gebhart/patrepeval huggingface dataset:
Purification and Characterization of Botulinum Neurotoxin FA from a Genetically Modified Clostridium botulinum Strain (2016)

Botulinum neurotoxins (BoNTs), produced by neurotoxigenic clostridial species, are the cause of the severe disease botulism in humans and animals. Early research on BoNTs has led to their classification into seven serotypes (serotypes A to G) based upon the selective neutralization of their toxicity in mice by homologous antibodies. Recently, a report of a potential eighth serotype of BoNT, designated "type H," has been controversial. This novel BoNT was produced together with BoNT/B2 in a dual-toxin-producing Clostridium botulinum strain. The data used to designate this novel toxin as a new serotype were derived from culture supernatant containing both BoNT/B2 and novel toxin and from sequence information, although data from two independent laboratories indicated neutralization by antibodies raised against BoNT/A1, and classification as BoNT/FA was proposed. The sequence data indicate a chimeric structure consisting of a BoNT/A1 receptor binding domain, a BoNT/F5 light-chain domain, and a novel translocation domain most closely related to BoNT/F1. Here, we describe characterization of this toxin purified from the native strain in which expression of the second BoNT (BoNT/B) has been eliminated. Mass spectrometry analysis indicated that the toxin preparation contained only BoNT/FA and confirmed catalytic activity analogous to that of BoNT/F5. The in vivo mouse bioassay indicated a specific activity of this toxin of 3.8 × 10(7) mouse 50% lethal dose (mLD50) units/mg, whereas activity in cultured human neurons was very high (50% effective concentration [EC50] = 0.02 mLD50/well). Neutralization assays in cells and mice both indicated full neutralization by various antibodies raised against BoNT/A1, although at 16- to 20-fold-lower efficiency than for BoNT/A1. IMPORTANCE Botulinum neurotoxins (BoNTs), produced by anaerobic bacteria, are the cause of the potentially deadly, neuroparalytic disease botulism. BoNTs have been classified into seven serotypes, serotypes A to G, based upon their selective neutralization by homologous antiserum, which is relevant for clinical and diagnostic purposes. Even though supportive care dramatically reduces the death rate of botulism, the only pharmaceutical intervention to reduce symptom severity and recovery time is early administration of antitoxin (antiserum raised against BoNTs). A recent report of a novel BoNT serotype, serotype H, raised concern of a "treatment-resistant" and highly potent toxin. However, the toxin's chimeric structure and characteristics indicate a chimeric BoNT/FA. Here we describe the first characterization of this novel toxin in purified form. BoNT/FA was neutralized by available antitoxins, supporting classification as BoNT/FA. BoNT/FA required proteolytic activation to achieve full toxicity and had relatively low potency in mice compared to BoNT/A1 but surprisingly high activity in cultured neurons.
Metabolism and Turnover of Lung Surfactant (1987)

Despite the grave difficulties that beset researchers who are trying to isolate and characterize the various intracellular and extracellular forms of lung surfactant; despite the serious ambiguities of interpretation of experimental data caused by the multicomponent nature of the surfactant; despite the inaccessibility for diagnostic purposes of this material, which functions deep in the lungs; despite the fact that incisive methods of protein chemistry and molecular biology have only recently been brought to bear on lung surfactant; despite all these problems, our knowledge and understanding of lung surfactant are rapidly increasing. We know now that it is a dynamic system with many parts, and that the reserves of these are normally not large and are recycled. We believe that tight metabolic control must exist to maintain these reserves, and we already have experimental techniques to raise or lower the reserves. Heroic methods of surfactant substitution are now being tested in patients whose deficiency or risk thereof is sufficiently desperate, and the results of these clinical trials, if they are carefully documented with lung function data, will add a new dimension to our knowledge of surfactant dynamics. We may expect in the future that more subtle alterations in surfactant function will become detectable and more sophisticated methods to manipulate the system will be invented. Essential to these will be a deeper understanding of surfactant forms, pathways, kinetics, and controls. Fortunately, research on surfactant structure, metabolism, and turnover intrigues many investigators. They, we may hope, will soon provide the necessary information.
Cooling Enhancements in Thin Films Supported by Flexible Complex Seals in the Presence of Ultrafine Suspensions (2003)

