gebhart/patrepeval huggingface dataset:
Could an Unrelated Live Attenuated Vaccine Serve as a Preventive Measure To Dampen Septic Inflammation Associated with COVID-19 Infection? (2020)

We propose the concept that administration of an unrelated live attenuated vaccine, such as MMR (measles, mumps, rubella), could serve as a preventive measure against the worst sequelae of coronavirus disease 2019 (COVID-19). There is mounting evidence that live attenuated vaccines provide nonspecific protection against lethal infections unrelated to the target pathogen of the vaccine by inducing "trained" nonspecific innate immune cells for improved host responses against subsequent infections. Mortality in COVID-19 cases is strongly associated with progressive lung inflammation and eventual sepsis. Vaccination with MMR in immunocompetent individuals has no contraindications and may be especially effective for health care workers who can easily be exposed to COVID-19. Following the lead of other countries conducting clinical trials with the live attenuated <i>Mycobacterium bovis</i> BCG (BCG) vaccine under a similar concept, a clinical trial with MMR in high-risk populations may provide a "low-risk-high-reward" preventive measure in saving lives during this unprecedented COVID-19 pandemic.
Interleukin-18 controls energy homeostasis by suppressing appetite and feed efficiency (2007)

Circulating levels of the cytokine interleukin 18 (IL-18) are elevated in obesity. Here, we show that administration of IL-18 suppresses appetite, feed efficiency, and weight regain in food-deprived male and female C57BL/6J mice. Intraperitoneal vs. intracerebroventricular routes of IL-18 administration had similar potency and did not promote formation of a conditioned taste aversion (malaise-like behavior). Mice partially (Il18(+/-)) or totally (Il18(-/-)) deficient in IL-18 were hyperphagic by young adulthood, with null mutants then becoming overweight by the fifth month of life. Adult Il18(-/-) mice gained 2- to 3-fold more weight than WT mice per unit energy consumed of low- or high-fat diet. Indirect calorimetry revealed reduced energy expenditure in female Il18(-/-) mice and increased respiratory exchange ratios [volume of carbon dioxide production (VCO(2))/volume of oxygen consumption (VO(2))] in mutants of both sexes. Hyperphagia continued in maturity, with overeating greatest during the mid- to late-dark cycle. Relative white fat-pad mass of Il18(-/-) mice was approximately 2- to 3-fold greater than that of WT, with gonadal, mesenteric, and inguinal depots growing most. The data suggest that endogenous IL-18 signaling modulates food intake, metabolism, and adiposity during adulthood and might be a central or peripheral pharmacological target for controlling energy homeostasis.
High Resolution Tertiary and Quaternary Structural Changes in Deoxy and Liganded Hemoglobin E (2008)

Abstract Hemoglobin (Hb) E (β26 Glu→Lys), known to be more unstable than HbA in vitro, remains an enigma in terms of its contributions to red blood cell (RBC) pathophysiological mechanisms. EE individuals exhibit a mild, chronic anemia while HbE-β thalassemia individuals show a range of clinical manifestations, including high morbidity and death, often resulting from cardiac disease. To determine pathophysiological consequences originating from HbE, we created a transgenic mouse expressing exclusively human HbE with equivalent α- and β-chains [Chen et al., Blood 106(11):892a, 2005]. This mice model exhibited hematological characteristics similar to human EE individuals: microcytic RBC with low MCV, low MCH but normal MCHC; target RBC; mild anemia with low Hb, low HCT, elevated reticulocytes; and decreased osmotic fragility. These RBC parameters correlated with indications of mild RBC oxidative stress. Importantly, the transgenic mouse model allows us to obtain purified HbE for crystal growth and dynamic studies, without the presence of human HbA2 (co-expressed in human HbE RBC and difficult to separate). We now present the low [PDB 1YVQ] and high salt [PDB 1YVT] liganded COHbE structures (1.8Å resolution) at or near physiological pH. The known in vitro instability of oxy HbE and its propensity for oxidation may be explained by the substitution of the β26 side-chain with Lys resulting in a positive charge repulsion with consequential changes to β117, and other key stabilizing residues at the α1β1 interface that impart normal association and oxidative stability to HbA. The specific alterations observed in this microenvironment may be the key to HbE instability, given the findings by Adachi et al. (Biochemistry, 42:10252, 2003) that β116 in normal HbA plays a critical role in stabilizing α1β1 interactions and inhibiting oxidation. Additionally, the difference in water structure observed in each of our COHbE structures from crystals generated under different conditions clearly suggests that resolved water structure is dependent simply upon crystallization conditions, and caution must be taken in interpretation of thermal instability. The 1.6 Å structure of deoxy HbE [PDB 3DUT] (crystallization conditions: pH 6.8, 1.8M ammonium phosphate/ammonium sulfate/citrate) exhibits definitive quaternary change compared to the deoxy HbA structure obtained under similar conditions. These structural findings, explain in part, our recent spectroscopic findings of alterations in oxy and deoxy HbE-nitrite interactions.
Exon and Intron Sequences, Respectively, Repress and Activate Splicing of a Fibroblast Growth Factor Receptor 2 Alternative Exon (1995)

