gebhart/patrepeval huggingface dataset:
Human Factor D of the Alternative Complement Pathway: Purification and Characterization (1977)

Abstract D̄ was purified to homogeneity from outdated human plasma by successive chromatography on Bio Rex 70, Sephadex G-200, Bio Rex 70, and Sephadex G-75. Column fractions were monitored for D̄ activity by a hemolytic diffusion plate assay. The overall yield was approximately 4% by activity. A m.w. of 22,900 daltons was established by sedimentation equilibrium. Amino acid analyses have been obtained and Isoleucine has been determined as the NH2-terminus. Incubation of D̄ with purified B and CoVF in the presence of Mg++ resulted in cleavage of B, as judged by SDS-polyacrylamide gel electrophoresis and immunoelectrophoresis. D̄ hydrolyzed certain synthetic amino acid esters of arginine, lysine, and tyrosine. Benzoyl-L-arginine methyl ester (BAME) was the most sensitive substrate for D̄ among those tested. The substrate profile of D̄ was distinct when compared to that of C1̄s, C1̄r, plasmin, urokinase, and trypsin. Both the enzymatic and hemolytic activity of D̄ were irreversibly inhibited by treatment with 10 mM DFP as well as by reduction and alkylation.
Comparison of Ultraviolet Absorbance, Chemiluminescence, and DOAS Instruments for Ambient Ozone Monitoring (2006)

This paper evaluates the accuracy of ozone measurements made by monitors that determine ozone concentrations in ambient air by UV absorption. These monitors are typically used to measure ozone for the purpose of establishing local compliance to air-quality standards. The study was predicated by the concern that commercially available UV absorbance O3 monitors may be subject to interference from volatile organic carbon (VOC) species that absorb light at 254 nm. To test for these and other effects, we compared simultaneous O3 measurements made by a commercial UV O3 monitor with an O3-NO chemiluminescence instrument, which is not subject to interference by VOC compounds. The comparisons were carried out in the summers of 1999 and 2000 at urban/industrial sites in Nashville and Houston, and in 2004 aboard a ship in the Gulf of Maine. In the two urban areas, we also compared the 03 measurements from these two methods with O3 measurements made by a long-path differential optical absorption spectrometer (DOAS). Our tests indicate that, with well-maintained monitors, there are no significant interferences even in areas with significant ambient concentrations of potentially interfering VOCs.
Effects of Slash Pile Burning on the Physical and Chemical Soil Properties of Vassar Soils (1998)

Abstract To determine the initial effects of slash pile burning on chemical and physical properties in the Vassar soil series, mineral soil samples from two depths (2.5 cm and 12.5 cm) were collected before and after burning slash piles of four fuel loadings (0.5 m, 1 m, 2 m and 3 m) over wet and dry soils, as well as from burned and unburned litter plots. Surface soil CEC decreased with increasing fuel loads, reflecting the increased combustion of fuels, longer residence time of the fires, and increased fire severity with these heavier loads. Available nitrogen increased with increasing fuel loads as a result of the increased total quantity of mineralization of organic N from the heavier fuels. While some cations (magnesium and sodium) increased after burning, others, such as calcium, in general decreased.
Diagnostic Applications of Sleep Deprivation (1986)

Four cases are described in which observation of the response to forty hour sleep deprivation was used in resolving the differential diagnosis between depression and dementia. In each case it was possible to conduct psychometric assessment of cognitive ability during the period of improvement of the clinical state. The utility of this approach and some of the difficulties associated with its use are discussed.
Phosphor for White Light Sources Using Blue/Near-Ultraviolet LEDs (2009)

