and low noise level with the reference measurements and outperformed the conventional measurement methods such as independent component analysis and principle component analysis in both the stationary and non-stationary scenarios.
Investigation of the applicability of a sequential digestion protocol using trypsin and leucine aminopeptidase M for protein identification by matrix-assisted laser desorption/ionization - time of flight mass spectrometry (2001)

An investigation of the applicability of a sequential digestion procedure involving endo- and exoprotease digestion of proteins is reported. The procedure involves the digestion of a protein sample with trypsin, yielding peptide fragments characteristic of the protein. The resulting mixture of peptide fragments is then subjected to N-terminal sequencing with leucine aminopeptidase M (LAP), with matrix-assisted laser desorption ionization-time of flight mass spectrometric analysis of the various digestion products. Several proteins in solution, as well as gel extracted proteins were subjected to this sequential enzyme digestion procedure. The results of these experiments reveal that LAP will preferentially cleave specific peptides of the trypsin digested sample with high efficiency, while leaving other peptides undigested. Also, the length of the amino acid sequence tags that can be generated with this method is limited; the longest sequence tag generated from a single tryptic peptide was four amino acids, even though the digestion was allowed to proceed for long times. In the experiments, N-terminal digestion products were detected as early as two minutes, or as late as 90 minutes, following the addition of LAP to the sample. The method was shown to be effective for subpicomole starting quantities of protein, although with some loss in digestion efficiency at lower concentrations of starting material. This method is useful in providing additional sequence information to increase the level of confidence in protein identification, as illustrated in the identification of bacterial proteins fractionated by high-performance liquid chromatography. In some instances, this method can provide additional sequence information where post source decay and nanospray mass spectrometry failed to generate fragment ion spectra. This is illustrated in an example where the procedure was applied to a membrane protein, CD9, that had been isolated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Although the sequential digestion procedure requires more human intervention, it is a straightforward method and can be readily implemented.
A research on photovoltaic energy controlling system with maximum power point tracking (2003)

This paper introduces a photovoltaic energy system, controlled by a DC-DC converter and a single phase bi-directional PWM converter to realize the inversion. A current controlling (MPPT) method of tracking the maximum power point and forcing the system to operate close to this point is used. An artificial neural network is used in the MPPT system and its robustness and insensitivity to the intermittent weather conditions is enhanced. Uc3854 is used as an inversion current controller, which has a high performance in harmonics and power factor.
Energetic Contributions and Topographical Organization of Ligand Binding Residues of Tissue Factor (1995)

Tissue factor is the cellular receptor and macromolecular enzymatic cofactor for the serine protease coagulation factor VIIa. The ligand binding extracellular domain of tissue factor consists of two structural modules which fold similar to fibronectin type III modules, consistent with the classification of tissue factor as a member of the class 2 cytokine receptor family. On the basis of the three-dimensional structure, we here analyze the importance of tissue factor residues for binding of ligand by scanning alanine mutagenesis. The identified significant binding contacts account for as much as 80% of the calculated total free energy of ligand binding. Most residues with energetic contributions to ligand binding are well exposed to solvent, and the area for ligand interaction extends from the cleft formed by the two structural modules (residues Lys20, Ile22, Lys48, Asp58, Arg135, Phe140) to the convex-shaped edge of the three- and four-stranded sheets characterized by a patch of surface-exposed hydrophobic side chains in the amino-terminal module (residues Gln37, Asp44, Trp45, Phe76, Tyr78). The binding residues are dispersed over an extended surface area, indicating adaptation to the recognition of specific structural modules of the macromolecular ligand factor VIIa. This analysis provides detailed insight into the three-dimensional organization of the ligand docking structure of the initiating cofactor for the coagulation pathways.
Expression of Hirudin Fusion Proteins in Mammalian Cells (1998)

Hirudin fusion proteins were expressed on mammalian cells, where they reduced local thrombin levels and inhibited fibrin formation. Regulated expression was achieved on activated cells by use of the cytoplasmic sequence from P-selectin. In vivo, these fusion proteins may prove useful transgenic or gene therapy agents for preventing intravascular thrombosis.
Differential gene expression in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Noncoordinate regulation of a TCDD-induced aldehyde dehydrogenase and cytochrome P-450c in the rat. (1988)

