gebhart/patrepeval huggingface dataset:
An insight into the mechanism of inhibition of unusual bi-subunit topoisomerase I from<i>Leishmania donovani</i>by 3,3′-di-indolylmethane, a novel DNA topoisomerase I poison with a strong binding affinity to the enzyme (2007)

DIM (3,3'-di-indolylmethane), an abundant dietary component of cruciferous vegetables, exhibits a wide spectrum of pharmacological properties. In the present study, we show that DIM is a potent inhibitor of Leishmania donovani topoisomerase I with an IC50 of 1.2 microM. Equilibrium dialysis shows that DIM binds strongly to the free enzyme with a binding constant of 9.73x10(-9) M. The binding affinity of DIM to the small subunit is 8.6-fold more than that of the large subunit of unusual LdTOP1LS (bi-subunit L. donovani topoisomerase I). DIM stabilizes topoisomerase I-DNA cleavage complexes in vitro and also in vivo. Like CPT (camptothecin), DIM inhibits the religation step when the drug was added to preformed topoisomerase I-DNA binary complex. Hence, DIM is similar to CPT with respect to its ability to form the topoisomerase I-mediated 'cleavable complexes' in vitro and in vivo. But unlike CPT, DIM interacts with both free enzyme and substrate DNA. Therefore DIM is a non-competitive class I inhibitor of topoisomerase I. DIM also inhibits the relaxation activity of the CPT-resistant mutant enzyme LdTOP1Delta39LS (N-terminal deletion of amino acids 1-39 of LdTOP1LS). The IC50 values of DIM in simultaneous and enzyme pre-incubation relaxation assays were 3.6 and 2.9 muM respectively, which are higher than that of wild-type topoisomerase I (LdTOP1LS), indicating that the affinity of DIM to LdTOP1Delta39LS is less than that for LdTOP1LS. This is the first report on DIM as an L. donovani topoisomerase I poison. Our study illuminates a new mode of action of enzyme inhibition by DIM that might be exploited for rational drug design in human leishmaniasis.
Structure and Assembly of a <i>T</i> =1 Virus-Like Particle in BK Polyomavirus (2005)

In polyomaviruses the pentameric capsomers are interlinked by the long C-terminal arm of the structural protein VP1. The T=7 icosahedral structure of these viruses is possible due to an intriguing adaptability of this linker arm to the different local environments in the capsid. To explore the assembly process, we have compared the structure of two virus-like particles (VLPs) formed, as we found, in a calcium-dependent manner by the VP1 protein of human polyomavirus BK. The structures were determined using electron cryomicroscopy (cryo-EM), and the three-dimensional reconstructions were interpreted by atomic modeling. In the small VP1 particle, 26.4 nm in diameter, the pentameric capsomers form an icosahedral T=1 surface lattice with meeting densities at the threefold axes that interlinked three capsomers. In the larger particle, 50.6 nm in diameter, the capsomers form a T=7 icosahedral shell with three unique contacts. A folding model of the BKV VP1 protein was obtained by alignment with the VP1 protein of simian virus 40 (SV40). The model fitted well into the cryo-EM density of the T=7 particle. However, residues 297 to 362 of the C-terminal arm had to be remodeled to accommodate the higher curvature of the T=1 particle. The loops, before and after the C-terminal short helix, were shown to provide the hinges that allowed curvature variation in the particle shell. The meeting densities seen at the threefold axes in the T=1 particle were consistent with the triple-helix interlinking contact at the local threefold axes in the T=7 structure.
Molecular dynamics simulation of reorientation of polyethylene chains under a high magnetic field (2006)

The purpose of this investigation is to clarify the dynamical process of reorientation of a polyethylene chains under high magnetic fields. Molecular dynamics (MD) simulations at constant temperature and pressure are carried out to study the reorientation of two polyethylene chains with different configurations. We utilized static homogeneous external magnetic fields of 25 T into the velocity Verlet integration algorithm through a suitable Taylor expansion. Simulations reveal that the gained potential energy through magnetic annealing facilitated the reorganization of the polyethylene chains closer to the direction of the applied magnetic field. The current study offer an alternative explanation for the orientation that was not available through the hydrodynamics continuum approach based on the diamagnetic susceptibilities as the driving force for reorientation.
Analyzing large-scale spiking neural data with HRLAnalysisâ„¢ (2014)

