gebhart/patrepeval huggingface dataset:
Rapid generation of circulating and mucosal decoy ACE2 using mRNA nanotherapeutics for the potential treatment of SARS-CoV-2 (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters through the airways and infects the lungs, causing lethal pulmonary damage in vulnerable patients. This virus contains spike proteins on its envelope that binds to human angiotensin-converting enzyme 2 (hACE2) expressed on the surface of airway cells, enabling entry of the virus for causing infection <sup>1,2</sup> . In severe cases, the virus enters the circulatory system, contributing to multiorgan failure. Soluble form of hACE2 binds to SARS-CoV-2 spike protein and prevents viral entry into target cells <sup>3</sup> . Moreover, soluble recombinant ACE2 ameliorates lung injury <sup>4</sup> but its short half-life limits its therapeutic utility <sup>5</sup> . Here, we engineered synthetic mRNA to encode a soluble form of hACE2 (hsACE2) to prevent viral infection. Novel lipid nanoparticles (LNPs) were used to package mRNA and transfect mammalian cells for enhanced production of secreted proteins. Intravenously administered LNP led to hepatic delivery of the mRNA. This elicited secretion of hsACE2 into the blood circulation within 2 h, and levels of circulating hsACE2 peaked at 6 h and gradually decreased over several days. Since the primary site of entry and pathogenesis for SARS-CoV-2 is the lungs, we instilled LNPs into the lungs and were able to detect hsACE2 in the bronchoalveolar lavage fluid within 24 h and lasted for 48 h. Through co-immunoprecipitation, we found that mRNA-generated hsACE2 was able to bind with the receptor binding domain of the SARS-CoV-2 spike protein. Furthermore, hsACE2 was able to strongly inhibit (over 90%) SARS-CoV-2 pseudovirus infection. Our proof of principle study shows that mRNA-based nanotherapeutics can be potentially deployed for pulmonary and extrapulmonary neutralization of SARS-CoV-2 and open new treatment opportunities for COVID-19.
Synthesis and characterization of bis[4-<i>N</i>-(cyclohexylimino)-2-pentanonato]magnesium(II) (2005)

A novel β-ketoimine, 4-N-(cyclohexylimino)-2-pentanone, was synthesized and reacted with dibutyl magnesium to afford the desired magnesium bis(β-ketoiminate). The complex, bis[4-N-(cyclohexylimino)-2-pentanonato]magnesium(II), has been structurally characterized by single-crystal X-ray diffraction methods. Crystallographic analysis shows the four-coordinate complex to be homoleptic and monomeric in the solid state. The geometry around the Mg(II) atom is a distorted tetrahedron. The bulky cyclohexyl groups provide enough steric bulk about magnesium to inhibit intermolecular interactions. The crystal structure of the complex is triclinic, space group , with a = 8.301(3), b = 11.301(4), c = 12.023(4) Å, α = 75.840(6), β = 88.867(6), γ = 84.611(6)°, Z = 2. The two normal Mg–O and Mg–N bond lengths are, respectively, 1.9162(11), 1.9265(11) and 2.0699(13), 2.0822(12) Å.
Constituents of Michelia rajaniana. Two New Germacranolide Amides (1988)

Six components have been isolated from the bark of Michelia rajaniana, and their structures have been determined by spectroscopic analysis. Four of the components have been reported previously: The germacranolide (-)-parthenolide and the oxoaporphinoid alkaloid liriodenine have been observed as constituents of several species, and (-)-bisparthenolidine and (+)-paramicholide have been reported recently by us as constituents of Paramichelia baillonii. The two new components 3 and 4, which are novel derivatives of parthenolide and contain an unusual N-acetyl substituent at C-13, have been given the names (+)-N-acetylparthenolidine and (+)-N-acetyl-8 alpha-hydroxyparthenolidine, respectively. The crude CHCl3 extract of the bark of M. rajaniana exhibited strong cytotoxicity in the KB cell culture assay.
Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages (2017)

