gebhart/patrepeval huggingface dataset:
Understanding evaluation and management of primary cutaneous and systemic ALCL. (2010)

Querfeld et al have written a comprehensive evaluation of primary cutaneous and systemic anaplastic large cell lymphoma (ALCL). The important similarities between them are outlined in the article, for example tumor cells expressing the CD30 antigen for both subtypes. In addition, important differences such as the wide spectrum of CD30+ lymphoproliferative disorders of the skin and the large differences in outcomes of the primary cutaneous vs systemic types of ALCL are discussed. Other important differences include expression of the anaplastic lymphoma kinase (ALK) protein. The ALK protein is activated most frequently through the nonrandom t(2;5) chromosome translocation, resulting in fusion of the nucleophosim (NPM) gene located at 5q35 to 2p23 and encoding the receptor tyrosine kinase, ALK. Most patients with primary cutaneous ALCL are ALK-negative, yet their 5-year disease-free survival rate is > 90%. Systemic ALCL is divided into ALK-positive and ALK-negative cases. Patients with systemic ALCL that is ALK-positive have a much higher 5-year survival rate of 70%, compared with a rate of 49% for those with systemic ALCL that is ALK-negative.[1]
Expression and Functions of Transmembrane Mucin MUC13 in Ovarian Cancer (2009)

MUC13, a transmembrane mucin, is normally expressed in gastrointestinal and airway epithelium. Its aberrant expression has been correlated with gastric colon and cancer. However, the expression and functions of MUC13 in ovarian cancer are unknown. In the present study, the expression profile and functions of MUC13 were analyzed to elucidate its potential role in ovarian cancer diagnosis and pathogenesis. A recently generated monoclonal antibody (clone PPZ0020) was used to determine the expression profile of MUC13 by immunohistochemistry using ovarian cancer tissue microarrays and 56 additional epithelial ovarian cancer (EOC) samples. The expression of MUC13 was significantly (P < 0.005) higher in cancer samples compared with the normal ovary/benign tissues. Among all ovarian cancer types, MUC13 expression was specifically present in EOC. For the functional analyses, a full-length MUC13 gene cloned in pcDNA3.1 was expressed in a MUC13 null ovarian cancer cell line, SKOV-3. Here, we show that the exogenous MUC13 expression induced morphologic changes, including scattering of cells. These changes were abrogated through c-Jun NH(2) kinase (JNK) chemical inhibitor (SP600125) or JNK2 siRNA. Additionally, a marked reduction in cell-cell adhesion and significant (P < 0.05) increases in cell motility, proliferation, and tumorigenesis in a xenograft mouse model system were observed upon exogenous MUC13 expression. These cellular characteristics were correlated with up-regulation of HER2, p21-activated kinase 1, and p38 protein expression. Our findings show the aberrant expression of MUC13 in ovarian cancer and that its expression alters the cellular characteristics of SKOV-3 cells. This implies a significant role of MUC13 in ovarian cancer.
Ice Model Testing of Structures With a Downward Breaking Cone at the Waterline JIP: Presentation, Set-Up and Objectives (2011)

Two large ice model test campaigns were performed in the period 2007–2010 as a part of a Joint Industry Project. The objectives of the project were to investigate different floater geometries and ice model test set-ups (model fixed to a carriage and pushed through the ice vs. ice pushed towards a floating model moored to the basin bottom) and their influence on the ice failure mode and structure responses in the various tested ice conditions. This paper presents the objectives and motivations for the project, the models tested, the target test set-up for the various tested configurations and the test matrix. Initial results from a fixed model tested in three first-year ice ridges with similar target ice properties are also presented and compared. Fixed models of both deep and shallow water platforms were tested in various ice conditions. All models except one had a downward breaking cone at the waterline. The influences of the waterline diameter, the angle of the downward breaking cone and the vertical cone height on the ice failure mode and the resulting ice load were investigated. Tests were conducted in level ice with a thickness ranging from 2 to 3 m and variable ice drift speeds ranging from 0.1 to 1.0 m/s in full scale values. The models were subjected to tests in managed level ice with varying speeds, ice concentrations and ice floe sizes. Fixed structures were also subjected to testing in typical first-year design ice ridge conditions with ridges of different depths and widths, as well as one multi-year ice ridge. One fixed model was also utilised for testing of the repeatability of scaled ice model testing. Moored models with the same waterline geometry as the fixed models were also tested. The moored models were tested in ice conditions similar to those of the fixed models with the objective of comparing their influences on the ice load due to structural responses.
The Benefits Of Using Low Accelerating Voltage To Assess Endodontic Instruments By Scanning Electron Microscopy (2004)

