gebhart/patrepeval huggingface dataset:
Extensively drug-resistant tuberculosis: new strains, new challenges (2008)

Extensively drug-resistant (XDR)-TB, defined as TB with resistance to at least isoniazid, rifampin, a fluoroquinolone and either amikacin, kanamycin or capreomycin, is a stark setback for global TB control. Overburdened public-health systems with inadequate resources for case detection and management and high HIV coinfection rates in many regions have contributed to the emergence of XDR-TB. Patients with XDR-TB have poor outcomes, prolonged infectious periods and limited treatment options. To prevent an epidemic of untreatable XDR-TB, improvements in XDR-TB surveillance, increased laboratory capacity for rapid detection of drug-resistant strains, better infection control and the development of new therapeutics are urgently needed.
Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system (2018)

Current single-particle cryo-electron microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size suitable for cryo-EM. Using a rigid continuous alpha helical linker, we connect a small 17-kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry. We show that the resulting construct is amenable to structural analysis by single-particle cryo-EM, allowing us to identify and solve the structure of the attached small protein at near-atomic detail, ranging from 3.5- to 5-Å resolution. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Furthermore, because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other protein or nucleic acid molecules, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryo-EM to proteins of typical size in the cell.
Malaria and other Apicomplexans: the "plant" connection. (1994)

Recent molecular studies point to the unorthodox conclusion that malaria parasites have a photosynthetic ancestry. Coupled with other phylogenetic evidence, this finding may apply across the phylum Apicomplexa, including other important pathogens such as the coccidia and piroplasms. We propose that an organelle corresponding to a residual plastid, performing unknown functions, is likely to reside in all, or many, of these organisms. The new findings discussed here highlight once more the pressing need to discover more about the basic biology of these economically important parasites. From such knowledge, new targets for chemotherapy may be identified.
Domain adaptive semantic diffusion for large scale context-based video annotation (2009)

Learning to cope with domain change has been known as a challenging problem in many real-world applications. This paper proposes a novel and efficient approach, named domain adaptive semantic diffusion (DASD), to exploit semantic context while considering the domain-shift-of-context for large scale video concept annotation. Starting with a large set of concept detectors, the proposed DASD refines the initial annotation results using graph diffusion technique, which preserves the consistency and smoothness of the annotation over a semantic graph. Different from the existing graph learning methods which capture relations among data samples, the semantic graph treats concepts as nodes and the concept affinities as the weights of edges. Particularly, the DASD approach is capable of simultaneously improving the annotation results and adapting the concept affinities to new test data. The adaptation provides a means to handle domain change between training and test data, which occurs very often in video annotation task. We conduct extensive experiments to improve annotation results of 374 concepts over 340 hours of videos from TRECVID 2005-2007 data sets. Results show consistent and significant performance gain over various baselines. In addition, the proposed approach is very efficient, completing DASD over 374 concepts within just 2 milliseconds for each video shot on a regular PC.
Two MHC Surface Amino Acid Differences Distinguish Foreign Peptide Recognition from Autoantigen Specificity (2001)

KRN T cells can recognize two self MHC alleles with differing biological consequences. They respond to the foreign peptide RN(42--56) bound to I-A(k) or alternatively initiate autoimmune arthritis by interacting with a self Ag, GPI(282--294), on I-A(g7). Five surface amino acid differences between the two MHC molecules collectively alter which peptide side chains are recognized by the KRN TCR. In this study, it is shown that mutation of only two of these residues, alpha 65 and beta 78, in I-A(k) to their I-A(g7) counterparts is sufficient to allow recognition of the TCR contacts from GPI(282--294). To provide a detailed mechanism for the specificity change, the distinct contributions of each of these two mutations to the global effect on peptide specificity were analyzed. The alpha65 mutation is shown to broaden the spectrum of amino acids permissible at P8 of the peptide. In contrast, the beta 78 mutation alone blocks KRN TCR interaction with I-A(k) and requires the simultaneous presence of the alpha 65 mutation to preserve recognition. In the presence of the alpha 65 mutation, the beta 78 residue broadens peptide recognition at P3 and prevents recognition of the P8 L in RN(42--56), thus producing the observed specificity shift. These results localize the functionally relevant differences between the surfaces of two self-restricted MHC molecules to two residues that have counterbalanced positive and negative contributions to interaction with a single TCR. They highlight how subtle structural distinctions attributable to single amino acids can stand at the interface between foreign Ag responsiveness and pathogenic autoreactivity.
Methane to methanol: Reactor design and process evaluation (1988)