The additional capabilities provided by high-performance neural simulation environments and modern computing hardware has allowed for the modeling of increasingly larger spiking neural networks. This is important for exploring more anatomically detailed networks but the corresponding accumulation in data can make analyzing the results of these simulations difficult. This is further compounded by the fact that many existing analysis packages were not developed with large spiking data sets in mind. Presented here is a software suite developed to not only process the increased amount of spike-train data in a reasonable amount of time, but also provide a user friendly Python interface. We describe the design considerations, implementation and features of the HRLAnalysis suite. In addition, performance benchmarks demonstrating the speedup of this design compared to a published Python implementation are also presented. The result is a high-performance analysis toolkit that is not only usable and readily extensible, but also straightforward to interface with existing Python modules.
Role of detergent builders in fabric washing formulations (1978)

Abstract The role of a detergent builder in fabric washing formulations is complex because the builder is multifunctional. The primary function of a builder is to counteract the detrimental effects of hardness ions (Ca 2+ and Mg 2+ ) which arise in the wash solution not only from the tap water but also from the washload. The need to control the free hardness ion level to 0.1 °FH is well established and is mainly required to release calcium bound soil and prevent further calcium soil interaction during the wash process. The most elegant way of doing this is with a sequestrant. Sodium triphosphate is the preferred material. Measurement of the equilibrium constants of sequestrants with Ca 2+ /Mg 2+ /Na + /H + as a function of temperature and ionic strength allows prediction of free hardness ion levels over a wide range of conditions such as temperature, pH, water hardness, and dosage. Secondary functions such as specific adsorption effects are important, and a true builder will aid not only soil removal but alleviate soil redeposition.
Geometrical model-based segmentation of the organs of sight on CT images (2008)

Segmentation of organs of sight such as the eyeballs, lenses, and optic nerves is a time consuming task for clinicians. The small size of the organs and the similar density of the surrounding tissues make the segmentation difficult. We developed a new algorithm to segment these organs with minimal user interaction. The algorithm needs only three seed points to fit an initial geometrical model to start an effective segmentation. The clinical evaluation shows that the output of our method is useful in clinical practice.
Intracellular calcium and ventricular fibrillation. Studies in the aequorin-loaded isovolumic ferret heart. (1991)

To elucidate the role of changes in [Ca2+]i in the induction of ventricular fibrillation (VF), Ca2+i signals, epicardial electrical potentials, and isovolumic left ventricular pressure were simultaneously recorded in isolated intact ferret hearts loaded with aequorin, a bioluminescent protein. When the preparations were perfused with 3 microM acetylstrophanthidin and 8 mM Ca2+, or with a low Na+ solution (18 mM Na+, 100 mM Li+), spontaneous transitions to the VF state were consistently observed within a short period of time. The initiation of spontaneous VF was preceded by development of a Ca2+i overload state, coincidental with the ascending phase of diastolic Ca2+i oscillations, and was followed by further elevation in Ca2+i levels, which were associated with augmented Ca2+i oscillations of a saw-toothed pattern. Pretreatment with 10 microM ryanodine, which blocked Ca2+i oscillations in the preparation, did not eliminate inducibility of VF by means of AC electrical stimulations; however, VF no longer occurred spontaneously, and the threshold for VF induction increased markedly. In the absence of a state of Ca2+i overload, spontaneous defibrillation occurred within a minute after the initiation of VF. We conclude that 1) VF can be induced in the absence of Ca2+i oscillations; however, 2) Ca2+i oscillations play a crucial role as a trigger for VF and therefore are an important determinant of the vulnerability to VF; and 3) the augmented Ca2+i oscillations after the transition to VF state may support the maintenance of this type of arrhythmia.
Using the axis of rotation of polar navigator echoes to rapidly measure 3D rigid‐body motion (2004)