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) regulates the transcription of a specific subset of genes through a receptor-mediated mechanism. We have isolated a cDNA to a TCDD-inducible rat liver aldehyde dehydrogenase and have shown that its induction by TCDD differs from that of another TCDD-induced gene, cytochrome P-450c, with regard to dose-response relationship, induction kinetics, and tissue specificity. At least a 10-fold higher dose of TCDD was required for half-maximal induction of TCDD-inducible rat liver aldehyde dehydrogenase in rat liver than the dose that half-maximally induced cytochrome P-450c. Further, the kinetics of induction of TCDD-inducible rat liver aldehyde dehydrogenase by TCDD in rat liver was delayed compared with that of cytochrome P-450c. Striking discrepancies were found in the capacity of various organs to induce both TCDD-inducible rat liver aldehyde dehydrogenase and cytochrome P-450c in a coordinated manner in response to TCDD. Organs that were able to evoke one of these responses to TCDD were not necessarily able to evoke coordinately the other response. The capacity of an organ to exhibit either of these two responses to TCDD did not correlate stringently with reported Ah receptor abundance. Our data suggest that TCDD can modulate the expression of specific genes in different ways and that regulatory pathways in addition to the classically defined Ah receptor may be involved.
High Mobility Group Box Protein 1 (HMGB1): The Prototypical Endogenous Danger Molecule (2015)

High mobility group box protein 1 (HMGB1) is an evolutionary ancient nuclear protein that exerts divergent biological tasks inside and outside of cells. The functions of HMGB1 depend on location, binding partners and redox states of the molecule. In the nucleus, HMGB1 organizes DNA and nucleosomes and regulates gene transcription. Upon cell activation or injury, nuclear HMGB1 can translocate to the cytoplasm, where it is involved in inflammasome activation and pyroptosis, as well as regulation of the autophagy/apoptosis balance. When actively secreted or passively released into the extracellular milieu, HMGB1 has cytokine, chemokine, neuroimmune and metabolic activities. Thus, HMGB1 plays multiple roles in the pathogenesis of inflammatory diseases and mediates immune responses that range from inflammation and bacterial killing to tissue repair. HMGB1 has been associated with divergent clinical conditions such as sepsis, rheumatoid arthritis and atherosclerosis. HMGB1 initiates and perpetuates immune responses during infectious and sterile inflammation, as the archetypical alarmin and damage-associated molecular pattern (DAMP) molecule. We here describe advances in the understanding of HMGB1 biology with focus on recent findings of its mission as a DAMP in danger sensing and as a therapeutic target in inflammatory diseases.
Reversible PEGylation:  A Novel Technology To Release Native Interferon α2 over a Prolonged Time Period (2004)

Many peptide and protein drugs have a short circulatory half-life in vivo. The covalent attachment of polyethylene glycol (PEG) chains (PEGylation) can overcome this deficiency, but pegylated peptides and proteins are often inactive. In this study, we present a novel PEG-IFNalpha2 conjugate, PEG(40)-FMS-IFNalpha2, capable of regenerating native interferon alpha2 (IFNalpha2) at a slow rate under physiological conditions. A 2-sulfo-9-fluorenylmethoxycarbonyl (FMS) containing bifunctional reagent, MAL-FMS-NHS, has been synthesized, enabling the linkage of a 40 kDa PEG-SH to IFNalpha2 through a slowly hydrolyzable bond. By use of a BIAcore binding assay, the in vitro rate of regeneration of native interferon was estimated to have a half-life of 65 h. Following subcutaneous administration to rats and monitoring circulating antiviral activity, active IFNalpha2 levels peaked at 50 h, with substantial levels still being detected 200 h after administration. This value contrasts with a half-life of about 1 h measured for unmodified interferon. The concentration of active IFNalpha2 scaled linearly with the quantity injected. Comparing subcutaneous to intravenous administration of PEG(40)-FMS-IFNalpha2, we found that the long circulatory lifetime of IFNalpha2 was affected both by the slow rate of absorption of the PEGylated protein from the subcutaneous volume and by the slow rate of discharge from the PEG in circulation. A numerical simulation of the results was in good agreement with the results observed in vivo. The pharmacokinetic profile of this novel IFNalpha2 conjugate combines a prolonged maintenance in vivo with the regeneration of active-native IFNalpha2, ensuring ready access to peripheral tissues and thus an overall advantage over currently used formulations.
Somatostatin receptors in human endocrine tumors. (1987)

