gebhart/patrepeval huggingface dataset:
Classification of Protein Binding in Hydroxyapatite Chromatography: Synergistic Interactions on the Molecular Scale (2011)

A protein library exhibiting a range of properties was employed to study protein binding behavior in hydroxyapatite systems. Chromatographic retention on ceramic hydroxyapatite (CHT) chromatography was determined using a sodium chloride gradient in the presence of different phosphate concentrations. Results from the column experiments were then analyzed using various quantitative structure property relationship (QSPR) based modeling approaches. Using the experimental data set in concert with new molecular descriptors, QSPR classification models were generated to provide improved understanding of protein binding in CHT systems. In addition, nonlinear SVM QSPR prediction models were generated and employed as a predictive tool for protein affinity in CHT. Interestingly, a class of descriptors which describe synergistic binding with both metal chelation and cation exchange interactions on the angstrom length scale was found to play a vital role for protein binding in all of the models developed for CHT. The importance of this descriptor suggests the importance of synergistic binding in CHT, which has not been previously described in the literature. This study provides a deeper understanding into the mechanisms and selectivity of protein adsorption in CHT and will help to create predictive models which could be used for methods development in bioseparation processes.
Yellow fever vaccine (2005)

Yellow fever, a mosquito-borne viral hemorrhagic fever, is one of the most lethal diseases of humankind. The etiologic agent is the prototype member of the genus Flavivirus, family Flaviviridae, a group of small, enveloped, positive-sense, single-strand RNA viruses. Approximately one in seven people who become infected develop a rapidly progressive illness, with hepatitis, renal failure, hemorrhage and cardiovascular shock, with a case fatality rate of 20-50%. Yellow fever occurs in sub-Saharan Africa and tropical South America, where it remains a continuing public health problem of varying magnitude, depending on the level of vaccination coverage in the human population and cyclical, ecologic and climatic factors that influence virus transmission.
Application of Melt-State NMR Spectroscopy for Polyolefin Characterization in Industry (2011)

Melt-state 13C NMR spectroscopy of polyolefins has been shown to be sensitive, quantitative and allow rapid sample throughput. The method was implemented in an industrial research and development environment and has proved to be both highly sensitive and versatile. For general problem solving melt-state MAS NMR was found to complement standard high-temperature solution state NMR. The main strength of the technique was found to be the possibility of high throughput, due to the combination of high sensitivity and rapid sample preparation. This was most clearly demonstrated for materials of low solubility. A broad scope of application of melt-state MAS NMR is demonstrated through the study of the whole family of polyolefins including HDPE homopolymers, HDPE copolymers, LLDPE, LDPE, LDPE copolymers, PP homopolymers and PP copolymers. The application of the techniques to the study of fractionated materials and filled materials is also demonstrated. Some key advantages as compared to standard solution-state NMR spectroscopy are emphasized and recent research on decoupling in the molten-state is presented.
Development of a multisensor road surveying measurement system (2012)

The construction of highways and federal roadways is subject to many restrictions and designing rules. The focus is on safety, comfort and smooth driving. Unfortunately, the planning information for roadways and their real constitution, course and their number of lanes and lane widths is often unsure or not available. Due to digital map databases of roads raised much interest during the last years and became one major cornerstone of innovative Advanced Driving Assistance Systems (ADAS), the demand for accurate and detailed road information increases considerably. Within this project a measurement system for collecting high accurate road data was developed. This paper gives a technical overview about the entire system, introduces the sensor configuration within the vehicle and shows some applications implemented in the post processing platform. The aim is to recover the origin parametric description of the roadway and the performance of the measurement system is being evaluated against several original road construction information. The system was developed for the Federal Highway Research Institute and is currently in a testing phase.
Delineating the core regulatory elements crucial for directed cell migration by examining folic-acid-mediated responses (2012)

