gebhart/patrepeval huggingface dataset:
[Buschke-Lowenstein penile tumor]. (2002)

The Buschke-Löwenstein genital tumour is a poorly defined, uncommon tumour. The distinction between benign lesions, potentially malignant lesions and carcinomatous lesions is difficult. The authors report a case of Human Papillomavirus (HPV) 11-associated Buschke-Löwenstein tumour with an area of micro-invasive carcinoma on histological examination of the surgical resection specimen. A 34-year-old patient was operated for recurrent condylomatous lesions of the penis with scrotal extension. Histological examination of the complete operative specimen confirmed the presence of Buschke-Löwenstein tumour as well as an area of dermal micro-invasion on one section. Molecular hybridization revealed the presence of HPV 11 DNA and immunohistochemistry showed basal cells weakly expressing mutant p53. The classification of Buschke-Löwenstein tumours is controversial. Some authors consider these tumours to be benign tumours or giant condylomata (non-metastatic, associated with HPV 6-11), while others consider these tumours to be borderline malignant (local extension and risk of progression to invasive carcinoma). The role of HPV as cofactor involved in carcinomatous transformation also remains controversial. The authors emphasize the need for surgical resection of this type of tumour with histological examination of the entire operative specimen looking for areas of micro-invasion. In the presence of micro-invasion with healthy resection margins and staging by clinical examination and complementary investigations, treatment essentially consists of regular surveillance.
Hydration Number and Water Activity Models for the Sucrose-Water System: A Critical Review (2000)

Abstract The nature of various molecular interactions occurring in the sucrose-water system and the structure of the aqueous solution are outlined briefly. The thermodynamic implications of these interactions are discussed, with special emphasis placed on the sucrose hydration number and the water activity coefficient. The existing "chemical" models of water activity, due to Scatchard (1921), Stokes and Robinson (1966), Schönert (1986), and Van Hook (1987), are evaluated in detail, including their predictive ability for dilute solutions and their limiting behavior in the region of high sucrose content. Some suggestions, based on the sucrose association mechanism, are made with regard to possible reformulations of the existing activity models that could result in a powerful thermodynamic model of the system. Keywords: activityaggregationassociationclusterhydrationsucrosethermodynamicswater.
Flow Classification in Information Centric Networking (1999)

For the ubiquitous and highly important Internet protocols (TCP, UDP,
IP), flows are conventionally identified by the 5-tuple of source
and destination IP addresses, source and destination port, and
protocol type in an IP packet. Information Centric Networking (ICN) is
a new paradigm where network communications are accomplished by
requesting named content, instead of sending packets to destination
addresses. This document describes mechanisms allowing ICN forwarders,
consumers, producers and other ICN nodes to encode, decode, and
process equivalence class identifiers (flows) at any desired
granularity of a routable name prefix and beyond the routable name
prefix. This document is a product of the IRTF Information- Centric
Networking Research Group (ICNRG).
Comparative Analysis of Single- and Dual-Media Thermocline Tanks for Thermal Energy Storage in Concentrating Solar Power Plants (2014)

A molten-salt thermocline tank is a low-cost option for thermal energy storage (TES) in concentrating solar power (CSP) plants. Typical dual-media thermocline (DMT) tanks contain molten salt and a filler material that provides sensible heat capacity at reduced cost. However, conventional quartzite rock filler introduces the potential for thermomechanical failure by successive thermal ratcheting of the tank wall under cyclical operation. To avoid this potential mode of failure, the tank may be operated as a single-medium thermocline (SMT) tank containing solely molten salt. However, in the absence of filler material to dampen tank-scale convection eddies, internal mixing can reduce the quality of the stored thermal energy. To assess the relative merits of these two approaches, the operation of DMT and SMT tanks is simulated under different periodic charge/discharge cycles and tank wall boundary conditions to compare the performance with and without a filler material. For all conditions assessed, both thermocline tank designs have excellent thermal storage performance, although marginally higher first- and second-law efficiencies are predicted for the SMT tank. While heat loss through the tank wall to the ambient induces internal flow nonuniformities in the SMT design over the scale of the entire tank, strong stratification maintains separation of the hot and cold regions by a narrow thermocline; thermocline growth is limited by the low thermal diffusivity of the molten salt. Heat transport and flow phenomena inside the DMT tank, on the other hand, are governed to a great extent by thermal diffusion, which causes elongation of the thermocline. Both tanks are highly resistant to performance loss over periods of static operation, and the deleterious effects of dwell time are limited in both tank designs.
Direct retrieval of stratospheric CO<sub>2</sub> infrared cooling rate profiles from AIRS data (2006)