Coronaviruses are positive-sense RNA viruses that generate double-stranded RNA (dsRNA) intermediates during replication, yet evade detection by host innate immune sensors. Here we report that coronavirus nonstructural protein 15 (nsp15), an endoribonuclease, is required for evasion of dsRNA sensors. We evaluated two independent nsp15 mutant mouse coronaviruses, designated N15m1 and N15m3, and found that these viruses replicated poorly and induced rapid cell death in mouse bone marrow-derived macrophages. Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3, which expresses a catalysis-deficient nsp15, activated MDA5, PKR, and the OAS/RNase L system, resulting in an early, robust induction of type I IFN, PKR-mediated apoptosis, and RNA degradation. Immunofluorescence imaging of nsp15 mutant virus-infected macrophages revealed significant dispersal of dsRNA early during infection, whereas in WT virus-infected cells, the majority of the dsRNA was associated with replication complexes. The loss of nsp15 activity also resulted in greatly attenuated disease in mice and stimulated a protective immune response. Taken together, our findings demonstrate that coronavirus nsp15 is critical for evasion of host dsRNA sensors in macrophages and reveal that modulating nsp15 stability and activity is a strategy for generating live-attenuated vaccines.
Facile Enzymatic Synthesis of Ketoses (2015)

Studies of rare ketoses have been hampered by a lack of efficient preparation methods. A convenient, efficient, and cost-effective platform for the facile synthesis of ketoses is described. This method enables the preparation of difficult-to-access ketopentoses and ketohexoses from common and inexpensive starting materials with high yield and purity and without the need for a tedious isomer separation step.
Bone Crystal Sizes: A Comparison of Transmission Electron Microscopic and X-Ray Diffraction Line Width Broadening Techniques (1994)

Bone crystals are particularly small and hence estimating their sizes have proved to be difficult and values obtained inconsistent. Here we use rat bone crystals of different ages, as well as different synthetic carbonate apatite crystals, to compare two methods commonly used for determining bone crystal sizes. One method involves direct measurement of crystal lengths and widths, but not thicknesses, from transmission electron microscope (TEM) photographs of dispersed crystals. The second method utilizes X-ray diffraction line width broadening to estimate the average length of crystals. We conclude that line width broadening values tend to reflect crystal coherence lengths rather than the physical dimensions of the whole crystal. TEM measurements provide reliable estimates of average crystal lengths and widths and their ranges. Sample preparation procedures, however, cause breakage of the fragile crystals, which probably results in underestimates of in vivo crystal sizes.
Fully automated diagnostic system with artificial intelligence using endocytoscopy to identify the presence of histologic inflammation associated with ulcerative colitis (with video) (2018)

Our CAD system potentially allows fully automated identification of persistent histologic inflammation associated with UC.
Video Compression Using Conditional Replenishment and Motion Prediction (1984)

A study of a low-rate monochrome video compression system is presented in this paper. This system is a conditional-replenishment coder that uses two-dimensional Walsh-transform coding within each video frame. The conditional-replenishment algorithm works by transmitting only the portions of an image that are changing in time. This system is augmented with a motion-prediction algorithm that measures spatial displacement parameters from frame to frame, and codes the data using these parameters. A comparison is made between the conditional-replen-ishment system with, and without, the motion-prediction algorithm. Subsampling in time is used to maintain the data rate at a fixed value. Average bit rates of 1 bit/picture element (pel) to 1/16 bit/pel are considered. The resultant performance of the compression simulations is presented in terms of the average frame rates produced.
Improved Photoelectrical Properties of MoS<sub>2</sub> Films after Laser Micromachining (2014)

Direct patterning of ultrathin MoS2 films with well-defined structures and controllable thickness is appealing since the properties of MoS2 sheets are sensitive to the number of layer and surface properties. In this work, we employed a facile, effective, and well-controlled technique to achieve micropatterning of MoS2 films with a focused laser beam. We demonstrated that a direct focused laser beam irradiation was able to achieve localized modification and thinning of as-synthesized MoS2 films. With a scanning laser beam, microdomains with well-defined structures and controllable thickness were created on the same film. We found that laser modification altered the photoelectrical property of the MoS2 films, and subsequently, photodetectors with improved performance have been fabricated and demonstrated using laser modified films.
Ion-implanted thin polycrystalline-silicon high-value resistors for high-density poly-load static RAM applications (1985)