A selection of 90 mainly endocrine but nonpituitary tumors have been tested for their content of specific somatostatin receptors using receptor autoradiography. Somatostatin receptors were detected in the following tumors: in all 5 meningiomas tested; in 3 of 39 malignant breast tumors; and in 3 growth hormone releasing factor-producing tumors, i.e., one mediastinal carcinoid, one intestinal carcinoma, and its liver metastasis. Receptor density varied greatly among individual tumors. Some of the positive tumors were biochemically characterized using in vitro binding assay and were shown to have saturable and high affinity receptors with pharmacological specificity for somatostatin. The following tumors did not contain somatostatin receptors: prostate carcinomas (n = 17); prostate hyperplasia (n = 2); ovarian carcinomas (n = 6); endometrial carcinomas (n = 4); primary liver cell carcinomas (n = 3); pheochromocytomas (n = 3); aldosteronomas (n = 2); medullary thyroid carcinomas (n = 2); one adrenocorticotropic hormone-secreting pulmonary carcinoid; one astrocytoma; one neurofibroma; one lung tumor; and one bladder tumor. Somatostatin receptors can be found in benign or malignant tumors, originating in part from tissue not primarily known as a somatostatin target. The biological function of such receptors is, therefore, partly unknown. If they can mediate antiproliferative properties, as has been suggested to be the case for somatostatin receptors in selected endocrine tumors in rats and humans, the present data could be of potential therapeutic interest.
The Landscape of the Liberal Arts (2013)

Abstract This chapter provides a rationale for the value of a liberal arts education, addressing briefly the recent history of the liberal arts, explaining the value of the liberal arts in diverse educational settings as opposed to simply residential liberal arts colleges, and exploring a contemporary rationale for the liberal arts.
Prediction of the Adaptability of Pseudomonas putida DOT-T1E to a Second Phase of a Solvent for Economically Sound Two-Phase Biotransformations (2005)

The strain Pseudomonas putida DOT-T1E was tested for its ability to tolerate second phases of different alkanols for their use as solvents in two-liquid-phase biotransformations. Although 1-decanol showed an about 10-fold higher toxicity to the cells than 1-octanol, the cells were able to adapt completely to 1-decanol only and could not be adapted in order to grow stably in the presence of a second phase of 1-octanol. The main explanation for this observation can be seen in the higher water and membrane solubility of 1-octanol. The hydrophobicity (log P) of a substance correlates with a certain partitioning of that compound into the membrane. Combining the log P value with the water solubility, the maximum membrane concentration of a compound can be calculated. With this simple calculation, it is possible to predict the property of an organic chemical for its potential applicability as a solvent for two-liquid-phase biotransformations with solvent-tolerant P. putida strains. Only compounds that show a maximum membrane concentration of less than 400 mM, such as 1-decanol, seem to be tolerated by these bacterial strains when applied in supersaturating concentrations to the medium. Taking into consideration that a solvent for a two-liquid-phase system should possess partitioning properties for potential substrates and products of a fine chemical synthesis, it can be seen that 1-decanol is a suitable solvent for such biotransformation processes. This was also demonstrated in shake cultures, where increasing amounts of a second phase of 1-decanol led to bacteria tolerating higher concentrations of the model substrate 3-nitrotoluene. Transferring this example to a 5-liter-scale bioreactor with 10% (vol/vol) 1-decanol, the amount of 3-nitrotoluene tolerated by the cells is up to 200-fold higher than in pure aqueous medium. The system demonstrates the usefulness of two-phase biotransformations utilizing solvent-tolerant bacteria.
Nanocrystal and Nanowire Synthesis and Dispersibility in Supercritical Fluids (2004)