Dictyostelium discoideum shows chemotaxis towards folic acid (FA) throughout vegetative growth, and towards cAMP during development. We determined the spatiotemporal localization of cytoskeletal and signaling molecules and investigated the FA-mediated responses in a number of signaling mutants to further our understanding of the core regulatory elements that are crucial for cell migration. Proteins enriched in the pseudopods during chemotaxis also relocalize transiently to the plasma membrane during uniform FA stimulation. In contrast, proteins that are absent from the pseudopods during migration redistribute transiently from the PM to the cytosol when cells are globally stimulated with FA. These chemotactic responses to FA were also examined in cells lacking the GTPases Ras C and G. Although Ras and phosphoinositide 3-kinase activity were significantly decreased in Ras G and Ras C/G nulls, these mutants still migrated towards FA, indicating that other pathways must support FA-mediated chemotaxis. We also examined the spatial movements of PTEN in response to uniform FA and cAMP stimulation in phospholipase C (PLC) null cells. The lack of PLC strongly influences the localization of PTEN in response to FA, but not cAMP. In addition, we compared the gradient-sensing behavior of polarized cells migrating towards cAMP to that of unpolarized cells migrating towards FA. The majority of polarized cells make U-turns when the cAMP gradient is switched from the front of the cell to the rear. Conversely, unpolarized cells immediately extend pseudopods towards the new FA source. We also observed that plasma membrane phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] levels oscillate in unpolarized cells treated with Latrunculin-A, whereas polarized cells had stable plasma membrane PtdIns(3,4,5)P3 responses toward the chemoattractant gradient source. Results were similar for cells that were starved for 4 hours, with a mixture of polarized and unpolarized cells responding to cAMP. Taken together, these findings suggest that similar components control gradient sensing during FA- and cAMP-mediated motility, but the response of polarized cells is more stable, which ultimately helps maintain their directionality.
Topical synthetic inhibitor of matrix metalloproteinases delays epidermal regeneration of human wounds* (2001)

Matrix metalloproteinases (MMPs) degrade extracellular proteins during epithelialization of wounds. To evaluate the biological significance of MMPs in epidermal healing, the synthetic broad-spectrum MMP inhibitor GM 6001 (also called Galardin and Ilomastat) was applied topically to standardized human wounds. GM 6001 (10 microg/microl) or vehicle alone was applied every second day onto 4 de-roofed 6 mm suction blister wounds on the volar forearm of healthy male volunteers for 12 days. GM 6001 delayed healing by 2-4 days as assessed macroscopically and microscopically. In situ hybridization or immunohistochemistry showed that MMP-1 (interstitial collagenase) was present in and MMP-2 (gelatinase A) close to laterally migrating keratinocytes whereas MMP-9 (gelatinase B) was seen during maturation of new epidermis. MMP-1 was undetectable in blister roofs (normal epidermis) and found in low levels in normal skin. Total MMP-1 activities increased about 100-fold in wounds, independent of treatment, compared to normal skin as analyzed by specific ELISA-based activity assay. By gelatin zymography, MMP-2, but not MMP-9, was detected in blister roofs and wound healing was associated with increased active MMP-2 and latent MMP-9 levels. GM 6001 prevented activation of MMP-2 and increased latent MMP-9 levels. GM 6001 delayed re-appearance of laminin-5, the synthesis of which correlated with epidermal regeneration. Restoration of stratum corneum, measured indirectly by transepidermal water loss, was also impaired (P<0.05) in the GM 6001 group. In conclusion, pharmacological MMP inhibition delayed epidermal regeneration in vivo, suggesting that MMPs are required to restore epidermis after epidermal ablation in humans.
Purification and characterization of a protein from chicken gizzard, which inhibits actin polymerization (1985)