An application of ion-implanted polycrystalline-silicon resistors for a 4- and 16-Mbit MOS static RAM cell is discussed. 4M and 16M static RAM's are designed with assumed minimum feature sizes of 0.5 and 0.25 µm of double-level polycrystalline-silicon process and power supply voltages of 3.0 and 1.5 V, respectively. The load current of the memory cell is kept at about 30 pA per cell, which is as low as that of state-of-the-art 64K static RAM's. LPCVD polycrystalline-silicon film of about 25-nm thickness is used to etch fine resistor patterns of 0.25 ∼ 0.5 µm feature sizes. Sheet resistances of 24 and 12 GΩ/ for 4M and 16M static RAM cells are controlled by arsenic implantation of about 4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</sup> and 3 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> at 10 keV, respectively. The ion-implanted polycrystalline-silicon resistors show nearly ideal linear current-voltage characteristics. Grain sizes of the polycrystalline-silicon films calculated from the current-voltage characteristics are in good agreement with those measured by transmission electromicrographs. It was shown that 4M and 16M static RAM's would be realized by combining the scaling-down of state-of-the-art 64K RAM cell of the double-level polycrystalline-silicon process and the thin ion-implanted polycrystalline-silicon resistors.
Multichannel combining and equalization for underwater acoustic MIMO channels (2008)

In order to achieve high data rate digital communications, multiple-input/multiple-output (MIMO) techniques have attracted growing interests in the underwater acoustic communication studies. In this paper, multichannel combining and decision feedback equalization (MCC/DFE) has been proposed for underwater acoustic MIMO channels. In order to overcome the difficulties introduced by the fast fluctuating channel, Doppler tracking and frequent channel estimation are performed. Then time reversal combining followed by a single channel DFE is used to demodulate individual symbol sequences transmitted by the multiple element source. To improve the performance, successive interference cancellation is also incorporated into the receiver structure. Using data from the Makai experiment conducted around Kauai Island, HI, 2005, we have shown that the achievable data rate can be increased up to 4 times using the same bandwidth as single source systems. For example, 32 kilobits/s could have been achieved by simultaneous transmission of four 4 kilosymbols/s 4-phase shift keying (QPSK) symbol sequences when both the source and the receiver were drifting at a 2 km range in the ocean.
Control of a class of nonlinear uncertain systems via compensated inverse dynamics approach (1994)

The tracking control problem of a class of nonlinear systems via inverse dynamics method is addressed. The motivation for the study stems from the need to control practical systems arising from aerospace and mechanical engineering. Because modeling uncertainties and external disturbances are always present in these systems, inverse dynamics technique is not applicable directly. A compensated inverse dynamics approach is proposed to account for the effect of uncertainties. The compensation is achieved by adaptive and robust schemes. Application of the proposed strategy to the vibration suppression of a two-bay flexible truss structure is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A simple nano-scale patterning technology for FinFET fabrication (2008)

In this paper, a simple low-cost sub-50 nm silicon fin patterning technology is proposed and experimentally demonstrated. The technology is based on a micro-meter level lithography equipment, that is, it does not need any critical photolithographic step. The masking layer for fin formation is the nitride caped oxide layer which is reduced in width from sub-micrometer scale to nano-meter scale through a lateral etching in BOE. The etching rate is shown to slow down as the etching process goes on. A nano-scale oxide hard mask can be achieved after the nitride is removal. Both the cross-sectional view and top view of the etching process are shown by SEM photographs. Results indicate the simple patterning way is of low cost and under good control, and applicable to FinFET technology.
Immunogenicity of a <i>Haemophilus influenzae</i> polysaccharide- <i>Neisseria meningitidis</i> outer membrane protein complex conjugate vaccine. (1990)

