gebhart/patrepeval huggingface dataset:
Prevalence of anal HPV infection in solid-organ transplant patients prior to immunosuppression (2004)

Patients that undergo organ transplantation have a high risk of developing various malignancies, depending on the duration and magnitude of immunosuppressive therapy. Among others, a 10-fold increased relative risk has been reported for the development of anal cancer. There is a strong association between persistent infection with high-risk mucosal types of human papillomavirus (HPV) and anogenital neoplasia. In this study we analysed the prevalence of anal HPV infection in organ transplant patients before starting immunosuppressive therapy. In a university transplant unit, patients ( n=60, 40 male, 20 female) that were undergoing solid-organ transplantation (kidney, liver) for the first time were routinely screened for anal HPV infection. Anal swabs were obtained within 24 h after transplantation and analysed for the presence of mucosal-type HPV DNA by liquid DNA/RNA hybridization [hybrid capture (HC) 2 test]. Overall, some type of HPV DNA was detected in 14/60 (23.3%) patients; 9/60 (15%) were positive for high-risk HPV and 8/60 (13.4%) were positive for low-risk HPV, and 3/60 (5%) were positive for both types. Prevalence of HPV infection tended to be higher in patients that were receiving liver transplants than in those receiving kidney transplants (29.4% vs. 20.9%), but the difference did not reach statistical significance. In our series of organ transplant patients the prevalence of previous HPV infection (23.3%) before immunosuppressive therapy was started was higher than that found in previous epidemiological studies or in a control group. In particular, there was a high rate (15%) of infection with oncogenic HPV types. These findings have important implications on screening and surveillance policies in this patient group at risk of developing neoplasias, including anal cancer.
First-in-Humans Imaging with 89Zr-Df-IAB22M2C Anti-CD8 Minibody in Patients with Solid Malignancies: Preliminary Pharmacokinetics, Biodistribution, and Lesion Targeting (2019)

Immunotherapy is becoming the mainstay for treatment of a variety of malignancies, but only a subset of patients responds to treatment. Tumor-infiltrating CD8-positive (CD8+) T lymphocytes play a central role in antitumor immune responses. Noninvasive imaging of CD8+ T cells may provide new insights into the mechanisms of immunotherapy and potentially predict treatment response. We are studying the safety and utility of <sup>89</sup>Zr-IAB22M2C, a radiolabeled minibody against CD8+ T cells, for targeted imaging of CD8+ T cells in patients with cancer. <b>Methods:</b> The initial dose escalation phase of this first-in-humans prospective study included 6 patients (melanoma, 1; lung, 4; hepatocellular carcinoma, 1). Patients received approximately 111 MBq (3 mCi) of <sup>89</sup>Zr-IAB22M2C (at minibody mass doses of 0.2, 0.5, 1.0, 1.5, 5, or 10 mg) as a single dose, followed by PET/CT scans at approximately 1-2, 6-8, 24, 48, and 96-144 h after injection. Biodistribution in normal organs, lymph nodes, and lesions was evaluated. In addition, serum samples were obtained at approximately 5, 30, and 60 min and later at the times of imaging. Patients were monitored for safety during infusion and up to the last imaging time point. <b>Results:</b><sup>89</sup>Zr-IAB22M2C infusion was well tolerated, with no immediate or delayed side effects observed after injection. Serum clearance was typically biexponential and dependent on the mass of minibody administered. Areas under the serum time-activity curve, normalized to administered activity, ranged from 1.3 h/L for 0.2 mg to 8.9 h/L for 10 mg. Biodistribution was dependent on the minibody mass administered. The highest uptake was always in spleen, followed by bone marrow. Liver uptake was more pronounced with higher minibody masses. Kidney uptake was typically low. Prominent uptake was seen in multiple normal lymph nodes as early as 2 h after injection, peaking by 24-48 h after injection. Uptake in tumor lesions was seen on imaging as early as 2 h after injection, with most <sup>89</sup>Zr-IAB22M2C-positive lesions detectable by 24 h. Lesions were visualized early in patients receiving treatment, with SUV ranging from 5.85 to 22.8 in 6 target lesions. <b>Conclusion:</b><sup>89</sup>Zr-IAB22M2C imaging is safe and has favorable kinetics for early imaging. Biodistribution suggests successful targeting of CD8+ T-cell-rich tissues. The observed targeting of tumor lesions suggests this may be informative for CD8+ T-cell accumulation within tumors. Further evaluation is under way.
2D QSAR Consensus Prediction for High‐Throughput Virtual Screening. An Application to COX‐2 Inhibition Modeling and Screening of the NCI Database. (2004)

