gebhart/patrepeval huggingface dataset:
Evaluation of Fluoromycobacteriophages for Detecting Drug Resistance in Mycobacterium tuberculosis (2011)

We tested a new method for detecting drug-resistant strains of Mycobacterium tuberculosis that uses a TM4 mycobacteriophage phAE87::hsp60-EGFP (EGFP-phage) engineered to contain the gene encoding enhanced green fluorescent protein (EGFP). After promising results in preliminary studies, the EGFP-phage was used to detect isoniazid (INH), rifampin (RIF), and streptomycin (STR) resistance in 155 strains of M. tuberculosis, and the results were compared to the resazurin microplate technique, with the proportion method serving as the reference standard. The resazurin technique yielded sensitivities of 94% for INH and RIF and 98% for STR and specificities of 97% for INH, 95% for RIF, and 98% for STR. The sensitivity of EGFP-phage was 94% for all three antibiotics, with specificities of 90% for INH, 93% for RIF, and 95% for STR. The EGFP-phage results were available in 2 days for RIF and STR and in 3 days for INH, with an estimated cost of ∼2$ to test the three antibiotics. Using a more stringent criterion for resistance improved the specificity of the EGFP-phage for INH and RIF without affecting the sensitivity. In preliminary studies, the EGFP-phage could also effectively detect resistance to the fluoroquinolones. The EGFP-phage method has the potential to be a valuable rapid and economic screen for detecting drug-resistant tuberculosis if the procedure can be simplified, if it can be adapted to clinical material, and if its sensitivity can be improved.
Trapping of Several Solitons in Annular Josephson Junctions (1992)

We have observed for the first time a chain of sine-Gordon solitons (flux quanta) trapped in an annular Josephson junction. The low-temperature electron microscopy technique has been used in order to trap in a controlled way one by one up to several solitons in the junction. We attribute the deviations of the soliton chain velocity from the single-soliton velocity with the effects of the interaction between solitons and their bunching at high velocity.
Specific Distribution within the <i>Enterobacter cloacae</i> Complex of Strains Isolated from Infected Orthopedic Implants (2009)

Bacteria belonging to the Enterobacter genus are frequently isolated from clinical samples but are unusual causative agents of orthopedic implant infections. Twelve genetic clusters (clusters I to XII) and one sequence crowd (sequence crowd xiii) can be distinguished within the Enterobacter cloacae nomenspecies on the basis of hsp60 sequence analysis, and until now, none of these clusters could be specifically associated with a disease. In order to investigate if specific genetic clusters would be involved in infections of orthopedic material, two series of bacterial clinical isolates identified as E. cloacae by routine phenotypic identification methods were collected either from infected orthopedic implants (n = 21) or from randomly selected samples of diverse anatomical origins (control; n = 52). Analysis of the hsp60 gene showed that genetic clusters III, VI, and VIII were the most frequent genetic clusters detected in the control group, whereas cluster III was poorly represented among the orthopedic implant isolates (P = 0.006). On the other hand, E. hormaechei (clusters VI and VIII), but not cluster III, is predominantly associated with infections of orthopedic implants and, more specifically, with infected material in the hip (P = 0.019). These results support the hypothesis that, among the isolates within the E. cloacae complex, E. hormaechei and hsp60 gene sequencing-based cluster III are involved in pathogenesis in different ways and highlight the need for more accurate routine Enterobacter identification methods.
Plastic Change of N-type Ca Channel Expression after Preconditioning Is Responsible for Prostaglandin E2-induced Long-lasting Allodynia (2003)