Two alternative exons, BEK and K-SAM, code for part of the ligand binding site of fibroblast growth factor receptor 2. Splicing of these exons is mutually exclusive, and the choice between them is made in a tissue-specific manner. We identify here pre-mRNA sequences involved in controlling splicing of the K-SAM exon. The short K-SAM exon sequence 5'-TAGGGCAGGC-3' inhibits splicing of the exon. This inhibition can be overcome by mutating either the exon's 5' or 3' splice site to make it correspond more closely to the relevant consensus sequence. Two separate sequence elements in the intron immediately downstream of the K-SAM exon, one of which is a sequence rich in pyrimidines, are both needed for efficient K-SAM exon splicing. This is no longer the case if either the exon's 5' or 3' splice site is reinforced. Furthermore, if the exon inhibitory sequence is removed, the intron sequences are not required for splicing of the K-SAM exon in a cell line which normally splices this exon. At least three elements are thus involved in controlling splicing of the K-SAM exon: suboptimal 5' and 3' splice sites, an exon inhibitory sequence, and intron activating sequences.
Parameters of adiabatic rapid passage in the 0-0 hyperfine transition ofRb87 (1984)

The parameters of adiabatic rapid passage (ARP) in the ground-state 0-0 hyperfine transition of $^{87}\mathrm{Rb}$ have been investigated. These parameters relate to how adiabatic and how rapid the passage through resonance must be in order to maximize the degree of population reversal. We find both experimentally and theoretically that the adiabaticity requirement is rather weak; and that once satisfied, it is more important to pass through the resonance rapidly. Furthermore, interpreting our results in the Bloch-vector model of ARP, we find that the Bloch vector is only required to precess a half revolution about the effective field in order to follow a 90\ifmmode^\circ\else\textdegree\fi{} change in the direction of that field. The applicability of the present results to ARP in general is discussed.
The Genetic Relevance of Human Induced Pluripotent Stem Cell-Derived Microglia to Alzheimer’s Disease and Major Neuropsychiatric Disorders (2019)

Microglia are the primary innate immune cell type in the brain that have been implicated in the pathogenesis of several neurodegenerative and neuropsychiatric disorders, most notably Alzheimer's disease (AD) and schizophrenia. Microglia generated from human induced pluripotent stem cells (hiPSCs) represent a promising in vitro cellular model for studying the neuroimmune interactions involved in these disorders. Among several methods of generating -hiPSC-derived microglia (iMG) - varying in duration and resultant purity - a recent protocol by Brownjohn et al. [Stem Cell Reports. 2018 Apr;10(4):1294-307] is particularly simple and efficient. However, the replicability of this method, transcriptomic similarity of these iMG to primary adult microglia, and their genetic relevance to disease (i.e., enrichment of disease risk loci in genes preferentially expressed in these cells) remains unclear. Using two hiPSC lines, we demonstrated that Brownjohn's protocol can rapidly generate iMG that morphologically and functionally resembled microglia. The iMG cells we generated were found to be transcriptionally similar to previously reported iMG, as well as fetal and adult microglia. Furthermore, by using cell type-specific gene expression to partition disease heritability, we showed that iMG cells are genetically relevant to AD but found no significant enrichments of risk loci of Parkinson's disease, schizophrenia, major depressive disorder, bipolar disorder, autism spectrum disorder, or body mass index. Across a range of neuronal and immune cell types, we found only iMG, primary microglia, and microglia-like cell types exhibited a significant enrichment for AD heritability. Our results thus support the use of iMG as a human cellular model for understanding AD biology and underlying genetic factors, as well as for developing and efficiently screening new therapeutics.
MARD: A Framework for Metamorphic Malware Analysis and Real-Time Detection (2014)