Scanning electron microscopy is often used to evaluate surface contamination and machining defects in dental and other medical instruments. Knowledge of the operating conditions of the SEM, in particular the accelerating voltage, is essential to properly interpret images of such material. We demonstrate the importance of using low accelerating voltages to detect surface features including contamination on NiTi rotary and hand files, and conclude that even recent studies may have significantly underestimated the amount of non-metallic debris (from the manufacturing process or from biological contamination) present on the surface of such instruments.
Quasi-Steady-State and Partial-Equilibrium Approximations in Chemical Kinetics: One Stage Beyond the Elimination of a Fast Variable (2021)

&lt;pre&gt;Classical approximations in chemical kinetics, the quasi-steady-state approximation (QSSA) and the partial-equilibrium approximation (PEA), are used to reduce rate equations for the concentrations and the extents of the reaction steps, respectively. We make precise two conditions on the rate constants necessary and sufficient to eliminate a well-chosen variable in the vicinity of a steady state. The first condition expresses that dynamics admits a small characteristic time associated with a fast variable. The second condition ensures that the fast variable is a concentration for QSSA and an extent for PEA. Both approximations exploit the zeroth order of a singular perturbation method. Eliminating a fast variable does not mean that it has reached a steady state. The fast evolution is considered over and the slow evolution of the eliminated variable is governed by the slow variables. The evolution of the slow variables occurs on a slow manifold in the space of the concentrations or the extents. In some cases the dynamics of the slow variables can be associated with a reduced chemical scheme. QSSA and PEA are applied to three chemical schemes associated with linear and nonlinear dynamics. We find that QSSA cannot be identified with the elimination of a reactive intermediate. The nonlinearities of the rate equations induce a more complex behavior.&lt;/pre&gt;
MEMS μ-wire magnetic field detection method@CERN (2015)

This work reports a novel construction of a micromachined MEMS magnetometer detecting static magnetic fields of CERN's reference dipole with a custom made capacitive read-out. The magnetic flux density is characterized via vibration modes of the MEMS structure which are sensed capacitively. The device consists of a single-crystal silicon clamped-free plate (cantilever) carrying a thin conductor. The cantilever and thin film metal electrodes are separated by a small gap, building a vibrating plate capacitor. Movements of the cantilever are read out conveniently by electronic circuits. A static magnetic field generates a force density acting on the conductor that alternates according to the frequency of the current. By knowing the electrical current, the deflection amplitude of the cantilever is a measure of the component of the magnetic flux density that points perpendicular to the current. The highest vibration amplitudes are expected, of course, in the vicinity of resonance frequencies of the micromachined structure. At ambient pressure the prototype sensor has a measured resonance frequency of 3.8 kHz for the fundamental mode and 20 kHz for the first antisymmetric mode. In experiments, the magnetic flux of the dipole has been characterized between 0.1 and 1 T, with a relative uncertainty of 3·10-4.
Inherent and transferable stabilization energies of carbon- and heteroatom-centred radicals on the same relative scale and their applications (2014)

