gebhart/patrepeval huggingface dataset:
A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by <i>Toxoplasma</i> (2005)

Apicomplexan parasites cause serious human and animal diseases, the treatment of which requires identification of new therapeutic targets. Host-cell invasion culminates in the essential cleavage of parasite adhesins, and although the cleavage site for several adhesins maps within their transmembrane domains, the protease responsible for this processing has not been discovered. We have identified, cloned, and characterized the five nonmitochondrial rhomboid intramembrane proteases encoded in the recently completed genome of Toxoplasma gondii. Four T. gondii rhomboids (TgROMs) were active proteases with similar substrate specificity. TgROM1, TgROM4, and TgROM5 were expressed in the tachyzoite stage responsible for the disease, whereas TgROM2 and TgROM3 were expressed in the oocyst stage involved in transmission. Although both TgROM5 and TgROM4 localized to the cell surface in tachyzoites, TgROM5 was primarily at the posterior of the parasite, whereas adhesins were sequestered in internal micronemes. Upon microneme secretion, as occurs during invasion, the MIC2 adhesin was secreted to the apical end and translocated to the posterior, the site of cleavage, where it colocalized only with TgROM5. Moreover, only TgROM5 was able to cleave MIC adhesins in a cell-based assay, indicating that it likely provides the key protease activity necessary for invasion. T. gondii rhomboids have clear homologues in other apicomplexans including malaria; thus, our findings provide a model for studying invasion by this deadly pathogen and offer a target for therapeutic intervention.
Low Initial Tau Phosphorylation in Human Brain Biopsy Samples (1997)

A rapid reversible tau phosphorylation at Ser 396/404 was observed in adult human cortical biopsy tissue and rat primary cortical cell cultures. Tau phosphorylation increased usually during the first 20-30 min in phosphate-buffered saline, followed by a decrease. The time course of tau phosphorylation and dephosphorylation in biopsy tissue could be lengthened by culturing in defined, oxygenated medium, instead of in phosphate-buffered saline. Phosphorylation of total protein in biopsy tissue occurred in two phases, with peaks at 30 and 90 min. The first peak of total protein phosphorylation coincided with the peak of tau phosphorylation, although both the first and second peaks of total protein phosphorylation coincided with the first and second peaks of neurofilament-H phosphorylation.
High-effective approach from amino acid esters to chiral amino alcohols over Cu/ZnO/Al2O3 catalyst and its catalytic reaction mechanism (2016)

Developing the high-efficient and green synthetic method for chiral amino alcohols is an intriguing target. We have developed the Mg(2+)-doped Cu/ZnO/Al2O3 catalyst for hydrogenation of L-phenylalanine methyl ester to chiral L-phenylalaninol without racemization. The effect of different L-phenylalanine esters on this title reaction was studied, verifying that Cu/ZnO/Al2O3 is an excellent catalyst for the hydrogenation of amino acid esters to chiral amino alcohols. DFT calculation was used to study the adsorption of substrate on the catalyst, and showed that the substrate adsorbs on the surface active sites mainly by amino group (-NH2) absorbed on Al2O3, and carbonyl (C=O) and alkoxy (RO-) group oxygen absorbed on the boundary of Cu and Al2O3. This catalytic hydrogenation undergoes the formation of a hemiacetal intermediate and the cleavage of the C-O bond (rate-determining step) by reacting with dissociated H to obtain amino aldehyde and methanol ad-species. The former is further hydrogenated to amino alcohols, and the latter desorbs from the catalyst surface.
An Accurate Tag Estimate Method for Improving the Performance of an RFID Anticollision Algorithm Based on Dynamic Frame Length ALOHA (2008)

In a radio-frequency identification (RFID) system, the dynamic frame length ALOHA protocol is widely adopted to solve the anticollision problem. Analysis for the anticollision problem can be divided into two primary parts. The concern of the first part is how to precisely estimate the number of tags. The other part involves determination of dynamic frame length to achieve maximum throughput or channel usage efficiency. In this paper, we present an accurate method for estimating tag quantity. This method is based on the maximum <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">posteriori</i> probability decision. We also derive the optimal frame length using radio channel efficiency. Simulation results indicate the tag estimate error of the proposed method is less than 4%. Use of our proposed tag estimate method together with optimal frame length can achieve close to the theoretical maximum throughput of the framed ALOHA algorithm.
Neutron Therapy (1983)

