gebhart/patrepeval huggingface dataset:
Complete nucleotide sequence of a highly divergent human T-cell leukemia (lymphotropic) virus type I (HTLV-I) variant from melanesia: genetic and phylogenetic relationship to HTLV-I strains from other geographical regions (1993)

The high prevalences of antibodies against human T-cell leukemia (lymphotropic) virus type I (HTLV-I) reported for remote populations in Papua New Guinea and the Solomon Islands and for some aboriginal populations in Australia have been verified by virus isolation. Limited genetic analysis of the transmembrane portion (gp21) of the envelope gene of these viruses indicates the existence of highly divergent HTLV-I strains in Melanesia. Here, we report the complete nucleotide sequence of an HTLV-I isolate (designated HTLV-IMEL5) from the Solomon Islands. The overall nucleotide divergence of HTLV-IMEL5 from the prototype HTLV-IATK was approximately 8.5%. The degree of variability in the amino acid sequences of structural genes ranged between 3 and 11% and was higher (8.5 to 25%) for the regulatory (tax and rex) genes and the other genes encoded by the pX region. Since HTLV-IMEL5 was as distantly related to HTLV-II as to the other known HTLV-I strains, it could not have arisen from a reocmbinational event involving HTLV-II but rather might be an example of independent viral evolution in this remote population. These data provide important insights and raise new questions about the origin and global dissemination of HTLV-I.
AM-to-PM conversion in a resonant microwave optical rectification detector (2017)

A LiNbO<sub>3</sub>-loaded microwave cavity pumped with weakly AM-modulated 30 fs optical pulses was used as a platform to investigate AM-to-PM conversion in the optical rectification process. Theoretical treatment of AM-to-PM conversion (i.e., peak-induced electrical phase deviation β<sub>i</sub> due to optical power modulation with index m) suggests that the dominant mechanism is self-group-velocity modulation due to χ<sup>(3)</sup> and cascaded χ<sup>(2)</sup> processes with a value of δ=β<sub>i</sub>/m=-151 dB, linearly dependent on the optical power at intensities of 6×10<sup>10</sup> W/m<sup>2</sup> in a 40 mm long LiNbO<sub>3</sub> crystal. This is in stark contrast to p-i-n photodiodes which can exhibit an AM-to-PM conversion gain δ>0 dB. In this experiment, we measured values of δ for a resonant optical rectification detector using typical mode-locked Ti:sapphire laser pulses (100 MHz, 30 fs, P<sub>avg</sub>≈100 mW) and found an instrumentation-limited lower bound of δ≈-43.5 dB, independent of the optical power.
Biodistribution of [S-35] Labeled Antisense Oligodeoxynuclotides Increased Tumor Targeting With Microsphere Coinjection (2002)

To elucidate the effect of microsphere coinjection on the administration of oligodeoxynucleotide (ODN), we have investigated biodistribution of [S-35]-labeled antisense ODN targeted to cAMP-dependent protein kinase (PKA) RI-a subunit in nude mice xenografted with WiDr (human colon cancer, ATCC CCL218). The strategy of using microsphere has been proposed for cancer treatment as a carrier of therapeutic ODN so that it could offer an advantage with respect to maintaining constant ODN levels in blood and obtaining higher therapeutic ODN concentration at tumor sites. Comparative biodistribution studies were performed in nude mice (female, 20 g of body weight, n = 4-6) xenografted with WiDr cancer cells, when 0.1 μCi (specific activity, 2.94 mCi/μmole) of [S-35]-labeled RI-α antisense ODN was injected alone or with microsphere (PLG-18, polylactic copolymer with cationic surfactant DDAB18). Peak tumor uptake of [S-35]-labeled ODN was significantly increased from 17.7% (at 6 h) of injected dose per gram of tissue (ID/g) to 42.5% (at 24 h) ID/g when microsphere was coinjected with ODN. The different biodistribution in the kidney accumulation (e.g., 100.2%ID/g for ODN alone and 54.9%/ID/g for microshpere coinjection) may contribute to higher blood concentration (e.g., 21.5%ID/ml for ODN alone and 37.5%ID/ml for microsphere coinjection) of radiolabeled ODN. Of importance is the fact that the whole body retention of radioactivity increased with microsphere coinjection from 50.8%ID/g to 68.0%ID/g after 24-h of injection. This decreased kidney accumulation and increased whole body retention of [S-35]-labeled ODN resulted in a significant improvement of ODN targeting to the tumor site. In conclusion, the coinjection of microsphere appears to be an important carrier system in vehiculation of antisense oligonucleotide to the tumor tissue in vivo.
Intrinsic pinning and the critical current scaling of clean epitaxial Fe(Se,Te) thin films (2013)

