gebhart/patrepeval huggingface dataset:
Proteomic Identification of saeRS -Dependent Targets Critical for Protective Humoral Immunity against Staphylococcus aureus Skin Infection (2015)

Recurrent Staphylococcus aureus skin and soft tissue infections (SSTIs) are common despite detectable antibody responses, leading to the belief that the immune response elicited by these infections is not protective. We recently reported that S. aureus USA300 SSTI elicits antibodies that protect against recurrent SSTI in BALB/c but not C57BL/6 mice, and in this study, we aimed to uncover the specificity of the protective antibodies. Using a proteomic approach, we found that S. aureus SSTI elicited broad polyclonal antibody responses in both BALB/c and C57BL/6 mice and identified 10 S. aureus antigens against which antibody levels were significantly higher in immune BALB/c serum. Four of the 10 antigens identified are regulated by the saeRS operon, suggesting a dominant role for saeRS in protection. Indeed, infection with USA300Δsae failed to protect against secondary SSTI with USA300, despite eliciting a strong polyclonal antibody response against antigens whose expression is not regulated by saeRS. Moreover, the antibody repertoire after infection with USA300Δsae lacked antibodies specific for 10 saeRS-regulated antigens, suggesting that all or a subset of these antigens are necessary to elicit protective immunity. Infection with USA300Δhla elicited modest protection against secondary SSTI, and complementation of USA300Δsae with hla restored protection but incompletely. Together, these findings support a role for both Hla and other saeRS-regulated antigens in eliciting protection and suggest that host differences in immune responses to saeRS-regulated antigens may determine whether S. aureus infection elicits protective or nonprotective immunity against recurrent infection.
Flow stimulates endothelial cells to release a nitrovasodilator that is potentiated by reduced thiol (1990)

We designed a novel system to study flow-mediated endothelium-dependent vasodilation. Vascular rings of rabbit thoracic aorta were mounted for isometric tension recording in a flow chamber filled with physiological saline solution. The flow chamber contained a stir bar and was mounted on a magnetic stirrer to induce vortical flow. Norepinephrine (NE, 10(-6) M) induced contraction of the vascular rings. Bovine endothelial cells on microcarrier beads added to the chamber had little effect on contraction to NE in the absence of flow. Flow induced endothelium-dependent relaxation of the vascular rings that was dependent on the flow rate. Relaxations were annulled or reversed to a contraction with methylene blue, bovine hemoglobin, or N-monomethyl-L-arginine. Conversely, N-acetyl-L-cysteine augmented the flow-mediated relaxation. Furthermore, in the presence of N-acetyl-L-cysteine, the half-life of the endothelium-dependent relaxing factor was increased. In conclusion, the stimulus of flow induces the release by endothelial cells of a diffusible, short-lived factor with the attributes of a nitrovasodilator. The action of this endogenous vasodilator is augmented by the reduced thiol N-acetyl-L-cysteine.
STUDY OF INHIBITORY EFFECTS OF AN ANTIANGIOGENIC SOMATOSTATIN-CAMPTOTHECIN CONJUGATE ON LASER-INDUCED CHOROIDAL NEOVASCULARIZATION IN RATS (2005)

Part 1: Camptothecin-somatostatin conjugate injected intravitreally appeared safe at concentrations of 10(-5)M or less. Part 2: Conjugate JF-10-81 at a concentration of 10(-5)M administered intravitreally 1 to 3 weeks after laser demonstrated statistically significant efficacy in the treatment of choroidal neovascularization.
BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers (2014)

http://dunbrack.fccc.edu/BAM.
KRS: An Environmentally Robutst Resist Based on Fast Reaction kinetics. (1995)

An environmentally stable resist with high contrast, sensitivity and resolution is presented. Delay stability in excess of 24 hr. has been achieved with insignificant change in linewidth. The resist also demonstrates extreme insensitivity to PEB, showing insignificant linewidth changes over a PEB temperature variation between 20C-100C. The resist is sensitive to DUV, X-ray and a-beam radiation. Linearity down to 0.25 t m using 0.5NA MSII (248 nm) tool has been demonstrated. The resist shows better than 0.8 m DOF and 15% DL at 0.25 m line and space pairs. Resolution down to 75 nm line and space pairs has been demonstrated with 100 KeV e-beam tool.
Effect of aging and Mn substitution on anisotropy of third generation piezoelectrics (2018)

