gebhart/patrepeval huggingface dataset:
Acoustic microcavitation: Its active and passive acoustic detection (1991)

In this work acoustic microcavitation in water is studied primarily at 0.75 MHz and 1% duty cycle. To detect cavitation, two kinds of acoustic detectors are used. The first one is an unfocused, untuned 1-MHz receiver transducer that serves as a passive detector. The other one is a focused 30-MHz transducer that is used in pulse-echo mode and is called the active detector. Cavitation itself is brought about by a focused PZT-8 crystal driven in pulse mode. The active detector is arranged confocally with respect to the cavitation transducer. Both the interrogating pulse and the cavitation pulse arrive simultaneously at the common focus, which is the region of cavitation. With the test chamber filled with clean water, no cavitation is observed, even when the cavitation transducer is driven to give its peak output of 22 bar peak negative. Cavitation is, however, observed when polystyrene microparticles are added to the host water. Our view of how these smooth, spherical, monodispersed microparticles give rise to cavitation is described with some estimates. An attempt has been made to understand whether the presence of "streaming" affects the thresholds, and it has been found that the active detector field affects the cavitation process.
Novel, Cross-Restricted, Conserved, and Immunodominant Cytotoxic T Lymphocyte Epitopes in Slow Progressors in HIV Type 1 Infection (1996)

HIV-specific cytotoxic T lymphocytes (CTLs) play an important role in the immune response to HIV infection. Long-term nonprogressors (LTNPs) or slow progressors (SPs) in HIV infection may make qualitatively different CTL responses compared to those generated by seropositive individuals who progress to disease at a faster rate. The class I molecule HLA-B*57 has been identified as one restriction element overrepresented in SP groups studied, and, together with the closely related molecule HLA-B*58, occurs commonly in ethnic groups where HIV is most prevalent. In this study, we have identified five new HLA-B*57-restricted CTL epitopes recognized by SP donors, one of which is also HLA-B*5801 restricted. These HLA-B*57-restricted responses represent the dominant HIV-specific CTL response in each of the SP donors tested. These and other such epitopes may be an important component in future vaccine design.
Diffraction from optically written persistent plasma gratings in doped compound semiconductors (1994)

We propose and demonstrate a new type of optical nonlinearity based on the properties of the DX center in doped compound semiconductors. We report measurements on samples of AlGaAs:Si which were exposed to interfering laser beams and find diffraction from a large, persistent refractive index change associated with the well-known persistent photoconductivity effect in this material. The new effect is shown to exhibit a refractive index change 30 times larger than that of conventional photorefractive materials. We explain the origin of the refractive index change in terms of the plasma effect and show that its expected magnitude is consistent with our observations.
Phosphate Stress in Cultures and Field Populations of the Dinoflagellate <i>Prorocentrum minimum</i> Detected by a Single-Cell Alkaline Phosphatase Assay (1999)

Alkaline phosphatase activity is a common marker of phosphate stress in many phytoplankton, but it has been difficult to attribute alkaline phosphatase activity to specific organisms or groups of phytoplankton in the field with traditional biochemical procedures. A new alkaline phosphatase substrate, ELF-97 (enzyme-labeled fluorescence), shows promise in this regard. When a phosphate group is cleaved from the ELF-97 reagent, the remaining molecule precipitates near the site of enzyme activity, thus fluorescently tagging cells with alkaline phosphatase activity. We characterized ELF-97 labeling in axenic cultures of a common dinoflagellate, Prorocentrum minimum, in order to understand ELF-97 labeling dynamics when phosphate nutrition varies. Enzyme activity, as detected by ELF-97 labeling, appears to be induced in late-log- or early-stationary-phase cultures if cells are grown in low-phosphate media and is lost when phosphate-stressed cells are refed with phosphate. ELF-97 appears to label an inducible intracellular alkaline phosphatase in P. minimum based on confocal microscopy studies. This may limit the use of this reagent to organisms that lack high levels of constitutive intracellular phosphatases. After laboratory cultures were characterized, ELF-97 was used to assay field populations of P. minimum in Narragansett Bay during two 1-week periods, and 12 to 100% of the P. minimum cells were labeled. The level of cell labeling was reduced by 3 days of incubation with added inorganic phosphate. Our results indicate that ELF-97 is an excellent new tool for monitoring phytoplankton phosphate stress in the environment when the data are supported by appropriate laboratory studies.
Real-time 2(1/2)-D head pose recovery for model-based video-coding (2001)