Here we review major breakthroughs in the rapidly developing research area of nanomaterial synthesis in supercritical fluids focusing on both the fundamental science and processing advantages in the application areas of separations, assembly and scale-up of synthesis. Density-tunable control of the solvation strength, along with favorable interfacial tensions, wetting, and transport properties make supercritical fluids (SCFs) unique and potentially superior solvent media for the synthesis and processing of nanoscale metals and semiconductors. The steric repulsion between particle cores may be tuned by adjusting the solvent density to control the nanocrystal size and polydispersity during single-phase synthesis, and to achieve size-selective nanocrystal precipitation. Compressed solvents at the vapor pressure can also be used to deposit nanocrystal monolayers at controlled evaporation rates without dewetting at higher rates than conventional solvents. The high synthetic temperatures accessible in SCFs can be used to promote the crystallization of covalent nanomaterials, while maintaining a reaction environment capable of solvating reactants and capping ligands. This allows semiconductor nanocrystals exhibiting size-dependent photoluminescence to be synthesized at temperatures well above the boiling point of conventional solvents. Finally, gold nanocrystal seed particles can be used to synthesize bulk quantities of defect-free silicon and germanium nanowires, several micrometers in length.
Advanced telerobotic controller (2002)

An advanced telerobotic control system has been developed for a subsea manipulator as part of the ARM (Automated Remote Manipulation) project. This project is being conducted by a consortium comprising Mobil North Sea Ltd (MNSL), the Offshore Supplies Office (OSO), Slingsby Engineering Ltd (SEL), Technical Software Consultants Limited (TSC) and University College London (UCL). The arm controls comprise a fast PC surface graphics control unit linked via the Remotely Operated Vehicle (ROV) umbilical to a 68000, VME-bus based subsea arm controller. This provides supervisory control of the manipulator, including manual master-slave tele-manipulation and fully automated, robotic task execution. A 3D video representation of the ROV, manipulator and work site is presented to the operator using solid shaded colour graphics, and can be used to monitor the arm whilst planning or executing tasks. The viewpoint can be modified to aid visualisation, and secondary windows used to display plan and elevation views of the arm and its work area. Also the arm can be viewed as if from an ROV mounted camera to give a close up which should correlate with actual television images. The arm can be controlled by a choice of input devices including keyboard, mouse, master arm or joysticks and operated in a variety of co-ordinate systems such as joint, world, tool, workpiece, etc. Standard serial communications have been used between the surface and subsea computers to improve readability and noise immunity. This requires a number of software modules to be implemented in both computers; these include inverse kinematics, path generation and collision detection routines. The topside computer has an update rate of 5 Hz which gives adequate sampling of the input device and refresh of the graphics. The subsea computer works at 50 Hz to give high bandwidth arm control. The first prototype arm has been fabricated and tests are in progress with the control software. This paper describes the operation of the arm undergoing a range of typical tasks. The tasks include tactile cylinder sizing and location to determine the trajectory of a nodal weld, and tracking round the weld with an inspection probe.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Brush polymer ion gels (2015)

ABSTRACT The structure, rheological response, and ionic conductivity of ABA brush block copolymer (BBCP) ion gels containing 1‐butyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide ([BMI][TFSI]) at polymer concentrations spanning 5‐50 wt % ( Φ gel ) were studied by small angle X‐ray scattering, dynamic mechanical analysis, and AC impedance spectroscopy. Application of a hard sphere form factor and Percus‐Yevick structure factor reveals trends in gel micellar structure as a function of BBCP molecular weight, A block volume fraction ( Φ A ), and Φ gel . Viscoelastic properties are strongly dependent on end‐block molar mass, with storage moduli ≤10 3 Pa at 25 °C. Impedance measurements reveal near liquid‐like dynamics in the matrix phase as evidenced by conductivities near 1 mS/cm at 25 °C that decrease with increasing Φ gel and Φ A . © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 292–300
Protein import into plant mitochondria: signals, machinery, processing, and regulation (2014)

The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.