We expand upon methods for retrieving thermal infrared cooling rate profiles, originally developed by Liou and Xue (1988) through application to the inversion of the stratospheric cooling rate produced by carbon dioxide (CO 2 ) and a formal description of the associated error budget. Specifically, we infer lower‐ and mid‐stratospheric cooling rates from the CO 2 ν 2 band on the basis of selected spectral channels and available data from the Atmospheric Infrared Sounder (AIRS). In order to establish the validity of our results, we compare our retrievals to those calculated from a forward radiative transfer program using retrieved temperature data from spectra taken by the Scanning High‐Resolution Interferometer Sounder (S‐HIS) on two aircraft campaigns: the Mixed‐Phase Arctic Cloud Experiment (MPACE) and the Aura Validation Experiment (AVE) both in Fall, 2004. Reasonable and consistent comparisons are illustrated, revealing that spectral radiance data taken by high‐resolution infrared sounders can be used to determine the vertical distribution of radiative cooling due to CO 2 .
Kinetics of H2 (D2) desorption from a Ge(100)-2×1:H (D) surface studied using scanning tunneling microscopy and temperature programmed desorption (2003)

The kinetics of H2 (D2) desorption from a Ge(100)-2×1:H (D) surface was studied using scanning tunneling microscopy (STM) and temperature programmed desorption (TPD). Inspection of STM images of surfaces at the saturation coverage of H (D) (θH(D)≃1.0 ML) revealed a 2×1 monohydride (monodeuteride) phase in which most H (D) atoms were paired on Ge-dimers. By counting the sites of H2 (D2) desorption in STM images taken after desorption of H2 (D2) at temperatures in the range Ts=500−550 K, the desorption of H2 (D2) was found to follow first order kinetics with an activation energy of Ed=1.65±0.1 eV (1.65±0.1 eV) and a pre-exponential factor of νd=(2.7±0.5)×1013 s−1 [(1.2±0.5)×1013 s−1]. These values of Ed and νd were used to simulate TPD spectra for the desorption of H2 (D2) from a Ge(100)-2×1:H (D) surface. The simulated spectra were in good agreement with the experimental TPD spectra. In contrast to the surfaces with saturated H coverage, which are characterized by pairs of H atoms on Ge-dimers, at the low H coverage of θH≃0.05 ML unpaired H atoms as well as paired H atoms were observed on the Ge-dimers on the surface, causing the desorption process to follow second order kinetics. At Ts∼300 K, the singly occupied dimers (SODs) appear to be favored over doubly occupied dimers (DODs). However, upon increasing the temperature (Ts) from 300 to 500 K, most SODs were rapidly converted into the thermodynamically favored DODs by the migration of H atoms. On the other hand, it is observed that even above Ts∼500 K, the onset temperature for H2 desorption from DODs, a non-negligible number of SODs remain on the surface due to the large entropic barrier to pairing. These results suggest that H adsorption in the low coverage is strongly influenced by the energetics of the pairing of H atoms.
Design, Specification, and Construction of a Light, Automated Drilling System (LADS) (2002)

