gebhart/patrepeval huggingface dataset:
<title>Monoclonal antibody-tagged receptor-targeted contrast agents for detection of cancers</title> (2001)

Oral cancer and precancer overexpress the epidermal growth factor receptor (EGFR) and monoclonal antibodies against EGFR coupled to photoactive dyes may have a potential both as a diagnostic and treatment modalities for oral premalignancy. We asked whether an anti-EGFR mab (C225) conjugated with the fluorescence dye indocyanine Cy5.5 could detect dysplastic changes in the hamster cheek pouch carcinogenesis model. Secondly, we tested whether the same antibody conjugated with the photosensitizer chlorin (e6) could be used together with illumination to reduce levels of expression of EGFR as evaluated by the immunophotodetection procedure. Increased fluorescence appeared to correlate with development of premalignancy when the C225-Cy5.5 conjugate was used. Areas with increased fluorescence signal were found in carcinogen-treated but clinically normal cheek pouches, that revealed dysplastsic changes by histology. The immunophotodetection procedure was carried out after photoummunotherapy with the C225-ce6 conjugate, and showed a significant reduction in fluorescence in the illuminated compared to the non-illuminated areas in the carcinogen- treated but not the normal cheek pouch. The results demonstrate that the use of anti-EGFR Mab targeted photoactive dyes may serve as a feedback controlled optical diagnosis and therapy procedure for oral premalignant lesions.
Learning-Based Object Identification and Segmentation Using Dual-Energy CT Images for Security (2015)

In recent years, baggage screening at airports has included the use of dual-energy X-ray computed tomography (DECT), an advanced technology for nondestructive evaluation. The main challenge remains to reliably find and identify threat objects in the bag from DECT data. This task is particularly hard due to the wide variety of objects, the high clutter, and the presence of metal, which causes streaks and shading in the scanner images. Image noise and artifacts are generally much more severe than in medical CT and can lead to splitting of objects and inaccurate object labeling. The conventional approach performs object segmentation and material identification in two decoupled processes. Dual-energy information is typically not used for the segmentation, and object localization is not explicitly used to stabilize the material parameter estimates. We propose a novel learning-based framework for joint segmentation and identification of objects directly from volumetric DECT images, which is robust to streaks, noise and variability due to clutter. We focus on segmenting and identifying a small set of objects of interest with characteristics that are learned from training images, and consider everything else as background. We include data weighting to mitigate metal artifacts and incorporate an object boundary field to reduce object splitting. The overall formulation is posed as a multilabel discrete optimization problem and solved using an efficient graph-cut algorithm. We test the method on real data and show its potential for producing accurate labels of the objects of interest without splits in the presence of metal and clutter.
Scanning Kelvin Probe Microscopy Investigation of the Role of Minority Carriers on the Switching Characteristics of Organic Field‐Effect Transistors (2016)

A method based on scanning Kelvin probe microscopy is developed to probe the effects of minority carriers on the switching characteristics of organic field-effect transistors. The mobility of the minority carriers is extracted and the role they play in screening of the gate potential in the OFF state and in recombination of trapped majority carriers trapped after an ON state is understood.
Ageing in tomato reduces the capacity of seeds to produce ethylene, while priming increases ethylene evolution during germination. (2003)