We report on the transport properties of clean, epitaxial Fe(Se,Te) thin films prepared on Fe-buffered MgO (001) single crystalline substrates by pulsed laser deposition. Near ${T}_{\mathrm{c}}$ a steep slope of the upper critical field for $H||ab$ was observed (74.1 T/K), leading to a very short out-of-plane coherence length, ${\ensuremath{\xi}}_{\mathrm{c}}(0)$, of 0.2 nm, yielding 2${\ensuremath{\xi}}_{\mathrm{c}}(0)\ensuremath{\approx}0.4\phantom{\rule{0.16em}{0ex}}\mathrm{nm}$. This value is shorter than the interlayer distance (0.605 nm) between the Fe-Se(Te) planes, indicative of modulation of the superconducting order parameter along the $c$ axis. An inverse correlation between the power law exponent $N$ of the electric field-current density($E$-$J$) curve and the critical current density ${J}_{\mathrm{c}}$ has been observed at 4 K, when the orientation of $H$ was close to the $ab$ plane. These results prove the presence of intrinsic pinning in Fe(Se,Te). A successful scaling of the angular dependent ${J}_{\mathrm{c}}$ and the corresponding exponent $N$ can be realized by the anisotropic Ginzburg Landau approach with appropriate $\ensuremath{\Gamma}$ values $2\ensuremath{\sim}3.5$. The temperature dependence of $\ensuremath{\Gamma}$ behaves almost identically to that of the penetration depth anisotropy.
Bat Salivary Gland Virus Carrier State in A Naturally Infected Mexican Freetail Bat (1966)

SummaryFour of 46 weak and nonflying Mexican free-tail bats (Tadarida brasiliensis mexicana) captured in Frio Cave, Uvalde County, Texas, were found to be infected with bat salivary gland virus. One of these four bats survived and was maintained in a nonhibernating state in the laboratory, and bat salivary gland virus was recovered from the saliva on 10 occasions over a period of 309 days after the bat was captured.
A tris(2,2′-bipyridine)ruthenium(<scp>ii</scp>) derivative tethered to a cis-PtCl<sub>2</sub>(amine)<sub>2</sub>moiety: syntheses, spectroscopic properties, and visible-light-induced scission of DNA (2006)

A tris(2,2'-bipyridine)ruthenium(II) derivative having two N-(3-ammoniopropyl)carbamoyl pendant units has been prepared and reacted with cis-PtCl2(DMSO)2 (DMSO = dimethyl sulfoxide) to give a heteronuclear Ru(II)Pt(II) dimer having a cis-Pt(II)Cl2(aliphatic amine)2 unit, [Ru(bpy)2(mu-bridge)PtCl2](PF6)2 (bpy = 2,2'-bipyridine, bridge = 4,4'-bis(N-(3-aminopropyl)carbamoyl)-2,2'-bipyridine). The ESI-TOF mass spectrum of the Ru(II)Pt(II) dimer shows a set of signals corresponding to {[Ru(bpy)2(mu-bridge)PtCl2](PF6)}(+) (m/z 1181.1). The MLCT (metal-to-ligand charge transfer) luminescence intensity is enhanced upon the platination of two amine units, presumably due to the formation of a relatively rigid metallocycle. More interestingly, the luminescence intensity is further enhanced by the complexation of the Ru(II)Pt(II) dimer with either 5'-GMP (guanosine 5'-monophosphate disodium salt) or calf thymus DNA. Visible-light-induced scission of supercoiled pBR322 DNA is found to be efficiently enhanced in the presence of the title Ru(II)Pt(II) dimer.
Loss kinetics of carbon atoms in low-pressure high density plasmas (2000)