Because of the financial and other gains attached with the growing malware industry, there is a need to automate the process of malware analysis and provide real-time malware detection. To hide a malware, obfuscation techniques are used. One such technique is metamorphism encoding that mutates the dynamic binary code and changes the opcode with every run to avoid detection. This makes malware difficult to detect in real-time and generally requires a behavioral signature for detection. In this paper we present a new framework called MARD for Metamorphic Malware Analysis and Real-Time Detection, to protect the end points that are often the last defense, against metamorphic malware. MARD provides: (1) automation (2) platform independence (3) optimizations for real-time performance and (4) modularity. We also present a comparison of MARD with other such recent efforts. Experimental evaluation of MARD achieves a detection rate of 99.6% and a false positive rate of 4%.
SHASTRA-an architecture for development of collaborative applications (2002)

The authors address the issue of design of architectures and abstractions to implement multimedia scientific manipulation systems in a concurrent engineering setting, where experts in a cooperating group communicate and interact to solve problems. They propose a model for the integration of software tools into a multi-user distributed and collaborative environment on the multimedia desktop, and describe a prototype CSCW infrastructure used to implement scientific problem solving tools. Finally, they briefly describe a prototype CE system built on this infrastructure. SHASTRA presents a unified prototype for some crucial enabling technologies for concurrent engineering-multimedia communication, framework integration, coordination, and enterprise integration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Polyiodized‐PCL as multisite transfer agent: Towards an enlarged library of degradable graft copolymers (2009)

Abstract Poly(ε‐caprolactone)‐based graft copolymers were prepared via a “grafting from” technique derived from iodine transfer polymerization. This copolymerization was done thanks to a poly(ε‐caprolactone‐co‐α‐iodo‐ε‐caprolactone) (PCL‐I), which was used as a multisite transfer agent. Styrene (Sty) and n ‐butyl acrylate ( n‐ BuA) were firstly used as model monomers to establish the feasibility of using PCL‐I as multisite transfer agent, and investigate some general properties of the polymerization. The formation of PCL‐ g ‐PSty and PCL‐ g ‐P( n‐ BuA) copolymers was confirmed by SEC and NMR analyzes of the copolymers before and after degradation of the PCL backbone. This method was extended to an acrylamide monomer, namely ( N,N ‐dimethyl) acrylamide (DMA), to prepare original amphiphilic copolymers with PCL as hydrophobic backbone and amido‐functionalized hydrophilic grafted chains. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5006–5016, 2009
Surface tension and wetting properties of rapeseed oil to biofuel conversion by-products (2018)

Abstract This work presents a study on the surface tension, density and wetting behaviour of distilled glycerol, technical grade glycerol and the matter organic non-glycerin fraction. The research was conducted to expand the knowledge about the physical properties of wastes from the rapeseed oil biofuel production. The results show that the densities of technical grade glycerol (1.300 g cm -3 ) and distilled glycerol (1.267 g cm -3 ) did not differ and were significantly lower than the density of the matter organic non-glycerin fraction (1.579 g cm -3 ). Furthermore, the surface tension of distilled glycerol (49.6 mN m -1 ) was significantly higher than the matter organic non-glycerin fraction (32.7 mN m -1 ) and technical grade glycerol (29.5 mN m -1 ). As a result, both technical grade glycerol and the matter organic non-glycerin fraction had lower contact angles than distilled glycerol. The examined physical properties of distilled glycerol were found to be very close to that of the commercially available pure glycerol. The results suggest that technical grade glycerol may have potential application in the production of glycerol/fuel blends or biosurfactants. The presented results indicate that surface tension measurements are more useful when examining the quality of biofuel wastes than is density determination, as they allow for a more accurate analysis of the effects of impurities on the physical properties of the biofuel by-products.
Reactive Integrated Mission and Motion Planning for Mobile Robotic Manipulators (2018)