Accurate G3(MP2)-RAD calculations are used to predict 264 R-H, R-CH3, R-Cl and R-R bond dissociation energies for a wide-ranging test set of carbon and non-carbon centred R˙ radicals. The data are used to calculate a set of inherent and transferrable radical stabilization energies, denoted RSEEt, which ranks the inherent stability of the 66 radicals studied on the same relative scale, irrespective of the nature of the radical centre. The Pauling electronegativity parameter for each radical is also calculated from the same data, along with the radical's inherent bonding ability D[R-R]calc. This latter quantity is defined as the R-R bond dissociation energy expected in the absence of direct steric or resonance interactions that are present in R-R but absent in R-CH3 and R-Cl. We show that the differences between D[R-R] and D[R-R]calc are typically very small except when R is sterically bulky, or there is a chain of (hyper)conjugation across the R-R bond. In such cases the difference between D[R-R] and D[R-R]calc provides a convenient means of quantifying the stabilization or destabilization of R-R due to these interactions. The predictability of the scheme is demonstrated by using these radical stabilities to calculate R-R' bond dissociation energies for 234 combinations of the 66 radicals studied, chosen to exclude steric or resonance interactions in the R-R' bond. The predicted bond energies lie within an average of 1.6 kcal mol(-1) from directly measured or calculated literature values.
Bandwidth enhancement and chirp reduction in DBR lasers by strong optical injection (2000)

Summary form only given.We have observed modulation bandwidth enhancement to 28 GHz and evidence of reduced chirp, beyond the optimally tuned free running case, in strongly injection-locked DBR lasers. Bandwidth enhancement occurs because the total modal photon density depends on the phase between the master and slave fields, which varies during modulation due to the dependence of index on carrier density. This results in an increased coupling between the carriers and photons, giving an effectively higher differential gain. This effect appears to be stronger than the similar amplitude-phase coupling that occurs with detuned loading. Chirp reduction occurs only for very strong injection, which can be explained by the fact that chirp reduction can only be achieved for modulation frequencies less than the locking range, which increases with injected power. For higher frequencies, the chirp reduction due to detuned loading dominates.
Complement Depletion with Naje haje Cobra Venom Factor Limits Prostaglandin Release and Improves Visceral Perfusion in Porcine Endotoxic Shock (1989)

We tested the hypothesis that complement (C')-dependent release of prostaglandin (PG) I2 is an important factor contributing to the development of hypotension and low systemic vascular resistance index (SVRI) in endotoxic shock. Two groups (n = 7) of pentobarbital-anesthetized pigs (12-15 kg) were infused over 40 min with Escherichia coli lipopolysaccharide (LPS; 200 micrograms/kg) and continuously resuscitated with normal saline (1 ml/kg min): LPS-Control (no pretreatment) and LPS-Decomplemented (pretreatment 18 hr before study with 500-1,500 units of Naje haje cobra venom factor, CVF). Prior treatment with CVF: i) decreased the mean titer of total hemolytic C' to 15.9% of pretreatment levels; ii) significantly decreased post-LPS plasma concentrations of immunoreactive TxB2 (TxA2 metabolite) and 6-keto-PGF1 alpha (PGI2 metabolite); iii) abrogated the early transient decrease in cardiac index observed in the LPS-Control group; iv) tended to improve post-LPS visceral perfusion assessed using radioactive microspheres; and v) had no discernible effect on the late sustained decrease in SVRI observed following infusion of LPS. We conclude that C' activation is a major determinant of LPS-induced prostanoid release in vivo, although our results do not support the view that C'-dependent release of PGI2 is an important factor contributing to low SVRI in resuscitated endotoxic shock.
Generalized matching from theory to application (1997)