Flow and heat transfer inside thin films supported by flexible soft seals having voids of a stagnant fluid possessing a large coefficient of volumetric thermal expansion βT are studied in the presence of suspended ultrafine particles. The study is conducted under periodically varying thermal load conditions. The governing continuity, momentum and energy equations are non-dimensionalized and reduced to simpler forms. The deformation of the seal is related to the internal pressure and lower plate’s temperature based on the theory of linear elasticity and a linearized model for thermal expansion. It is found that enhancements in the cooling are achieved by an increase in the volumetric thermal expansion coefficient, thermal load, thermal dispersion effects, softness of the supporting seals and the thermal capacitance of the coolant fluid. Further, thermal dispersion effects are found to increase the stability of the thin film. The noise in the thermal load is found to affect the amplitude of the thin film thickness, Nusselt number and the lower plate temperature however it has a negligible effect on their mean values.
Identification of a novel subpopulation of Caspase-4 positive Non-Small Cell Lung Cancer patients. (2020)

Abstract Background . Therapy/prognosis of Non-Small Cell Lung Cancer (NSCLC) patients are strongly related to gene alteration/s or protein expression. However, more than 50% of NSCLC patients are negative to key drugable biomarkers. Methods: We used human samples of NSCLC and mouse models of lung adenocarcinoma. Results . We showed that caspase-4 was highly present in the tumor mass compared to non-cancerous human tissues. Interestingly, the orthologue murine caspase-11 promoted lung carcinogenesis in mice. Carcinogen-exposed caspase-11 knockout mice had lower tumor lesions than wild type mice, due to the relevance of caspase-11 in the structural lung cell as demonstrated by bone marrow transplantation and adoptive transfer experiments. Similarly to what observed in mice, caspase-4 was correlated to the stage of lung cancer in humans in that it induced cell proliferation in a K-Ras, c-MyC and IL-1α dependent manner. Caspase-4 positive adenocarcinoma (79.3%) and squamous carcinoma (88.2%) patients had lower median survival than patients who had lower levels of caspase-4. Moreover, PD-L1 expression and gene mutation (i.e. EGFR) were not correlated to caspase-4 expression. Instead, NSCLC patients who had K-Ras or c-MyC gene alteration were positively correlated to higher levels of caspase-4 and lower survival rate. Conclusions . We identified a subgroup of NSCLC patients as caspase-4 positive among which double and triple positive caspase-4, K-Ras and/or c-MyC patients which prognosis was poor. Because K-Ras and c-MyC are still undrugable, the identification of caspase-4 as a novel oncoprotein could introduce novelty in the clinical yet unmet needs for NSCLC patients.
A hierarchical approach to wrapper induction (1999)

With the tremendous amount of information that becomes available on the Web on a daily basis, the ability to quickly develop information agents has become a crucial problem.
Removal of grapefruit juice furanocoumarins by four edible fungi (2008)

Furanocoumarins (FCs), a class of phenolic compounds, are known to inhibit the human cytochrome P450 3A4 (CYP 3A4) activity responsible for the metabolism of certain medications. This inhibition increases the oral bioavailability of these medications, leading to potential toxic effects. These interactions, overriding the potential health benefits of grapefruit consumption, have adversely affected the grapefruit industry, and have led to a need to remove the FCs from grapefruit juice (GFJ). Previously, we showed that autoclaved Aspergillus niger adsorbs FCs in GFJ, and that the fungus-treated GFJ showed a reduced inhibition of CYP 3A4. However, A. niger is not an edible fungus, thus prompting us to investigate edible fungi. In this study, autoclaved edible ascomycetes (Morchella esculenta and Monascus purpureus) and basidomycetes (Pleurotus sapidus, and Agaricus bisporus) were mixed with GFJ, and the levels of two of the major furanocoumarins 6´,7´-dihydroxybergamottin (DHB) and bergamottin (BM) were compared in the treated GFJ and in the control, untreated GFJ. These FCs were removed by the heat-killed fungi, suggesting that production of FC-removed GFJ may be achieved.
Method and apparatus for heating or heating and reduction of raw materials for a metallurgical furnace utilizing waste gases from the same furnace (1984)