An actin-polymerization-inhibiting protein, that occurs in crude preparations of vinculin from chicken gizzard, has been purified by DEAE-cellulose and carboxymethyl ion-exchange chromatography. According to sodium dodecyl sulfate (SDS)/polyacrylamide gel electrophoresis and to gel filtration the polymerization-inhibiting protein is heterogeneous and the molecular mass ranges from 20 kDa to 80 kDa. After treatment with acid the polymerization-inhibiting activity was found to migrate on a SDS/polyacrylamide gel as a single band of molecular mass about 32 kDa. The mechanism of the action of the polymerization-inhibiting protein on actin assembly was investigated by the effect on the kinetics of actin polymerization. The polymerization-inhibiting protein blocks elongation of actin filaments at substoichiometric ratios but does not nucleate actin filaments. The equilibrium constant for binding of the polymerization-inhibiting protein to the barbed end of an actin filament was estimated to be 2 X 10(6) M-1 in 100 mM KCl and 2 mM MgCl2, and 35 X 10(6) M-1 in 2 mM MgCl2.
Notes on a programme of work on informal construction in Africa (2011)

The overall aim of this program is to increase understanding of, and help improve, the estimation of the value, volume and price levels of construction activity in African countries and other developing countries in which household own-account construction is common. Specific objectives are to investigate: the value of construction activity included in, and excluded from, national accounts; how best to distinguish the forms of small and micro-scale informal construction activities which characterize own-account construction in Africa, and which are usually unregulated and under-enumerated; the range and types of such informal construction; the resource (input) prices (particularly, labor and material prices) for these activities; options to improve the collection of purchase price and rental values for informal housing; and the production of PPPs for informal construction. In the longer term, outputs of the research will contribute to improved construction output data, national accounts, construction PPPs and poverty analyses. These will be useful for national and international agencies, development experts and academics and others. The work reported below will demonstrate what is possible, provide preliminary results and indicate what a fuller study will involve and produce.
Morphologic and functional effects of <i>Clostridium difficile</i> enterotoxin in tissue culture (1982)

The effects of the Clostridium difficile toxin were examined in HeLa and mouse adrenal tumor (MAT) cells. Cytotoxicity was evaluated by vital dye exclusion and 51Cr release. In both HeLa and MAT cells, C. difficile toxin caused rounding of virtually 100% of cells. This rounding was distinguishable from rounding produced by the Escherichia coli heat-labile enterotoxin (LT): (1) LT was inactive in HeLa cells; (2) in MAT cells, C. difficile toxin produced uniformly rounded cells, while LT-rounded cells usually had cytoplasmic extensions and a regular background of flattened cells. In C. difficile toxin affected HeLa cells, there were less than mitotic figures per 1000 cells compared with 15-18 in controls. Clostridium difficile toxin treated HeLa cells showed less than 10% cytotoxicity in 24 h and no more than 30% by 74 h, similar to control cells. However, paralleling the suppression of mitotic figures, cell multiplication was inhibited in C. difficile toxin treated cells when subcultured in a short-term (72 h) assay compared with up to a 500% increase in control cells. This inhibition was also seen in a 6-week cloning assay in which C. difficile toxin treated cells had a cloning efficiency of less than 1% compared with approximately 10% in controls. We conclude that the major effect of the C. difficile toxin is inhibition of growth rather than immediate cell death. The relationship of this growth inhibition to colitis remains to be elucidated.
Operating System Concepts Essentials (2010)

Straightforward coverage of the core concepts of operating systems Open-source operating systems, virtual machines, and clustered computing are among the leading fields of operating systems and networking that are rapidly changing. This book covers the core concepts of operating systems without any unnecessary jargon or text. The authors put you on your way to mastering the fundamental concepts of operating systems while you also prepare for todays emerging developments. Covers the core concepts of operating systems Bypasses unnecessary and wordy text or jargon Encourages you to take your operating system knowledge to the next level Prepares you for todays emerging developments in the field of operating systems Operating Systems Concepts Essentials is a soup-to-nuts guide for all things involving operating systems!
A comparison of homologous recombination rates in bacteria and archaea (2008)

It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.
Polymerase Chain Reaction (2012)

This book is intended to present current concepts in molecular biology with the emphasis on the application to animal, plant and human pathology, in various aspects such as etiology, diagnosis, prognosis, treatment and prevention of diseases as well as the use of these methodologies in understanding the pathophysiology of various diseases that affect living beings.
Development of a new host vector system in mycobacteria (1991)