Background Although considerable evidence indicates neuronal Ca channels play significant roles in pain perception, their possible importance in hypersensitization after acute inflammation has not been investigated. Methods Using carrageenan for inducing hypersensitization, the authors investigated the analgesic effects of intrathecally administered N- and P/Q-type channel blockers, omega-conotoxin GVIA and omega-agatoxin IVA, respectively, and also examined the level of N-type channel expression. Results Acute inflammation, produced by carrageenan injection in a rat hind paw, caused mechanical hypersensitivity that resolved within several days. Injection of prostaglandin E2 into the same hind paw after resolution caused a markedly prolonged mechanical allodynia lasting more than 4 h. Similar but less potent prolonged allodynia was also induced in the contralateral hind paws. Intrathecal administration of omega-conotoxin GVIA (0.03-0.3 microg) produced dose-dependent inhibition of the allodynia in both control and carrageenan-preconditioned rats. However, the potency of omega-conotoxin GVIA was significantly lower in carrageenan-preconditioned paws than in those in the contralateral and saline-preconditioned paws. In contrast, omega-agatoxin IVA (0.01-0.1 microg) did not reduce the allodynia. Significant up-regulation of N-type channel expression was observed in both dorsal root ganglia and the spinal cord ipsilateral to the carrageenan-preconditioned hind paw. Conclusions The results suggest an aggravating role of the N-type channel in pain sensation and a selective plastic change of this channel expression that could underlie the mechanism of hypersensitization after acute inflammation.
Delayed two steps PRP injection strategy for the improvement of fat graft survival with superior angiogenesis (2020)

Platelet-rich plasma (PRP) has been widely used to improve the fat retention rate in autologous fat transplantation since it possesses a good angiogenesis capability in vivo. However, due to the short half-life of growth factors released from PRP and its uneven distribution in injected fat tissue, the strategy of PRP in fat transplantation needs further improvement. Since the capillaries started to grow into fat grafts in 1 week and vascular growth peaks in the second week after transplantation, we hypothesized that delayed two-steps PRP injection into the interior of grafts, accompanied with the extent of neovascularization might theoretically promote microvessel growth inside transplanted adipose tissue. 24 nude mice were divided into three groups: Blank group (0.35 mL fat mixed with 0.15 mL saline, N = 8), Single step group (0.35 mL fat mixed with 0.15 mLPRP, N = 8), and Two steps group (0.35 mL fat (day 0) + 0.075 mL PRP (day 7) + 0.075 mL PRP (day 14), N = 8). At 6 and 14 weeks post-transplantation, grafts were dissected, weighted, and assessed for histology, angiogenesis, fat regeneration and inflammation level. The weight and volume of the fat samples revealed no statistical difference among the three groups at 6 weeks after fat transplantation. The weight and volume of the Two steps group fat samples showed significantly higher compared to that in Blank and Single step groups at 14 weeks after fat transplantation (weight: 137.25 ± 5.60 mg versus 87.5 ± 3.90 mg,106.75 ± 2.94 mg, respectively; volume: 0.13 ± 0.01 mL versus 0.08 ± 0.01 mL, 0.09 ± 0.01 mL, respectively). Histological assessments indicated that delayed two-steps PRP injection strategy helps to improve adipose tissue content and reduce the composition of fibrous connective tissue at 14 weeks after fat transplantation. At 6 weeks and 14 weeks after transplantation, CD31 immunofluorescence indicated that delayed two-steps PRP injection strategy helps to improve angiogenesis and significantly higher compared to that in Blank and Single step groups (6 weeks: 28.75 ± 4.54 versus 10.50 ± 2.06, 21.75 ± 1.85; 14 weeks: 21.75 ± 2.86 versus 9.87 ± 2.08, 11.75 ± 1.47, respectively). Preadipocyte count indicated delayed two-steps PRP injection strategy might promote fat regeneration and significantly higher compared to that in Blank and Single step groups at 14 weeks (129.75 ± 6.57 versus 13.50 ± 3.50, 17.12 ± 6.23, respectively). In this study, we demonstrated that the novel delayed two-steps PRP injection strategy remarkably enhanced the long-term fat retention rate and improved the neovascularization extent in the interior of the fat graft. Platelet-rich plasma, Delayed two-steps injection, Angiogenesis, Fat transplantation.
Assessment of Cognitive and Motor Deficits in a Marmoset Model of Stroke (2003)

The Stroke Therapy Academic Industry Roundtable noted the need for standardized, well-accepted primate models of stroke to help develop both neuroprotective and restorative therapies. One primate model has been developed using the marmoset, a small New World species of monkey, in which long-term functional deficits can be assessed. The surgery and postoperative care of the animals is described, as well as the behavioral tests used to quantify the postoperative disability. The types of deficits seen are illustrated by reference to some of the findings with neuroprotective treatments. Nevertheless, the long-term nature and consistency of the motor deficits make this model ideal for assessing the worth of restorative therapies.
Les polymères végétaux : polymères pariétaux et alimentaires non azotés (1980)