This paper discusses a 2(1/2)-D tracking method allowing real-time recovery of the three-dimensional (3-D) position and orientation of a head moving in its image plane. The described method uses a two-dimensional (2-D) elliptical head model, region- and edge-based matching algorithms, and a linear Kalman filter estimator. The resulting motion tracking system works in a realistic environment without makeup on the face, with an uncalibrated camera, normal lighting conditions, and an unknown background.
Synchronization in scale-free dynamical networks: robustness and fragility (2002)

Recently, it has been demonstrated that many large complex networks display a scale-free feature, that is, their connectivity distributions are in the power-law form. In this paper, we investigate the synchronization phenomenon in scale-free dynamical networks. We show that if the coupling strength of a scale-free dynamical network is greater than a positive threshold, then the network will synchronize no matter how large it is. We show that the synchronizability of a scale-free dynamical network is robust against random removal of nodes, but is fragile to specific removal of the most highly connected nodes.
Neutronics and Transient Analysis of a Small Fast Reactor Cooled with Natural Circulation of Lead : ELECTRA: European Lead Cooled Training Reactor (2014)

In this thesis, neutronics and some relevant transient analyses of the European Lead-Cooled Training Reactor (ELECTRA) are analyzed. ELECTRA is a low-power lead-cooled fast reactor intended for training purpose. The design concept aims for the total nominal power of 0.5 MWth to be fully removed by natural circulation of pure lead, eliminating the need for pumps. A very small compact core with (Pu0.4Zr0.6)N fuel, which relies on neutron reflector to achieve criticality, results in unique reflector dominant neutronic characters. Moreover, a very hard neutron spectrum due to the choice of the fuel and the coolant leads to nearly zero Doppler feedback, relatively small effective delayed neutron fraction as well as short prompt neutron reproduction time. Nevertheless, dynamic stability and safety performance during unprotected transient scenarios are shown to be inherently ensured by the other reactivity feedbacks including the negative coolant temperature. Furthermore, the nature of the natural circulation provides favorable conditions during the studied accident cases.
Gene expression analysis of renal carcinoma: adipose differentiation‐related protein as a potential diagnostic and prognostic biomarker for clear‐cell renal carcinoma (2005)

The gene expression profiles of 33 renal cell carcinomas (RCCs) and nine normal kidney samples were examined using high-density oligonucleotide microarrays in an attempt to identify biomolecular markers for the diagnosis of tumour subtypes and also for prediction of prognosis. Hierarchical clustering demonstrated that clear-cell RCC, chromophobe RCC, and normal kidney tissue showed distinctive gene expression profiles. The mean expression levels of 149 of 12 500 genes were more than three times higher in clear-cell RCC than in chromophobe RCC and normal kidney tissue. Among the genes whose expression was upregulated in clear-cell RCC, adipose differentiation-related protein (ADFP) and nicotinamide N-methyltransferase (NNMT) were selected for further analysis. Consistent with the results of the microarray, increased levels of ADFP and NNMT mRNA were found more frequently in clear-cell RCCs than in other non-clear-cell tumour subtypes using real-time quantitative PCR. Immunohistochemistry for ADFP showed strong and unique tumour cell staining patterns in the majority of clear-cell RCCs. More importantly, patients bearing tumours with higher AFDP mRNA levels showed significantly better survival in both univariate and multivariate analyses. ADFP is a lipid storage droplet-associated protein and its transcription is considered to be regulated by the von Hippel-Lindau/hypoxia-inducible factor pathway. It is known that clear-cell RCC contains abundant lipids and cholesterols. Thus it is likely that sustained upregulation of ADFP following VHL inactivation is involved in the morphological appearance of clear-cell RCC. Moreover ADFP expression status may provide useful prognostic information as a biomolecular marker in patients with clear-cell RCC.
On-line solid-phase preconcentration for sensitivity enhancement in capillary electrophoresis. (2001)