Abstract A "typical" North Slope well is a thing of the past. Twenty years ago, a rig would sit on a Prudhoe pad and drill dozens of 10,000 bopd wells. Today, a rig might drill multi-laterals one month, and exploration wells 60 miles from infrastructure the next. Diverse well types and changing economic drivers warranted a new look at North Slope rig designs. In 1997, BP Alaska began researching what the drilling machine of the future should look like. Conceptual drawings were drafted and several new design tenets emerged. First, the rig had to be safer and more automated. Second, it had to reduce well costs. Third, it had to be lighter and smaller. Fourth, it had to be better suited for cross-tundra rig moves. In May 2000, BP chose Phoenix Alaska Technology (PAT) to finalize the design, construct, and operate the rig. In March 2001, PAT began constructing a state-of-the-art, fully automated drilling rig that is expected to commence operations on the North Slope in early 2002. The rig weighs less than half that of a conventional North Slope rig of equivalent horsepower. A single operator controls all drilling, tripping, and horizontal setback operations from a computerized control station. This paper discusses the first four stages of this project: 1) The conceptual design phase by the operator, BP, 2) conceptual design phase by the contractor, PAT, 3) final engineering and specification by PAT and its subcontractors, and 4) rig fabrication. This case study also explores the basis for the design and the features of a light automated drilling system (LADS) that is expected to meet the objectives.
Real-Time Optical Spectrum Fourier Transformation (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. Malacarne, Y. Park, M. Li, S. LaRochelle, and J. Azaña, "Real-Time Optical Spectrum Fourier Transformation," in Conference on Lasers and Electro-Optics 2012, OSA Technical Digest (online) (Optica Publishing Group, 2012), paper CW3D.5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Optimization of a Soft Ensemble Vote Classifier for the Prediction of Chimeric Virus-Like Particle Solubility and Other Biophysical Properties (2020)

Chimeric virus-like particles (cVLPs) are protein-based nanostructures applied as investigational vaccines against infectious diseases, cancer, and immunological disorders. Low solubility of cVLP vaccine candidates is a challenge that can prevent development of these very substances. Solubility of cVLPs is typically assessed empirically, leading to high time and material requirements. Prediction of cVLP solubility <i>in silico</i> can aid in reducing this effort. Protein aggregation by hydrophobic interaction is an important factor driving protein insolubility. In this article, a recently developed soft ensemble vote classifier (sEVC) for the prediction of cVLP solubility was used based on 91 literature amino acid hydrophobicity scales. Optimization algorithms were developed to boost model performance, and the model was redesigned as a regression tool for ammonium sulfate concentration required for cVLP precipitation. The present dataset consists of 568 cVLPs, created by insertion of 71 different peptide sequences using eight different insertion strategies. Two optimization algorithms were developed that (I) modified the sEVC with regard to systematic misclassification based on the different insertion strategies, and (II) modified the amino acid hydrophobicity scale tables to improve classification. The second algorithm was additionally used to synthesize scales from random vectors. Compared to the unmodified model, Matthew's Correlation Coefficient (MCC), and accuracy of the test set predictions could be elevated from 0.63 and 0.81 to 0.77 and 0.88, respectively, for the best models. This improved performance compared to literature scales was suggested to be due to a decreased correlation between synthesized scales. In these, tryptophan was identified as the most hydrophobic amino acid, i.e., the amino acid most problematic for cVLP solubility, supported by previous literature findings. As a case study, the sEVC was redesigned as a regression tool and applied to determine ammonium sulfate concentrations for the precipitation of cVLPs. This was evaluated with a small dataset of ten cVLPs resulting in an <i>R</i> <sup>2</sup> of 0.69. In summary, we propose optimization algorithms that improve sEVC model performance for the prediction of cVLP solubility, allow for the synthesis of amino acid scale tables, and further evaluate the sEVC as regression tool to predict cVLP-precipitating ammonium sulfate concentrations.
Immunotherapy for prostate cancer - recent progress in clinical trials. (2007)

Prostate cancer is the most common malignancy affecting men in the United States. Traditional therapy with radical prostatectomy or radiation therapy can be curative for localized disease, but metastatic prostate cancer is currently incurable. The only treatments known to prolong survival in patients with metastatic disease are androgen-deprivation therapy and chemotherapy, both of which have significant side effects. Immunotherapy approaches offer hope in providing new treatments to delay disease progression, ideally with fewer side effects. The results from nearly all early immunotherapy clinical trials for prostate cancer conducted to date have shown minimal toxicity, and many have suggested clinical benefit in terms of delaying disease progression. Several phase III clinical trials are currently under way in patients with metastatic, androgen-independent prostate cancer. The current article reviews recent trials evaluating immune-modulating agents, antigen-specific active immunotherapy, and combination therapies in clinical development for the treatment of prostate cancer.
Adaptive channel access tuning and QoS support for multimedia applications over IEEE 802.11e WLANs (2011)