Using classification (SOM, LVQ, Binary, Decision Tree) and regression algorithms (PLS, BRANN, k-NN,\nLinear), this paper details the building of eight 2D-QSAR models from a 266 COX-2 inhibitor training set.\nThe predictive performances of these eight models were subsequently compared using an 88 COX-2 inhibitor\ntest set. Each ligand is described by 52 2D descriptors expressed as van der Waals Surface Areas (P_VSA)\nand its COX-2 binding IC&lt;sub&gt;50&lt;/sub&gt;. One of our best predictive models is the neural network model (BRANN),\nwhich is able to select a subset, from the 88 ligand test set, that contains 94% COX-2 active inhibitors\n(pIC&lt;sub&gt;50&lt;/sub&gt; &gt; 7.5) and detects 71% of all the actives. We then introduce a QSAR consensus prediction protocol\nthat is shown to be more predictive than any single QSAR model: our C3 consensus approach is able to\nselect a subset from the 88 ligand test set that contains 94% active inhibitors and 83% of all the actives. The\n2D QSAR consensus protocol was finally applied to the high-throughput virtual screening of the NCI database,\ncontaining 193 477 organic compounds.
Cavitation Therapy Monitoring of Commercial Microbubbles With a Clinical Scanner (2020)

The ability to monitor cavitation activity during ultrasound and microbubble-mediated procedures is of high clinical value. However, there has been little reported literature comparing the cavitation characteristics of different clinical microbubbles, nor have current clinical scanners been used to perform passive cavitation detection in real time. The goal of this work was to investigate and characterize standard microbubble formulations (Optison, Sonovue, Sonazoid, and a custom microbubble made with similar components as Definity) with a custom passive cavitation detector (two confocal single-element focused transducers) and with a Philips EPIQ scanner with a C5-1 curvilinear probe passively listening. We evaluated three different methods for investigating cavitation thresholds, two from previously reported work and one developed in this work. For all three techniques, it was observed that the inertial cavitation thresholds were between 0.1 and 0.3 MPa for all agents when detected with both systems. Notably, we found that most microbubble formulations in bulk solution behaved generally similarly, with some differences. We show that these characteristics and thresholds are maintained when using a diagnostic ultrasound system for detecting cavitation activity. We believe that a systematic evaluation of the frequency response of the cavitation activity of different microbubbles in order to inform real-time therapy monitoring using a clinical ultrasound device could make an immediate clinical impact.
COEXISTENCE OF NUMEROUS SYNCHRONIZED AND DESYNCHRONIZED STATES IN A MODEL OF TWO PHASE OSCILLATORS COUPLED WITH DELAY (2008)

When two phase oscillators interact with a time-delay, new synchronized and desynchronized regimes appear, in this way giving rise to the phenomenon of multistability. The number of coexisting stable states grows with an increase of the delay, and their frequencies quantize. We show that, while the number of synchronized solutions grows linearly with the delay and/or coupling, the set of the desynchronized solutions, i.e. those with different average frequencies of the individual oscillators, raises quadratically with increasing delay. For the synchronized states, we analyze the mutual arrangement of the basins of attraction, and conclude that the structure and size of the basins are apparently the same for each state. We discuss possible implications for desynchronizing brain stimulation techniques.
Synthesis, Structure, and Chemical Property of the First Fluorine-Containing Porphycene (2003)

[structure: see text] A pyrrolic macrocycle, beta-tetrakis(trifluoromethyl)porphycene, is the first example of a fluorine-containing porphycene. Four electron-withdrawing CF(3) substituents provide a highly distorted structure and an attractive electron-deficient nature for the porphycene framework. From the electrochemical study, it is found that the LUMO energy level for the beta-trifluoromethylporphycene is 1.24 V more stabilized compared to that for etioporphyrin. Moreover, the deprotonation of the inner N[bond]H proton in the porphycene was observed upon the addition of DBU.
Estimation of the Weibull parameters by the fracture strength of weakest fiber embedded in FRM and the strength of FRM. (1988)