The luminescence properties of orange-yellow-emitting Eu2+-activated Sr3SiO5 were optimized for application to blue/near ultraviolet n-UV light-emitting diodes LEDs . Sr2.97SiO5:Eu0.03 2+ showed strong orange-yellow emission peaking at 580 nm under blue and n-UV light of 450 and 405 nm, respectively, and the effects of Ca and Ba substitutions into Sr2+ sites on the emission band change were investigated. For the substitution of Ca, Ca3SiO5:Eu 2+ showed no orange-yellow emission under blue light due to the different crystal structures of Ca3SiO5 monoclinic and Sr3SiO5 tetragonal . The redshift and blueshift of the emission band of Sr1−xBax 3SiO5:Eu were explained by the competition between crystal field effect and Nephelauxetic effect. The 460 nm-emitting blue LED-pumped white LED with Sr3SiO5:Eu 2+ or a mixture of Sr3SiO5:Eu 2+ and green phosphor Ba2SiO4:Eu were fabricated and they showed color coordinates of 0.343, 0.281 and 0.349, 0.339 , respectively. © 2009 The Electrochemical Society. DOI: 10.1149/1.3106042 All rights reserved.
Role of Immunoregulatory Donor T Cells in Suppression of Graft-Versus-Host Disease Following Donor Leukocyte Infusion Therapy (1999)

In murine models of allogeneic bone marrow transplantation (BMT), MHC-mismatched recipients given a delayed infusion of donor leukocytes (DLI) at 21 days posttransplant develop significant GVHD whereas MHC-matched recipients do not. The current study was initially designed to test the hypothesis that small numbers of T cells in the MHC-mismatched donor bone marrow (BM) graft exacerbated graft-vs-host disease (GVHD) when DLI was administered at 21 days after BMT. Ex vivo depletion of Thy1+ cells from the donor BM had no impact on the severity of GVHD after DLI. However, depletion of donor T cells in vivo with a Thy1 allele-specific mAb given after BMT resulted in significantly more severe GVHD after DLI. Similar results were obtained in a MHC-matched model of allogeneic BMT, indicating that this was a general phenomenon and not model dependent. These results indicated that a population of donor-derived Thy1+ cells suppressed graft-vs-host reactivity after DLI. Results of experiments with thymectomized recipients demonstrated that an intact thymus was required for generation of the immunoregulatory donor cells. Experiments using TCR beta-chain knockout mice as BM donors indicated that the immunosuppressive Thy1+ cells coexpressed alphabetaTCR heterodimers. Similar experiments with CD4 and CD8 knockout donor BM suggested that the immunoregulatory Thy1+alphabetaTCR+ cells consisted of two subpopulations: a CD4+CD8- subpopulation and a CD4-CD8- subpopulation. Together, these results show that thymus-derived, Thy1+alphabetaTCR+ donor cells generated early after allogeneic BMT suppress the graft-vs-host reactivity of T cells given as DLI. These cells may mediate dominant peripheral tolerance after allogeneic BMT.
[A review on integration methods for single-cell data]. (2021)

The emergence of single-cell sequencing technology enables people to observe cells with unprecedented precision. However, it is difficult to capture the information on all cells and genes in one single-cell RNA sequencing (scRNA-seq) experiment. Single-cell data of a single modality cannot explain cell state and system changes in detail. The integrative analysis of single-cell data aims to address these two types of problems. Integrating multiple scRNA-seq data can collect complete cell types and provide a powerful boost for the construction of cell atlases. Integrating single-cell multimodal data can be used to study the causal relationship and gene regulation mechanism across modalities. The development and application of data integration methods helps fully explore the richness and relevance of single-cell data and discover meaningful biological changes. Based on this, this article reviews the basic principles, methods and applications of multiple scRNA-seq data integration and single-cell multimodal data integration. Moreover, the advantages and disadvantages of existing methods are discussed. Finally, the future development is prospected.
Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning (2017)

Background. Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. Method. In this study, we present a novel method to predict real-valued angles by combining clustering and deep learning. That is, we first generate certain clusters of angles (each assigned a label) and then apply a deep residual neural network to predict the label posterior probability. Finally, we output real-valued prediction by a mixture of the clusters with their predicted probabilities. At the same time, we also estimate the bound of the prediction errors at each residue from the predicted label probabilities. Result. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Conclusions. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.
Fake it Till You Make it: Self-Supervised Semantic Shifts for Monolingual Word Embedding Tasks (2021)

