gebhart/patrepeval huggingface dataset:
[Fibrin fragment beta 15-118. Inhibitory and complex-forming properties]. (1996)

Peptide beta 15-118 isolated from desAABB-NDSK preserves fibrin polymerization active site "B", inhibits polymerization process at 12 degrees C, eliminates the inhibitory properties of plasmin D-D-fragment but does not influence inhibitory properties of a D-monomer fragment. Complex formation between peptide beta 15-118 and both D- and D-D fragments was electrophoretically demonstrated. Peptide beta 15-118 forms more stable complex with the D-D fragment which does not dissociate in the medium of polymerizing fibrin as the complex of the peptide with monomer D fragment does. Gel filtration data confirm dimerization of D-monomer fragments after their complexing with beta 15-118. This phenomenon suggests that mutual affinity of D-domains in fibrin increases after loci interactions of the "B"-"b" type.
Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines (2021)

Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SARS-CoV-2 outbreak in a local hospital and used nanopore sequencing with a modified ARTIC protocol employing 1200 bp long amplicons. We detected a long deletion of 168 nucleotides in the ORF8 gene in 76 samples from the hospital outbreak. This deletion is difficult to identify with the classical amplicon sequencing procedures since it removes two amplicon primer-binding sites. We analyzed public SARS-CoV-2 sequences and sequencing read data from ENA and identified the same deletion in over 100 genomes belonging to different lineages of SARS-CoV-2, pointing to a mutation hotspot or to positive selection. In almost all cases, the deletion was not represented in the virus genome sequence after consensus building. Additionally, further database searches point to other deletions in the ORF8 coding region that have never been reported by the standard data analysis pipelines. These findings and the fact that ORF8 is especially prone to deletions, make a clear case for the urgent necessity of public availability of the raw data for this and other large deletions that might change the physiology of the virus towards endemism.
TU‐F‐CAMPUS‐J‐05: Fast Volumetric MRI On An MRI‐Linac Enables On‐Line QA On Dose Deposition in the Patient (2015)

Purpose: The introduction of the MRI‐linac in radiotherapy brings MRI‐guided treatment with daily plan adaptions within reach. This paradigm demands on‐line QA. With its ability to perform continuous volumetric imaging in an outstanding soft‐tissue contrast, the MRI‐ linac promises to elucidate the dose deposition process during a treatment session. Here we study for a prostate case how dynamic MRI combined with linac machine parameters and a fast dose‐engine can be used for on‐line dose accumulation. Methods: Prostate imaging was performed in healthy volunteer on a 1.5T MR‐scanner (Philips, Best, NL) according to a clinical MR‐sim protocol, followed by 10min of dynamic imaging (FLASH, 4s/volume, FOV 40×40×12cm 3 , voxels 3×3×3mm 3 , TR/TE/α=3.5ms/1.7ms/5°). An experienced radiation oncologist made delineations, considering the prostate CTV. Planning was performed on a two‐compartment pseudoCT (air/water density) according to clinical constraints (77Gy in PTV) using a Monte‐Carlo (MC) based TPS that accounts for magnetic fields. Delivery of one fraction (2.2Gy) was simulated on an emulator for the Axesse linac (Elekta, Stockholm, SE). Machine parameters (MLC settings, gantry angle, dose rate, etc.) were recorded at 25Hz. These were re‐grouped per dynamic volume and fed into the MC‐engine to calculate a dose delivered for each of the dynamics. Deformations derived from non‐rigid registration of each dynamic against the first allowed dose accumulation on a common reference grid. Results: The DVH parameters on the PTV compared to the optimized plan showed little changes. Local deformations however resulted in local deviations, primarily around the air/rectum interface. This clearly indicates the potential of intra‐fraction adaptations based on the accumulated dose. Application in each fraction helps to track the influence of plan adaptations to the eventual dose distribution. Calculation times were about twice the delivery time. Conclusion: The current Result paves the way to perform on‐line treatment delivery QA on the MRI‐linac in the near future.
Class-based graph anonymization for social network data (2009)