A study was conducted to compare ethylene production in a tomato seed lot after moderate aging and compare the relationship between seed priming and ethylene production in aged and non-aged seeds using ethylene-insensitive tomato (cv. Moneymaker) mutants. Seeds were stored at 4°C or room temperature (∼23°C) for 18 months and osmotically primed in aerated 3% KNO3 solution for 7 days at 20°C in the dark and subsequently dried at room temperature for 24 h to 8.2±1.1% moisture content. In separate Petri dishes, seeds were imbibed on water or 5 mM ACC for 12, 24, 36, 48 and 60 h. Seeds aged for 18 months had reduced vigour as indicated by radicle emergence after 60 h. Seeds imbibed on water evolved less ethylene than those imbibed on ACC. Non-primed aged seeds began to evolve ethylene 24 h later than non-primed non-aged seeds. Even between seed lots with comparable viability, reduced vigour results in a reduced capacity to produce ethylene. Non-primed seeds attained 50% radicle protrusion after 77 h, while primed seeds required only ∼36 h. At 48 h, primed seeds produced ten times the ethylene of non-primed seeds. Primed aged and non-aged seeds had similar radicle emergence percentages after 48 h. However, ethylene production, though enhanced, was significantly lower in primed aged seeds than primed non-aged seeds. Endogenous ACC content in seed following priming was 4.0±0.9 pmol per seed vs. 0.69±0.08 and 1.1±0.06 pmol per seed in non-primed non-aged and non-primed aged seeds, respectively. Priming significantly increased ACC oxidase activity.
DELAYED HYPERSENSITIVITY (1960)

The capacity to develop the delayed type of hypersensitivity to diphtheria toxoid and ovalbumin may persist in guinea pigs and rabbits that have received doses of x-ray sufficient to eliminate a detectable antibody response. Larger doses of x-irradiation can prevent development of delayed-type hypersensitivity in rabbits.
Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure (2019)

Abstract Rationale A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of MS/MS reference spectra in public databases. Currently, scientists purchase databases or use public databases such as GNPS. The MSMS-Chooser workflow empowers the creation of MS/MS reference spectra directly in the GNPS infrastructure. Methods An MSMS-Chooser sample template was completed with the required information and sequence tables were generated programmatically. Standards in methanol-water (1:1) solution (1 μM) were placed into wells individually. An LC-MS/MS system using data-dependent acquisition in positive and negative modes was used. Species that may be generated under typical ESI conditions are chosen. The MS/MS spectra and MSMS-Chooser sample template were subsequently uploaded to MSMS-Chooser in GNPS for automatic MS/MS spectral annotation. Results Data acquisition quickly and effectively collected MS/MS spectra. MSMS-Chooser was able to accurately annotate 99.2% of the manually validated MS/MS scans that were generated from the chemical standards. The output of MSMS-Chooser includes a table ready for inclusion in the GNPS library (after inspection) as well as the ability to directly launch searches via MASST. Altogether, the data acquisition, processing, and upload to GNPS took ~2 hours for our proof-of-concept results. Conclusions The MSMS-Chooser workflow enables the rapid data acquisition, analysis, and annotation of chemical standards, and uploads the MS/MS spectra to community-driven GNPS. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.
Stress-strain behaviour analysis of Middle Polish glacial tills from Warsaw (Poland) based on the interpretation of advanced field and laboratory tests (2016)

Abstract The selected parameters of the Wartanian and Odranian tills, with relation to their spatial occurrence, grain size distribution, mineralogical composition, matric suction and other physical characteristics, are presented. The assessment of the lithogenesis and stress history on the microstructure is attempted. The comparison of the compression and permeability characteristics from field and laboratory tests has been performed. Laboratory consolidation tests carried out with up to 20MPa vertical stress, revealed two yield stress values, one in the range of a couple hundreds kPa, the other in the range of a couple thousands kPa. Based on those results, the reliability of the soil preconsolidation assessment, with the use of the two different methods is discussed. The aspect of the triaxial strength reduction under the dynamic loading of diverse frequency and amplitude is raised. The research results depict a variety of possible geological-engineering characteristics, under the divergent constraints scenarios, of compression or strength weakening origin. The effects of the specialized research program will widen the possibilities of physio-mechanical and structural characterization of soils for geological-engineering purposes.
Reconfigurable visible nanophotonic switch for optogenetic applications (Conference Presentation) (2017)

