gebhart/patrepeval huggingface dataset:
Crystal Structure and Spectroscopic Characterization of a Luminescent Europium Chelate (1996)

We report the crystal structure at 1 Å resolution of europium bound to diethylenetriaminepentaacetate covalently coupled to an organic chromophore, carbostyril 124 (DTPA-cs124; carbostyril 124 = 7-amino-4-methyl-2(1H)-quinolinone). The complex is highly luminescent in solution and in the crystal form. The Eu-DTPA-cs124 crystallizes in the space group C2/c with two molecules in the asymmetric unit. The two molecules form a dimer which is stabilized by π-stacking of two carbostyrils and by the ligation of the carbonyl oxygen of one cs124 to the europium of the second half of the dimer. This ligation removes the last water bound to the primary coordination sphere of europium, resulting in no waters bound to the lanthanide. The crystal structure also shows the amide oxygen between the cs124 and the DTPA is ligated to the metal. Spectroscopic measurements of the europium luminescence in the crystal show that 66% of the luminescence is centered around 617 nm with a full width at half-maximum of 2.5 nm. In solution, 48% of the europium luminescence intensity is in the 617 nm peak, with a fwhm of 3.5 nm. The europium lifetime in the crystal structure is 0.90 ms; the lifetime of the monomeric Eu-DTPA-cs124 is 0.62 ms in H2O solution and 2.4 ms in D2O solution. The differing lifetimes can be explained by the well-known effects of H2O on nonradiative europium emission rates and by postulating an electric (crystal) field surrounding the Eu which is more anisotropic in the crystal than in the solution, creating a faster radiative rate of Eu excited state deactivation. This greater anisotropy is expected on the basis of the crystal structure. The crystal structure also suggests improvements in the linkage of cs124 to DTPA which may improve the energy transfer between the organic chromophore and the europium and sharpen the Eu emission spectrum in solution.
Long-Term Effects on QT Prolongation of Pretomanid Alone and in Combinations in Patients with Tuberculosis (2019)

Concentration-QTc modeling was applied to pretomanid, a new nitroimidazooxazine antituberculosis drug. Data came from eight phase 2 and phase 3 studies. Besides pretomanid alone, various combinations with bedaquiline, linezolid, moxifloxacin, and pyrazinamide were considered; special attention was given to the bedaquiline-pretomanid-linezolid (BPaL) regimen that has demonstrated efficacy in the Nix-TB study in subjects with extensively drug-resistant or treatment-intolerant or nonresponsive multidrug-resistant tuberculosis. Three heart rate corrections to QT were considered: Fridericia's QTcF, Bazett's QTcB, and a population-specific correction, QTcN. QTc increased with the plasma concentrations of pretomanid, bedaquiline's M2 metabolite, and moxifloxacin in a manner described by a linear model in which the three slope coefficients were constant across studies, visits within study, and times postdose within visit but where the intercept varied across those dimensions. The intercepts tended to increase on treatment to a plateau after several weeks, a pattern termed the secular trend. The slope terms were similar for the three QTc corrections, but the secular trends differed, suggesting that at least some of the secular trend was due to the elevated heart rates of tuberculosis patients decreasing to normal levels on treatment. For pretomanid 200 mg once a day (QD) alone, a typical steady-state maximum concentration of drug in plasma (<i>C</i><sub>max</sub>) resulted in a mean change from baseline of QTcN of 9.1 ms, with an upper 90% confidence interval (CI) limit of 10.2 ms. For the BPaL regimen, due to the additional impact of the bedaquiline M2 metabolite, the corresponding values were 13.6 ms and 15.0 ms. The contribution to these values from the secular trend was 4.0 ms.
Field test reliability of a new lens opacity rating system utilizing slit-lamp examination. (1989)