An improved technique to prospectively correct three-dimensional rigid-body motion using polar spherical navigator (pNAV) echoes is presented. The technique is based on acquiring pNAVs of an object in a baseline and rotated position and determining the axis of rotation (AOR) between data sets, thereby reducing 3D rotations to a 2D, planar rotation. Finding the AOR is simplified by prerotating the baseline trajectory, which forces the axis to lie within a specific polar region of a spherical shell in k-space. Orbital navigator echoes are interpolated from the pNAV data in planes orthogonal to the AOR and cross-correlated to determine the 2D rotation. The rotation about the AOR is used in conjunction with its orientation to calculate the overall 3D rotation. The pNAV-AOR technique was tested for its precision, accuracy, and processing speed in detecting compound rotations and translations of varying magnitude. In comparison to the spherical navigator echo technique, the pNAV-AOR technique is noniterative, fast, and independent of rotation magnitude and direction. At low SNR, the technique can detect compound rotations to 0.5 degrees accuracy in an estimated 100 msec, indicating that prospective 3D rigid-body motion correction may be feasible with this technique.
Interfacing an Electric Vehicle to the Grid with Modular Conversion Unit: A Case Study of a Charging Station and its Control Framework (2018)

In response to vehicle-to-grid (V2G) application, promising solutions for fast charging stations of electric vehicles (EV) are still demanding with considerations of their interfaced requirements on the AC distribution network. An integrating periodic loads with different energy storage technologies to the common DC bus is strong alternative to the existing infrastructures. This paper addresses a key role of rectification topology in fast charging stations with respect to higher scalability, redundancy and its capacity to compensate unbalanced loads or total harmonic distortion (THD) at the point of common coupling (PCC). It is achieved through the operational performance of the Modular Multilevel Converter (MMC) deployed to transfer AC power generated by medium-voltage grid to common DC bus feeding multiple EV batteries. The developed control framework is constructed by two-layer configuration, in which a first-layer finite control set-model predictive control (FCS-MPC) methodology provides an initial controlled variables to regulate the rectifier module voltages and currents at the connected loads. The second-layer iterative controller is embedded into an integrated perturbation analysis and sequential quadratic programming (IPA-SQP) algorithm for handling nonlinearities and updating weighting factors. The control objectives are improving the computational burden with variables constraints, lowering the dc ripples and grid current harmonic contents. The feasibility assessment of load-leveling approach is also studied when large energy storage systems are in operation. To prove a functionality of the proposed design, numerical simulations are conducted and some results are presented.
Development of an enzyme-linked immunosorbent assay for alachlor and its application to the analysis of environmental water samples (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDevelopment of an enzyme-linked immunosorbent assay for alachlor and its application to the analysis of environmental water samplesPaul C. C. Feng, Stephen J. Wratten, Susan R. Horton, C. Ray Sharp, and Eugene W. LoguschCite this: J. Agric. Food Chem. 1990, 38, 1, 159–163Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jf00091a034https://doi.org/10.1021/jf00091a034research-articleACS PublicationsRequest reuse permissionsArticle Views99Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Integrated free-space optical interconnects for chip-to-chip communications (2002)

Free-space optics can help alleviate the communications problems of electronic computers by its large spatial and temporal bandwidth. For compact packaging, the concept of planar-integrated free-space optics is used. Here, we give an overview of the design, fabrication and thermal management of planar optical interconnects.
Structural Analysis of New Antihypertensive Peptides Derived from Cheese Whey Protein by Proteinase K Digestion (1998)