High spatiotemporal resolution deep-brain optical excitation for optogenetics would enable activation of specific neural populations and in-depth study of neural circuits. Conventionally, a single fiber is used to flood light into a large area of the brain with limited resolution. The scalability of silicon photonics could enable neural excitation over large areas with single-cell resolution similar to electrical probes. However, active control of these optical circuits has yet to be demonstrated for optogenetics. Here we demonstrate the first active integrated optical switch for neural excitation at 473 nm, enabling control of multiple beams for deep-brain neural stimulation. Using a silicon nitride waveguide platform, we develop a cascaded Mach-Zehnder interferometer (MZI) network located outside the brain to direct light to 8 different grating emitters located at the tip of the neural probe. We use integrated platinum microheaters to induce a local thermo-optic phase shift in the MZI to control the switch output. We measure an ON/OFF extinction ratio of >8dB for a single switch and a switching speed of 20 microseconds. We characterize the optical output of the switch by imaging its excitation of fluorescent dye. Finally, we demonstrate in vivo single-neuron optical activation from different grating emitters using a fully packaged device inserted into a mouse brain. Directly activated neurons showed robust spike firing activities with low first-spike latency and small jitter. Active switching on a nanophotonic platform is necessary for eventually controlling highly-multiplexed reconfigurable optical circuits, enabling high-resolution optical stimulation in deep-brain regions.
How Far Can We Push Polymer Architectures? (2013)

We here report the synthesis and characterization of a complex polymeric architecture based on a block copolymer with a cylindrical brush block and a single-chain polymeric nanoparticle block folded due to strong intramolecular hydrogen-bonds. The self-assembly of these constructs on mica surfaces was studied with atomic force microscopy, corroborating the distinct presence of block copolymer architectures.
Proteome analysis of Escherichia coli K‐12 by two‐dimensional native‐state chromatography and MALDI‐MS (2003)

To identify proteins expressed in Escherichia coli K-12 MG1655 during exponential growth in defined medium, we separated soluble proteins of E. coli over two dimensions of native-state high-performance liquid chromatography, and examined the components of the protein mixtures in each of 380 fractions by peptide mass fingerprinting. To date, we have identified the products of 310 genes covering a wide range of cellular functions. Validation of protein assignments was made by comparing the assignments of proteins to specific first-dimension fractions to proteins visualized by two-dimensional gel electrophoresis. Co-fractionation of proteins suggests the possible identities of components of multiprotein complexes. This approach yields high-throughput gel-independent identification of proteins. It can also be used to assign identities to spots visualized by two-dimensional gels, and should be useful to evaluate differences in expressed proteome content and protein complexes among strains or between different physiological states.
Synthesis of HighPerformance Analog Circuits in ASTRX/OBLX (2009)

We present a new synthesis strategy that can automate fully the path from an analog circuit topology and performance specifications to a sized circuit schematic. This strategy relies on asymptotic waveform evaluation to predict circuit performance and simulated annealing to solve a novel unconstrained optimization formulation of the circuit synthesis problem. We have implemented this strategy in a pair of tools called ASTRX and OBLX. To show the generality of our new approach, we have used this system to resynthesize essentially all the analog synthesis benchmarks published in the past decade; ASTRX/OBLX has resynthesized circuits in an afternoon that, for some prior approaches, had required months. To show the viability of the approach on difficult circuits, we have resynthesized a recently published (and patented), high-performance operational amplifier; ASTRX/OBLX achieved performance comparable to the expert manual design. And finally, to test the limits of the approach on industrial-sized problems, we have synthesized the component cells of a pipelined A/D converter; ASTRX/OBLX successfully generated cells 2-3?? more complex than those published previously.
Effect of genetic background on Cav2 channel alpha1 and beta subunit messenger RNA expression in cerebellum of N-type Ca2+ channel alpha1B subunit-deficient mice. (2004)

