gebhart/patrepeval huggingface dataset:
Slow formation of aggregation‐resistant β‐sheet folding intermediates (2009)

Protein folding has been studied extensively for decades, yet our ability to predict how proteins reach their native state from a mechanistic perspective is still rudimentary at best, limiting our understanding of folding-related processes in vivo and our ability to manipulate proteins in vitro. Here, we investigate the in vitro refolding mechanism of a large beta-helix protein, pertactin, which has an extended, elongated shape. At 55 kDa, this single domain, all-beta-sheet protein allows detailed analysis of the formation of beta-sheet structure in larger proteins. Using a combination of fluorescence and far-UV circular dichroism spectroscopy, we show that the pertactin beta-helix refolds remarkably slowly, with multiexponential kinetics. Surprisingly, despite the slow refolding rates, large size, and beta-sheet-rich topology, pertactin refolding is reversible and not complicated by off-pathway aggregation. The slow pertactin refolding rate is not limited by proline isomerization, and 30% of secondary structure formation occurs within the rate-limiting step. Furthermore, site-specific labeling experiments indicate that the beta-helix refolds in a multistep but concerted process involving the entire protein, rather than via initial formation of the stable core substructure observed in equilibrium titrations. Hence pertactin provides a valuable system for studying the refolding properties of larger, beta-sheet-rich proteins, and raises intriguing questions regarding the prevention of aggregation during the prolonged population of partially folded, beta-sheet-rich refolding intermediates. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
A Review of Visual Perception Research in Optical See-Through Augmented Reality (2020)

In the field of augmented reality (AR), many applications involve user interfaces (UIs) that overlay visual information over the user's view of their physical environment, e.g., as text, images, or three-dimensional scene elements. In this scope, optical seethrough head-mounted displays (OST-HMDs) are particularly interesting as they typically use an additive light model, which denotes that the perception of the displayed virtual imagery is a composite of the lighting conditions of one's environment, the coloration of the objects that make up the virtual imagery, and the coloration of physical objects that lay behind them. While a large body of literature focused on investigating the visual perception of UI elements in immersive and flat panel displays, comparatively less effort has been spent on OST-HMDs. Due to the unique visual effects with OST-HMDs, we believe that it is important to review the field to understand the perceptual challenges, research trends, and future directions. In this paper, we present a systematic survey of literature based on the IEEE and ACM digital libraries, which explores users' perception of displaying text-based information on an OST-HMD, and aim to provide relevant design suggestions based on the meta-analysis results. We carefully review 14 key papers relevant to the visual perception research in OST-HMDs with UI elements, and present the current state of the research field, associated trends, noticeable research gaps in the literature, and recommendations for potential future research in this domain.
Low-Temperature Atomic Ordering of Oriented L1<SUB>0</SUB>-FePtCu Nanoparticles with High Areal-Density Characterized by Transmission Electron Microscopy and Electron Diffraction (2007)

Oriented and densely dispersed L10-FePtCu nanoparticles have been directly synthesized by co-evaporation of Fe, Pt and Cu using rf-magnetron sputtering onto NaCl substrate kept at 563–613 K without any post-deposition annealing. Formation of the L10-type structure in the specimens fabricated as low a substrate temperature as 563 K (Fe40Pt50Cu10) was confirmed by electron microscopy and electron diffraction, while the coercivity measured at room temperature was very low and the intensity of the superlattice reflections was quite weak. The atomic ordering was promoted in the specimen fabricated at 613 K with a composition of Fe37Pt52Cu11, resulted in a higher coercivity exceeding 1 kOe at room temperature as well as appearance of clear superlattice reflections. In addition to the evolution of atomic ordering, 〈100〉 oriented growth was enhanced as the substrate temperature increased. Particle size dependence of long-range order (LRO) is considered to be responsible for the decrease of coercivity with particle size reduction as well as thermal fluctuation of magnetization. High coercivity was obtained for specimens with Cu concentration near 10 at% under the present sputtering condition. The LRO in the FePtCu ternary phase is considered to sensitively depend on the alloy concentration.
Gasdynamic laser based on air gasification of carbon (1985)