The recent rise in popularity of social networks, such as Facebook and MySpace, has created large quantities of data about interactions within these networks. Such data contains many private details about individuals so anonymization is required prior to attempts to make the data more widely available for scientific research. Prior work has considered simple graph data to be anonymized by removing all non-graph information and adding or deleting some edges. Since social network data is richer in details about the users and their interactions, loss of details due to anonymization limits the possibility for analysis. We present a new set of techniques for anonymizing social network data based on grouping the entities into classes, and masking the mapping between entities and the nodes that represent them in the anonymized graph. Our techniques allow queries over the rich data to be evaluated with high accuracy while guaranteeing resilience to certain types of attack. To prevent inference of interactions, we rely on a critical "safety condition" when forming these classes. We demonstrate utility via empirical data from social networking settings. We give examples of complex queries that may be posed and show that they can be answered over the anonymized data efficiently and accurately.
Interpenetrated and interlocked molecules via bis(pyridinium)ethanes. (1999)

This thesis deals with the synthesis of [2]pseudorotaxane, [2]-, and [3]rotaxane architectures utilizing bis(pyridinium)ethane dications and 24-membered crown ethers as templating agents. Eight bis(pyridinium)ethane dications 2a--h were synthesized and their complexation behaviour with six 24C8 derivatives 3a--f was examined. All the dications formed [2]pseudorotaxane geometries in solution with the crown ethers except for 2c which did not form a complex with any of 3a--f due to steric: constraints. Association constants for pseudorotaxane formation were determined by 1H NMR spectroscopy for all the complexes formed and the thermodynamics of formation of the pseudorotaxanes involving 2g and 3a--f . The crystal structures of [2]pseudorotaxanes 2e:3c, 2f:3c, and 2g:3c were determined. [2]Pseudorotaxane 2e:3c was converted to [2]rotaxanes 7 and 9 by two different synthetic routes. The 1H NMR spectra were examined and the crystal structures of 7 and 9 were determined. Two axle-shaped tetracations 11 and 12 were synthesized and converted, via benzylation in the presence of 3c, to the respective [3]rotaxanes 14 and 15, and [2]rotaxane molecular shuttles 16 and 17. The 1H NMR spectra of these compounds was examined and compared to the non-mechanically bonded benzylated, products 18 and 19. The dynamic behaviour of the [2]rotaxane shuttles was investigated by 1H NMR spectroscopy to determine the free energy of activation. In addition, it was established that molecular shuttle 17 displayed preference for one translational isomer. The crystal structures of 14 and 17 were also determined. Paper copy at Leddy Library: Theses &amp; Major Papers - Basement, West Bldg. / Call Number: Thesis1999 .W57. Source: Dissertation Abstracts International, Volume: 62-10, Section: B, page: 4556. Adviser: Stephen Loeb. Thesis (Ph.D.)--University of Windsor (Canada), 1999.
Therapeutic Potential of Fluoxetine in Neurological Disorders (2008)

The selective serotonin reuptake inhibitor (SSRI) fluoxetine, which is registered for a variety of psychiatric disorders, has been found to stimulate the cAMP-responsive element binding protein (CREB), increase the production of brain-derived neurotrophic factor (BNDF) and the neurotrophic peptide S100beta, enhance glycogenolysis in astrocytes, block voltage-gated calcium and sodium channels, and decrease the conductance of mitochondrial voltage-dependent anion channels (VDACs). These mechanisms of actions suggest that fluoxetine may also have potential for the treatment of a number of neurological disorders. We performed a Pubmed search to review what is known about possible therapeutic effects of fluoxetine in animal models and patients with neurological disorders. Beneficial effects of fluoxetine have been noted in animal models of stroke, multiple sclerosis, and epilepsy. Fluoxetine was reported to improve neurological manifestations in patients with Alzheimer's disease, stroke, Huntington's disease, multiple sclerosis, traumatic brain injury, and epilepsy. Clinical studies so far were small and often poorly designed. Results were inconclusive and contradictory. However, the available preclinical data justify further clinical trials to determine the therapeutic potential of fluoxetine in neurological disorders.
Experimental determination of two-dimensional critical current density distribution in YBCO coated conductors (2001)