Capillary electrophoresis is attractive for the analysis of biological samples because only a few nanoliters of sample need to be injected. Indeed, optimal resolution is achieved when the injected volume is 1% or less of the total capillary volume. Unfortunately, this advantage leads to severe detection limitations compounded by the fact that many analytes in a biological sample are present at very low concentrations. To overcome the detection sensitivity limitations of CE, nonspecific, on-line preconcentration has been employed in a variety of applications. This technique is based on inserting a small quantity of reversed-phase material (e.g., C18 particles or membrane) near the inlet of the CE capillary for sample enrichment by solid-phase extraction. A detachable cartridge containing the solid phase is relatively simple to construct and permits the injection of large sample volumes (1-100 microL) into the capillary. Elution of adsorbed analyte in less than 100 nL of solvent permits a 100-1000 fold improvement in the effective concentration limit of detection, depending on the hydrophobicity of the compound. Detection of analytes present in complex mixtures at concentrations as low as 20 amol/microL has been reported when using an on-line preconcentration device in conjunction with CE-mass spectrometry. In this review, the potential merits of the technique are described and some examples of direct analysis of biological samples without rigorous off-line pretreatment are given.
Time and calcium dependence of activation and inactivation of calcium-induced release of calcium from the sarcoplasmic reticulum of a skinned canine cardiac Purkinje cell. (1985)

Microprocessor-controlled changes of [free Ca2+] at the outer surface of the sarcoplasmic reticulum (SR) wrapped around individual myofibrils of a skinned canine cardiac Purkinje cell and aequorin bioluminescence recording were used to study the mechanism of Ca2+-induced release of Ca2+ from the SR. This Ca2+ release is triggered by a rapid increase of [free Ca2+] at the outer surface of the SR of a previously quiescent skinned cell. Ca2+-induced release of Ca2+ occurred under conditions that prevented any synthesis of ATP from ADP, was affected differentially by interventions that depressed the SR Ca2+ pump about equally, and required ionic conditions incompatible with all known Ca2+-releasing, uncoupled, partial reactions of the Ca2+ pump. Increasing the [free Ca2+]trigger up to an optimum increased the amount of Ca2+ released. A supraoptimum increase of [free Ca2+] trigger inactivated Ca2+-induced release of Ca2+, but partial inactivation was also observed at [free Ca2+] below that necessary for its activation. The amplitude of the Ca2+ release induced by a given increase of [free Ca2+] decreased when the rate of this increase was diminished. These results suggest that Ca2+-induced release of Ca2+ is through a channel across the SR membrane with time- and Ca2+-dependent activation and inactivation. The inactivating binding site would have a higher affinity for Ca2+ but a lower rate constant than the activating site. Inactivation appeared to be a first-order kinetic reaction of Ca2+ binding to a single site at the outer face of the SR with a Q10 of 1.68. The removal of inactivation was the slowest step of the cycle, responsible for a highly temperature-dependent (Q10 approximately 4.00) refractory period.
Macromol. React. Eng. 4/2007 (2007)

Cover: The picture on the cover depicts a semi‐batch polymerization with three monomers forming a branched polymer owing to transfer reactions and to the presence of two double bonds in one monomer. Molecular weight, sequence distributions and average molecular radius of gyration are predicted using population balance equations in terms of generating functions. Further details can be found in the article by R. C. S. Dias and M. R. P. F. N. Costa * on page 440.
PEG-liposomal oxaliplatin potentialization of antitumor efficiency in a nude mouse tumor-xenograft model of colorectal carcinoma (2011)