The use of language is subject to variation over time as well as across social groups and knowledge domains, leading to differences even in the monolingual scenario. Such variation in word usage is often called lexical semantic change (LSC). The goal of LSC is to characterize and quantify language variations with respect to word meaning, to measure how distinct two language sources are (that is, people or language models). Because there is hardly any data available for such a task, most solutions involve unsupervised methods to align two embeddings and predict semantic change with respect to a distance measure. To that end, we propose a self-supervised approach to model lexical semantic change by generating training samples by introducing perturbations of word vectors in the input corpora. We show that our method can be used for the detection of semantic change with any alignment method. Furthermore, it can be used to choose the landmark words to use in alignment and can lead to substantial improvements over the existing techniques for alignment. We illustrate the utility of our techniques using experimental results on three different datasets, involving words with the same or different meanings. Our methods not only provide significant improvements but also can lead to novel findings for the LSC problem.
Empirical specification of field‐aligned plasma density profiles for plasmasphere refilling (2006)

Sounding measurements from the radio plasma imager (RPI) on the IMAGE satellite are used to derive electron density distributions along magnetic field lines in the nightside plasmasphere and plasmatrough for three midlatitude passes. These passes occurred during (1) a magnetic storm, (2) a prolonged quiet time, and (3) a sudden commencement of a storm, respectively. It is found that the density profiles of filled (in the inner plasmasphere) and depleted (in the plasmatrough or outer plasmasphere) flux tubes have different field line dependence. A multivariant least squares fit with a simple analytical function is used to model the density profiles. The fitting parameters in the function define the field line dependence of a density profile, i.e., the steepness of the density profile at high latitudes and the flatness at low latitudes. In each pass the density profiles along the filled and depleted flux tubes can be well modeled with the selected functional form, with two different sets of fitting parameter values for filled and depleted flux tubes. For the three passes examined, the fitting parameter values are not sensitive to the geomagnetic activity for the inner plasmasphere density profiles but vary slightly for the plasmatrough or outer plasmasphere density profiles from case to case. The equatorial densities extrapolated from the measured density profiles approximately have a power law relation with L values. The results suggest that the selected function has potential of being able to construct realistic global empirical plasmasphere/plasmatrough models. Furthermore, it is now feasible to empirically determine the density profiles along the depleted flux tubes for plasmasphere refilling studies.
Room-temperature operation at 333 nm of Al0.03Ga0.97N/Al0.25Ga0.75N quantum-well light-emitting diodes with Mg-doped superlattice layers (2000)

We demonstrate room-temperature deep ultraviolet (UV) current injection emission from Al0.03Ga0.97N/Al0.25Ga0.75N multiquantum-well (MQW) light-emitting diodes (LEDs) fabricated by metalorganic vapor phase epitaxy. The electroluminescence (EL) peaked at 333.0 nm under pulsed current injection. To our knowledge, this is the shortest wavelength ever reported for nitride QW LEDs. A Mg-doped GaN/AlGaN superlattice (SL) hole conductive layer was used as a p-type layer in order to enable current injection into such deep-level AlGaN QWs. We observed single-peak near band-edge emission from the QWs. The output intensity did not saturate up to current densities of 0.33 kA/cm2. We obtained a reasonable well width dependence on the EL peak wavelength of Al0.01Ga0.99N MQW LEDs, which confirms that the main emission peak originates from the QW regions. These results revealed that the Mg-doped SL hole conductive layers are highly suitable for application to GaN-based UV light-emitting devices.
REGULATION OF COLLECTING DUCT Na<sup>+</sup> REABSORPTION BY ANP 31–67 (1995)