Vacuum ultraviolet absorption spectroscopy (VUVAS) with a carbon hollow cathode lamp was applied to the measurement of decay rate of C atom density in the afterglow of CO and CO/H2 inductively coupled plasmas. The transition line used for the measurement was 2p3s 3P2–2p2 3P2 at 165.7 nm. The influence of background absorption by the species in plasma other than C atoms on the transition line of C atoms was found to be negligible. This was clarified by measuring the absorption intensities around the center wavelength of C atoms in plasmas with VUVAS employing a xenon microhollow cathode lamp. Moreover, the dependence of the decay rate of C atom density on pressure revealed that C atoms were dominantly lost at the surface rather than in the gas phase in both CO and CO/H2 plasmas. However, in the case of CO/H2 plasma at higher pressures over about 5.0 Pa, C atoms were lost in the gas phase as well as at the surface. The diffusion constants of C atoms in both CO and CO/H2 plasmas were also determined to be 3.1×104 and 3.7×104 cm2 Pa s−1, respectively.
Orthopaedic wear particle‐induced bone loss and exogenous macrophage infiltration is mitigated by local infusion of NF‐κB decoy oligodeoxynucleotide (2017)

Excessive production of wear particles from total joint replacements induces chronic inflammation, macrophage infiltration, and consequent bone loss (periprosthetic osteolysis). This inflammation and bone remodeling are critically regulated by the transcription factor NF-κB. We previously demonstrated that inhibition of NF-κB signaling by using the decoy oligodeoxynucleotide (ODN) mitigates polyethylene wear particle-induced bone loss using in vitro and in vivo models. However, the mechanisms of NF-κB decoy ODN action, and in particular its impact on systemic macrophage recruitment, remain unknown. In the current study, this systemic macrophage infiltration was examined in our established murine femoral continuous particle infusion model. RAW264.7 murine macrophages expressing a luciferase reporter gene were injected into the systemic circulation. Quantification of bioluminescence showed that NF-κB decoy ODN reduced the homing of these reporter macrophages into the distal femurs exposed to continuous particle delivery. Particle-induced reduction in bone mineral density at the distal diaphysis of the femur was also mitigated by infusion of decoy ODN. Histological staining showed that the decoy ODN infusion decreased osteoclast and macrophage numbers, but had no significant effects on osteoblasts. Local infusion of NF-κB decoy ODN reduced systemic macrophage infiltration and mitigated particle-induced bone loss, thus providing a potential strategy to treat periprosthetic osteolysis. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3169-3175, 2017.
Reactions of cyclopalladated compounds and alkynes: New pathways for organic synthesis? (1990)

Abstract Cyclometallated compounds, obtained by direct intramolecular C–H activation of a ligand by transition metals, are fairly reactive [especially those derived from palladium(II)] towards insertion of internal alkynes into their metal‐carbon bond. This reaction leads to either new organometallic compounds by inclusion of one to three alkynes into the M‐C bond, or organic compounds which are either carbocyclic or heterocyclic, their nature depending upon the alkyne substituents as well as upon the cyclometallated ligand.
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII (2005)

Thus far, identification of functionally important residues in Type II restriction endonucleases (REases) has been difficult using conventional methods. Even though known REase structures share a fold and marginally recognizable active site, the overall sequence similarities are statistically insignificant, unless compared among proteins that recognize identical or very similar sequences. Bsp6I is a Type II REase, which recognizes the palindromic DNA sequence 5'GCNGC and cleaves between the cytosine and the unspecified nucleotide in both strands, generating a double-strand break with 5'-protruding single nucleotides. There are no solved structures of REases that recognize similar DNA targets or generate cleavage products with similar characteristics. In straightforward comparisons, the Bsp6I sequence shows no significant similarity to REases with known structures. However, using a fold-recognition approach, we have identified a remote relationship between Bsp6I and the structure of PvuII. Starting from the sequence-structure alignment between Bsp6I and PvuII, we constructed a homology model of Bsp6I and used it to predict functionally significant regions in Bsp6I. The homology model was supported by site-directed mutagenesis of residues predicted to be important for dimerization, DNA binding and catalysis. Completing the picture of sequence-structure-function relationships in protein superfamilies becomes an essential task in the age of structural genomics and our study may serve as a paradigm for future analyses of superfamilies comprising strongly diverged members with little or no sequence similarity.
Dynamic Segmentation : Detecting Complex Topology 3D-object (2005)