The critical current density (Jc) distribution in YBCO coated conductors is attracting interest from the viewpoint of its influence on their AC loss characteristics as well as from material science and process engineering. A two-dimensional Jc distribution in a YBCO coated conductor made by the IBAD (ion-beam assisted deposition) and the PLD (pulse-laser deposition) method can be determined by the magnetic-knife method with spatial resolutions of 0.2 mm lateral and 10 mm longitudinal directions, respectively. In an up-to-date 80A-class YBCO coated conductor, the Jc is relatively uniform in the central part and reaches \mbox{7$×$109 A m-2, } while the Jc fluctuates spatially in the central part of a tape fabricated earlier and with less critical current. Near the edges of the tapes, the Jc is higher or lower than in the central part and the experimentally determined Jc distributions are far from uniform. This suggests that a presumption of a uniform Jc for AC loss estimations is not always reasonable and can lead to a large error in the estimated AC losses.
The Kinematics and Kinetics of Slipknots for Arthroscopic Bankart Repair (2001)

An apparatus has been developed to enable the in vitro measurement of the kinematics and kinetics of a slipknot, both while the knot is being tightened and with the knot in place and the tension removed. During tightening, the apparatus provides a linearly increasing resistance, which may be considered analogous to the resistance experienced when the labrum is drawn toward and apposed to the edge of the glenoid cavity during a Bankart repair. The tension to close the knot is measured with a tensiometer, in tandem with the closure of the capsule model onto the bone anchor, which is measured with a datalogger. The tightening tension was limited to 25 N and intraoperator and interoperator comparisons were made for four knots tied by six participants. Failure of a knot was taken to be reverse slippage of 2 mm. A second criterion of ease of slide was used to assess each knot. We found wide interoperator variability with regard to slipknot tying. A methodology for quality control of slipknot tying is presented.
Ultrasonic Sensors For Measuring Coronary Blood Flow (1988)

During the last 15 years we have developed and applied several types of catheter-mounted ultrasonic Doppler transducers for sensing coronary blood flow in man. Validation studies in the laboratory and in animals have shown that these catheters can accurately measure velocity from a small sample volume located ahead of the catheter tip. The Doppler transducers have been miniaturized enough to be mounted on the tip of a balloon angioplasty catheter without compromising any of the normal functions of the catheter. Good quality, high fidelity velocity signals have been recorded from many sites within the coronary circulation of patients during coronary arteriography and during balloon angioplasty.
Confocal fundus imaging with a scanning laser ophthalmoscope in eyes with cataract. (1995)

SLO imaging was found to be superior to fundus photography for viewing the retina in eyes with cataract. Owing to the inhomogeneous nature of cataracts, the optimal choice of confocal aperture and laser wavelength is not simple and must be individualised.
Electrochemical nanoparticle–enzyme sensors for screening bacterial contamination in drinking water (2015)

Traditional plating and culturing methods used to quantify bacteria commonly require hours to days from sampling to results. We present here a simple, sensitive and rapid electrochemical method for bacterial detection in drinking water based on gold nanoparticle-enzyme complexes. The gold nanoparticles were functionalized with positively charged quaternary amine headgroups that could bind to enzymes through electrostatic interactions, resulting in inhibition of enzymatic activity. In the presence of bacteria, the nanoparticles were released from the enzymes and preferentially bound to the bacteria, resulting in an increase in enzyme activity, releasing a redox-active phenol from the substrate. We employed this strategy for the electrochemical sensing of Escherichia coli and Staphylococcus aureus, resulting in a rapid detection (<1 h) with high sensitivity (10(2) CFU mL(-1)).
Occurrence and Activity of Myofibroblasts in Human Capsular Tissue Surrounding Mammary Implants (1981)