A field test of a lens opacity rating system was run. Findings were graded in 7 categories: Cortex: (1) Waterclefts, Vacuoles, & Flakes (WVF, 4 grades), (2) Wedges & Spokes graded by number of Quadrants affected (WS-Q), and (3) Inward extent of Wedges & Spokes (WS-I, 3 grades); Nucleus: (4) Opacification (NUC-O) and (5) Coloration (NUC-C), each using 4 grades; and Subcapsular areas: (6) Anterior (SUB-A) and (7) Posterior (SUB-P) opacification, each using 5 grades. An instruction booklet with corresponding guidelines, sketches, and photographs was developed. Reproducibility of grading was tested in 3 clinics using 16 ophthalmologist-examiners. At each clinic, examiners were randomly paired. They independently performed slit-lamp exams of assigned patients (9 on average) on the same day (inter-examiner) and 1-2 weeks later (intra-examiner). To test intra-examiner reliability, examiners were divided into two groups (one from each pair), with gradings analyzed by group. For each group, 53 to 58 patients had evaluable examinations. Intra-examiner concordance for each lens category (defined as at most one grade difference in one lens) was as follows (for examiner groups 1 and 2, resp.): WVF: 98% & 97%; WS-Q: 96% & 100%; WS-I: 100% & 100%; NUC-O: 98% & 100%; NUC-C: 100% & 98%; SUB-A: 90% & 100%; and, SUB-P: 92% & 100%. Inter-examiner concordances were slightly lower than those found for intra-examiner. Grading lens findings in the manner described above appears to have potential utility in large scale studies.
Stress-sharing between the fluid and solid components of articular cartilage under varying rates of compression. (1993)

This paper investigates the factors affecting the mechanical behavior of the articular cartilage matrix with special emphasis on the effect of compressive strain-rate on the short and long term responses of the fluid and the solid components. The relationships expressed in the general theory of one-dimensional consolidation are generalized to account for strain-rate in the deformation process with the result that the stiffness due to the fluid and the solid components, and a parameter representing the degree of drag, can be calculated explicitly.
Biofilms (2001)

Abstract The attachment of bacteria to surfaces, followed by their growth and the production of extracellular polymers, results in the formation of a bacterial biofilm. The biofilm community is a complex assemblage of different metabolic types of microorganisms, which may interact through a variety of physiological, genetic and behavioural processes.
Customized Shape Detection Algorithms for Radiometric Calibration of Multispectral Imagers for Precision Agriculture Applications (2020)

Dual panel relative radiometric calibration is an important tool for multispectral imagers mounted on UAV's for small farm precision agriculture. A customized dual panel detection technique integrated into the multispectral calibration routine is developed in this work. Otsu segmentation was the most precise method to find square reflectance panels with a controlled background. Canny edge detection proved less noisy than Laplacian of Gaussian filters and more robust to environmental changes than Otsu's method. More post processing on the images was required inside of edge detection algorithms, as the zero crossing edge detection methods amplified noise inside the image. Both hole filling algorithms and morphological filters were employed to reduce the noise. Morphological erosion filters caused under segmented images. This resulted in the desired low false positive rates, and negative volume similarity metrics for the regions of interest. A fast and reliable dual reflection panel detection technique was implemented for radiometric calibration for small farm monitoring where time is of the essence.
ProfileMe: hardware support for instruction-level profiling on out-of-order processors (2002)

Profile data is valuable for identifying performance bottlenecks and guiding optimizations. Periodic sampling of a processor's performance monitoring hardware is an effective, unobtrusive way to obtain detailed profiles. Unfortunately, existing hardware simply counts events, such as cache misses and branch mispredictions, and cannot accurately attribute these events to instructions, especially on out-of-order machines. We propose an alternative approach, called ProfileMe, that samples instructions. As a sampled instruction moves through the processor pipeline, a detailed record of all interesting events and pipeline stage latencies is collected. ProfileMe also supports paired sampling, which captures information about the interactions between concurrent instructions, revealing information about useful concurrency and the utilization of various pipeline stages while an instruction is in flight. We describe an inexpensive hardware implementation of ProfileMe, outline a variety of software techniques to extract useful profile information from the hardware, and explain several ways in which this information can provide valuable feedback for programmers and optimizers.
Structure and Electronic Properties ofMoS2Nanotubes (2000)