The non-selectivity of chemotherapeutics between normal tissue and pathological sites poses a challenge for the treatment strategy for advanced colorectal carcinoma. To obtain sufficient antitumor activity, optimization of the therapeutic regimen is of great importance. We investigated PEG-liposomal oxaliplatin potentialization of antitumor efficiency in a nude mouse tumor-xenograft model of colorectal carcinoma. A tumor-bearing nude mouse model, intravenous injections of (Dio)-labeled PEG-liposomes via tail vein and fluorescence imaging with in vivo imaging system were employed. Mice were treated with free L-oHP, PEG-liposomal L-oHP via the tail vein, followed by analysis of the accumulation of L-oHP in tumor tissues by high-performance liquid chromatography (HPLC), observation of the tumor volume and the survival rate. Apoptosis and proliferation of tumors were detected by TUNEL assay and immunohistochemistry. The mRNA and protein levels of Bcl-2, Bax, caspase-3 (P17) and Ki-67 were determined by RT-PCR and Western blotting. Fluorescence imaging with in vivo imaging showed PEG-liposome targeting in tumor tissues. After intravenous injections of PEG-liposomal oxaliplatin, tumor tissue maximum accumulation of L-oHP was 9.37 ± 0.79 µg/g at 24 h; The tumor volume was significantly suppressed, and mice showed longer survival, compared with the free oxaliplatin group. Apoptosis increased, but proliferation decreased in tumor tissues. The mRNA expression of Bcl-2 and Ki-67 was down-regulated, while Bax and caspase-3 expression was up-regulated. Protein expression of Bcl-2 was down-regulated, while Bax and P17 expression was up-regulated. The results indicate that PEG-liposomal oxaliplatin can improve antitumor efficiency in a nude mouse tumor-xenograft model of colorectal carcinoma.
Enhanced vertical transport in p-type AlGaN∕GaN superlattices (2004)

We report on p-type AlGaN∕GaN superlattice designs with significantly improved vertical and lateral electrical conductivities (σV and σL). Composition-graded p-AlGaN layers produce a polarization charge distribution, which together with an appropriate Mg doping in the structure leads to more than an eightfold reduction of barrier height and a ∼50% increase in the sheet hole density in the p-GaN wells compared to typical modulation-doped superlattice structures. Using the optimized structure, more than 13 orders of magnitude and 35 times improvement is shown for σV, compared to typical superlattice and σL, compared to bulk p-GaN, respectively. Both σV and σL are found to improve significantly at higher temperatures in the optimized structure.
[The influence on the biodegradation of phenanthrene by nonionic surfactant, Tween20]. (2004)

The objective of this study was to quantify the bioavailability of phenanthrene solubilized in surfactants by a mixed phenanthrene-degrading culture isolated from the petroleum contaminated soils. An nonionic surfactant, Tween20, was used. The effects of Tween20 on the microbial degradation of phenanthrene were evaluated depending on the rotary flasks experiments. The results showed that the concentrations of Tween20 above the critical micelle concentration (CMC) could increase the solubility of phenanthrene on great extent and were not toxic to the phenanthrene-degrading bacteria, and that the presence of surfactant micelles did not inhibit the biodegradation of phenanthrene. Phenanthrene solubilized in the micelles of Tween20 in liquid media was bioavailable and degradable by the mixed culture of bacteria.
Variational encoding of complex dynamics (2018)

Often the analysis of time-dependent chemical and biophysical systems produces high-dimensional time-series data for which it can be difficult to interpret which individual features are most salient. While recent work from our group and others has demonstrated the utility of time-lagged covariate models to study such systems, linearity assumptions can limit the compression of inherently nonlinear dynamics into just a few characteristic components. Recent work in the field of deep learning has led to the development of the variational autoencoder (VAE), which is able to compress complex datasets into simpler manifolds. We present the use of a time-lagged VAE, or variational dynamics encoder (VDE), to reduce complex, nonlinear processes to a single embedding with high fidelity to the underlying dynamics. We demonstrate how the VDE is able to capture nontrivial dynamics in a variety of examples, including Brownian dynamics and atomistic protein folding. Additionally, we demonstrate a method for analyzing the VDE model, inspired by saliency mapping, to determine what features are selected by the VDE model to describe dynamics. The VDE presents an important step in applying techniques from deep learning to more accurately model and interpret complex biophysics.
Double Michelson Interferometer for Contactless Length Change Measurements. (1978)