A method for estimating the Weibull Parameters of reinforcing-fiber embedded in a matrix has been proposed. In general, the weakest fibers fracture first in FRM, and the strength is variable as shown by tensile-testing several times. That is to say, the strength is a random variable based on the order statistics, and the Weibull parameters can be estimated by applying a single Weibull distribution to it. B4C coated boron fiber reinforced Al composites produced by hot-pressing were employed as the test materials. The fracture of the weakest fibers was identified by the AE method. The result showed that the shape parameter obtained from the present method gave a smaller value compared to that obtained from the conventional extracted-fiber test, and the scale parameter gave a larger value. Using these Weibull parameters, the strength distribution curves of the composites, reported by Harlow-Phoenix, were predicted. The curves by the present parameters were in good agreement with the experimental data of the composites, as compared with the those by the conventional test parameters. Additionally, the efficiency of the present method was discussed from the Weibull parameters converted by the moment method, on the condition that the fiber strength was given by the bi-modal Weibull distribution.
Avis en réponse à la saisine HCB - dossier C/NL/06/01_001. Paris, le 17 octobre 2018 (2018)

Le Haut Conseil des biotechnologies (HCB) a été saisi le 14 août 2018 par les autorités compétentes françaises (le ministère de l’Agriculture et de l’Alimentation) d’une demande d’avis relative au dossier C/NL/06/01_001 de demande de renouvellement d’autorisation de mise sur le marché de la lignée d’oeillets génétiquement modifiés 123.8.12 (identificateur unique FLO- 40689-6) à des fins d’importation et de commercialisation de fleurs coupées. Ce dossier a été déposé par la société Suntory Flowers Limited auprès des autorités compétentes néerlandaises sur le fondement de la directive 2001/18/CE. Conformément à cette directive, la Commission européenne a adressé le rapport d’évaluation des Pays-Bas ainsi que le dossier du pétitionnaire à l’ensemble des Etats membres, qui disposent de 60 jours pour faire des commentaires, demander des informations complémentaires ou émettre des objections à la mise sur le marché. Par cette saisine, les autorités compétentes françaises consultent le HCB dans cette perspective, en amont du vote des Etats membres à la Commission européenne. Le Comité scientifique (CS)2 du HCB a examiné le dossier en séance du 17 octobre 2018 sous la présidence de Jean-Christophe Pagès. Le présent avis a été adopté en séance et publié le 23 octobre 2018.
Zeros of discretized continuous systems expressed in the Euler operator-an asymptotic analysis (2005)

The structure of the zeros of SISO continuous time systems which are discretized via a zero order hold and expressed in the Euler operator, /spl epsiv/ (/spl epsiv/=(x-1)/T), is studied. It is shown that when state space descriptions of linear SISO continuous time systems with relative degree /spl ges/2 are discretized, the zero dynamics of the resulting discrete system is singularly perturbed and shows a reparation of time scale; the fast time scale corresponding to the zeros introduced by the sampling process. Finally, implications of the result to control design based on pole zero cancellation is discussed.
Supplemental Table 5 from Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA (2023)

&lt;p&gt;Available therapies and clinical trials&lt;/p&gt;
Nanoscale chromatin structure characterization for optical applications: a transmission electron microscopy study (Conference Presentation) (2017)

Structural and biological origins of light scattering in cells and tissue are still poorly understood. We demonstrate how this problem might be addressed through the use of transmission electron microscopy (TEM). For biological samples, TEM image intensity is proportional to mass-density, and thus proportional to refractive index (RI). By calculating the autocorrelation function (ACF) of TEM image intensity of a thin-section of cells, we essentially maintain the nanoscale ACF of the 3D cellular RI distribution, given that the RI distribution is statistically isotropic. Using this nanoscale 3D RI ACF, we can simulate light scattering through biological samples, and thus guiding many optical techniques to quantify specific structures. In this work, we chose to use Partial Wave Spectroscopy (PWS) microscopy as a one of the nanoscale-sensitive optical techniques. Hela cells were prepared using standard protocol to preserve nanoscale ultrastructure, and a 50-nm slice was sectioned for TEM imaging at 6 nm resolution. The ACF was calculated for chromatin, and the PWS mean sigma was calculated by summing over the power spectral density in the visible light frequency of a random medium generated to match the ACF. A 1-µm slice adjacent to the 50-nm slice was sectioned for PWS measurement to guarantee identical chromatin structure. For 33 cells, we compared the calculated PWS mean sigma from TEM and the value measured directly, and obtained a strong correlation of 0.69. This example indicates the great potential of using TEM measured RI distribution to better understand the quantification of cellular nanostructure by optical methods.
Modified Poisson–Boltzmann equations for characterizing biomolecular solvation (2013)