National audience
The Basis of Choice (2010)

Chapter 9 suggested that enterprise should be seen as one of the options for people for trying to get what they want out of life. This chapter looks at the possible influences on the choice people make between it and the other options.
Impact of lexical filtering on overall opinion polarity identification (2005)

One approach to assessing overall opinion polarity (OvOP) of reviews, a concept defined in this paper, is the use of supervised machine learning mechanisms. In this paper, the impact of lexical filtering, applied to reviews, on the accuracy of two statistical classifiers (Naive Bayes and Markov Model) with respect to OvOP identification is observed. Two kinds of lexical filters, one based on hypernymy as provided by Word-Net (Fellbaum 1998), and one hand-crafted filter based on part-of-speech (POS) tags, are evaluated. A ranking criterion based on a function of the probability of having positive or negative polarity is introduced and verified as being capable of achieving 100% accuracy with 10% recall. Movie reviews are used for training and evaluation of each statistical classifier, achieving 80% accuracy.
Reduction of buffer leakage current in AlGaN/GaN high-electron-mobility-transistor structure on Si substrate by reducing the dislocation density in AlN buffer layer (2007)

We investigated preferable way of decrease of vertical leakage current in GaN-based high-electron-mobility-transistor structure on Si(111) substrate. It is found that the leakage current is much improved as the dislocation density in thin A1N buffer layer decreases. It has been successfully obtained the leakage current less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 200 V although the total epitaxial layer thickness is about only 1 mum.
Detection, quantifications and pharmacokinetics of toltrazuril sulfone (Ponazuril<sup>®</sup>) in cattle (2008)

Toltrazuril sulfone (Ponazuril) is a triazine-based anti-protozoal agent with highly specific actions against apicomplexan group of organisms, which are undergoing intensive investigation. Toltrazuril sulfone may have clinical application in the treatment of Neospora. caninum and other protozoal infections in cattle. To evaluate absorption, distribution, and elimination characteristics of toltrazuril sulfone in cattle, a sensitive validated quantitative high-pressure liquid chromatography method for toltrazuril sulfone in bovine biological fluids was developed. After a single oral dose of toltrazuril sulfone at 5 mg/kg (as 150 mg/g of Marquis; Bayer HealthCare, Shawnee Mission, KS, USA), samples from six cows showed good plasma concentrations of toltrazuril sulfone, which peaked at 4821 ng/mL +/- 916 (SD) at 48 h postadministration. Thereafter, plasma concentration declined to 1950 ng/mL +/- 184 (SD) at 192 h after administration with an average plasma elimination half-life of approximately 58 h. Following oral dose of toltrazuril sulfone, the observed peak plasma concentrations were in relatively close agreement ranging from the lowest 3925 ng/mL to the highest of 6285 ng/mL with the mean peak plasma concentration being 4821 ng/mL. This study shows that toltrazuril sulfone is relatively well absorbed after oral dose in cattle. These results are therefore entirely consistent with and support the reported clinical efficacy of toltrazuril sulfone in the treatment of experimentally induced clinical cases of N. caninum and other protozoal-mediated bovine diseases.
Identifying Cryptic Relationships (2011)

Cryptic relationships such as first-degree relatives often appear in studies that collect population samples such as the case-control genome-wide association studies (GWAS). Cryptic relatedness not only creates increased type 1 error rate but also affects other aspects of GWAS, such as population stratification via principal component analysis. Here we discuss two effective methods, as implemented in PREST and PLINK, to detect and correct for the problem of cryptic relatedness using high-throughput SNP data collected from GWAS or next-generation sequencing (NGS) experiments. We provide the analytical and practical details involved using three application examples.
Mapping the energy surface of PbTiO<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mrow/><mml:mn>3</mml:mn></mml:msub></mml:math>in multidimensional electric-displacement space (2011)