Although the N-type Ca2+ channel plays a role in a variety of neuronal functions, N-type Ca2+ channel alpha1B-deficient mice exhibit normal life span without apparent behavioral or histologic abnormalities. To examine whether the reason for their normal behavior is compensation by other Cav2 channel alpha1 or beta subunit genes and to analyze whether genetic background influences the subunit expression pattern, we studied the alpha1A, alpha1E, beta1b, beta2, beta3 and beta4 subunit mRNA levels in cerebellum of alpha1B-deficient mice with CBA x C57BL/6 or CBA/JN background. In cerebellum of the mice with a CBA x C57BL/6 background, alpha1A mRNA was expressed at a higher level than that in wild-type or heterozygous mice, but difference in the expression levels of alpha1E, beta1b, beta2, beta3 and beta4 subunits was not found among wild-type, heterozygous, and homozygous mice. In cerebellum of alpha1B-deficient mice with CBA/JN background, beta4 mRNA was expressed at a higher level than that in wild-type or heterozygous mice, but alpha1A, alpha1E, beta1b, alpha2, beta3 and transcripts were expressed at similar levels in all genotypes. Therefore, a possible explanation of the normal behavior of alpha1B-deficient mice is that Cav2 channel family members compensate for the deficiency, and that the change of functional subunit expression pattern for compensation differs in animals with different genetic backgrounds.
Accuracy of error propagation exemplified with ratios of random variables (2000)

The method of error propagation provides a convenient tool for calculating mean and variance of a measurand from means and variances of primarily measured quantities. However, being based on a (usually first-order) Taylor approximation of the measurement function, it only yields approximate results with unknown accuracy. We develop a method for estimating the accuracy of (Nth-order) error propagation for an arbitrary number of correlated random quantities, and apply our findings to the ratio of two random variables (RVs). A comparison with some analytically solved expressions for certain probability density functions (PDFs) as well as with some computer simulations reveals the excellent quality of our estimates as long as the involved PDFs are not significantly skew. For the ratio of two RVs it turns out that conventional, first-order error propagation is safely applicable (with about 1% accuracy) as long as the denominator’s mean is larger than about 12 times its standard deviation. Using second-order error propagation, the approximation for the ratio’s mean can be refined, yielding 1% accuracy if the denominator’s mean is larger than about four times its standard deviation.
Distributed parallel volume rendering applied to virtual endoscopy (2002)

Improved realism in virtual endoscopy may be achieved by using volume rather than surface rendering, which preserves grayscale information and fine detail from the original CT dataset. Since volume rendering is computationally intensive, parallelization of the calculations is attractive. A distributed parallel rendering algorithm has been applied to calculation of volume rendered cine sequences in a few seconds per frame when using a modest number of readily available workstations.
Cryptococcus neoformans Capsular Enlargement and Cellular Gigantism during Galleria mellonella Infection (2011)

We have studied infection of Cryptococcus neoformans in the non-vertebrate host Galleria mellonella with particular interest in the morphological response of the yeast. Inoculation of C. neoformans in caterpillars induced a capsule-independent increase in haemocyte density 2 h after infection. C. neoformans manifested a significant increase in capsule size after inoculation into the caterpillar. The magnitude of capsule increase depended on the temperature, being more pronounced at 37°C than at 30°C, which correlated with an increased virulence of the fungus and reduced phagocytosis at 37°C. Capsule enlargement impaired phagocytosis by haemocytes. Incubation of the yeast in G. mellonella extracts also resulted in capsule enlargement, with the polar lipidic fraction having a prominent role in this effect. During infection, the capsule decreased in permeability. A low proportion of the cells (<5%) recovered from caterpillars measured more than 30 µm and were considered giant cells. Giant cells recovered from mice were able to kill the caterpillars in a manner similar to regular cells obtained from in vivo or grown in vitro, establishing their capacity to cause disease. Our results indicate that the morphological transitions exhibited by C. neoformans in mammals also occur in a non-vertebrate host system. The similarities in morphological transitions observed in different animal hosts and in their triggers are consistent with the hypothesis that the cell body and capsular responses represent an adaptation of environmental survival strategies to pathogenesis.
Changing Acute Renal Failure Treatment from Intermittent Hemodialysis to Continuous Hemofiltration: Impact on Azotemic Control (1999)

Changing the form of renal replacement therapy from intermittent hemodialysis to continuous hemofiltration is associated with improved control of azotemia. The superior adequacy of small solute clearance achieved during CVVHDF provides additional support for its preferential use in the management of acute renal failure in the ICU.
In vitro and in vivo anticancer activities of synthetic macrocyclic ketone analogues of halichondrin B. (2001)