An apparatus for heating or heating and reduction of raw material for a metallurgical furnace, utilizing high temperature waste gases which are released from the same furnace, has one or plural numbers of reactor(s) capable of holding the raw materials in the amount which can be charged in plural numbers of processing in the metallurgical furnace, where the reactor(s) is (are) disposed on a bypass passage connected to a pipe of a waste gas processing apparatus for cooling and scrubbing the waste gases from the metallurgical furnace. A part or all the waste gases are introduced into the reactor(s) and come into contact with the raw materials therein when the blowing in the furnace is performed to a full scale, and the reactor is cut off at the initial and final stage of blowing, whereby the heating or the heating and reduction raw material of a metallurgical furnace is effectively performed.
A Thermal Imaging Instrument with Uncooled Detectors (2017)

In this work, we performed an instrument concept study for sustainable thermal imaging over land with uncooled detectors. We evaluated two different uncooled detector technologies uncooled microbolometers and thermopiles. We have also evaluated materials for use in in a uncooled thermopile detector concept.
Superhydrophilicity of Rutile TiO2 Prepared by Anodic Oxidation in High Concentration Sulfuric Acid Electrolyte (2008)

Abstract The contact angles of rutile TiO2 prepared by anodic oxidation in an electrolyte with a high concentration of sulfuric acid is almost zero without UV illumination. The water droplet spread across the surface within 1 ms because of the strong interaction with the hydroxy groups.
A novel, fast and cost effective graphene-modified graphite pencil electrode for trace quantification of<scp>l</scp>-tyrosine (2015)

A simple and novel method for detecting<sc>l</sc>-tyrosine in urine was introduced using a graphene-modified graphite pencil electrode (GR-modified GPE).
Manipulating perceptual brightness during retinal electrical stimulation using pulse trains (2005)

Most experimental work examining the effects of retinal electrical stimulation in human patients has focused on single pulses. However, a successful implant will require continuous stimulation using high frequency pulse trains. We report here data examining stimulation using pulse trains in three patients with advanced retinitis pigmentosa implanted with a 4×4 epiretinal electrode array. Stimuli were 200ms biphasic electrical pulse trains that varied in the number of pulses (1–45). Individual pulses had durations of 0.075ms or 0.975ms for both cathodic and anodic phases. We measured amplitude threshold using a yes-no paradigm. Additionally, we carried out brightness matching to determine the amplitude needed for two pulses of different frequencies to match in brightness. The current needed to reach threshold decreases with the number of pulses, but the necessary total charge increases linearly. A similar loss of charge efficiency occurs supra-threshold. This efficiency decrease is more pronounced for long than short pulses, and does not depend on the inter-phase interval or on the temporal separation between pulses, over 1–40msec. These data are consistent with the idea that indirect inhibition mediated by amacrine cells may be stronger for long than for short pulses.
Virtualized reality: constructing virtual worlds from real scenes (1997)

A new visual medium, Virtualized Reality, immerses viewers in a virtual reconstruction of real-world events. The Virtualized Reality world model consists of real images and depth information computed from these images. Stereoscopic reconstructions provide a sense of complete immersion, and users can select their own viewpoints at view time, independent of the actual camera positions used to capture the event.
Kinetics and structural evolution of sorbents at high temperatures. Final report, September 1, 1993--August 31, 1994 (1995)

The focus of this project is on furnace sorbent injection technology using dry, calcium-based sorbents for flue gas desulfurization. The goal is to provide fundamental research kinetics and the effects of sorbent properties, aimed at improving S0{sub 2} removal and increasing sorbent utilization in a cost-effective fashion. The fourth year work has been carried out in three phases: (1) structural evolution of sorbent, (2) modified sorbent studies, and (3) development of mathematical model. The results, their interpretation, and discussions are the primary focus of this report.
Design and evaluation of a music video summarization system (2005)