ABSTRACT In recent years considerable progress has been made in the application of neutron sources to the treatment of cancer. The development of this field is outlined, and a review is given of the current status of published clinical experience. A variety of sources can be used for neutron therapy and their relative merits are discussed. Proposals for an Australian facility for neutron therapy are put forward.
Learning to Set Waypoints for Audio-Visual Navigation (2020)

In audio-visual navigation, an agent intelligently travels through a complex, unmapped 3D environment using both sights and sounds to find a sound source (e.g., a phone ringing in another room). Existing models learn to act at a fixed granularity of agent motion and rely on simple recurrent aggregations of the audio observations. We introduce a reinforcement learning approach to audio-visual navigation with two key novel elements: 1) waypoints that are dynamically set and learned end-to-end within the navigation policy, and 2) an acoustic memory that provides a structured, spatially grounded record of what the agent has heard as it moves. Both new ideas capitalize on the synergy of audio and visual data for revealing the geometry of an unmapped space. We demonstrate our approach on two challenging datasets of real-world 3D scenes, Replica and Matterport3D. Our model improves the state of the art by a substantial margin, and our experiments reveal that learning the links between sights, sounds, and space is essential for audio-visual navigation. Project: http://vision.cs.utexas.edu/projects/audio_visual_waypoints.
1-Methoxyhexane-3-thiol, a Powerful Odorant of Clary Sage (Salvia sclarea L.) (2002)

The peculiar and highly diffusive odor signal of flowering clary-sage plants (Salvia sclarea L.) was identified to derive from trace amounts of 1-methoxyhexane-3-thiol (1) by mass-spectrometry analysis and confirmed by comparison with synthetic racemic thiol (±)-1. The enantiomers (S)- and (R)-1 were prepared by enantioselective synthesis, and the absolute configuration of (S)-1 was fully corroborated by X-ray-diffraction analysis of the crystalline thioester (1′S,1S)-2. Compound (S)-1 is one of the most powerful odorants known, with a detection threshold of 0.04⋅10−3 ng/l air, and is, with its herbaceous-green, alliaceous, and perspiration profile, key to the fragrance of clary-sage flowers and of the freshly distilled essential oil. As a consequence of its unique odor, 1 was also suspected to be part of the volatiles of a Ruta species where it was subsequently identified together with its homologue, 1-methoxyheptane-3-thiol (3), 1-methoxy-4-methylpentane-3-thiol (4), and the known 4-methoxy-2-methylbutane-2-thiol (5). The syntheses of (±)-3 and (±)-4 as well as of the enantiomer (R)-4 are described. In both natural fractions, the ratio (S)-1/(R)-1 was slightly in favor of the (S)-enantiomer. Natural 4 has (R)-configuration.
Hidden-Markov-Model Based Speech Enhancement (2017)

The goal of this contribution is to use a parametric speech synthesis system for reducing background noise and other interferences from recorded speech signals. In a first step, Hidden Markov Models of the synthesis system are trained. Two adequate training corpora consisting of text and corresponding speech files have been set up and cleared of various faults, including inaudible utterances or incorrect assignments between audio and text data. Those are tested and compared against each other regarding e.g. flaws in the synthesized speech, it's naturalness and intelligibility. Thus different voices have been synthesized, whose quality depends less on the number of training samples used, but much more on the cleanliness and signal-to-noise ratio of those. Generalized voice models have been used for synthesis and the results greatly differ between the two speech corpora. Tests regarding the adaptation to different speakers show that a resemblance to the original speaker is audible throughout all recordings, yet the synthesized voices sound robotic and unnatural in smaller parts. The spoken text, however, is usually intelligible, which shows that the models are working well. In a novel approach, speech is synthesized using side information of the original audio signal, particularly the pitch frequency. Results show an increase of speech quality and intelligibility in comparison to speech synthesized solely from text, up to the point of being nearly indistinguishable from the original.
Predictors of Mortality in Verapamil Overdose: Usefulness of Serum Verapamil Concentrations (2010)