Methods for computing electrostatic interactions often account implicitly for the solvent, due to the much smaller number of degrees of freedom involved. In the Poisson–Boltzmann (PB) approach the electrostatic potential is obtained by solving the Poisson–Boltzmann equation (PBE), where the solvent region is modeled as a homogeneous medium with a high dielectric constant. PB however is not exempt of problems. It does not take into account for example the sizes of the ions in the atmosphere surrounding the solute, nor does it take into account the inhomogeneous dielectric response of water due to the presence of a highly charged surface. In this paper we review two major modifications of PB that circumvent these problems, namely the size-modified PB (SMPB) equation and the Dipolar Poisson–Boltzmann Langevin (DPBL) model. In SMPB, steric effects between ions are accounted for with a lattice gas model. In DPBL, the solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. This model results in a dielectric profile that transits smoothly from the solute to the solvent region as well as in a variable solvent density that depends on the charges of the solute. We show successful applications of the DPBL formalism to computing the solvation free energies of isolated ions in water. Further developments of more accurately modified PB models are discussed.
Leukocyte/Endothelial Cell Adhesion and Ischemia/Reperfusion Injury (2019)

The early restitution of blood flow to ischemic tissues is essential to halt the progression of cellular injury associated with decreased delivery of oxygen and metabolic substrates, and for removal of potentially harmful metabolic byproducts. However, it is now apparent that reperfusion also initiates a complex series of pathologic events that paradoxically injure tissues. The microcirculation appears to be particularly vulnerable to the deleterious effects of reperfusion in that microvascular dysfunction precedes the development of parenchymal cell injury. When blood flow to certain organs is reinstituted after ischemia, a large proportion of capillaries fail to reperfuse, a phenomenon referred to as capillary no-reflow. Leukocyte/capillary plugging has also been suggested to underlie development of capillary no-reflow in postischemic tissues. While this may contribute to the reduction in capillary perfusion during ischemia, physical impaction of leukocytes within the capillaries does not appear to play a role in the pathogenesis of no-reflow in skeletal muscle when normal perfusion pressures are established at reperfusion.
Artificial Magnetic Conductor(AMC) Polarizer Backed Circular-Polarized(CP) Antenna (2010)

인공 자기 도체 편파 변환기를 이용한 원형 편파 안테나를 소개하고 특성을 분석한다. 기존 원형 편파 안테나들의 한계였던 얇은 구조의 광대역 축비 대역폭을 구현할 수 있음을 인공 자기 도체 이론에 근거하여 이론적으로 설명하고 실험적으로 검증한다. 기존의 안테나들은 방사체 표면 전류에 의해 원형 편파 특성이 구현됨에 따라 축비 대역폭이 방사체 구조에 의존적이었던 반면, 제안된 구조는 선형 편파 다이폴 안테나를 사용하면서 접지면의 격자 구조를 통해 원형 편파 특성을 구현하였다. 이러한 인공 자기 도체 편파 변환기는 접지면에 전기적으로 인접한 다이폴 안테나가 효율적으로 방사할 수 있도록 도와줄 뿐 아니라, 표면 격자의 기하 구조에 따라 축비 대역폭을 조절할 수 있다는 장점을 동시에 가진다. 인공 자기 도체 편파 변환기를 통해 발생된 원형 편파의 축비 특성을 이론적으로 분석하고, 임피던스 정합 특성, 원형 편파 방사 패턴 및 축비 패턴, 축비 대역폭, 격리도 등을 측정하여 논의한다. A new type of circularly polarized(CP) antenna that is characterized by having both low-profile and greater axial-ratio bandwidth(ARBW) beyond existing antennas is introduced through analysis of artificial magnetic conductor(AMC) polarizer, and experimentally demonstrated. Although it is made use of a linear-polarized dipole antenna with close proximity to ground plane, it is backed by AMC polarizer so as to efficiently radiate with circularly changed polarization whose ARBW is determined by the texture geometry, whereas existing antennas exhibit CP surface-current on radiators, which limit ARBW. The mechanism of the polarization conversion is theoretically analyzed for ARBW, and the experimental properties including the impedance matching, CP radiation pattern, axial-ratio pattern, ARBW, and two-port isolation are discussed.
Development of zircaloy clad hafnium rods for BWR long life neutron absorbers. (1986)