Capsular tissue obtained from a series of 16 patients with silicone mammary implants was exposed in vitro to smooth-muscle stimulants and relaxants. Capsule relaxation was produced in 75 percent of the patients. The most active antagonists were papaverine and veratrine. Capsule contracture was produced in 69 percent of the patients. The most active agonists were histamine and epinephrine. Myofibroblasts were identified in several capsules. These data support the hypothesis that the myofibroblasts is a probable cause of capsular contracture.
Evaluation of a New Viral Vaccine Vector in Mice and Rhesus Macaques: J Paramyxovirus Expressing Hemagglutinin of Influenza A Virus H5N1 (2021)

H5N1, an avian influenza virus, is known to circulate in many Asian countries, such as Bangladesh, China, Cambodia, Indonesia, and Vietnam. The current FDA-approved H5N1 vaccine has a moderate level of efficacy. A safe and effective vaccine is needed to prevent outbreaks of highly pathogenic avian influenza (HPAI) H5N1 in humans. Nonsegmented negative-sense single-stranded viruses (NNSVs) are widely used as a vector to develop vaccines for humans, animals, and poultry. NNSVs stably express foreign genes without integrating with the host genome. J paramyxovirus (JPV) is a nonsegmented negative-strand RNA virus and a member of the proposed genus <i>Jeilongvirus</i> in the family <i>Paramyxoviridae</i>. JPV-specific antibodies have been detected in rodents, bats, humans, and pigs, but the virus is not associated with disease in any species other than mice. JPV replicates in the respiratory tract of mice and efficiently expresses the virus-vectored foreign genes in tissue culture cells. In this work, we explored JPV as a vector for developing an H5N1 vaccine using intranasal delivery. We incorporated hemagglutinin (HA) of H5N1 into the JPV genome by replacing the small hydrophobic (SH) gene to generate a recombinant JPV expressing HA (rJPV-ΔSH-H5). A single intranasal administration of rJPV-ΔSH-H5 protected mice from a lethal HPAI H5N1 challenge. Intranasal vaccination of rJPV-ΔSH-H5 in rhesus macaques elicited antigen-specific humoral and cell-mediated immune responses. This work demonstrates that JPV is a promising vaccine vector. <b>IMPORTANCE</b> A highly pathogenic avian influenza (HPAI) H5N1 outbreak in Southeast Asia destroyed millions of birds. Transmission of H5N1 into humans resulted in deaths in many countries. In this work, we developed a novel H5N1 vaccine candidate using J paramyxovirus (JPV) as a vector and demonstrated that JPV is an efficacious vaccine vector in animals. Nonsegmented negative-sense single-stranded viruses (NNSVs) stably express foreign genes without integrating into the host genome. JPV, an NNSV, replicates efficiently in the respiratory tract and induces robust immune responses.
Design of a non-scaling FFAG accelerator for proton therapy (2005)

In recent years there has been a revival of interest in Fixed Field Alternating Gradient (FFAG) accelerators. 1In Japan a number have been built, or are under construction.A new non-scaling approach to the FFAG reduces the required orbit offsets during acceleration and the size of the required aperture, while maintaining the advantage of the low cost magnets associated with fixed fields.An advantage of the non-scaling FFAG accelerator, with respect to synchrotrons, is the fixed field and hence the possibility of high current and high repetition rate for spot scanning.There are possible advantages of the nonscaling design with respect to fixed-field cyclotrons.The non-scaling FFAG allows strong focusing and hence smaller aperture requirements compared to scaling designs, thus leading to very low losses and better control over the beam.We present, here, a non-scaling FFAG designed to be used for proton therapy.
[Evaluation of morphine metabolism in presence of amantadine and dextromethorphan in human serum by high performance liquid chromatography coupled with mass spectrometry (LC/MS) method]. (2008)