The continuous model of an image to segment can be used to consider the segmenting problem as the evolution of a 3D surface (modelised by spline tensorial products) under strenghts comparable to those used in active contours or snakes. The advantage of this method is that this evolution can be modelled with a simple differential system, the variables of which are the coefficients of the B-splines representing the frontier. Moreover, this method is by nature adaptive : it is easy to control the number of B-spline used to represent the frontier, which makes it possible to improve progressively the result of the segmentation. Aprioriknowledge can easily be taken into account if provided under the form of a CAD model of the object to segment. Some topological problems may appear : surfaces topologically equivalent to spheres may have to be transformed into more complex topology surfaces (torus for instance). We propose a method to solve that problem.
220 An Experimental Attempt at Reducing Unburnt Particle Emission in the Recycled PET-Resin Powder Combustion (2005)

The possibility of thermal recycling of wasted PET-resin has been investigated in the open atmospheric operation by supplying PET-resin powder as an auxiliary fuel to a proposed twin-fuelled burner. In the preceding experiments, in order to reduce an amount of unburnt PET-particles in the open atmospheric operation, reactive flows and burning processes of PET-particles were investigated using PIV/PTV measurements. Appearances of flying PET-particles were also observed by using the pulse laser and the particle diameter was evaluated as an equivalent diameter. According to the results, some key factors for reducing the unburnt rate of PET-particles were clarified. In this paper, by taking these factors into consideration, an experimental attempt at reducing unburnt particle emission in the recycled PET-resin powder combustion is carried out by varying the PET-powder supply pipe diameter. The result specifies experimentally that the increase in the dispersion degree of PET-particles reduces the unbunt rate of PET-powder.
Hydration Study of Cementitious Materials using Semi-Adiabatic Calorimetry (2007)

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Modelling Attempts to Predict Fretting-Fatigue Life on Turbine Components (2004)

Whenever two or more turbine components are in tight contact, Fretting-Fatigue becomes a relevant failure mechanism. Despite of on-going research on Fretting Fatigue, life prediction under fretting conditions continues being a challenge. To analytically predict fretting-fatigue life, key driving factors need to be identified and quantified in mechanical terms (stress and strain). Due to the intrinsic characteristics of contact, stress and strain fields around contact areas evolve with the loading history. They, together with material non-linearity and contact conditions need to be taken into account in order to perform a reliable life prediction. The present paper focuses on identifying the driving factors for fretting damage on blade-disk attachment under real engine conditions. Two-dimensional finite element contact calculations were carried out to quantify the influence of the key factors on mechanical quantities (stress and strain). Special attention was paid to material models and surface interaction (friction coefficient and contact conditions) in order to balance computational effort with result's accuracy. Finally, the multi-axial fatigue criteria developed by Dang Van and co-workers is used to predict failure. For validation purposes life prediction is compared with experimental results.
Organic Films Containing Trinuclear Ruthenium Clusters that Exhibit Redox-state-dependent Heat-shielding Characteristics (2009)

Abstract We report here an unprecedented utility of redox-active transition-metal complexes as heat-shielding materials. A poly(vinyl alcohol) film containing mixed-valent cluster [Ru3(μ3-O)(μ-CH3CO2)6(mbpy+)3](PF6)3 (1) (mbpy+ = 1-methyl-4,4′-bipyridinium cation), which strongly absorbs light in the near-infrared region, shows heat-shielding characteristics whose efficiency is found to highly depend on the redox state of the cluster dye.
Pre-EUCREX Intercomparison of Airborne Humidity Measuring Instruments (1994)