Amplification and stimulated emission of radiation of the 10.6 μ wavelength was observed as a result of supersonic mixing of carbon dioxide with the products of air gasification of carbon.
KEY PRINCIPLES OF BIOSECURITY (2003)

The goal of our research program is to put science into biosecurity protocols. We realize that bigger issues such as siting, pig proximity, and aerosol transmission offer risks that we cannot control in many cases. Thus, our research has focused on the details within production units that we can control - specifically the role of people as mechanical vectors in transmitting porcine pathogens. These details are important because we most likely track pathogens among groups of pigs before we observe the clinical signs of an outbreak.
Implication of a retrovirus‐like glycoprotein peptide in the immunopathogenesis of Ebola and Marburg viruses (2006)

Ebola and Marburg viruses can cause hemorrhagic fever (HF) outbreaks with high mortality in primates. Whereas Marburg (MARV), Ebola Zaire (ZEBOV), and Ebola Sudan (SEBOV) viruses are pathogenic in humans, apes, and monkeys, Ebola Reston (REBOV) is pathogenic only in monkeys. Early immunosuppression may contribute to pathogenesis by facilitating viral replication. Lymphocyte depletion, intravascular apoptosis, and cytokine dysregulation are prominent in fatal cases. Here we functionally characterize a 17 amino acid domain in filoviral glycoproteins that resembles an immunosuppressive motif in retroviral envelope proteins. Activated human or rhesus peripheral blood mononuclear cells (PBMC) were exposed to inactivated ZEBOV or a panel of 17mer peptides representing all sequenced strains of filoviruses, then analyzed for CD4+ and CD8+ T cell activation, apoptosis, and cytokine expression. Exposure of human and rhesus PBMC to ZEBOV, SEBOV, or MARV peptides or inactivated ZEBOV resulted in decreased expression of activation markers on CD4 and CD8 cells; CD4 and CD8 cell apoptosis as early as 12 h postexposure; inhibition of CD4 and CD8 cell cycle progression; decreased interleukin (IL)-2, IFN-gamma, and IL12-p40 expression; and increased IL-10 expression. In contrast, only rhesus T cells were sensitive to REBOV peptides. These findings are consistent with the observation that REBOV is not pathogenic in humans and have implications for understanding the pathogenesis of filoviral HF.
Role of buoyancy in fuel-thermal-stability studies (1995)

A unique methodology is used to investigate the effects of gravity on fuel flowing through the small-bore heated tubes that are often used in the study of fuel-thermal- stability characteristics. The copper block that houses the fuel tube (or test section) is located on a swivel, and experiments are conducted for different tube orientations, namely; horizontal, vertical with flow from bottom to top and vice versa. Results obtained for different fuel-flow rates and block temperatures are discussed. An axisymmetric, time-dependent numerical model is used to simulate the flow patterns in the test section. This model solves momentum, energy, species, and k-e turbulence equations. The buoyance term is included in the axial-momentum equation. Natural flow resulting from buoyancy was found to have a significant effect on heat transfer and oxygen consumption for fuel-flow rates up to 100 cc/min (Reynolds numbers up to 2.3 x 10 3). Flow instabilities were observed when the fuel was flowing downward in a vertically mounted test section. The effect of block temperature and flow rate on these instabilities was also studied.
Simulation of the Mean Flow in the Cylinder of a Motored 4-Valved Spark Ignition Engine (1995)

<div class="htmlview paragraph">The Computational Fluid Dynamics (CFD) code KIVA II has been applied to simulate the in-cylinder mean air motion (tumble) and turbulence levels in a motored 4-stroke single cylinder engine with pentroof combustion chamber geometry, having two inlet and two exhaust valves.</div> <div class="htmlview paragraph">In-cylinder flow during intake and compression strokes were simulated and a comparison between computational and experimental results were made. The mean turbulent kinetic energy and tumble ratio variation during the compression stroke obtained with CFD, have been compared with computational and experimental data from published literature. The simulation shows general similarity of flow structure and magnitude with published data on engines with similar geometry and initial flow conditions in the cylinder.</div>
Induced resistance: an enhancement of basal resistance? (2002)