Structural and electronic properties as well as the stability of MoS2 nanotubes are studied using the density-functional-based tight-binding method. It is found that MoS2 zigzag ( n,0) nanotubes exhibit a narrow direct band gap and MoS2 armchair ( n,n) possess a nonzero moderate direct gap. Interestingly, the ( n,n) tubes show a small indirect gap similar to the direct gap of ( n,0) nanotubes. Simulated electron diffraction patterns confirm the existence of armchair and zigzag disulphide nanotubes. The structure of the MoS2 nanotube tips is explained by introducing topological defects which produce positive and negative curvature.
Connectivity of Heterogeneous Wireless Networks (2011)

We address the percolation-based connectivity of large-scale ad hoc heterogeneous wireless networks, where secondary users exploit channels temporarily unused by primary users and the existence of a communication link between two secondary users depends on not only the distance between them but also the transmitting and receiving activities of nearby primary users. We introduce the concept of connectivity region defined as the set of density pairs-the density of secondary users and the density of primary transmitters - under which the secondary network is connected. Using theories and techniques from continuum percolation, we analytically characterize the connectivity region of the secondary network and reveal the tradeoff between proximity (the number of neighbors) and the occurrence of spectrum opportunities. Specifically, we establish three basic properties of the connectivity region-contiguity, monotonicity of the boundary and uniqueness of the infinite connected component, where the uniqueness implies the occurrence of a phase transition phenomenon in terms of the almost sure existence of either zero or one infinite connected component; we identify and analyze two critical densities which jointly specify the profile as well as an outer bound on the connectivity region; we study the impacts of secondary users' transmission power on the connectivity region and the conditional average degree of a secondary user and demonstrate that matching the interference ranges of the primary and the secondary networks maximizes the tolerance of the secondary network to the primary traffic load. Furthermore, we establish a necessary condition and a sufficient condition for connectivity, which lead to an outer bound and an inner bound on the connectivity region.
Effect of urapidil on rat brain catecholamine synthesis (1986)

The effects of urapidil, a clinically effective antihypertensive drug, on the in-vivo rate of synthesis of rat brain noradrenaline (NA) and dopamine (DA) was determined. A significant dose-dependent increase in dopa concentration by urapidil after dopa decarboxylase inhibition by NSD 1015 was observed in brain stem (3-30 mg kg-1 i.p.) and striatum (10-30 mg kg-1 i.p.), indicating increased NA and DA turnover, respectively, most probably a result of central blockade of brainstem alpha 1-adrenergic and striatal DA receptors. These results indicate that urapidil may possibly exert its central hypotensive action in part by a reduced influence on brain stem NA, thus reducing central sympathetic outflow.
Appearance of New Lipoxygenases in Soybean Cotyledons after Germination and Evidence for Expression of a Major New Lipoxygenase Gene (1992)

The appearance and subsequent disappearance of lipoxygenase activity at pH 6.8 in germinated cotyledons of soybean (Glycine max [L.]) was shown using a variant soybean cultivar (Kanto 101) that lacks the two lipoxygenase isozymes, L-2 and L-3, that are present in dry seeds of a normal soybean cultivar (Enrei). Three new lipoxygenases, designated lipoxygenase L-4, L-5, and L-6, were purified using anionic or cationic ion exchange chromatography. The major lipoxygenase in 5-day-old cotyledons of the variant soybean was lipoxygenase L-4. Lipoxygenases L-5 and L-6 preferentially produced 13(S)-hydroperoxy-9(Z), 11(E)-octadecadienoic acid (13S-HPOD) as a reaction product of linoleic acid, whereas lipoxygenase L-4 produced both 13S-HPOD and 9(S)-hydroperoxy-10(E), 12(Z)-octadecadienoic acid. All three isozymes have pH optima of 6.5, no activity at pH 9.0, and preferred linolenic acid to linoleic acid as a substrate. Partial amino acid sequencing of lipoxygenase L-4 showed that this isozyme shares amino acid sequence homology with lipoxygenases L-1, L-2, and L-3 but is not identical to any of them. This indicates that a new lipoxygenase, L-4, is expressed in cotyledons.
Multiplex qPCR assay for simultaneous quantification of CYP51‐S524T and SdhC‐H152R substitutions in European populations of Zymoseptoria tritici (2020)