The hybrid plasmid pYT72/pYT92 constructed from an Escherichia coli plasmid pACYC177 and mycobacterial plasmid pMSC262 isolated from Mycobacterium scroflaceum strain W262 transformed both E. coli and BCG. Phage-sensitive mutants S-10 and S-20 isolated from BCG Tokyo strain showed higher frequency of transformation than the wild-type strain. Frequency of transformation was dependent on age of the culture and the electroporation condition used. Several deletion mutants were generated from pYT72/92 to determine the minimum region for the replication in the mycobacteria. A 2.3-kb fragment of pMSC262 was found to contain an essential region. Using this fragment and pACYC177, a small shuttle vector pYT937 containing two drug-resistance markers, kanamycin- and ampicillin-resistance, was constructed. pYT937 contains AatII, BamHI, BbvII, GsuI, HincII, PstI, ScaI and XbaI cloning sites.
Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography (2015)

Two-tensor UKF tractography provides the ability to trace a larger volume AF than single-tensor streamline tractography in the setting of peritumoral edema in brain tumor patients.
Evidence that anti–tumor necrosis factor therapy with both etanercept and infliximab induces apoptosis in macrophages, but not lymphocytes, in rheumatoid arthritis joints: Extended report (2005)

In RA patients, both etanercept and infliximab are able to induce cell type-specific apoptosis in the monocyte/macrophage population. This suggests a potential pathway that would account for the diminished synovial inflammation and the decreased numbers of synovial macrophages evident after TNF blockade.
A novel method for detection of HBVcccDNA in hepatocytes using rolling circle amplification combined with in situ PCR (2014)

RCA combined with IS-PCR is an effective and practicable method which could detect the presence of low copy number of cccDNA sensitively and specifically, and reflect the relationship between cccDNA expression level and liver tissue pathological characteristics.
Synthesis of a Biotinated Lipofullerene as a New Type of Transmembrane Anchor (2000)

As a prototype for a new class of lipid membrane components, the lipophilic fullerene derivative (so-called lipofullerene) 1 was synthesized and characterized. This mixed [1:5]-hexakisadduct consists of ten long alkyl chains within five didodecyl malonate addends and a linker malonate carrying a (+)-biotin unit as part of an amphiphilic spacer. The malonates are attached to the fullerene core in an octahedral addition pattern, which was achieved by two successive cyclopropanation sequences with the functional precursor malonate 8 and dodecyl malonate 10. The final step of the synthesis of 1 was the attachment of activated biotin 5 with the deprotected precursor 11. Binding experiments followed by reflectometric interference spectroscopy [RIfS] proved the capability of 1 to bind specifically the protein streptavidin (SA) through the biotin unit. The amphiphilic behavior of 1 was demonstrated by Langmuir Blodgett (LB) film investigations.
In vivo efficacy of antimicrobial-coated fabric from prosthetic heart valve sewing rings. (1998)

These results suggest that silver-coated sewing rings may not prove to be clinically anti-infective. In contrast, antimicrobial-coated sewing rings that produce effective zones of inhibition, particularly those coated with M/R, are likely to be clinically protective.
The Effect of Tapering the Optical Fiber on Evanescent Wave Measurements (1992)

Abstract Optical biosensors are analytical tools employed in environmental, biotechnology and clinical fields. For remote evanescent wave detection with optical fibers, the majority of the fiber remains cladded while only a small portion of the core is exposed to perform the analysis. To improve the sensitivity of this type of fiber optic biosensor, tapering the sensing region of the fiber was investigated. Silica fibers were tapered into two geometries: step and continuous tapers. To determine the effect of tapering on detection levels, a fluoroimmunoassay was performed on fibers with nontapered, step-tapered and continuously tapered geometries. Solutions containing a fluorescent analyte were circulated over an antibody-coated fiber and the fluoresence signal measured The minimum detection limit for fibers with 10 cm sensing region was 1.56 nM, 0.31 nM and 0.16 nM for nontapered, step-tapered and continuously tapered fibers, respectively. Continuous tapering of the sensing region of an optical fiber offered a 10-fold increase in the sensitivity of the optical biosensor.
Electrolytic-capacitor-less AC/DC electric vehicle on-board battery charger for universal line applications (2011)