In recent years, methods have been developed that allow first-principles electronic-structure calculations to be carried out under conditions of fixed electric field. For some purposes, however, it is more convenient to work at fixed electric displacement field. Initial implementations of the fixed-displacement-field approach have been limited to constraining the field along one spatial dimension only. Here, we generalize this approach to treat the full three-dimensional displacement field as a constraint and compute the internal-energy landscape as a function of this multidimensional displacement-field vector. Using PbTiO${}_{3}$ as a prototypical system, we identify stable or metastable tetragonal, orthorhombic, and rhombohedral structures as the displacement field evolves along the [001], [110], and [111] directions, respectively. The energy minimum along [001] is found to be deeper than that along [110] or [111], as expected for a system having a tetragonal ground state. The barriers connecting these minima are found to be quite small, consistent with the current understanding that the large piezoelectric effects in PbTiO${}_{3}$ arise from the easy rotation of the polarization vector.
Evidence that the N-terminal part of the S-layer protein from Bacillus stearothermophilus PV72/p2 recognizes a secondary cell wall polymer (1997)

The S-layer of Bacillus stearothermophilus PV72/p2 shows oblique lattice symmetry and is composed of identical protein subunits with a molecular weight of 97,000. The isolated S-layer subunits could bind and recrystallize into the oblique lattice on native peptidoglycan-containing sacculi which consist of peptidoglycan of the A1gamma chemotype and a secondary cell wall polymer with an estimated molecular weight of 24,000. The secondary cell wall polymer could be completely extracted from peptidoglycan-containing sacculi with 48% HF, indicating the presence of phosphodiester linkages between the polymer chains and the peptidoglycan backbone. The cell wall polymer was composed mainly of GlcNAc and ManNAc in a molar ratio of 4:1, constituted about 20% of the peptidoglycan-containing sacculus dry weight, and was also detected in the fraction of the S-layer self-assembly products. Extraction experiments and recrystallization of the whole S-layer protein and proteolytic cleavage fragments confirmed that the secondary cell wall polymer is responsible for anchoring the S-layer subunits by the N-terminal part to the peptidoglycan-containing sacculi. In addition to this binding function, the cell wall polymer was found to influence the in vitro self-assembly of the guanidinium hydrochloride-extracted S-layer protein. Chemical modification studies further showed that the secondary cell wall polymer does not contribute significant free amino or carboxylate groups to the peptidoglycan-containing sacculi.
A semiclassical approach to Coulomb scattering of conduction electrons on ionized impurities in nondegenerate semiconductors (2003)

In the proposed model of mobility, the time of electron–ion interaction equals the time taken by the conduction electron to pass a spherical region, corresponding to one impurity ion in crystal, and the minimum scattering angle is determined after Conwell–Weisskopf. We consider the acts of electron scattering on ions as independent and incompatible events. It is shown in the approximation of quasimomentum relaxation time, that for nondegenerate semiconductors, the mobility μi, limited by the elastic scattering by impurity ions with the concentration Ni, is proportional to T/Ni2/3; the Hall factor equals 1.4. The calculated dependences of the mobility of the majority charge carriers upon their concentration for different temperatures T agree well with known experimental data. It is shown, that the Brooks–Herring formula μBH∝T3/2/Ni gives overestimated values of mobility. Comparison of the calculations of mobility in degenerate semiconductors with experimental data also yields μi&lt;μBH.
Specificity of p47 <sup> <i>phox</i> </sup> SH3 Domain Interactions in NADPH Oxidase Assembly and Activation (1997)

The delineation of molecular structures that dictate Src homology 3 (SH3) domain recognition of specific proline-rich ligands is key to understanding unique functions of diverse SH3 domain-containing signalling molecules. We recently established that assembly of the phagocyte NADPH oxidase involves multiple SH3 domain interactions between several oxidase components (p47phox, p67phox, and p22phox). p47phox was shown to play a central role in oxidase activation in whole cells by mediating interactions with both the transmembrane component p22phox and cytosolic p67phox. To understand the specific roles of each SH3 domain of p47phox in oxidase assembly and activation, we mutated critical consensus residues (Tyr167 or Tyr237-->Leu [Y167L or Y237L], W193R or W263R, and P206L or P276L) on each of their binding surfaces. The differential effects of these mutations indicated that the first SH3 domain is responsible for the p47phox-p22phox interaction and plays a predominant role in oxidase activity and p47phox membrane assembly, while the second p47phox SH3 domain interacts with the NH2-terminal domain of p67phox. Binding experiments using the isolated first SH3 domain also demonstrated its involvement in intramolecular interactions within p47phox and showed a requirement for five residues (residues 151 to 155) on its N-terminal boundary for binding to p22phox. The differential effects of nonconserved-site mutations (W204A or Y274A and E174Q or E244Q) on whole-cell oxidase activity suggested that unique contact residues within the third binding pocket of each SH3 domain influence their ligand-binding specificities.
Optical damage in transition metal doped ferroelectrics (1978)