We present a novel approach for post-mapping optimization. We exploit the concept of generalised matching, a technique that finds symbolically all possible matching assignments of library cells to a multi-output network specified by a Boolean relation. Several objectives are targeted: area minimization under delay constraints; power minimization under delay constraints; and unconstrained delay minimization. We describe the theory of generalized matching and the algorithmic optimization required for its efficient and robust implementation. A tool based on generalized matching has been implemented and tested on large examples of the MCNC'91 benchmark suite. We obtain sizable improvements in: speed (6% in average, up to 20.7%); area under speed constraints (13.7% an average, up to 29.5%); and power under speed constraints (22.3% in average, up to 38.1%).
Absolute oxygen tension (pO<sub>2</sub>) in murine fatty and muscle tissue as determined by EPR (2005)

The absolute partial pressure of oxygen (pO(2)) in the mammary gland pad and femoral muscle of female mice was measured using EPR oximetry at 700 MHz. A small quantity of lithium phthalocyanine (LiPc) crystals was implanted in both mammary and femoral muscle tissue of female C3H mice. Subsequent EPR measurements were carried out 1-30 days after implantation with or without control of core body temperature. The pO(2) values in the tissue became stable 2 weeks after implantation of LiPc crystals. The pO(2) level was found to be higher in the femoral muscle than in the mammary tissue. However, the pO(2) values showed a strong dependence on the core body temperature of the mice. The pO(2) values were responsive to carbogen (95% O(2), 5% CO(2)) breathing even 44-58 days after the implantation of LiPc. The LiPc linewidth was also sensitive to changes in the blood supply even 60 days after implantation of the crystals. This study further validates the use of LiPc crystals and EPR oximetry for long-term non-invasive assessment of pO(2) levels in tissues, underscores the importance of maintaining normal body core temperature during the measurements, and demonstrates that mammary tissue functions at a lower pO(2) level than muscle in female C3H mice.
Monte Carlo modeling of electron backscattering from carbon nanotube forests (2010)

The authors present a new Monte Carlo tool capable of simulating electron trajectories in nanotube forests, taking into account the underlying nanoscale nature of the material. The scattering angle distribution is adaptively modified at each step of the simulation according to the local environment (how the nanotubes are positioned, their diameters, and internanotube distances). This provides additional degrees of freedom in the Monte Carlo simulation that are directly related to the internal structure of the nanotube forest, allowing the model to closely match experimental data.
Oxidation of DNA bases, deoxyribonucleosides and homopolymers by peroxyl radicals (1998)

DNA base oxidation is considered to be a key event associated with disease initiation and progression in humans. Peroxyl radicals (ROO. ) are important oxidants found in cells whose ability to react with the DNA bases has not been characterized extensively. In this paper, the products resulting from ROO. oxidation of the DNA bases are determined by gas chromatography/MS in comparison with authentic standards. ROO. radicals oxidize adenine and guanine to their 8-hydroxy derivatives, which are considered biomarkers of hydroxyl radical (HO.) oxidations in cells. ROO. radicals also oxidize adenine to its hydroxylamine, a previously unidentified product. ROO. radicals oxidize cytosine and thymine to the monohydroxy and dihydroxy derivatives that are formed by oxidative damage in cells. Identical ROO. oxidation profiles are observed for each base when exposed as deoxyribonucleosides, monohomopolymers and base-paired dihomopolymers. These results have significance for the development, utilization and interpretation of DNA base-derived biomarkers of oxidative damage associated with disease initiation and propagation, and support the idea that the mutagenic potential of N-oxidized bases, when generated in cellular DNA, will require careful evaluation. Adenine hydroxylamine is proposed as a specific molecular probe for the activity of ROO. in cellular systems.
Cross‐validation of MIPAS/ENVISAT and GPS‐RO/CHAMP temperature profiles (2004)