During the pre-EUCREX (European Cloud and Radiation Experiment) intercomparison of airborne instrumentation in January 1992, nine hygrometers mounted on three different aircraft were compared. Although the different instruments are based on completely different principles and the three aircraft have very different flying characteristics, humidity data from both vertical profiles as well as horizontal flight legs showed good agreement. Despite the different aircraft limitations the intercomparison was done with the aircraft in close formation. In terms of relative difference in mixing ratio, most instruments agreed to within ±5% for values down to about 0.1 g kg−1. For mixing ratios between 0.03 and 0.1 g kg−1 most instruments agreed to within ±15%. Systematic differences between the instruments suggest that in joint experiments where data will be shared, the same algorithms for evaluating and converting humidity parameters should be used whenever possible.
New Details of the Human Corneal Limbus Revealed With Second Harmonic Generation Imaging (2015)

By using SHG imaging, new details of the collagen architecture of human corneal limbal area were elucidated. High resolution images with volumetric analysis revealed two novel collagen structures.
Joint Optimization Of Lcmv Beamforming And Acoustic Echo Cancellation (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Nomograms for prognostication of patients with esophageal and gastroesophageal carcinoma undergoing definitive chemoradiotherapy. (2012)

82 Background: Level-1 evidence for definitive chemoradiotherapy (bimodality therapy or BM therapy) has been established for patients with esophageal and gastroesophageal junction cancers (EGEJC) who otherwise do not qualify for surgery; however, tools to estimate individual patient’s prognosis are unavailable. We used a number of clinical pre-treatment and post-treatment parameters to establish two nomograms (for overall survival [OS] and relapse-free survival [RFS]). Methods: From 2002 through 2010, 257 consecutive patients with EGJEC who received BM therapy and had pre- and post-treatment positron emission tomography (PET) and post-treatment endoscopic biopsies among other assessments were analyzed from a prospectively maintained database. Standard statistical methods were used to generate the nomograms. Results: The median follow -up time was 39.2 months (95% confidence interval [CI], 35.7 – 50.1). None of 257 patients underwent surgery. Persistent or recurrent cancer was documented in 187 (72.8%) patients. The estimated median survival duration for all 257 patients was 21.1 months (95% CI, 18.9-27.1) and median RFS duration was 11.6 months (95% CI, 9.43-15.0). The estimated OS and RFS rates at 3 years were 37.3% (95% CI, 31.2%-44.7%) and 25.1% (95% CI, 19.9%-31.6%), respectively. After BM therapy, 155 (60.3%) patients achieved a clinical complete response (cCR). In the multivariate analyses, initial standardized uptake value maximum and cCR were independent prognostic variables for OS (P=0.038, P<0.001). Nomogram concordance indices of 0.70 for OS and 0.77 for RFS were established by 200 bootstrap resampling for each of the two outcomes. Conclusions: Our data suggest that in patients with EGEJC, pre- and post-treatment clinical parameters contribute to the establishment of OS and RFS prognostic nomograms. Upon validated, these nomograms could prove useful in the clinic to individualize therapy.
A Simple Calculation of Structural and Depletion Forces for Fluids/Suspensions Confined in a Film (2001)

By use of the analytic result for the Laplace transform of the radial distribution function for two large hard spheres dispersed in a fluid of the smaller hard spheres, simple equations for the film interaction energy and film disjoining pressure, due to the structural and depletion forces, are derived. The proposed equations satisfy some known exact results and explicitly express the energy and pressure as a function of the film thickness and volume fraction of the small hard spheres. The predicted results for the film energy and film disjoining pressure are compared with existing computer simulation data. The proposed simple analytical expressions can be applied to understand the stability of liquid films containing colloidal particles and the stability of suspensions, foams, and emulsions.
Lymphomatoid papulosis in children: a series of 25 cases (2014)

Paediatric LyP belongs to the group of CD30-positive CTLPDs including C-ALCL. Children have to be carefully followed up lifelong, even if the prognosis appears good. The high frequencies of an associated viral infection, atopic dermatitis, marked eosinophilic infiltrate and a good outcome suggest that paediatric LyP could be considered a reactional disease rather than a malignant disorder.