The design of a supersonic nozzle reactor for controlling the partial oxidation of methane to methanol and alternative condenser and gas separation systems were investigated. GENMIX, a simplified fluid dynamics code available at Los Alamos, was modified to simulate mixing and simultaneous chemical reaction in the reaction vessel. Preliminary studies indicate that complete mixing of reactants in a coaxial supersonic expansion nozzle is impossible in the time scale of reaction. A global kinetic model was regressed from computer simulations of the complete reaction mechanism. The global model is felt to be sufficient for preliminary nozzle simulations in a temperature range of 800-1000 K, initial pressure of 60 atm, and initial oxygen concentrations of approximately 33 mol%. Attempts to incorporate global kinetics into the fluid dynamics code were not successful because of code limitations. Two condenser system configurations for the removal of methanol from the process stream were evaluated by simulation with ASPEN PLUS. A two-step series condensation is less energy intensive and has a lower equipment cost than a system consisting of a condenser and distillation column. However, the condenser and distillation system have a higher methanol recovery and product purity. Investigation of possible methods for the separation of methanemore » and carbon monoxide from the process stream revealed that membrane techniques, pressure swing adsorption, and adsorption into propane are feasible alternatives. 27 refs.« less
Detection and classification of anomalous events in water quality datasets within a smart city-smart bay project (2014)

Continual measurement is key to understanding sudden and gradual changes in chemical and biological quality of water, and for taking reactive remedial action in the case of contamination. Monitoring of water bodies will increase in future within Europe to comply with legislative requirements such as the Water Framework Directive and globally owing to pressure from climate change. Establishing high quality long-term monitoring programs is regarded as essential if the implementation of pertinent legislation is to be successful. However, conventional discrete sampling programs and laboratory-based analysis techniques can be costly, and are unlikely to provide timely and reliable estimates of true ranges of deterministic physicochemical variability in a water body with marked temporal or spatial variability. \nOnly continual or near continual measurements have the capacity to detect ephemeral or sporadic events, thus providing the potential for on-line event detection and classification. The aim of this work is to demonstrate the potential role of continuous data acquisition in decision support as part of a smart city project. In this work, a multi-modal smart sensor network system framework for large scale estuarine and marine water quality monitoring is proposed. The application of a number of evolving techniques that allow automated detection and clustering of events from data generated by in situ sensors within environmental time series datasets is described. We provide examples of how change in the range of variables such as turbidity and salinity might be detected and clustered to provide the end user with greater ability to detect the onset of environmentally significant events. Finally, we discuss the acquisition of data from in situ water quality sensors and its utility within the framework a smart city-smart bay integrated project.
The effect of the interruption of agitation on plateletquality during storage for transfusion (2001)

Interruption of agitation of PCs for 1 day, either on the agitator or in the shipping container, produces no platelet damage measurable by these in vitro techniques. However, an interruption of agitation for 2 days can result in significant damage in some components. Further studies will be required to learn more about the mechanisms that lead to the metabolic changes described and to determine if the same generalizations apply to apheresis PCs and PCs prepared from pooled buffy coats.
Understanding Molecular Interactions of Asphaltenes in Organic Solvents Using a Surface Force Apparatus (2011)

A surface force apparatus was used to study the intermolecular forces of asphaltenes in toluene and heptane. The repulsive interaction forces measured between two asphaltene surfaces in toluene were shown to have a steric nature and could be described by the Alexander–de Gennes theory on steric repulsion between two interacting polymer layers in good solvents at short separation distances under high compression forces. On the other hand, the adhesion forces measured between asphaltenes in heptane can be described by van der Waals forces, which are responsible for asphaltene aggregation and precipitation in paraffinic solvents. The asphaltene films adsorbed on mica were found to swell significantly in toluene but only moderately in heptane. In addition, an adhesion force was observed between an asphaltene surface and a mica surface in toluene. The results from this study provide an insight into the basic interaction mechanisms of asphaltenes in organic media and hence in crude oil and bitumen production.
DINGPOS: High sensitivity GNSS platform for deep indoor scenarios (2010)