The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on board the ENVISAT and the Global Positioning System (GPS) receiver on the Challenging Mini‐Satellite Payload (CHAMP) provide temperature profiles by limb‐viewing midinfrared emission and radio occultation (RO) measurements, respectively. The MIPAS temperatures retrieved at the Institut für Meteorologie und Klimaforschung (IMK) are compared with the GPS‐RO/CHAMP observations derived at Jet Propulsion Laboratory (JPL) and GeoForschungsZentrum (GFZ) Potsdam. The three data sets show generally good agreement. The global mean differences averaged between 8 and 30 km in 14 days of September/October 2002 are −0.44 ± 0.02 K and 0.07 ± 0.02 K for MIPAS/GPS‐RO JPL and GFZ comparisons, respectively. The MIPAS global mean temperatures below 25 km are slightly lower than those of GPS‐RO JPL and GFZ by less than 1 K and 0.2 K, respectively. Above 25 km, the MIPAS temperatures are higher than the JPL and GFZ data, in particular near both poles and the equator, with maxima of 1 K for JPL and 1.5 K for GFZ at 30 km. The standard deviations are ∼2–4 K. Possible explanations for the observed differences include (1) effect of spatial and temporal mismatch between the correlative measurements on the observed standard deviations, in particular in regions and episodes of enhanced wave activity; (2) a negative bias in GPS‐RO/CHAMP temperatures in regions of increased humidity; (3) a mapping of initialization temperature profiles on GPS‐RO/CHAMP retrievals at altitudes where low refraction contains no information on air density; and (4) measurement errors of both instruments, particularly the errors due to insufficient knowledge of the instrument line shape and spectroscopy in current MIPAS retrievals.
The dire sexual health crisis among MSM in the Philippines: an exploding HIV epidemic in the absence of essential health services (2015)

The rate of HIV is exploding in the men who have sex with men (MSM) population in the Philippines. There is a paucity of information with respect to sexual behaviour, condom use, psychological health, and the prevalence of other STIs in the MSM subpopulation. At present there are no existing private or public clinical services in the country that focus on health services of MSM. We discuss the current epidemic situation and the steps needed to further define the rapidly evolving epidemic among MSM.
Weather and Climate Science in the Digital Era (2019)

Abstract. The need for open science has been recognized by the communities of meteorology and climate science. However, while these domains are mature in terms of applying digital technologies, these are lagging behind where the implementation of open science methodologies is concerned. In a session on Weather and Climate Science in the Digital Era at the 14th IEEE International eScience conference domain specialists and data and computer scientists discussed the road towards open weather and climate science. The studies presented in the conference session showed the added value of shared data, software and platforms through, for instance, combining data sets from disparate sources, increased accuracy and skill of simulations and forecasts at local scales, and improved consistency of data products. We observed that sharing data and code is important, but not sufficient to achieve open weather and climate science and that here are important issues to address. At the level of technology, the implementation of the FAIR principles to many datasets used in weather and climate science remains a challenge due to their origin, scalability, or legal barriers. Furthermore, the complexity of current software platforms limits collaboration between researchers and optimal use of open science tools and methods. The main challenges we observed, however, were non-technical and impact the system of science as a whole. There is a need for new roles and responsibilities at the interface of science and digital technology, e.g., data stewards and research software engineers. This requires the personnel portfolio of academic institutions to be more diverse, and in addition, a broader consideration of the impact of academic work, beyond publishing and teaching. Besides, new policies regarding open weather and climate science should be developed in an inclusive way to engage all stakeholders, including non-academic parties such as meteorological institutions. We acknowledge that open weather and climate science requires effort to change, but the benefits are large. As can already be observed from the studies presented in the conference it leads to much faster progress in understanding the world.
Video delivery over heterogeneous cellular networks: Optimizing cost and performance (2014)

Video delivery to mobile users is one of the largest challenges that network operators face today. In this work we consider a heterogeneous cellular network with storage capable small-cell base stations, and study this problem for pre-stored video files that can be encoded with two different schemes, namely versions or layers, in various qualities. We introduce a framework for the joint derivation of video caching and routing policies for users with different quality requirements. This allows the operator to optimize a balanced objective of incurred servicing cost, and users experienced delay, according to his priorities. The numerical results indicate that versions and layers may have different impact on the delay and servicing cost, depending on the diversity of users' demand, and that the cost-delay trade off is affected by the network's load.