In the present study we assessed by LC/MS method the influence of amantadine and dextromethorphan on morphine metabolism in humans in order to explain clinically observed phenomenon of amplification of analgesic action of morphine by these drugs. Neither dextromethorphan nor amantadine influenced the rate of morphine degradation and concentration of morphine metabolites. Thus, our results suggest pharmacodynamical, not pharmacokinetic mechanism of interaction.
Manufacturing of two and three-dimensional micro/nanostructures by integrating optical tweezers with chemical assembly (2004)

Optical tweezers have been used as versatile tools for non-contact manipulation of micrometer-sized particles. This paper proposes a hybrid micro/nanoscale manufacturing system using optical tweezers and chemical linkages for fabricating 2D and 3D micro/nanostructures. A holographic multiple trap optical tweezer system is first used to trap particles in a desired pattern. The particles are then connected to form rigid units using suitable chemistry. Different connection schemes based on gold seeding, complimentary-DNA linkage and streptavidinbiotin chemistry are presented and possible applications of this technique are explored. This method combines the advantages of top-down and bottom-up approaches and is compatible with organic and inorganic materials.
CCDC 1406900: Experimental Crystal Structure Determination (2016)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Enzyme assays to detect preovulatory human luteinizing hormone surge. (1983)

Nonradioisotopic enzyme assays have been developed to detect the preovulatory luteinizing hormone (LH) surge in the unextracted urine of normally menstruating women. The amino groups on 6-mm glass beads were activated and coupled to the anti-LH-gamma-globulin for enzyme immunoassay or to the LH receptor prepared from bovine corpora lutea for enzyme receptorassay. The LH was conjugated with alkaline phosphatase. The enzyme assays detected preovulatory LH surge in the morning urine samples of 12 normally menstruating women. The LH surge was coincidental with preovulatory serum estradiol rise, shift in basal body temperature, and 4+ spinnbarkeit of the cervical mucus. The serum estradiol and progesterone levels in the luteal phase were indicative of corpus luteum formation.
A Programmable Impulse Generator for Spin-Lattice Relaxation Time Measurements in High Resolution NMR (1970)

This paper describes the design of a precision, programmable impulse generator capable of producing repetitive impulse trains of accurately defined parameters, selectable over a wide range. The generator was conceived for the specific purpose of gating the audio modulation of the applied magnetic field in an HA 100 Varian NMR spectrometer. The basic circuit is much more general, however, and may be used for the generation of a wide variety of impulse trains. The present configuration is capable of producing repetitive trains of one π pulse followed by several equidistant 2π pulses. The width of these pulses, their number, their separation, and the repetition rate of the sequence are independently selectable. The selections may be made manually or by remote control from an on-line digital computer. All times are increments of a basic clock period, derived in our case from the 16.7 MHz crystal oscillator of the spectrometer. Construction is modular and TTL integrated circuits are used throughout for simplicity.
Mutations in the rpoB gene of Mycobacterium tuberculosis that interfere with PCR-single-strand conformation polymorphism analysis for rifampin susceptibility testing (1997)

Rifampin susceptibility of 32 rifampin-resistant and 26 rifampin-susceptible Mycobacterium tuberculosis strains was analyzed by PCR-single-strand conformation polymorphism (SSCP) and DNA sequencing within the 157-bp region of the rpoB gene (Ala500 to Val550). Two false-positive PCR-SSCP results were observed among the susceptible strains due to the silent mutation Gln513 (CAA-->CAG) and the deletion mutation Thr508 and Ser509. Another silent mutation [Leu511 (CTG-->CTA)], combined with the mutation Ser531-->Leu, was observed in a resistant strain. These results suggest that to rule out false-positive PCR-SSCP results, sequencing of the target DNA is required.