We present a system that summarizes the textual, audio, and video information of music videos in a format tuned to the preferences of a focus group of 20 users. First, we analyzed user-needs for the content and the layout of the music summaries. Then, we designed algorithms that segment individual song videos from full music video programs by noting changes in color palette, transcript, and audio classification. We summarize each song with automatically selected high level information such as title, artist, duration, title frame, and text as well as audio and visual segments of the chorus. Our system automatically determines with high recall and precision chorus locations, from the placement of repeated words and phrases in the text of the song's lyrics. Our Bayesian belief network then selects other significant video and audio content from the multiple media. Overall, we are able to compress content by a factor of 10. Our second user study has identified the principal variations between users in their choices of content desired in the summary, and in their choices of the platforms that should support their viewing.
Advances in technology and practice for land-based aquaculture systems: tank-based recirculating systems for finfish production. (2009)

Abstract: Recirculating systems for aquaculture production are much talked about but often not very well understood. Proponents state that recirculating systems, systems that recycle water through a number of filters and components to clean the water and reuse it, are the way to a sustainable future for aquaculture. Detractors state with equal conviction that recirculating systems are too expensive to build and operate and are not and will not be an economically viable way to grow aquacultured products. As with most issues, there is no ‘black and white’ simple answer. This chapter seeks to highlight the required unit processes that must be dealt with in order to succeed when utilizing recirculating technology for tank-based finfish production. Additionally, examples of state-of-the-art components are provided. Wherever possible, commercially available technology is referenced. Further, the chapter closes with the description of what the authors consider a well thought-out and implemented commercial-scale recirculating aquaculture production system.
Detection of Noncovalent Complexes in Biological Samples by Intensity Fading and High-Mass Detection MALDI-TOF Mass Spectrometry (2006)

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has not yet contributed widely to the study of intact noncovalent biomolecular complexes, because MALDI is known to cause dissociation of the interaction partners and induce formation of nonspecific aggregates. Here, we present a new strategy to circumvent this problem. It is based on intensity fading (in the low m/z range) and high-mass detection MALDI mass spectrometry (MS), using a cryodetector (in the high m/z range), with and without chemical cross-linking of the interaction partners. The study focuses on noncovalent interactions between the human enzyme carboxypeptidase A (hCPA) and three protease inhibitors (PCI, TCI, and LCI) present in heterogeneous mixtures of other nonbinding molecules derived from a biological source, an extract from leech (Hirudo medicinalis). Another example involves an extract of the sea anemone Stichodactyla helianthus, which is used without previous fractionation to detect the specific complex between the enzyme trypsin and the endogenous SphI-1 inhibitor. The results give insight into the mechanism of intensity fading MS and demonstrate that the specificity of binding is greatly favored when the overall concentrations of the analytes (nonbinding molecules, protease inhibitor and target enzyme) present in a biological sample of interest are kept at low concentrations, in the sub-micromolar range. Higher concentrations may lead to unspecific interactions and the formation of aggregates both during the MALDI process and during reaction with the cross-linking reagents. This strategy is expected to advance the field of high-throughput affinity-based approaches, by taking advantage of a new generation of high mass detectors for MALDI-TOF instruments.
Exploring Key Weather Factors From Analytical Modeling Toward Improved Solar Power Forecasting (2017)

Accurate solar power forecasting plays a critical role in ensuring the reliable and economic operation of power grids. Most of existing literature directly uses available weather conditions as input features, which might ignore some key weather factors and the coupling among weather conditions. Therefore, a novel solar power forecasting approach is proposed in this paper by exploring key weather factors from photovoltaic (PV) analytical modeling. The proposed approach is composed of three engines: (1) analytical modeling of PV systems; (2) machine learning methods for mapping weather features with solar power; and (3) a deviation analysis for solar power forecast adjustment. In contrast to the existing research that directly uses available weather conditions, this paper explores the physical knowledge from PV models. Different irradiance components and PV cell temperatures are derived from PV analytical modeling. These weather features are used to reformulate the input of machine learning methods, which helps achieve a better forecasting performance. Moreover, based on the historical forecasting deviations, a compensation term is presented to adjust the solar power forecast. Case studies based on measured datasets from PV systems in Australia demonstrate that the forecasting performance can be highly improved by taking advantage of the key weather features derived from PV models.
Identification of alternatively spliced mRNAs encoding variants of MDK1, a novel receptor tyrosine kinase expressed in the murine nervous system. (1995)