1. The bulk of studies of the actions of atrial natriuretic peptides (ANP) have focussed on the carboxyterminal derivative (ANP 99-126) of the prohormone (ANP 1-126), but recent evidence indicates that an additional peptide derived from ANP 1-126, namely, ANP 31-67 also circulates, and has natriuretic actions. 2. The effects of ANP 31-67 on inner medullary collecting duct (IMCD) Na+ transport have been examined in freshly prepared suspensions of rabbit IMCD cells. Like ANP 99-126, ANP 31-67 reduces Na+ transport in these cells. 3. However, unlike ANP 99-126, this effect is not mediated by cGMP, and does not result from inhibition of apical Na+ channels. Rather, ANP 31-67 inhibits basolateral Na/K-ATPase, probably via the stimulation of PGE2 synthesis. 4. These results are discussed in the context of other natriuretic substances (interleukin 1 and endothelin), which also inhibit Na+ reabsorption by PGE2-mediated inhibition of Na/K-ATPase.
Audio-Visual Speech Enhancement Using Conditional Variational Auto-Encoders (2020)

Variational auto-encoders (VAEs) are deep generative latent variable models that can be used for learning the distribution of complex data. VAEs have been successfully used to learn a probabilistic prior over speech signals, which is then used to perform speech enhancement. One advantage of this generative approach is that it does not require pairs of clean and noisy speech signals at training. In this article, we propose audio-visual variants of VAEs for single-channel and speaker-independent speech enhancement. We develop a conditional VAE (CVAE) where the audio speech generative process is conditioned on visual information of the lip region. At test time, the audio-visual speech generative model is combined with a noise model based on nonnegative matrix factorization, and speech enhancement relies on a Monte Carlo expectation-maximization algorithm. Experiments are conducted with the recently published NTCD-TIMIT dataset as well as the GRID corpus. The results confirm that the proposed audio-visual CVAE effectively fuses audio and visual information, and it improves the speech enhancement performance compared with the audio-only VAE model, especially when the speech signal is highly corrupted by noise. We also show that the proposed unsupervised audio-visual speech enhancement approach outperforms a state-of-the-art supervised deep learning method.
CD85j (Leukocyte Ig-Like Receptor-1/Ig-Like Transcript 2) Inhibits Human Osteoclast-Associated Receptor-Mediated Activation of Human Dendritic Cells (2005)

Immature dendritic cells (DCs) derived from freshly isolated human monocytes were used to evaluate the effect of the inhibiting receptor CD85j (leukocyte Ig-like receptor-1/ILT2) on activation induced by cross-linking of the human osteoclast-associated receptor (hOSCAR). CD85j and hOSCAR were expressed consistently at the same density on monocytes and on monocyte-derived DCs (both immature and mature). Cross-linking of hOSCAR, which activates via the FcR-associated gamma-chain, induced Ca(2+) flux in DCs. Concomitant cross-linking of anti-CD85j mAb abolished this early activation event. Likewise, CD85j stimulation strongly reduced IL-8 and IL-12 production by hOSCAR-activated DCs. Inhibition of DCs via CD85j also impaired their ability to enhance Ag-specific T cell proliferation induced by hOSCAR. Finally, because hOSCAR prevents apoptosis of DCs in the absence of growth/survival factors, CD85j cross-linking was able to counteract completely this antiapoptotic effect and to reduce Bcl-2 expression enhanced by hOSCAR stimulation. Thus, CD85j is an inhibiting receptor that is functional in human DCs.
Studies on the Synthesis of Furo[3,2-<i>d</i>]pyrimidine C-Nucleosides: New Inosine Analogues with Antiprotozoan Activity (1990)

Abstract Methods are described for the synthesis of the α and β anomers of 7-D−ribofuranosylfuro[3,2-d]pyrimidines substituted at C-4 with either amino, oxo, thiono, or methylthio groups. The analogous 2,4-dithiono compounds are also described. The key steps involve the LDA-promoted cyclizations of the cyano ethers 3 and 14 to give, respectively, the substituted furan C-nucleosides A and 16. After separation of anomers, these compounds were subjected to a number of pyrimidine-ring-forming reactions to give the desired bicyclic C-nucleosides. The adenosine analogue 13 is markedly cytotoxic to mouse L1210 cells in vitro, and the inosine analogue 20 shows activity against the pathogenic protozoans Leishmania donovani and Trypanosoma gambiense.
Expression, purification and characterization of soluble red rooster laforin as a fusion protein in Escherichia coli (2014)