Abstract Demethylation inhibitor (DMI) and succinate dehydrogenase inhibitor (SDHI) fungicides are currently relied upon for the control of septoria tritici blotch (STB) in European wheat fields. However, multiple mutations have occurred over time in the genes encoding the targeted proteins that have led to a practical loss of fungicide efficacies. Among the different amino acid substitutions in Zymoseptoria tritici associated with resistance to these fungicides, S524T in CYP51 (DMI target) and H152R in SdhC (SDHI target) are regarded as conferring the highest resistance factors to DMI and SDHI, respectively. To facilitate further studies on the monitoring and selection of these substitutions in Z . tritici populations, a multiplex allele‐specific quantitative PCR (qPCR) assay allowing for estimation of both allele frequencies in bulk DNA matrices was developed. The assay was then used on complex DNA samples originating from a spore trap network set up in Belgium, Denmark, Sweden, and Ireland in 2017 and 2018, as well as on leaf samples with symptoms. The S524T allele was present in all field samples and its proportion was significantly higher in Ireland than in Belgium, whereas the proportion of H152R was only sporadically present in both countries. The frequency of S524T varied greatly in the airborne inoculum of all four countries; however, the H152R allele was never detected in the airborne inoculum. The method developed in this study can be readily adopted by other laboratories and used for multiple applications including resistance monitoring in field populations of Z . tritici .
Mutation spectrum inEscherichia coliDNA mismatch repair deficient (mutH) strain (1987)

The Dam-directed post-replicative mismatch repair system of Escherichia coli removes base pair mismatches from DNA. The products of the mutH, mutL and mutS genes, among others, are required for efficient mismatch repair. Absence of any of these gene products leads to persistence of mismatches in DNA with a resultant increase in spontaneous mutation rate. To determine the specificity of the mismatch repair system in vivo we have isolated and characterized 47 independent mutations from a mutH strain in the plasmid borne mnt repressor gene. The major class of mutations comprises AT to GC transitions that occur within six base pairs of the only two 5'-GATC-3' sequences in the mnt gene. In the wild type control strain, insertion of the IS1 element was the major spontaneous mutational event. A prediction of the Dam-directed mismatch repair model, that the mutation spectra of dam and mutH strains should be the same, was confirmed.
The Spreading and Overlay Codes for the L1C Signal (2007)

ABSTRACT: We describe the rationale and construction of the family of L1C spreading codes and the associated family of overlay codes. The length-10230 spreading codes comprise 210 pilot/data sequence pairs. The codes are perfectly balanced and exhibit good even and odd auto- and crosscorrelation. They are constructed using prime-length Weil codes: selected length-10223 Weil-codes were padded with a fixed 7-bit pad. A search over all Weil codes and insertion points yielded a set of 739 codes from which the final set of 420 codes was chosen. Two separate families of codes were optimized based on modulation scheme (BOC(1,1) and MBOC). The length-1800 overlay codes are truncated linear feedback shift register sequences of length 2047, including both m-sequences and Gold sequences. Besides full period even auto- and cross-correlation, the overlay code search considered the correlation when a small subsequence (100 or 200 symbols) is correlated against the full code.
VANCOMYCIN-TOLERANT STREPTOCOCCUS PNEUMONIAE AND ITS CLINICAL SIGNIFICANCE (2001)

St. Jude Children’s Research Hospital and the University of Tennessee Health Science Center, Memphis, TN
[Early and late postoperative results of mitral and tricuspid valve insufficiency surgical treatment using edge-to-edge central coaptation procedure]. (2002)

Edge-to-edge approximation of the mitral leaflets and creation of a double-orifice mitral valve (Jatene-Alfieri procedure), for mitral regurgitation surgical treatment was effective in most cases, especially for patients who had rheumatic and degenerative valve disease, traumatic or ischemic mitral valve insufficiency. Positive results of double-orifice technique encourages to use this method to correct some forms of tricuspid insufficiency. Triple-orifice repair procedure is a lot more effective to correct central prolapses in all of the three leaflets (extraordinary elongated chordaes) and/or degenerative tricuspid annular dilation than the ordinary routine procedures. This study aims to evaluate early and long-term postoperative outcomes for 29 patients after mitral double-orifice and/or triple orifice repair procedures. It also determines clinical and echocardiographic results at follow-up period for more than two years.
Vibration and sound radiation of a cylindrical shell under a circumferentially moving load (1995)