Deep indoor scenarios are one of the most challenging areas of application for Global Navigation Satellite Systems (GNSS) in personal navigation devices. Especially severe signal attenuation, as well as heavy multipath constrain the use of GNSS in this environment. The project DINGPOS is focusing on the development of a platform for pedestrian users which can acquire and track GNSS signals also under most adverse indoor signal conditions. The main idea of the concept is the extension of the coherent signal integration time of the GNSS receiver to the length of several seconds, which increases the correlation gain significantly. To facilitate this goal, a very long and very precise signal replica is needed. Therefore the system must reproduce the user motion, the navigation message data bits and the satellite constellation precisely. Hence, the system uses a sensor suite of several state of the art indoor positioning sensors and innovative fusion algorithms. The integrating element of the system is a software receiver using Ultra-Tightly Coupling (UTC) implemented by vector tracking. The presented work was performed under the ESA funded contract DINGPOS, ESTEC Ctr. No. 20834.
Hypopigmentation and Maternal-Zygotic Embryonic Lethality Caused by a Hypomorphic <i>Mbtps1</i> Mutation in Mice (2012)

The site 1 protease, encoded by Mbtps1, mediates the initial cleavage of site 2 protease substrates, including sterol regulatory element binding proteins and CREB/ATF transcription factors. We demonstrate that a hypomorphic mutation of Mbtps1 called woodrat (wrt) caused hypocholesterolemia, as well as progressive hypopigmentation of the coat, that appears to be mechanistically unrelated. Hypopigmentation was rescued by transgenic expression of wild-type Mbtps1, and reciprocal grafting studies showed that normal pigmentation depended upon both cell-intrinsic or paracrine factors, as well as factors that act systemically, both of which are lacking in wrt homozygotes. Mbtps1 exhibited a maternal-zygotic effect characterized by fully penetrant embryonic lethality of maternal-zygotic wrt mutant offspring and partial embryonic lethality (~40%) of zygotic wrt mutant offspring. Mbtps1 is one of two maternal-zygotic effect genes identified in mammals to date. It functions nonredundantly in pigmentation and embryogenesis.
Modeling ESD protection (2005)

This work presents the modeling and simulation of ESD circuit design protection. The electrostatic discharge (ESD) is a charge rebalancing process between two adjacent ICs. The ESD can cause IC failure during the manufacturing, the testing, the handling and the assembly of integrated circuits (ICs). ESD protection design methodology needs to be as systematic and transferable as possible. The empirical, trial and error method for creating ESD protection schemes is based on fabricating several test protection structures, gradually applying increasing voltage pulses and then measuring the functionality of the protection structures. This method is time consuming and destructive in nature. The model could be used to optimize the ESD circuit's design and predict its protection performance. A combination of bias conditions and layout parameters could maximize the ESD robustness device. This optimization can be achieved by developing simulation tools for ESD circuits. ESD is a phenomenon that causes reliability problems and even permanent damages to the IC since the goal is to find the voltage and the current limits before the device fails permanently.
High resolution virtual reality (1992)

article High resolution virtual reality Share on Author: Michael Deering Sun Microsystems Computer Corporation, 2550 Garcia Avenue, MountainView, CA Sun Microsystems Computer Corporation, 2550 Garcia Avenue, MountainView, CAView Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 26Issue 2July 1992 pp 195–202https://doi.org/10.1145/142920.134039Online:01 July 1992Publication History 154citation2,872DownloadsMetricsTotal Citations154Total Downloads2,872Last 12 Months138Last 6 weeks14 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Learning and mathematical reasoning using adaptive signal processing techniques (1989)

The MLS (machine learning system) approach offers a more generic solution to the problem of fault diagnosis and adjustments in electronic devices and systems than the classical ESs. The MLS is capable of learning the relationships between the inputs and the outputs of a system by looking at a number of examples which include features and corresponding desired action. Therefore the performance of the MLS depends on how the features have been selected. The authors present a technique for finding the correlation between the selected features, the significance of each individual feature and the interaction between the outcomes. This enables one to modify the feature set and also the training sequence. The main limitations of this approach are (a) the combiners are a linear structure, therefore they can not be used to model nonlinear relationships and (b) the decisions of the DAP are based on the estimates of the correlation matrices. In order to resolve the first problem it is intended to look at nonlinear structures such as neural networks for the implementation of the MLS. The second problem may be solved by either using a large number of training examples or introducing some form of memory into the structure of the DAP so that the present decisions are not only based on the present correlation matrices but also on the previous decisions.<
 >
Light‐microscopic and electron‐microscopic evaluation of short‐term nerve regeneration using a biodegradable poly (DL‐lactide‐ε‐caprolacton) nerve guide (1996)