Upon primary pathogen attack, plants activate resistance mechanisms at the site of infection. Besides this so-called basal resistance, plants have also the ability to enhance their defensive capacity against future pathogen attack. There are at least two types of biologically induced resistance. Classic systemic aquired resistance (SAR) results from infection by a necrotizing pathogen and is dependant on endogenous accumulation of salicylic acid (SA). Root colonization by non-pathogenic rhizobacteria can trigger an induced systemic resistance (ISR) response as well, which functions independantly of SA and requires intact responsiveness to the plant hormones jasmonic acid (JA) and ethylene (ET). A screen for genotypes impaired in either ISR or SAR revealed that ecotypes RLD1 and Ws-0, as well as the enhanced disease suspectibility mutants eds4-1, eds8-1 and eds10-1, are impaired in WCS417r-mediated ISR, whereas mutants eds5-1 and eds12-1 are impaired in pathogen-induced SAR. Analysis of JA-, ET- and SA-responsiveness revealed that the ISR-impaired genotypes are affected in signaling compounds contributing to JA/ET-dependent basal against P. syringae, while the SAR-impaired genotypes are affected in compounds contributing to SA-dependent basal resistance against P. syringae. To further examine the relationship between basal resistance and induced resistance, the effectiveness of SAR and ISR was assessed against different Arabidopsis pathogens that are resisted through JA/ET-dependent basal resistance, SA-dependent basal resistance, or a combination of JA/ET- and SA-dependent basal resistance. This analysis revealed that ISR is effective predominantly against pathogens that are resisted through JA/ET-dependent basal resistance, whereas SAR is effective against pathogens that are resisted through SA-dependent basal resistance. Collectively, our results suggest that ISR constitutes an enhancement of JA/ET-dependent basal resistance, whereas SAR is achieved through an enhanced expression of SA-dependent basal resistance.
<i> <scp>ADGRL</scp> 3 ( <scp>LPHN</scp> 3) </i> variants are associated with a refined phenotype of <scp>ADHD</scp> in the <scp>MTA</scp> study (2016)

The detection of susceptibility conferred by ADGRL3 variants in the extreme phenotype of continued diagnosis of ADHD-C from childhood to adolescence provides additional support that the association of ADGRL3 and ADHD is not spurious. Exploring genetic effects in longitudinal cohorts, in which refined, age-dependent phenotypes are documented, is crucial to understand the natural history of ADHD.
The Effect of X-Ray Irradiation upon the Sequence of Immune Globulins Following Initial Immunization in the Rabbit (1964)

Summary The effect of x-ray irradiation upon the sequential formation of immune globulins was studied. With increasing doses of total body irradiation, a delay in the appearance of γ2-globulin antibody was observed, whereas only a slight delay in the timing of the initial detection and minimal diminution in the over-all titer of γ1M-macroglobulin antibody was noted. After lethal irradiation during which various portions of the animal's lymphoid tissue was shielded, a prolonged period of exclusive γ1M-macroglobulin synthesis was demonstrated. The restoration of immunopoietic tissue during the shielding procedures could be accomplished with the cells of the spleen, appendix, hind limb and peripheral blood. Simultaneous immunization of shielded and normal tissue after lethal irradiation demonstrated a normal sequential formation of antibodies to that antigen used to inject the shielded tissue but specific inhibition of γ2-globulin antibody to that antigen used to inject irradiated tissue. Various hypotheses which attempt to explain the relative resistance of the γ1M-macroglobulin phase of the immune response as compared to the γ2-globulin phase to total body irradiation were discussed.
Differential gas–liquid chromatographic behaviour in diastereoisomeric systems. Part III. Symmetrically substituted dichiral ethers, alkoxysiloxanes, and disiloxanes (1971)