Verapamil poisoning may result in life-threatening cardiovascular morbidities and fatalities. To date, prognosticators of mortality have been poorly investigated and the use of serum verapamil concentration for prognosis remains unclear. We aimed to evaluate the ability of usual clinical and laboratory parameters including serum verapamil concentrations measured on admission to predict outcome (survival versus death) in verapamil poisoning. We reviewed the medical records of all intentional and symptomatic verapamil poisonings admitted over 8 years to two medical intensive care units. Clinical and laboratory parameters were measured in 65 patients, and final outcomes of survival or death recorded. A multivariable analysis was conducted to evaluate the prognostic values of recorded parameters. Life-threatening complications of verapamil poisonings included shock (62%), atrioventricular blocks (24%), sinoatrial blocks (20%), acute respiratory distress syndrome (19%) and cardiac arrest (11%) resulting in death (8%). Verapamil concentration measured on intensive care unit admission was the only independent factor associated with mortality (p = 0.01). The optimal verapamil cut-off point was 5.0 μM (100% sensitivity, 91% specificity), which conferred a 2.76-times increase in odds of fatality. In conclusion, cardiovascular monitoring and assessment of organ failure are vital in symptomatic verapamil poisonings. The serum verapamil concentration has excellent prognostic ability for predicting fatality in verapamil overdose.
Rapid Evaluation of Plant Extracts and Essential Oils for Antifungal Activity Against <i>Botrytis cinerea</i> (1997)

A rapid assay to determine antifungal activity in plant extracts and essential oils is described. Wells in microtiter plates were loaded with Botrytis cinerea spores and plant extracts or essential oils. Subsequent changes in optical density following spore germination in the wells was measured after 24 h using an automatic microtiter plate reader driven by a software program developed for this purpose. Extracts from 345 plants and 49 essential oils were evaluated for their antifungal activity against B. cinerea. Among 345 plant extracts analyzed, 13 showed high levels of antifungal activity, with species of Allium and Capsicum predominating. Among the 49 essential oils tested, palmarosa (Cymbopogon martini), red thyme (Thymus zygis), cinnamon leaf (Cinnamomum zeylanicum), and clove buds (Eugenia caryophyllata) demonstrated the most antifungal activity against B. cinerea. The most frequently occurring constituents in essential oils showing high antifungal activity were: D-limonene, cineole; β-myrcene; α-pinene, β-pinene; and camphor.
Extracting 3D facial animation parameters from multiview video clips (2002)

We propose an accurate and inexpensive procedure that estimates 3D facial motion parameters from mirror-reflected multiview video clips. We place two planar mirrors near a subject's cheeks and use a single camera to simultaneously capture a marker's front and side view images. We also propose a novel closed-form linear algorithm to reconstruct 3D positions from real versus mirrored point correspondences in an uncalibrated environment. Our computer simulations reveal that exploiting mirrors' various reflective properties yields a more robust, accurate, and simpler 3D position estimation approach than general-purpose stereo vision methods that use a linear approach or maximum-likelihood optimization. Our experiments show a root mean square (RMS) error of less than 2 mm in 3D space with only 20-point correspondences. For semiautomatic 3D motion tracking, we use an adaptive Kalman predictor and filter to improve stability and infer the occluded markers' position. Our approach tracks more than 50 markers on a subject's face and lips from 30-frame-per-second video clips. We've applied the facial motion parameters estimated from the proposed method to our facial animation system.
Inductive activity of recombinant human growth and differentiation factor-5 (2000)

Growth and differentiation factor-5 (GDF-5) is a divergent member of the transforming growth factor-beta/bone morphogenetic protein (BMP) superfamily that is required for proper skeletal patterning and development in the vertebrate limb. Based on the homology of GDF-5 with other bone-inducing BMP family members, the inductive activity of a recombinant form of human GDF-5 (rhGDF-5) was evaluated in a series of in vitro assays and in vivo bone-formation models. The in vitro response to rhGDF-5 resulted in the formation of chondrogenic nodules in fetal rat calvarial cells cultured in the context of collagen or collagen/hyaluronate extracellular matrices. Matrices loaded with rhGDF-5 induced ectopic cartilaginous and osseous tissue when implanted in subcutaneous or intramuscular sites. In non-human primate long-bone-defect and spinal-fusion models, rhGDF-5 combined with a mineralized collagen matrix induced bone formation in a manner equivalent to autogenous bone. These results highlight the unique potential of rhGDF-5 in a wide variety of orthopaedic applications.
Characterization of the magnetohydrodynamic effect as a signal from the surface electrocardiogram during cardiac magnetic resonance imaging (2006)