Click to increase image sizeClick to decrease image sizeKEYWORDS: nuclear reactor materialscontrol rodsneutron absorbersZircaloy-2hafniumcladdingcoatingfabricationdiffusion bondingadhesion testsnodular corrosion testscorrosion tests
Computational Assessment and Understanding of C6 Product Selectivity for Chromium Phosphinoamidine Catalyzed Ethylene Trimerization (2021)

One approach to selectively generate 1-hexene is through ethylene trimerization using highly active Cr N-phosphinoamidine catalysts ((P,N)Cr). Depending on the ligand, (P,N)Cr catalysts can either generate nearly pure 1-hexene or form 1-hexene with significant mixtures of other C6 mass products, for example methylenecyclopentane. Here we report DFT transition state modeling examining 1-hexene catalysis pathways as well as pathways that lead to alternative C6 mass products. This provided qualitative and semi-quantitative modeling of the experimental 1-hexene purity values for several (P,N)Cr catalysts. Consistent with previous computational studies, the key 1-hexene purity-determining transition states were determined to be β-hydrogen transfer structures from the metallacycloheptane intermediate. The origin of selectivity for these (P,N)Cr catalysts can be attributed to steric effects in the transition-state structure with coordinated ethylene that leads to C6 impurities.
Diacylglycerol Lipase Î± Knockout Mice Demonstrate Metabolic and Behavioral Phenotypes Similar to Those of Cannabinoid Receptor 1 Knockout Mice (2015)

After creating >4650 knockouts (KOs) of independent mouse genes, we screened them by high-throughput phenotyping and found that cannabinoid receptor 1 (Cnr1) KO mice had the same lean phenotype published by others. We asked if our KOs of DAG lipase a or b (Dagla or Daglb), which catalyze biosynthesis of the endocannabinoid (EC) 2-Arachidonoylglycerol (2-AG), or Napepld, which catalyzes biosynthesis of the EC anandamide, shared the lean phenotype of Cnr1 KO mice. We found that Dagla KO mice, but not Daglb or Napepld KO mice, were among the leanest of 3651 chow-fed KO lines screened. In confirmatory studies, chow- or high fat diet-fed Dagla and Cnr1 KO mice were leaner than wild type (WT) littermates; when data from multiple cohorts of adult mice were combined, body fat was 47% and 45% lower in Dagla and Cnr1 KO mice, respectively, relative to WT values. In contrast, neither Daglb nor Napepld KO mice were lean. Weanling Dagla KO mice ate less than WT mice and had body weight similar to pair-fed WT mice, and adult Dagla KO mice had normal activity and VO2 levels, similar to Cnr1 KO mice. Our Dagla and Cnr1 KO mice also had low fasting insulin, triglyceride and total cholesterol levels, and after a glucose challenge had normal glucose but very low insulin levels. Dagla and Cnr1 KO mice also showed similar responses to a battery of behavioral tests. These data suggest: 1) the lean phenotype of young Dagla and Cnr1 KO mice is mainly due to hypophagia; 2) in pathways where ECs signal through Cnr1 to regulate food intake and other metabolic and behavioral phenotypes observed in Cnr1 KO mice, Dagla alone provides the 2-AG that serves as the EC signal; and 3) small molecule Dagla inhibitors with a pharmacokinetic profile similar to that of Cnr1 inverse agonists are likely to mirror the ability of these Cnr1 inverse agonists to lower body weight and improve glycemic control in obese patients with type 2 diabetes, but may also induce undesirable neuropsychiatric side-effects.
Self-Assembled Two-Dimensional Heteromolecular Nanoporous Molecular Arrays on Epitaxial Graphene (2013)

The development of graphene functionalization strategies that simultaneously achieve two-dimensional (2D) spatial periodicity and substrate registry is of critical importance for graphene-based nanoelectronics and related technologies. Here, we demonstrate the generation of a hydrogen-bonded molecularly thin organic heteromolecular nanoporous network on epitaxial graphene on SiC(0001) using room-temperature ultrahigh vacuum scanning tunneling microscopy. In particular, perylenetetracarboxylic diimide (PTCDI) and melamine are intermixed to form a spatially periodic 2D nanoporous network architecture with hexagonal symmetry and a lattice parameter of 3.45 ± 0.10 nm. The resulting adlayer is in registry with the underlying graphene substrate and possesses a characteristic domain size of 40-50 nm. This molecularly defined nanoporous network holds promise as a template for 2D ordered chemical modification of graphene at lengths scales relevant for graphene band structure engineering.