Whey protein was digested with one of seven kinds of proteases at 37 degrees C (trypsin, proteinase K, actinase E, thermolysin, or papain) or at 25 degrees C (pepsin or chymotrypsin) for 24 h. The digested samples were assayed for the inhibitory activity of angiotensin-converting enzyme and for changes in the systolic blood pressure caused in spontaneously hypertensive rats after gastric intubation. The strongest depressive effect on the systolic blood pressure (-55 mm Hg) was observed at 6 h after gastric intubation of the whey protein that was digested by proteinase K. Finally, six peptides were chromatographically isolated from the proteinase K digest by a combination of hydrophobic reversed-phase HPLC and gel filtration. The amino acid sequences and their origins were clarified as follows: Val-Tyr-Pro-Phe-Pro-Gly [beta-casein (CN); f 59-64], Gly-Lys-Pro (beta 2-microglobulin; f 18-20), Ile-Pro-Ala (beta-lactoglobulin; f 78-80), Phe-Pro (serum albumin; f 221-222; beta-CN, f 62-63, f 157-158, and f 205-206), Val-Tyr-Pro (beta-CN; f 59-61), and Thr-Pro-Val-Val-Val-Pro-Pro-Phe-Leu-Gln-Pro (beta-CN; f 80-90). Chemical synthesis of these six peptides confirmed that all peptides, except an undecapeptide, have antihypertensive activity in spontaneously hypertensive rats. The synthetic tripeptide Ile-Pro-Ala, originating from beta-lactoglobulin, showed the strongest antihypertensive activity (-31 mm Hg).
<title>Detection of weapons of mass destruction</title> (2003)

High Energy X-ray cargo screening is a mature technology that has proven its value in the detection of contraband material hidden within cargo including fully loaded sea containers. To date high energy screening has been largely applied to manifest verification and to drug detection. However, the dramatic change in world terrorism has altered the application. Now it is essential that weapons of mass destruction (WMD’s) be interdicted with incredibly high accuracy. The implication of a missed detection has gone from loss of revenue or the lowering of the street price of drugs to potentially stopping, at least for some significant time, most world commerce. Screening containers with high energy x-rays (~250+ mm of steel penetration) is capable of detecting all nuclear threats at a fraction of the strategically important mass. The screening operation can be automated so that no human decisions are required with very low false alarms. Finally, the goal of 100% inspection of cargo inbound to the United States from the twenty largest international ports is an achievable goal with hardware costs in the area of that already spent on airport security.
Deoxyribonucleic Acid Homology Among Lactic Streptococci (1981)

A comparison was made by deoxyribonucleic acid homology of 45 strains of lactic streptococci, using two strains of Streptococcus cremoris and three strains of Streptococcus lactis as reference strains. All S. cremoris strains were grouped together by deoxyribonucleic acid homology. S. lactis strains formed a second group, except that three strains of S. lactis showed a high degree of homology with S. cremoris strains. The three Streptococcus diacetylactis strains could not be differentiated from S. lactis strains. In spite of these differences between S. lactis and S. cremoris strains, the majority of S. cremoris, S. lactis, and S. diacetylactis strains studied had at least 50% of their base sequences in common. In contrast, Streptococcus thermophilus strains generally showed little relationship with the other strains of lactic streptococci. The relevance of these findings to the selection of starter strains for cheese making is discussed.
Enantioselective Synthesis with Lithium/(−)‐Sparteine Carbanion Pairs (1997)

Abstract “Chiral carbanions”—that is, enentiomerically enriched lithium–carbanion pairs in which the carbanionic center carries the chiral information—were regarded until recently as “exotic species.” In the past ten years it has become clear that they can, in fact, play a meaningful role in enantioselective synthesis, since substitution for lithium occurs here stereospecifically, usually with retention of configuration. They are also more readily and commonly accessible than was originally assumed. The trick lies in the use of lithium cations with chiral ligands, whether in the form of alkyllithium species used as bases in kinetically controlled, enantiotopically discriminating deprotonation, or in thermodynamically controlled equilibration in configurationally labile epimeric ion pairs. The lupine alkaloid (−)‐sparteine has shown itself admirably suited as a chiral bidentate ligand, and its efficiency and breadth of application are so far unsurpassed. This contribution constitutes an overview of the preparation of chiral reagents, convering primarily “umpoled” synthons such as homoenolates. 1‐oxyalkanides with a broad pattern of substitution, and α‐aminobenzyl anions.
Infection Rate of Percutaneous Kirschner Wire Fixation for Distal Radius Fractures (2010)