G.l.c. resolution of diastereomers containing an asymmetric silicon atom as alkoxysiloxane was studied and compared with that of similar compounds of the ether and of the disiloxane series. The resolution factors of some diastereomers containing an asymmetric silicon atom are ca. 1·04 and complete separation is achieved on an efficient capillary column coated with Apiezon L.
Acute effects of carbon monoxide on cardiac electrical stability. (1990)

The objective of this project was to determine the effects of acute carbon monoxide exposure on cardiac electrical stability. To obtain a comprehensive assessment, diverse biological models were employed. These involved cardiac electrical testing in the normal and ischemic heart in anesthetized and conscious dogs. The experimental plan was designed both to examine the direct effects of carbon monoxide exposure on the myocardium and to evaluate possible indirect influences through alterations in platelet aggregability or changes in central nervous system activity in the conscious animal. Our results indicate that exposure to relatively high levels of carbon monoxide, leading to carboxyhemoglobin concentrations of up to 20 percent, is without significant effect on ventricular electrical stability. This appears to be the case in the acutely ischemic heart as well as in the normal heart. It is important to note that the total exposure period was in the range of 90 to 124 minutes. The possibility that longer periods of exposure or exacerbation from nicotine in cigarette smoke could have a deleterious effect cannot be excluded. We also examined whether or not alterations in platelet aggregability due to carbon monoxide exposure could be a predisposing factor for cardiac arrhythmias. A model involving partial coronary artery stenosis was used to simulate the conditions under which platelet plugs could lead to myocardial ischemia and life-threatening arrhythmias. We found no changes either in the cycle frequency of coronary blood flow oscillations or in platelet aggregability during carbon monoxide exposure. Thus, carbon monoxide exposure does not appear to alter platelet aggregability or its effect on coronary blood flow during stenosis. In the final series of experiments, we examined the effects of carbon monoxide exposure in the conscious state. The rationale was to take into consideration possible adverse consequences mediated by the central nervous system. We found no adverse effects on cardiac excitable properties in response to either a 2-hour or 24-hour-exposure paradigm. This appears to argue against major deleterious influences of carbon monoxide exposure as a result of direct myocardial actions or indirect actions mediated through effects on central nervous system activity.
Hierarchical structural matching algorithms for registration of aerospace images (2004)

The aim of investigation was developing the image registration algorithms dealing with the aerial and cosmic pictures taken in different seasons from differing view points, or formed by differing kinds of sensors (visible, IR, SAR). The task could not be solved using the traditional correlation based approaches, thus we chose the structural juxtaposition of the stable specific details of pictures as the general image matching technique. Structural matching was usually applied in the expert systems where the rather reliable results were based on the target specific algorithms, but our algorithms deal with the aerospace photographs of arbitrary contents for which the application specific approaches could not be used. The chosen form of structural descriptions should provide distinguishing between the similar simple elements in the huge multitudes of image contours, thus the descriptions were made hierarchical: we grouped the contour elements belonging to the separate compact image regions. The structural matching was carried out in two levels: matching the simple elements of every group in the first image with the ones of every group in the second image; matching the groups as the wholes. The top-down links were used to enhance the lower level matching using the higher level matching results.
A semi-continuous stochastic trajectory model for phoneme-based continuous speech recognition (2002)

We propose a model of phoneme-based speech unit, called semi-continuous stochastic trajectory model (SC-STM), which generalizes our stochastic trajectory models (STM). As STMs, the SC-STMs focus on the modeling of speech segments (called trajectories) in their parameter space, and can therefore handle segmental information, which is critical for large vocabulary continuous speech recognition. Compared to the STMs, the SC-STMs improve the resolution of the trajectory modeling, while keeping a moderate number of free parameters by sharing state probability density functions. The SC-STM can therefore maintain a good trade-off between detailed acoustic modeling and limited training data. We tested the idea on a 2010 words, speaker-dependent, continuous speech database. Preliminary results show that SC-STM gives a word accuracy close to that of STM, without using heuristic techniques that enhanced STM.
Vision et visualisation (1992)