IEEE 802.11e Enhanced Distributed Channel Access (EDCA) standard defines multiple Access Categories (AC) to support MAC-level Quality of Service (QoS). However, the values of the main parameters of each AC are static and do not take the wireless channel condition and the channel density into account. Therefore, the default EDCA parameters only yield good performance for few scenarios. In this paper, we propose a new cross-layer adaptation scheme that improves the IEEE 802.11e Quality of Service (QoS) by tuning the Medium Access Control (MAC) layer channel access parameters. Proposed scheme is based on the number of mobile nodes on the channel, their traffic types, application layer QoS requirements and physical layer (PHY) channel conditions. Simulation results indicate that our scheme outperforms the standard implementation and provides desired QoS for multimedia applications.
Monolithic integration of vertical SiNx microrings on a ridge waveguide to achieve multi-channel photonic coupling (2017)

Multi-channel vertical photonic coupling was observed, by integrating two different SiNx vertical microring couplers (VμRC) monolithically on a single ridge waveguide. This work represents a critical step to 3D photonic integration using VμRC’s.
Grain size dependence of dielectric relaxation in cerium oxide as high-k layer (2013)

Cerium oxide (CeO2) thin films used liquid injection atomic layer deposition (ALD) for deposition and ALD procedures were run at substrate temperatures of 150°C, 200°C, 250°C, 300°C, and 350°C, respectively. CeO2 were grown on n-Si(100) wafers. Variations in the grain sizes of the samples are governed by the deposition temperature and have been estimated using Scherrer analysis of the X-ray diffraction patterns. The changing grain size correlates with the changes seen in the Raman spectrum. Strong frequency dispersion is found in the capacitance-voltage measurement. Normalized dielectric constant measurement is quantitatively utilized to characterize the dielectric constant variation. The relationship extracted between grain size and dielectric relaxation for CeO2 suggests that tuning properties for improved frequency dispersion can be achieved by controlling the grain size, hence the strain at the nanoscale dimensions.
Carcinoembryonic Antigen Family Receptor Recognition by Gonococcal Opa Proteins Requires Distinct Combinations of Hypervariable Opa Protein Domains (2002)

Neisserial Opa proteins function as a family of adhesins that bind heparan sulfate proteoglycan (HSPG) or carcinoembryonic antigen family (CEACAM) receptors on human host cells. In order to define the CEACAM binding domain on Opa proteins, we tested the binding properties of a series of gonococcal (strain MS11) recombinants producing mutant and chimeric Opa proteins with alterations in one or more of the four surface-exposed loops. Mutagenesis demonstrated that the semivariable domain, present in the first loop, was completely dispensable for CEACAM binding. In contrast, the two hypervariable (HV) regions present in the second and third loops were essential for binding; deletion of either domain resulted in loss of receptor recognition. Deletion of the fourth loop resulted in a severe decrease in Opa expression at the cell surface and could therefore not be tested for CEACAM binding. Chimeric Opa variants, containing combinations of HV regions derived from different CEACAM binding Opa proteins, lost most of their receptor binding activity. Some chimeric variants gained HSPG binding activity. Together, our results indicate that full recognition of CEACAM receptors by Opa proteins requires a highly coordinate interplay between both HV regions. Furthermore, shuffling of HV regions may result in novel HSPG receptor binding activity.
Facile Synthesis of 5.ALPHA.-Fluorocholestan-3-one from 4-Cholesten-3-one via Molecular Fluorine Addition and Reductive Defluorination. (1994)