Formal design of integrated task and motion planning of mobile manipulators in a common workspace, where other agents can also manipulate objects in the workspace, is a challenging research question due to the tight coupling between agents, dynamic environments, and the complexity of mission specifications. We are therefore motivated to propose a multi-layered reactive integrated mission and motion planning for mobile-robotic manipulator systems that are operating in a partially known environment. At the high-level, it receives high-level mission specifications that are expressed in linear temporal logic, and a mission planner constructs a symbolic two-player game between the robots and their environment to synthesize a strategy that adapts to changes in the workspace imposed by other robots. A bilateral synergistic layer is developed to map the designed mission plan to an integrated task and motion planner, which constructs a set of robot tasks to move the objects according to the mission strategy. In the low-level planning stage, verifiable motion controllers are designed that can be incrementally composed to guarantee a safe motion planning for each high-level induced task.
Long non-coding RNA DLEU1 contributes to the development of endometrial cancer by sponging miR-490 to regulate SP1 expression. (2018)

This study aimed to investigate the role of long non-coding RNA DLEU1 in endometrial cancer (EC) development. The DLEU1 expression in EC tissues and cells (HHUA, KLE, Ishikawa, and ECC-1) were detected. The expression of DLEU1 was suppressed by transfection with sh-DLEU1 and the effects of DLEU1 suppression on the malignant behaviors of Ishikawa cells, including cell viability, apoptosis, migration and migration were then detected. In addition, the interaction of DLEU1 and miR-490 as well as between miR-490 and SP1 in EC were investigated. Furthermore, the regulatory relationship between DLEU1 and PI3K/AKT/GSK-3β pathway was explored. DLEU1 was upregulated in EC tissues and cells. Suppression of DLEU1 significantly inhibited Ishikawa cell viability, promoted cell apoptosis, decreased BCL-2 expression and increased the expression of Bax, cleaved-caspase-3 and cleaved-caspase-3, suppressed cell migration and invasion, and inhibited EMT via increasing the expression of E-cadherin and decreasing the expression of N-cadherin, Snail and Vimentin. In addition, DLEU1 could sponge miR-490 and miR-490 inhibition significantly reversed the effects of DLEU1 suppression on the malignant behaviors of Ishikawa cells. Furthermore, SP1 was verified as a target of miR-490, and SP1 knockdown could reverse the effects of miR-490 inhibition on the malignant behaviors of Ishikawa cells. Besides, suppression of DLEU1 inhibited PI3K/AKT/GSK-3β pathway, while miR-490 inhibition activated this pathway that could be neutralized by SP1 knockdown. Our findings indicate that DLEU1 contributes to EC development by sponging miR-490 to regulate SP1 expression. DLEU1/miR-490/SP1 axis may provide a new strategy for EC therapy.
Tripyrrindione as a Redox‐Active Ligand: Palladium(II) Coordination in Three Redox States (2015)

The tripyrrin-1,14-dione scaffold of urinary pigment uroerythrin coordinates divalent palladium as a planar tridentate ligand. Spectroscopic, structural and computational investigations reveal that the tripyrrindione ligand binds as a dianionic radical, and the resulting complex is stable at room temperature. One-electron oxidation and reduction reactions do not alter the planar coordination sphere of palladium(II) and lead to the isolation of two additional complexes presenting different redox states of the ligand framework. Unaffected by stability problems common to tripyrrolic fragments, the tripyrrindione ligand offers a robust platform for ligand-based redox chemistry.
Augmentation of interleukin 1 (IL-1) release by murine macrophages stimulated with FK-565. (1984)