The results of a detailed study of optically induced refractive index changes (optical damage) in undoped and doped LiNbO3 are presented. The quantitative relationships between the sensitivity to optical damage and the concentrations of Fe ions are determined. The concentrations of Fe2+ and Fe3+ ions have been evaluated from EPR, acoustic EPR and optical spectra. The optimal parameters of LiNbO3: Fe crystals for obtaining the highest photorefractive sensitivity are determined.
Large Displacement Optical Flow: Descriptor Matching in Variational Motion Estimation (2010)

Optical flow estimation is classically marked by the requirement of dense sampling in time. While coarse-to-fine warping schemes have somehow relaxed this constraint, there is an inherent dependency between the scale of structures and the velocity that can be estimated. This particularly renders the estimation of detailed human motion problematic, as small body parts can move very fast. In this paper, we present a way to approach this problem by integrating rich descriptors into the variational optical flow setting. This way we can estimate a dense optical flow field with almost the same high accuracy as known from variational optical flow, while reaching out to new domains of motion analysis where the requirement of dense sampling in time is no longer satisfied.
Ludovico Ariosto - Poet and Poem in the Italian Renaissance (1968)

Journal Article LUDOVICO ARIOSTO—POET AND POEM IN THE ITALIAN RENAISSANCE Get access C. P. BRAND C. P. BRAND Edinburgh Search for other works by this author on: Oxford Academic Google Scholar Forum for Modern Language Studies, Volume IV, Issue 1, January 1968, Pages 87–101, https://doi.org/10.1093/fmls/IV.1.87 Published: 01 January 1968
Sensitive and Rapid Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA by Loop-Mediated Isothermal Amplification (2005)

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method in which reagents react rapidly and efficiently, with a high specificity, under isothermal conditions. We used a LAMP assay for the detection of herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and varicella-zoster virus (VZV). The virus specificities of primers were confirmed by using 50 HSV-1, 50 HSV-2, and 8 VZV strains. The assay was performed for 45 min at 65 degrees C. The LAMP assay had a 10-fold higher sensitivity than a PCR assay. An analysis of nucleotide sequence variations in the target and primer regions used for the LAMP assay indicated that 3 of 50 HSV-1 strains had single nucleotide polymorphisms. No HSV-2 or VZV strains had nucleotide polymorphisms. Regardless of the sequence variation, there were no differences in sensitivity with the HSV-1-specific LAMP assay. To evaluate the application of the LAMP assay for clinical diagnosis, we tested clinical samples from 40 genital herpes patients and 20 ocular herpes patients. With the LAMP assay, 41 samples with DNA extraction and 26 direct samples without DNA extraction were identified as positive for HSV-1 or HSV-2, although 37 samples with DNA extraction and just one without DNA extraction were positive by a PCR assay. Thus, the LAMP assay was less influenced than the PCR assay by the presence of inhibitory substances in clinical samples. These observations indicate that the LAMP assay is very useful for the diagnosis of HSV-1, HSV-2, and VZV infections.
Turbo decoding for high spectral efficiency satellite communications (2002)

The problem of efficient utilization of the frequency spectrum for coded satellite systems is investigated; one which results as a consequence of highly crowding adjacent channels. An analytical characterization of the resulting interference channel is introduced based on concepts in statistical decision theory and is then exploited for interference cancellation. A joint implementation of MMSE interference cancellation and forward error control (FEC) decoding is considered where soft-input soft-output (SISO) modules are used along with the iterative structure. It is shown that, for example, one can operate a satellite system with convolutionally encoded QPSK modulation that uses practical pulse shaping at the channel spacing valve of 0.75 of the symbol rate, or bandwidth efficiency level of 2.67 bits-per-second/Hz, with minimum additional energy requirement. (This corresponds to a spectral efficiency improvement of 55% compared with a conservative baseline system.).