The magnetohydrodynamic (MHD) effect was investigated in the electrocardiogram (ECG) during MRI. ECGs were obtained for 10 healthy subjects inside and outside a 3.0T MRI scanner. The MHD effect was characterized as the difference in voltage between the mean beat from the ECG taken inside the magnet and the one taken outside the magnet. A significant deflection was observed and was found to primarily correspond to the flow of blood in the aortic arch. When subjects were in supine position, the mean amplitude of this deflection was 0.19 ± 0.04 mV, and its mean duration was 0.34 ± 0.02 secs; when in prone position, the mean amplitude of this deflection was 0.21 ± 0.08 mV, and its mean duration was 0.33 ± 0.02 secs. An axial orientation 2D phase contrast MRI scan was performed to allow blood flow and velocity measurements. By characterizing the MHD signal, we can obtain flow information and can develop improved subtraction techniques for ECG during MRI. 1.
Growth and Characterization of Al<sub>2</sub>O<sub>3</sub> Atomic Layer Deposition Films on sp<sup>2</sup>-Graphitic Carbon Substrates Using NO<sub>2</sub>/Trimethylaluminum Pretreatment (2015)

The growth of Al2O3 films by atomic layer deposition (ALD) on model sp(2)-graphitic carbon substrates was evaluated following a nitrogen dioxide (NO2) and trimethylaluminum (TMA) pretreatment to deposit an Al2O3 adhesion layer. Al2O3 ALD using TMA and water (H2O) as the reactants was used to grow Al2O3 films on exfoliated highly ordered pyrolitic graphite (HOPG) at 150 °C with and without the pretreatment procedure consisting of five NO2/TMA cycles. The Al2O3 films on HOPG substrates were evaluated using spectroscopic ellipsometry and electrochemical analysis to determine film thickness and quality. These experiments revealed that five NO2/TMA cycles at 150 °C deposited an Al2O3 adhesion layer with a thickness of 5.7 ± 3.6 Å on the HOPG substrate. A larger number of NO2/TMA cycles at 150 °C deposited thicker Al2O3 films until reaching a limiting thickness of ∼80 Å. Electrochemical impedance spectroscopy (EIS) measurements revealed that five cycles of NO2/TMA pretreatment enabled the growth of high quality insulating Al2O3 films with high charge-transfer resistance after only 20 TMA/H2O Al2O3 ALD cycles. In contrast, with no NO2/TMA pretreatment, EIS measurements indicated that 100 TMA/H2O Al2O3 ALD cycles were necessary to produce an insulating Al2O3 film with high charge-transfer resistance. Al2O3 films grown after the NO2/TMA pretreatment at 150 °C were also demonstrated to have better resistance to dissolution in an aqueous environment.
Vorinostat Inhibits Brain Metastatic Colonization in a Model of Triple-Negative Breast Cancer and Induces DNA Double-Strand Breaks (2009)

We report the first preclinical data for the prevention of brain metastasis of triple-negative breast cancer. Vorinostat is brain permeable and can prevent the formation of brain metastases by 62%. Its mechanism of action involves the induction of DNA double-strand breaks, suggesting rational combinations with DNA active drugs or radiation.
<i>Borrelia burgdorferi</i> Lacking BBK32, a Fibronectin-Binding Protein, Retains Full Pathogenicity (2006)