Gg-laforin is more soluble and stable than human laforin in vitro, and possesses similar activity as a glucan phosphatase. Therefore, it can be used to model human laforin in structure-function studies. We have established a protocol for purifying recombinant Gg-laforin in sufficient quantity for crystallographic and other biophysical analyses, in order to better understand the function of laforin and define the molecular mechanisms of Lafora disease.
Stability of a Lithium-Drifted Silicon Detector (1994)

The instability of a radiation detector has been studied by means of 1150 nm infrared light. The change in the detector sensitivity is exhibited in photocurrent measurements. Several resonancelike bumps were observed in the conductance of the detector when the aging was incomplete. Using the observed data, we discuss the possible mechanisms which affect detector stability.
[Selective suppression of polymerase chain reaction]. (1999)

The selective suppression of the polymerase chain reaction and methods based upon it (construction of cDNA libraries from low amounts of biological material, subtractive hybridization and differential display of mRNA, fast cloning of full-size cDNA, chromosome walking, cloning in vitro, and others) are reviewed. These methods display a high effectiveness and, taken together, enable intricate DNA analyses to be performed--from the search for nontrivial sequences to the total sequencing of the corresponding genes.
Low-cost implementation of a self-paced treadmill by using a commercial depth sensor (2013)

A self-paced treadmill that can simulate overground walking has the potential to improve the effectiveness of treadmill training for gait rehabilitation. We have implemented a self-paced treadmill without the need for expensive equipment such as a motion capture system and an instrumented treadmill. For this, an inexpensive depth sensor, ASUS XtionTM, substitutes for the motion capture system, and a low-cost commercial treadmill is considered as the platform of the self-paced treadmill. The proposed self-paced treadmill is also convenient because the depth sensor does not require markers placed on user's body. Through pilot tests with two healthy subjects, it is quantitatively and qualitatively verified that the proposed self-paced treadmill achieves similar performance as one which utilizes a commercial motion capture system (VICON) as well as an instrumented treadmill.
Design and Control of a Passively Morphing Quadcopter (2019)

This paper presents a novel quadcopter design that uses passive rotary joints to enable rapid aerial morphing without the use of additional actuators. The normally rigid connections between the arms of the quadcopter and the central body are replaced by sprung hinges that allow for the arms of the quadcopter to fold downward when low thrusts are produced by the propellers, resulting in a reduction of the largest dimension of the vehicle by approximately 50%. The ability of the vehicle to reduce its size during flight allows, e.g., for the traversal of gaps through which a non-morphing quadcopter could not pass. The vehicle is designed such that existing quadcopter controllers and trajectory generation algorithms can be used, provided that some additional constraints on the control inputs are met. The nonlinear dynamics of the system are presented, and design rules are given that minimize transition time between configurations and maximize the available range of control inputs. A method for performing gap traversal maneuvers is proposed and validated experimentally.
Time-Delay Identification in a Chaotic Semiconductor Laser With Optical Feedback: A Dynamical Point of View (2009)

A critical issue in optical chaos-based communications is the possibility to identify the parameters of the chaotic emitter and, hence, to break the security. In this paper, we study theoretically the identification of a chaotic emitter that consists of a semiconductor laser with an optical feedback. The identification of a critical security parameter, the external-cavity round-trip time (the time delay in the laser dynamics), is performed using both the auto-correlation function and delayed mutual information methods applied to the chaotic time-series. The influence on the time-delay identification of the experimentally tunable parameters, i.e., the feedback rate, the pumping current, and the time-delay value, is carefully studied. We show that difficult time-delay-identification scenarios strongly depend on the time-scales of the system dynamics as it undergoes a route to chaos, in particular on how close the relaxation oscillation period is from the external-cavity round-trip time.