Polysaccharide-protein conjugate vaccines made with different carriers vary in their ability to elicit antipolysaccharide IgG antibody responses in young infants and an adult mouse model, suggesting that the carrier proteins used in the conjugate vaccines differ in their ability to act as carriers, or that additional mechanisms of immunogenicity play a role. A conjugate vaccine of Haemophilus influenzae PRP coupled to the outer membrane protein complex (OMPC) of Neisseria meningitidis serogroup B is immunogenic in children as young as 2 mo of age and is immunogenic in infant rhesus monkeys, an animal model for infant humans. In the present study, PRP-OMPC was found to induce efficient IgM to IgG switching of anti-PRP serum antibody in adult mice, whereas PRP conjugated to two other protein carriers did not. Thus the PRP-OMPC conjugate was examined in order to determine why PRP coupled to OMPC was so immunogenic, even more immunogenic than conjugates made with other carrier proteins. The OMPC carrier differs from the other protein carriers in that the proteins are present in a liposomal form containing lipids (including LPS) derived from the outer membrane of N. meningitidis. We studied the OMPC to see whether the different components or the nature of the OMPC carrier could contribute to its enhanced immunogenicity. Specifically we evaluated the OMPC for both classic Th cell carrier activity and adjuvanticity, and the LPS component of OMPC for systemic polyclonal B cell activation. Carrier recognition of the OMPC moiety of PRP-OMPC was demonstrated. In addition the PRP-OMPC conjugate vaccine was observed to have adjuvant properties for both T cell-dependent and T cell-independent Ag in the absence of LPS-induced systemic polyclonal B cell activation. These observations suggest that in addition to functioning as a classic protein carrier whereby the proteins in OMPC provide Th cell epitopes, the OMPC also has adjuvant activity that distinguishes it from other protein carriers and may contribute to the increased immunogenicity of PRP-OMPC conjugates in animal models.
Application of Particle Swarm Optimization-Based Support Vector Machine in Fault Diagnosis of Turbo-Generator (2008)

Support vector machine (SVM) is a new machine learning method based on statistical learning theory, which is a powerful tool for solving the problem with small sample, nonlinear and high dimension. However, the practicability of SVM is affected due to the difficulty of selecting appropriate SVM parameters. Particle swarm optimization (PSO) is a new optimization method, which is motivated by social behavior of bird flocking or fish schooling. The optimization method not only has strong global search capability, but also is very easy to implement. Thus, in the study, the proposed PSO-SVM model is applied to fault diagnosis of turbo-generator, among which PSO is used to determine free parameters of support vector machine. Finally, the effectiveness and correctness of this method are validated by the results of fault diagnosis examples. Consequently, PSO-SVM is a proper method in fault diagnosis of turbo-generator.
Highly scalable, resonantly cladding-pumped, Er-doped fiber laser with record efficiency (2009)

We report the performance of a resonantly cladding-pumped, Yb-free, Er-doped fiber laser. We believe this is the first reported resonantly cladding-pumped fiber-Bragg-grating-based, Er-doped, large-mode-area (LMA) fiber laser. The laser, pumped by fiber-coupled InGaAsP/InP laser diode modules at 1,532.5 nm, delivers approximately 48 W of cw output at 1,590 nm. It is believed to be the highest power ever reported from a Yb-free Er-doped LMA fiber. This fully integrated laser also has the optical-to-optical efficiency of approximately 57%, to the best of our knowledge, the highest efficiency reported for cladding-pumped unidirectionally emitting Er-doped laser.
Notch Model for Photoresist Dissolution (1999)

A new model for photoresist dissolution rate as a function of photoactive compound concentration is presented. This semiempirical model combines elements of previous kinetic models in order to better fit recent experimental dissolution rate behavior. In particular, rate data exhibiting a dissolution notch can be well fit by this model. ©1998 The Electrochemical Society
Efficient insertional mutagenesis in rice using the maize <i>En</i>/<i>Spm</i> elements (2005)

We have developed a novel system for insertional mutagenesis in rice (Oryza sativa) based on the maize (Zea mays) enhancer/suppressor mutator (En/Spm) element. In this system, a single T-DNA construct with Spm-transposase and the non-autonomous defective suppressor mutator (dSpm) element is used in conjunction with green fluorescent protein (GFP) and Discosoma sp. Red Fluorescence Protein (DsRed) fluorescent markers to select unlinked stable transpositions of dSpm. Using this system, we could demonstrate high frequencies of unlinked germinal transposition of dSpm in rice. Analysis of dSpm flanking sequences from 353 stable insertion lines revealed that the dSpm insertions appear to be widely distributed on rice chromosomes with a preference for genic regions (70%). The dSpm insertions appear to differ from Activator-Dissociation (Ac-Ds) elements in genomic distribution and exhibit a greater fraction of unlinked transpositions when compared with Ds elements. The results obtained in this study demonstrate that the maize En/Spm element can be used as an effective tool for functional genomics in rice and can complement efforts using other insertional mutagens. Further, the efficacy of the non-invasive fluorescence-based selection system is promising for its application to other crops.
A disheartening story: Aprotinin in cardiac surgery (2006)