A novel member of the eck/eph family of receptor tyrosine kinases (RTKs), termed mouse developmental kinase 1 (MDK1), was identified and shown to be closely related to the Eek, Ehk1/Cek7, Ehk2, Cek4/Mek4/hek and Sek/Cek8 subfamily. Northern blot analysis revealed MDK1 mRNA transcripts of 6.8, 5.7, 4.0, 3.2 and 2.6 kb that encode apparent splice variants. Sequence analyses of MDK1 cDNA clones from adult mouse brain predict the existence of at least five isoforms, including two truncated receptor variants lacking the kinase domain. Northern blot and in situ hybridization analysis indicate that in the adult mouse MDK1 RNA expression is restricted to brain, testes and spleen. The distinct patterns of MDK1 gene expression during mouse development suggest an important role in the formation of neuronal structures and possibly other morphogenic processes.
Porridge: a method of providing resilient and scalable cloud-attestation-as-a-service (2017)

Effectively establishing trust in Cloud Computing is a critical requirement for achieving wider adoption of hybrid and public cloud. Although a number of Trusted Cloud concepts have been proposed, they suffer from limitations in resilience, scalability and dynamism. We tackle these limitations with the creation of a distributed attestation service, Porridge. Porridge achieves resiliency, as multiple attestation workers are employed and redundant workers assigned for attesting each Virtual Machine (VM); scalability, as the attestation load and responsibility is automatically distributed evenly among workers; adaptivity to cloud dynamism, as each VM's virtual Trusted Platform Module (vTPM) is mapped to a stable set of physical Trusted Platform Modules (TPM) in the host and then the workers TPMs. Overall the attestation scheme enables flexible vTPM-TPM bindings while hiding details of cloud infrastructure, with the root-of-trust for the VM not bound to its underlying host's TPM, but to its managing workers. This concept can be extended to support more advanced cloud security through the introduction of Trusted Service Providers providing Cloud Attestation as a Service (CAaaS).
Reducing Wind Tunnel Data Requirements Using Neural Networks (1997)

The use of neural networks to minimize the amount of data required to completely define the aerodynamic performance of a wind tunnel model is examined. The accuracy requirements for commercial wind tunnel test data are very severe and are difficult to reproduce using neural networks. For the current work, multiple input, single output networks were trained using a Levenberg-Marquardt algorithm for each of the aerodynamic coefficients. When applied to the aerodynamics of a 55% scale model of a U.S. Air Force/ NASA generic fighter configuration, this scheme provided accurate models of the lift, drag, and pitching-moment coefficients. Using only 50% of the data acquired during, the wind tunnel test, the trained neural network had a predictive accuracy equal to or better than the accuracy of the experimental measurements.
Three-dimensional EIT imaging of breast tissues: system design and clinical testing (2002)

Results of development and testing of the new medical imaging system are described. The system uses a planar array consisting of 256 electrodes and enables obtaining images of the three-dimensional conductivity distribution in regions below the skin's surface up to several centimeters deep. The developed measuring system and image reconstruction algorithm can be used for breast tissue imaging and diagnostics, in particular for malignant tumor detection. Examples of tomographic images obtained in vivo during clinical tests are presented. The mammary gland, being an organ-target, alters at the background with such physiological events as menstrual cycle, pregnancy, lactation, and postmenopause. The objectives of this paper include estimation of the possibilities of electrical impedance mammography for investigation of mammary glands' state among women with different hormonal status. We found that electrical impedance mammograms from different groups had clear visual distinctions and statistically significant differences in mammary glands' conductivity. Our data on conductivity distribution in the mammary gland during different physiological periods will allow us to use it as normal values in the future, to continue this research on mammary glands with different pathology.