A facile synthesis of 5α-fluorocholestan-3-one from 4-cholesten-3-one has been accomplished. Direct fluorination of the enone by molecular fluorine gave the cis-vicinal difluoride. Treatment of this adduct with triphenyltin hydride in the presence of azobisisobutyronitrile afforded the title compound.
Thymus-Related Cellular Immune Mechanisms in Sex-Associated Resistance to Experimental Murine Cysticercosis (Taenia crassiceps) (1993)

The role of sex, thymus, and cellular immune mechanisms in mouse resistance to experimental cysticercosis with Taenia crassiceps was studied in male and female susceptible mice treated with cyclophosphamide, as well as in mice neonatally thymectomized and passively transferred with T-enriched lymphoid cells. High doses of cyclophosphamide increased delayed hypersensitivity and resistance of mice of both sexes without affecting antibody production. Neonatal thymectomy diminished resistance in both sexes but depressed delayed hypersensitivity in females only, without significantly affecting antibody response in either sex. Passive transfer of T-enriched lymphoid cells to thymectomized mice restored resistance to control levels without greatly affecting delayed hypersensitivity. Thus, our results indicate that cell-associated immune mechanisms are implicated in resistance to murine cysticercosis with T. crassiceps. Because neonatal thymectomy nearly equalized the intensity of infection of female and male mice, it is argued that the thymus is importantly involved in the interaction between gonads and the immune system in the control of this cysticercosis.
Effect of Fumonisin on Growth of Ruminal Bacteria in Batch Culture (2009)

Fumonisin (FMN) is a mycotoxin produced by Fusarium species and has been found in feeds fed to dairy cattle. The effects of FMN on ruminal bacterial growth and fermentation were measured with batch culture. Experimental feeds contained 0, 100 or 200 ppm FMN and were arranged as a completely randomized design (CRD). All feeds were incubated at 39°C with buffer and strained ruminal fluid. Culture optical density (OD) was measured to estimate microbial populations. The cultures were sampled at 0, 6, 12, 24 and 36 h to measure the fermentation end products, pH and OD. OD increased over time with no differences among treatments except at 12 h. At 12 h, OD was higher for cultures fed diets containing FMN at 100 (1.66) and 200 (1.62) ppm versus feed without FMN (1.41). Culture pH decreased over time and was not significantly different due to treatments over the entire study. Total concentration of VFA and concentrations of acetic acid, propionic acid, and butyric acid increased over time with no differences among treatments. Feed containing no FMN supported higher concentrations of ammonia and branch chain VFA (BCVFA) versus the other treatments from 6 h through 36 h. There was a high correlation between ammonia and BCVFA concentrations at sample times (r = 0.97). The results indicated that FMN changed ruminal microbial fermentation of protein as measured by changes in BCVFA and ammonia in this in vitro fermentation system. The effect of these changes in rumen fermentation on animal performance should be investigated.
Dynamics of a two-state quantum dot laser with saturable absorber (2007)

In this paper, we report on both experimental and theoretical investigations on the dynamics of self-pulsation regimes in a two-section QD laser that is operating simultaneously on the GS and ES transitions. We show that the competition between the two states results in anti-phase dynamics. We also found a sub-harmonic sequence that leads ultimately to chaos.
Catalytic Aerobic Oxidation of Alcohols using Recoverable IAPNO α‐Hydrogen Nitroxyl Radicals (2015)

Abstract α‐Hydrogen‐substituted nitroxyl radicals are of considerable interest as catalysts for oxidation and polymerization, but are usually inherently unstable. We report herein the catalytic activity of a new family of stable iso‐azaphenalene (IAPNO) α‐hydrogen nitroxyl radicals in the copper/bipyridine/ N ‐methylimidazole co‐catalyzed aerobic oxidation of alcohols. The nitroxyl radical Mes/TIPSO‐IAPNO (TIPSO=triisopropyloxy, IAPNO=isoazaphenalene N‐oxyl) displays higher activity than TEMPO in the oxidation of benzylic and allylic alcohols. Alkyl, benzyl, allyl, and propargyl alcohols are oxidized with yields up to 96 %. The readily prepared nitroxyl catalysts are recovered in 75–90 % yield after purification of the reaction mixture and are recycled.