BBK32, a fibronectin-binding protein of Borrelia burgdorferi, is one of many surface lipoproteins that are differentially expressed by the Lyme disease spirochete at various stages of its life cycle. The level of BBK32 expression in B. burgdorferi is highest during infection of the mammalian host and lowest in flat ticks. This temporal expression profile, along with its fibronectin-binding activity, strongly suggests that BBK32 may play an important role in Lyme pathogenesis in the host. To test this hypothesis, we constructed an isogenic BBK32 deletion mutant from wild-type B. burgdorferi B31 by replacing the BBK32 gene with a kanamycin resistance cassette through homologous recombination. We examined both the wild-type strain and the BBK32 deletion mutant extensively in the experimental mouse-tick model of the Borrelia life cycle. Our data indicated that B. burgdorferi lacking BBK32 retained full pathogenicity in mice, regardless of whether mice were infected artificially by syringe inoculation or naturally by tick bite. The loss of BBK32 expression in the mutant had no adverse effect on spirochete acquisition (mouse-to-tick) and transmission (tick-to-mouse) processes. These results suggest that additional B. burgdorferi proteins can complement the function of BBK32, fibronectin binding or otherwise, during the natural spirochete life cycle.
Fungal Immunomodulatory Protein from <i>Flammulina velutipes</i> Induces Interferon-γ Production through p38 Mitogen-Activated Protein Kinase Signaling Pathway (2004)

FIP-fve is a fungal immunomodulatory protein purified from Flammulina velutipes, an edible golden needle mushroom thought to possess potent immunomodulatory properties. When examined for its effects on lymphocytes, FIP-fve exhibited potent mitogenic effects on human peripheral blood lymphocytes, inducing G1/G0 to S phase proliferation. T cells activated by FIP-fve show significant production and secretion of interferon-gamma (IFN-gamma) associated with intercellular adhesion molecule 1 expression but low detectable levels of interleukin-4 in vitro or in vivo. However, SB203580, the p38 mitogen-activated protein kinase (p38 MAPK) inhibitor, can fully abolish the production of IFN-gamma induced by FIP-fve. At the same time, SB203580 only partially prevents the lymphocytes from progressing from G1 to S phase of the cell cycle. These findings demonstrate that FIP-fve is a potent T-cell activator, mediating its effects via cytokine regulation of p38 MAPK. The immunoprophylatic effects of FIP-fve in Th2-mediated allergic anaphylaxis are believed to be associated with the ability of FIP-fve to enhance activation of IFN-gamma-releasing Th1 cells.
A "Precharged" Positive Plate for the Lead–Acid Automotive Battery: I . Positive Plate Allowing Direct Incorporation of (1984)

A process to manufacture the positive plate of the lead‐acid battery that eliminates conventional curing and formation steps via the direct incorporation of active material into the grid is described. "Precharged" plates made from a mixture of tetrabasic lead sulfate, , and water were found to be strong and capable of delivering first cycle (i.e., with no formation) cranking rate capacity which was 35% of conventionally produced plates tested in the same format. Full capacity is obtainable within three to five charge‐discharge cycles. At this point, the precharged plates were found to be structurally indistinguishable from conventionally processed plates. To ensure in these initial studies that the was electrochemically active, the material was obtained from electrochemically formed conventional positive plates. The successful use of chemically prepared is demonstrated in the following paper. This new process is simple and will allow the manufacture of ready-to-use plates on modern automated expanded metal platemaking equipment.
iSAID: A Large-scale Dataset for Instance Segmentation in Aerial Images (2019)

Existing Earth Vision datasets are either suitable for semantic segmentation or object detection. In this work, we introduce the first benchmark dataset for instance segmentation in aerial imagery that combines instance-level object detection and pixel-level segmentation tasks. In comparison to instance segmentation in natural scenes, aerial images present unique challenges e.g., a huge number of instances per image, large object-scale variations and abundant tiny objects. Our large-scale and densely annotated Instance Segmentation in Aerial Images Dataset (iSAID) comes with 655,451 object instances for 15 categories across 2,806 high-resolution images. Such precise per-pixel annotations for each instance ensure accurate localization that is essential for detailed scene analysis. Compared to existing small-scale aerial image based instance segmentation datasets, iSAID contains 15$\times$ the number of object categories and 5$\times$ the number of instances. We benchmark our dataset using two popular instance segmentation approaches for natural images, namely Mask R-CNN and PANet. In our experiments we show that direct application of off-the-shelf Mask R-CNN and PANet on aerial images provide suboptimal instance segmentation results, thus requiring specialized solutions from the research community. The dataset is publicly available at: https://captain-whu.github.io/iSAID/index.html