Expanded AbstractCitationMangano DT, Tudor IC, Dietzel C: The risk associated with aprotinin in cardiac surgery. N Engl J Med 2006, 354:353–365 [1].BackgroundThe majority of patients undergoing surgical treatment for ST-elevation myocardial infarction receive antifibrinolytic therapy to limit blood loss. This approach appears counterintuitive to the accepted medical treatment of the same condition – namely, fibrinolysis to limit thrombosis. Despite this concern, no independent, large-scale safety assessment has been undertaken.MethodsDesign and settingProspective observational cohort study in 69 institutions in North and South America, the Middle East, Europe, and Asia.Subjects4374 patients undergoing coronary-artery revascularization. All patients were >18 years old and completed a pre-surgery interview. Patients were classified as undergoing primary surgery (no previous heart surgery and no other surgery besides a coronary artery bypass graft), or complex surgery (all other surgery).InterventionNone.MeasurementsThe authors prospectively assessed three agents (aprotinin [1295 patients], aminocaproic acid [883], and tranexamic acid [822]) as compared with no agent (1374 patients) with regard to serious cardiovascular, renal, and cerebrovascular outcomes by propensity and multivariable methods.ResultsIn propensity-adjusted, multivariable logistic regression (C-index, 0.72), use of aprotinin was associated with a doubling in the risk of renal failure requiring dialysis among patients undergoing complex coronary-artery surgery (odds ratio, 2.59; 95 percent confidence interval, 1.36 to 4.95) or primary surgery (odds ratio, 2.34; 95 percent confidence interval, 1.27 to 4.31). Similarly, use of aprotinin in the latter group was associated with a 55 percent increase in the risk of myocardial infarction or heart failure (P < 0.001) and a 181 percent increase in the risk of stroke or encephalopathy (P = 0.001). Neither aminocaproic acid nor tranexamic acid was associated with an increased risk of renal, cardiac, or cerebral events. Adjustment according to propensity score for the use of any one of the three agents as compared with no agent yielded nearly identical findings. All the agents reduced blood loss.ConclusionThe association between aprotinin and serious end-organ damage indicates that continued use is not prudent. In contrast, the less expensive generic medications aminocaproic acid and tranexamic acid are safe alternatives.
Pharmacological inhibition of TLR9 activation blocks autoantibody production in human B cells from SLE patients (2010)

Autoreactive B cells persist in SLE patients during disease remission in the circulating B-cell memory pool. TLR9-dependent activation of memory B cells by pathogens could be one of the mechanisms triggering relapses in SLE. Compounds targeting the TLR/MyD88 pathway may be used as novel therapeutic tools to treat acute disease and to prevent relapses in SLE patients.
Polyhalogenated Cyclopentadienes in [4+2] Cycloadditions: Preparative Aspects (1997)

Abstract [4+2] Cycloadditions of cyclopentadienes 1a–1i with arylsubstituted cyclic and open‐chain dienophiles usually gave single endo ‐cycloadducts in high yield. Assignment of the product structures involved 1 H‐NMR spectroscopy including ( 1 H, 1 H) long‐range coupling and ( 1 H, 19 F) through‐bond and through‐space coupling.
Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection <sup>*</sup> (2020)

Photochemical stability is one of the most important parameters that determine the usefulness of organic dyes in different applications. This Review addresses key factors that determine the dye photostability. It is shown that photodegradation can follow different oxygen-dependent and oxygen-independent mechanisms and may involve both <sup>1</sup>S<sub>1</sub>-<sup>3</sup>T<sub>1</sub> and higher-energy <sup>1</sup>S<sub>n</sub>-<sup>3</sup>T<sub>n</sub> excited states. Their involvement and contribution depends on dye structure, medium conditions, irradiation power. Fluorescein, rhodamine, BODIPY and cyanine dyes, as well as conjugated polymers are discussed as selected examples illustrating photobleaching mechanisms. The strategies for modulating and improving the photostability are overviewed. They include the improvement of fluorophore design, particularly by attaching protective and anti-fading groups, creating proper medium conditions in liquid, solid and nanoscale environments. The special conditions for biological labeling, sensing and imaging are outlined.