The infection rate after percutaneous Kirschner wire fixation is unacceptable. Kirschner wires should be buried under the skin to decrease the infection rate.
Characterization of the Properties of Human- and Dairy-Derived Probiotics for Prevention of Infectious Diseases in Fish (2001)

The present study aimed to investigate the potential probiotic properties of six lactic acid bacteria (LAB) intended for human use, Lactobacillus rhamnosus ATCC 53103, Lactobacillus casei Shirota, Lactobacillus bulgaricus, L. rhamnosus LC 705, Bifidobacterium lactis Bb12, and Lactobacillus johnsonii La1, and one for animal use, Enterococcus faecium Tehobak, for use as a fish probiotic. The strains for human use were specifically chosen since they are known to be safe for human use, which is of major importance because the fish are meant for human consumption. The selection was carried out by five different methods: mucosal adhesion, mucosal penetration, inhibition of pathogen growth and adhesion, and resistance to fish bile. The adhesion abilities of the seven LAB and three fish pathogens, Vibrio anguillarum, Aeromonas salmonicida, and Flavobacterium psychrophilum, were determined to mucus from five different sites on the surface or in the gut of rainbow trout. Five of the tested LAB strains showed considerable adhesion to different fish mucus types (14 to 26% of the added bacteria). Despite their adhesive character, the LAB strains were not able to inhibit the mucus binding of A. salmonicida. Coculture experiments showed significant inhibition of growth of A. salmonicida, which was mediated by competition for nutrients rather than secretion of inhibitory substances by the probiotic bacteria as measured in spent culture liquid. All LAB except L. casei Shirota showed tolerance against fish bile. L. rhamnosus ATCC 53103 and L. bulgaricus were found to penetrate fish mucus better than other probiotic bacteria. Based on bile resistance, mucus adhesion, mucus penetration, and suppression of fish pathogen growth, L. rhamnosus ATCC 53103 and L. bulgaricus can be considered for future in vivo challenge studies in fish as a novel and safe treatment in aquaculture.
Morphological and postural sexual dimorphism of the lumbar spine facilitates greater lordosis in females (2016)

Previous work suggests females are evolutionarily adapted to have greater lumbar lordosis than males to aid in pregnancy load-bearing, but no consensus exists. To explore further sex-differences in the lumbar spine, and to understand contradictions in the literature, we conducted a cross-sectional retrospective study of sex-differences in lumbar spine morphology and sacral orientation. In addition, our sample includes data for separate standing and supine samples of males and females to examine potential sex-differences in postural loading on lumbosacral morphology. We measured sagittal lumbosacral morphology on 200 radiographs. Measurements include: lumbar angle (L1-S1), lumbar vertebral body and disc wedging angles, sacral slope and pelvic incidence. Lumbar angle, representative of lordotic curvature between L1 and S1, was 7.3° greater in females than males, when standing. There were no significant sex-differences in lumbar angle when supine. This difference in standing lumbar angle can be explained by greater lordotic wedging of the lumbar vertebrae (L1-L5) in females. Additionally, sacral slope was greater in females than males, when standing. There were no significant sex-differences in pelvic incidence. Our results support that females have greater lumbar lordosis than males when standing, but not when supine - suggesting a potentially greater range of motion in the female spine. Furthermore, sex-differences in the lumbar spine appear to be supported by postural differences in sacral-orientation and morphological differences in the vertebral body wedging. A better understanding of sex-differences in lumbosacral morphology may explain sex-differences in spinal conditions, as well as promote necessary sex-specific treatments.
Oxidized Forms of Glutathione in Peripheral Blood as Biomarkers of Oxidative Stress (2006)

With the use of artifact-free measurement methods, GSH, GSSG, and PSSG are potentially powerful and reliable biomarkers of oxidative stress status and can be used to evaluate whether, and to what extent, oxidative stress may be involved in various diseases.
ChemInform Abstract: N,N′‐DIPHOSPHORYLATED 1,3,2‐DIAZAPHOSPHOLANES (1985)

Abstract o‐Phenylendiamin (I) wird mit Phosphortrichlorid oder dem Triamidophosphit (IV) zu Benzodiazaphospholanen (II) bzw. (V) cyclisiert.