Isolation of FK-1 56 (lactyl-L-Ala-y-D-Glu-(L)ra^0-a,e-A2pm(L)-GlyOH), a new low-molecular-weight immunopotentiator, from culture filtrates of Streptomyces olivaceogriseus sp. nov. and Streptomyces violaceus has been reported.1 ~3) Chemists in our laboratory have succeeded in synthesizing FK-156 and a series of structurally related peptides according to the methods previously reported.4) FK-156 and its synthetic derivatives enhanced the natural resistance of experimental animals against microbial invasion and tumor transplants.5~7) Among them, FK-565 (heptanoyl-y-D-Glu-(L)m^9-a,e-A2pm(L)-D-AlaOH)
1‐Alkoxy‐2,5‐diphenylphospholane and ‐phospholanium Salts in Rhodium‐Catalyzed Asymmetric Hydrogenation (2006)

Abstract A series of chiral enantiopure phosphinites was synthesized in four steps starting from phosphinic acid. New species were obtained as alkoxyphosphonium compounds. They can be used in the asymmetric hydrogenation of functionalized alkenes. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
An Improved Dynamic Model for Bearingless Induction Motor Considering Rotor Eccentricity and Load Change (2021)

In the process of establishing a bearingless induction motor (BL-IM) traditional dynamic model, the magnetomotive force of rotor winding, the influence of suspension winding on torque, and the influence of torque winding on radial force are ignored. To solve the problem of insufficient accuracy in the traditional analytical model, based on fixed-pole rotor structure designed by the research group, which comprehensively considers the effect of suspension winding, torque winding, and rotor winding, an improved dynamic model is proposed. First, the spatial variation equation of air gap under rotor eccentricity is established, the composite magnetomotive force of three sets of windings according to the law of magnetic circuit is deduced, and the analytical model of magnetic coenergy in air gap is built. Second, using virtual displacement theorem to find partial derivative, the torque and radial force analytical model are obtained. Third, the improved BL-IM dynamic model is established. Finally, finite element analysis simulations based on controlled variable method prove the accuracy of improved dynamic model. The change trend of torque is verified with respect to suspension current, phase difference between suspension current and torque current, as well as rotor eccentricity. The change characteristics of radial force under no-load, load, and load disturbance are analyzed. In experiments, the controllers based on the traditional dynamic model and the improved dynamic model are compared and analyzed for speed, radial displacement, and centroid trajectory. The effectiveness of the improved dynamic accurate model is verified.
Variable region sequence modulates periplasmic export of a single-chain Fv antibody fragment in Escherichia coli. (1995)

Using PCR, we have cloned antibody heavy and light chain variable region (VH and VL) coding sequences specific for a recombinant hepatitis B virus surface antigen (HBsAg) and assembled these for expression as single-chain Fv (scFv) fragments in Escherichia coli periplasm using the ompA signal peptide. The vectors also encoded N- or C-terminal His6 extensions to allow for the purification of the expressed proteins using immobilized metal affinity chromatography (IMAC). We found that the VH-linker-VL configuration of the scFv was not exported to the periplasm but remained associated with cellular insoluble material, from which it could be extracted, renatured to its active form by gentle dialysis and purified using IMAC. The molecular size of the scFv suggests that the ompA signal peptide was not processed. Based on previous reports, we hypothesized that the arginine in framework 1 (FR1) of the VH might interfere with translocation to the periplasm by means of the signal peptide. Because no arginines are present in FR1 of VL, we reversed the order of the V-regions in the scFv and observed efficient export of the active scFv to the periplasm. Furthermore, when the arginine in FR1 of VH was mutated to glycine in the original VH-linker-VL construct, active scFv was also exported to the periplasm. Thus, exposed positive charges near the signal peptide may account for at least some of the often-encountered difficulties in bacterial scFv expression.
Energy renormalization for coarse-graining polymers having different segmental structures (2019)

Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy <i>s</i> <sub><i>c</i></sub> in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to <i>s</i> <sub><i>c</i></sub> are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass "fragility". We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.