The use of a two-channel, or double Michaelson, interferometer for measuring the absolute thermal strain epsilon of a small test sample (e.g., 4-in. long) is described. This method is contactless inasmuch as laser beams reflect off the ends of the sample. Real-time strain changes are recorded automatically to a resolution of lambda/8L sub s, where L sub s is the sample length. Analysis shows that the measurement errors are approximately proportional to the sample temperature excursion, with the strain error varying from .48 to 2 x 10 to the -7 power as Delta T sub s varies from 25 to 250 C. An average coefficient of thermal expansion for ultralow-expansion glass, measured with additional fringe interpolation by photo-detector signal analysis, would be known to + or - 1.2 times 10 to the -9th power/deg C.
Isolation of Escherichia coli 0157 from raw meat products (1996)

This study has evaluated an enrichment and four subculture procedures for detection of Escherichia coli O157 in raw meat products. The combination of enrichment in modified tryptone broth incubated at 42 degrees C for 6 h, followed by immunomagnetic separation and subculture on to cefixime, tellurite sorbitol MacConkey agar was the most sensitive and selective procedure. Traditional subculture using 10 microliters and 100 microliters inocula and culture of centrifuged deposits were less satisfactory. A most probable number method was used to enumerate E. coli O157 in naturally contaminated samples associated with human cases. The results indicated that the samples contained < 0.3 to 2300 cfu g-1 of E. coli O157 which confirms that the infective dose for this organism is low.
Immunocytochemical Demonstration of Hormones in Pancreatic and Pituitary Tissue Embedded in Methyl Methacrylate (1997)

We describe the immunocytochemical demonstration of hormones in pancreatic and pituitary tissue embedded in the plastic methyl methacrylate. Semithin sections were prepared for high resolution light microscopy and a broad spectrum of antibodies applied. Excellent immunocytochemical staining was reliably achieved with all the antibodies investigated combining strong positivity with good tissue morphology. The results were superior to similar studies we have previously performed with other acrylic plastic embedding media, and the method can be routinely employed in a diagnostic laboratory. (The J Histotechnol 20:35, 1997)
The 5′ Terminal Trailer Region of Vesicular Stomatitis Virus Contains a Position-Dependent <i>cis</i> -Acting Signal for Assembly of RNA into Infectious Particles (1999)

The cis-acting genomic RNA requirements for the assembly of vesicular stomatitis virus (VSV) ribonucleocapsids into infectious particles were investigated. Using a biological assay based on particle infectivity, we demonstrated that subgenomic replicons that contained all four possible combinations of the natural genomic termini, the 3' leader (Le) and 5' trailer (Tr) regions, were replication competent; however, a 3' copyback replicon (3'CB), containing the natural 3' terminus but having the 5' Tr replaced by a sequence complementary to the 3' Le for 46 nucleotides, was unable to assemble infectious particles, despite efficient replication. When a copy of Tr was inserted 51 nucleotides from the 5' end of 3'CB, infectious particles were produced. However, analysis of the replication products of these particles showed that the 51 nucleotides which corresponded to the Le complement sequences at the 5' terminus were removed during RNA replication, thus restoring the wild-type 5' Tr to the exact 5' terminus. These data showed that a cis-acting signal was necessary for assembly of VSV RNAs into infectious particles and that this signal was supplied by Tr when located at the 5' end. The regions within Tr required for assembly were analyzed by a series of deletions and exchanges for Le complement sequences, which demonstrated that the 5' terminal 29 nucleotides of Tr allowed assembly of infectious particles but that the 5' terminal 22 nucleotides functioned poorly. Deletions in Tr also altered the balance between negative- and positive-strand genomic RNA and affected levels of replication. RNAs that retained fewer than 45 but at least 22 nucleotides of the 5' terminus could replicate but were impaired in RNA replication, and RNAs that retained only 14 nucleotides of the 5' terminus were severely reduced in ability to replicate. These data define the VSV Tr as a position-dependent, cis-acting element for the assembly of RNAs into infectious particles, and they delineate RNA sequences that are essential for negative-strand RNA synthesis. These observations are consistent with, and offer an explanation for, the absence of 3' copyback defective interfering particles in nature.