Le sys~me optique de l'oeil fonne, au niveau de la r6tine, une image du monde exltrieur qui CSt analysa: parle cerveau. Cette image rtinienne, constitu&: d'une distribution bidimensionnelle el mul variable de lumire, est transform6e en un signal neuronal par la mosaque des photolicepteurs; ce signal subit d'abord un prtraitement au niveau n!tinien puis est transmis au cerveau o des op.5rations plus complexes de traitement sont effoctu&:s pour extraire les attribul$ sensoriels de la scne visuelle.
ZYGADENUS ALKALOIDS. II. THE OCCURRENCE OF HYPOTENSIVE GERMINE ESTERS IN ZYGADENUS VENENOSUS (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTZYGADENUS ALKALOIDS. II. THE OCCURRENCE OF HYPOTENSIVE GERMINE ESTERS IN ZYGADENUS VENENOSUSS. Morris Kupchan and C. V. DeliwalaCite this: J. Am. Chem. Soc. 1952, 74, 12, 3202Publication Date (Print):June 1, 1952Publication History Published online1 May 2002Published inissue 1 June 1952https://pubs.acs.org/doi/10.1021/ja01132a539https://doi.org/10.1021/ja01132a539research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Development of a Novel Molecular Assay for the Ultra-Rapid Diagnosis of Acute Promyelocytic Leukemia by RT-Q-LAMP Technology (2016)

Acute promyelocytic leukemia (APL) accounts for 10% of cases of acute myeloid leukemia and is characterized by a particularly aggressive disease progression. Its peculiarity is the presence at diagnosis, 80% of cases, of a severe hemorrhagic syndrome. This dysfunction is often manifested in the form of hemorrhage at brain level that, before the advent of the revolutionary therapy with ATRA (All-Trans Retinoic Acid) caused the early death of almost 20% of patients. At the genetic level, the disease is caused in 99% of cases by a balanced translocation between chromosomes 15 and 17, leading to the formation of the chimeric protein PML-RAR. In RARA gene, the breakpoint constantly occurs in intron 2, while is variable in PML gene, resulting in three different isoforms (bcr1, bcr2 and bcr3). Due to the fast and dramatic progression of the disease and to exploit the availability of life-saving drug it is necessary to have a very quick method of diagnosis, therefore the object of this work is the development of a molecular assay for the ultra-rapid diagnosis of APL, based on the molecular technology LAMP (loop mediated isothermal amplification), a non-PCR method for the amplification of nucleic acids, very rapid and highly specific. LAMP is a quite recent technology, developed in Japan, originally based on the detection of the amplification signal with turbidimetry. The detection method has been greatly improved at DiaSorin, exploiting the use of fluorescent probes. This innovation allowed the detection of different targets in real-time and in multiplex format, thanks to the use of probes emitting at different wavelenghts. A further point of improvement has been the introduction of an engineered polymerase can perform the reverse transcription of RNA in a single step and in a single tube. Two assays have been developed, based on RT-Q-LAMP technology, ultra-rapid and simple to perform, which, starting directly from RNA, are able to identify and discriminate in 15 minutes, the three transcripts bcr1, bcr2 and bcr3, together with an internal control for the validation of negative results. Sensitivity and specificity of the assays have been evaluated on plasmids and validated on positive (n = 88) and negative (n = 94) clinical samples. The results obtained with RT-Q-LAMP assays have been compared with the reference method (PCR or sequencing), giving 100% agreement on the final result. The assays have proven to be highly specific on RNAs negative for the PML-RARA translocations (n = 282) and on water samples (NTC, n = 627). Moreover, both assays demonstrated to be very robust, even when used on suboptimal RNA, with low concentration or poor purity and quality. Compared to current methods, such as PCR, expensive in terms of time, reagents, and which require specialized staff, these new RT-Q-LAMP assays, thanks to the characteristics mentioned above, prove to be extremely competitive and suitable for actual clinical needs.