Halichondrin B is a highly potent anticancer agent originally found in marine sponges. Although scarcity of the natural product has hampered efforts to develop halichondrin B as a new anticancer drug, the existence of a complete synthetic route has allowed synthesis of structurally simpler analogues that retain the remarkable potency of the parent compound. In this study, we show that two macrocyclic ketone analogues of halichondrir B, ER-076349 and ER-086526, have sub-nM growth inhibitory activities in vitro against numerous human cancer cell lines as well as marked in vivo activities at 0.1-1 mg/kg against four human xenografts: MDA-MB-435 breast cancer, COLO 205 colon cancer, LOX melanoma, and NIH: OVCAR-3 ovarian cancer. ER-076349 and ER-086526 induce G2-M cell cycle arrest and disruption of mitotic spindles, consistent with the tubulin-based antimitotic mechanism of halichondrin B. This is supported further by direct binding of the biotinylated analogue ER-040798 to tubulin and inhibition of tubulin polymerization in vitro by ER-076349 and ER-086526. Retention of the extraordinary in vitro and in vivo activity off halichondrin B in structurally simplified, fully synthetic analogues establishes the feasibility of developing halichondrin B-based agents as highly effective, novel anticancer drugs.
Protective efficacy of P7C3-S243 in the 6-hydroxydopamine model of Parkinson's disease (2015)

Abstract Background: There are currently no therapeutic options for patients with Parkinson's disease that prevent or slow the death of dopaminergic neurons. We have recently identified the novel P7C3 class of neuroprotective molecules that blocks neuron cell death. AIMS: The aim of this study was to determine whether treatment with highly active members of the P7C3 series blocks dopaminergic neuron cell death and associated behavioral and neurochemical deficits in the rat 6-hydroxydopamine (6-OHDA) model of Parkinson's disease. Methods: After unilateral injection of 6-OHDA into the median forebrain bundle, rats were assessed for behavioral function in the open field, cylinder test, and amphetamine-induced circling test. Thereafter, their brains were subjected to neurochemical and immunohistochemical analysis of dopaminergic neuron survival. Analysis was conducted as a function of treatment with P7C3 compounds, with administration initiated either before or after 6-OHDA exposure. Results: Animals administered P7C3-A20 or P7C3-S243, two of the most advanced agents in the P7C3 series of neuroprotective compounds, both before and after 6-OHDA exposure showed evidence of protective efficacy in all measures. When P7C3-S243 administration was initiated after 6-OHDA exposure, rats also showed protective efficacy in all measures, which included blocking dopaminergic neuron cell death in ipsilateral substantia nigra pars compacta, preservation of dopamine and its metabolites in ipsilateral striatum, and preservation of normal motor behavior. Conclusions: The P7C3 series of compounds may form the basis for developing new therapeutic agents for slowing or preventing progression of Parkinson's disease.
A Bibliometric Survey of Paraffin/Olefin Separation Using Membranes (2019)

Bibliometric studies allow to collect, organize and process information that can be used to guide the development of research and innovation and to provide basis for decision-making. Paraffin/olefin separations constitute an important industrial issue because cryogenic separation methods are frequently needed in industrial sites and are very expensive. As a consequence, the use of membrane separation processes has been extensively encouraged and has become an attractive alternative for commercial separation processes, as this may lead to reduction of production costs, equipment size, energy consumption and waste generation. For these reasons, a bibliometric survey of paraffin/olefin membrane separation processes is carried out in the present study in order to evaluate the maturity of the technology for this specific application. Although different studies have proposed the use of distinct alternatives for olefin/paraffin separations, the present work makes clear that consensus has yet to be reached among researchers and technicians regarding the specific membranes and operation conditions that will make these processes scalable for large-scale commercial applications.
Application of dielectric resonators to surface impedance measurements of microwave susceptors (2019)

In this work, application of split-post and single-post dielectric resonator to the measurements of surface impedance of microwave susceptors is discussed.