The aim of this study was to evaluate short-term peripheral nerve regeneration across a 10-mm gap, using a biodegradable poly(DL,-lactide-ϵ-caprolacton) nerve guide, with an internal diameter of 1.5 mm and a wall thickness of 0.30 mm. To do so, we evaluated regenerating nerves using light microscopy, transmission electron microscopy and morphometric analysis after implantation of 12-mm nerve guides in the sciatic nerve of the rat. Evaluation times ranged from 3–10 weeks. Three weeks after reconstruction, myelinated nerve fibers could be observed in the distal nerve stump. Ten weeks after reconstruction, the regenerating nerves already resembled normal nerves. In conclusion, we show that poly(DL,-lactide-ϵ-caprolacton) nerve guides can be successfully applied in the reconstruction of severed nerves in the rat model. Furthermore, we have observed the fastest nerve regeneration described thus far, after reconstruction using a biodegradable nerve guide. © 1996 John Wiley & Sons, Inc.
Evaluation of Application Technologies of Entomopathogenic Nematodes for Control of the Black Vine Weevil (2005)

Black vine weevil, Otiorhynchus sulcatus (F.), is a severe pest of small fruit and nursery crops around the world. These studies were conducted to determine the efficacy of three species of entomopathogenic nematodes (Heterorhabditis marelatus, Heterorhabditis bacteriophora, and Steinernema riobrave) applied in infected host cadavers or as aqueous applications for black vine weevil larval control. Experiments were conducted in the greenhouse and outdoors. Application of three infected host cadavers or 40 infective juvenile nematodes (IJs) /cm2 were made to pots of Impatiens walleriana 5-7 d after larval infestation. Efficacy was assessed at 14 d in the greenhouse and at 14 and 28 d after nematode application in outdoor trials. In the greenhouse, all treatments with the exception the S. riobrave (cadaver and aqueous applications) provided nearly 100% efficacy after 14 d. The S. riobrave applications, although significantly better than the control, only provided 40-70% control and were not included in the outdoor trials. Nematode efficacy was slowed in the outdoor trials particularly in the cadaver applications. In the initial outdoor trial (soil temperatures < 12 degrees C), there were no significant differences between any nematode treatment and the control after 14 d. The nematode efficacy in the initial outdoor trial after 28 d was improved from the 14-d evaluation but not to the level seen in the second trial. In the second outdoor trial, in which soil temperatures were higher (> 12 degrees C), the aqueous applications of H. marelatus and H. bacteriophora provided nearly complete control after 14 d. The cadaver applications also provided nearly complete control in the second outdoor trial after 28 d. Even though the potential total number of IJs estimated per pot was higher in the cadaver-applied treatments, cool soil temperatures apparently delayed or potentially reduced IJ emergence from cadavers resulting in delayed control.
Crowdsourcing based radio map anomalous event detection system for calibration-on-demand (2014)

Calibrations for Wi-Fi Indoor Positioning Systems (IPS) are expensive and time-consuming. Recalibrations are necessary periodically to compensate the drifts of radio map. Many crowdsourcing-based approaches have been proposed to calibrate the radio map strategically with user-contributed data. However, these approaches still suffer from several drawbacks. Calibration-on-demand is desirable to reduce the maintenance cost and to enhance the reliability of the Wi-Fi IPS. Wi-Fi IPS degrades only when the radio map changes significantly and lastingly. Such changes are caused by radio map anomalous events. Examples of these events include changes in indoor environment, existence of spurious data from the sensing system and unexpected failure in utility infrastructures. This paper presents a theoretical and experimental study of a crowdsourcing online Wi-Fi radio map anomalous event detection system. Detection of these events will enhance the operation intelligence of Wi-Fi IPS and enable high-level context-aware services. This system is consisted of an outlier detector for abnormal signal identification and an event discriminator for determination of event occurrence. Real world smartphone data and simulated data are used to test the performance of the system. Initial results show that the system is able to detect over 92% of simulated events and 87.5% of real world events with a low false alarm rate.
Microcavity effects in the photoluminescence of hydrogenated amorphous silicon nitride (1998)

Fabry-Perot microcavities are used for the alteration of photoluminescence in hydrogenated amorphous silicon nitride grown with and without ammonia. The photoluminescence is red-near-infrared for the samples grown without ammonia, and blue-green for the samples grown with ammonia. In the Fabry- Perot microcavities, the amplitude of the photoluminescence is enhanced, while its linewidth is reduced with respect to the bulk hydrogenated amorphous silicon nitride. The microcavity was realized by a metallic back mirror and a hydrogenated amorphous silicon nitride--air or a metallic front mirror. The transmittance, reflectance, and absorbance spectra were also measured and calculated. The calculated spectra agree well with the experimental spectra. The hydrogenated amorphous silicon nitride microcavity has potential for becoming a versatile silicon based optoelectronic device such as a color flat panel display, a resonant cavity enhanced light emitting diode, or a laser.