Proposed is an electrolytic-capacitor-less AC/DC on-board charger for electric vehicles. To remove the high-voltage electrolytic capacitor, the proposed charger uses a rectified AC type link voltage generated by an isolated resonant converter, and harmonic and charge controls are achieved through a discontinuous conduction mode buck–boost converter. It provides normal control operation under wide input voltage range with only a single control loop. The feasibility has been verified with a 3 kW prototype.
Reductive dehalogenation by cytochrome P450CAM: Substrate binding and catalysis (1993)

Biological reductive dehalogenation reactions are important in environmental detoxification of organohalides. Only scarce information is available on the enzymology underlying these reactions. Cytochrome P450CAM with a known X-ray structure and well-studied oxygenase reaction cycle, has been studied for its ability to reduce carbon-halogen bonds under anaerobic conditions. The reductive reactions functioned with NADH and the physiological electron-transfer proteins or by using artificial electron donors to reduce cytochrome P450CAM. Halogenated methane and ethane substrates were transformed by a two-electron reduction and subsequent protonation, beta-elimination, or alpha-elimination to yield alkanes, alkene, or carbene-derived products, respectively. Halogenated substrates bound to the camphor binding site as indicated by saturable changes in the Fe(III)-heme spin state upon substrate addition. Hexachloromethane was bound with a dissociation constant (KD) of 0.7 microM and caused > 95% shift from low- to high-spin iron. Ethanes bearing fewer chlorine substituents were bound with increasing dissociation constants and gave lesser degrees of iron spin-state change. Camphor competitively inhibited hexachloroethane reduction with an inhibitor constant (KI) similar to the dissociation constant for camphor (KI = KD = 0.9 microM). Rate determinations with pentachloroethane indicated a 100-fold higher enzyme V/K compared to the second-order rate constant for hematin free in solution. These studies on substrate binding and catalysis will help reveal how biological systems enzymatically reduce carbon-halogen bonds in the environment.
ChemInform Abstract: Synthesis of Some Phenanthrene Derivatives Structurally Related to Certain Analgesic and Antipyretic Drugs. (1990)

Abstract The spiro compound (VII), which combines the moieties of phenanthrene and pyrazole, is synthesized in order to have an access to compounds which may possess a higher analgesic activity than phenanthrenes or pyrazoles.
Evidence for double resistance to permethrin and malathion in head lice: reply from authors (2000)

Journal Article Evidence for double resistance to permethrin and malathion in head lice: reply from authors Get access A.M.R. Downs, A.M.R. Downs Department of Dermatology, Search for other works by this author on: Oxford Academic Google Scholar K.A. Stafford, K.A. Stafford Veterinary Science and Search for other works by this author on: Oxford Academic Google Scholar I. Harvey, I. Harvey Department of Dermatology,Public Health, University of Bristol, Bristol BS2 8HW, U.K. Search for other works by this author on: Oxford Academic Google Scholar G.C. Coles G.C. Coles Veterinary Science and Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 142, Issue 5, 1 May 2000, Page 1067, https://doi.org/10.1046/j.1365-2133.2000.03515.x Published: 01 May 2000
Low-energy ion scattering spectroscopy observations of <i>c</i>-axis-oriented YBa2Cu3O7−<i>x</i> thin films: Effects of in-vacuum annealing (1991)

The atomic structure of (001) surfaces of c-axis-oriented YBa2Cu3O7−x (YBCO) thin films was studied by low-energy ion scattering spectroscopy (ISS) after annealing in ultrahigh vacuum. This is the first report on the surface analysis of superconducting oxide evaluated by ISS. A clean surface of YBCO (001) 1×1 is produced by annealing at around 500 °C. The surface structure is discussed in terms of the blocking and the nonblocking effects caused by the desorption of O(4) atoms. We conclude that the (001) surfaces are stabilized by Cu(1)-O chains.