A theoretical model is developed to evaluate the vibration and sound radiation of a thin cylindrical shell excited by a constant point load continuously traveling along the circumferential direction at a rotational speed Ω. This rotating load model takes into account the exterior fluid loading due to the sound pressure radiated by the shell. The three equations of the vibroacoustic problem are the shell equations of motion, the Helmholtz equation in the exterior fluid medium and the continuity equation at fluid–shell interface. The rotating load model is based on a frequency-domain solution which is convenient for the interpretation of the vibratory and acoustic responses in terms of shell modes. The equations of motion are expanded over the shell modes to give the modal equations of motion. A frequency-domain representation of the rotating load shows that its frequency content is a series of equal amplitude harmonics NΩ. Each harmonic excites exclusively the circumferential mode N. For this rotating excitation, vibration and radiation critical speeds are identified. They give, respectively, an indication at which rotational speeds high vibration levels and sound radiation efficiency are expected. Finally, a good correlation between the rotating load model and experiments are obtained.
Quantitative defect etching of GaAs on Si: Is it possible? (1988)

The Wright etch [M. W. Jenkins, J. Electrochem. Soc. 124, 757 (1977)], hitherto used to reveal defects in silicon, has been examined as a defect etchant for GaAs epitaxial layers on silicon. Various calibration techniques, including transmission electron microscopy of etched epitaxial layers, have been used to establish that etch features correspond with dislocations. Problems involved in direct comparisons of defect densities measured by different methods are discussed.
Mise au point de la quantification des HAP contenus dans des extraits aqueux de sols et de produits résiduaires organiques (2009)

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Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L. (2019)

Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic mosaic theory of coevolution predicts that coevolutionary interactions vary across geographic scales. Consequently, plant specialized metabolite diversity is expected to be highest in coevolutionary hotspots, geographic regions, which exhibit strong reciprocal selection on the interacting species. Despite being well-established theoretical frameworks, technical limitations have precluded rigorous hypothesis testing. Here we aim at understanding how geographic separation over evolutionary time may have impacted chemical differentiation in the cosmopolitan plant genus <i>Euphorbia</i>. We use a combination of state-of-the-art computational mass spectral metabolomics tools together with cell-based high-throughput immunomodulatory testing. Our results show significant differences in specialized metabolite diversity across geographically separated phylogenetic clades. Chemical structural diversity of the highly toxic <i>Euphorbia</i> diterpenoids is significantly reduced in species native to the Americas, compared to Afro-Eurasia. The localization of these compounds to young stems and roots suggest a possible ecological relevance in herbivory defense. This is further supported by reduced immunomodulatory activity in the American subclade as well as herbivore distribution patterns. We conclude that computational mass spectrometric metabolomics coupled with relevant ecological data provide a strong tool for exploring plant specialized metabolite diversity in a chemo-evolutionary framework.
Tumor markers in hairy cell leukemia (2011)

Despite the availability of highly effective therapies for hairy cell leukemia, including cladrabine, deoxycoformycin, and interferon α, a significant fraction of patients relapse. The use of flow cytometry, bone marrow examination for minimal residual disease, and peripheral blood counts provides details about the level of disease activity, but the optimal method for following patient response and risk for relapse has not been established. Flow cytometry provides accurate assessments of circulating malignant cell counts even at very low levels, but does not provide details on the extent of bone marrow involvement. Bone marrow involvement can be assessed by biopsy, but is a painful procedure, and the extent of involvement by hairy cell leukemia is not always uniform. Thus, a single biopsy may not identify active disease when it is present. Magnetic resonance imaging is being evaluated as a means for assessing total body burden of disease in the marrow and shows great promise. Tumor markers that can be measured in the serum provide a method for assessing total body disease burden. Cell surface proteins can be shed by tumor cells through proteolytic cleavage to release portions of their extracellular domains. These proteolytic degradation products can be measured in the serum and provide a tool to monitor disease burden and response to therapy. Three cell surface molecules expressed by the malignant hairy cells, CD25, CD22, and CD307, have been used to monitor disease activity and follow patients at risk for relapse. Serum tumor markers provide a reliable, inexpensive, and non-invasive means of following patients with hairy cell leukemia for response to treatment and relapse.