We study the aging and Mn doping effect on third generation lead based relaxor single crystals. We measured the polarization (PE) and strain with applied field on two perpendicular orientations of the rhombohedral pseudocubic [001] poled crystal. To understand these effects along the average dipoles/defect dipoles direction, we adopt a simple model with direction cosine and sine of polarization and strain. We found that when the PE measurement is perpendicular to average defect dipoles, a double loop is observed, and when it is parallel an asymmetric response is observed. We propose that the varied response found in PE measurements depend on the relative direction of average dipoles/defect dipoles to the measurement direction.
Evaluation of adaptive phased array antenna, far-field nulling performance in the near-field region (1990)

A theory for analyzing the behavior of adaptive phased array antennas illuminated by a near-field interference test source is presented. Conventional phased array near-field focusing is used to produce an equivalent far-field antenna pattern at a range distance of one to two aperture diameters from the adaptive antenna under test. The antenna is assumed to be a linear array of isotropic receive elements. The interferer is assumed to be a bandlimited noise source radiating from an isotropic antenna. The theory is developed for both partially and fully adaptive arrays. Results are presented for the fully adaptive array case with single and multiple interferers. The results indicate that near-field and far-field adaptive nulling can be equivalent. The adaptive nulling characteristics studied in detail are the array radiation patterns, adaptive cancellation, covariance matrix eigenvalues, and adaptive array weights.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structural and Functional Characterization of 4‐Hydroxyphenylacetate 3‐Hydroxylase from Escherichia coli (2019)

The hydroxylation of phenols into polyphenols, which are valuable chemicals and pharmaceutical products, is a challenging reaction. The search for green synthetic processes has led to considering microorganisms and pure hydroxylases as catalysts for phenol hydroxylation. Herein, we report the structural and functional characterization of the flavin adenine dinucleotide (FAD)-dependent 4-hydroxyphenylacetate 3-monooxygenase from Escherichia coli, named HpaB. It is shown that this enzyme enjoys a relatively broad substrate specificity, which allows the conversion of a number of non-natural phenolic compounds, such as tyrosol, hydroxymandelic acid, coumaric acid, hydroxybenzoic acid and its methyl ester, and phenol, into the corresponding catechols. The reaction can be performed by using a simple chemical assay based on formate as the electron donor and the organometallic complex [Rh(bpy)Cp*(H<sub>2</sub> O)]<sup>2+</sup> (Cp*: 1,2,3,4,5-pentamethylcyclopentadiene, bpy: 2,2'-bipyridyl) as the catalyst for FAD reduction. The availability of a crystal structure of HpaB in complex with FAD at 1.8 Å resolution opens up the possibility of the rational tuning of the substrate specificity and activity of this interesting class of phenol hydroxylases.
Large environment rendering using plenoptic primitives (2003)

One of the most difficult tasks in computer graphics is to enable virtual walkthroughs in very large and complicated environments that are photorealistic, seamless, and in real time. Current image-based rendering techniques, while capable of photorealism and interactive speeds, have failed in practice to extend to visualizations of such environments. We demonstrate an approach that defines a virtual walkthrough experience using plenoptic primitives (PPs). A PP can be any type of local visual experience: 360/spl deg/ static panorama, panoramic video (PV), lumigraph/light field representation, or concentric mosaics (CMs). By combining them judiciously, user experience can be authored with significantly reduced effort while maintaining high-quality user experience. We illustrate our technique on synthetic and real environments using PVs and CMs and show how the problem of achieving smooth transitions among PVs and CMs can be solved by using position-dependent local geometries.
About the ferroelastic phase transition in phenothiazine (1992)

Abstract A detailed Brillouin scattering study of the low temperature phase of phenothiazine reasonably explains the slightly 1rst order character of this structural phase transition (SPT) and the non observation of any soft optical mode due to a non negligible order parameter relaxation time. Results also confirm the possibility of a pure ferroelastic SPT.
A Generic Strategy Framework for Policy-directed Autonomous Trading Agents (2010)

Abstract: In this paper, a strategy framework for coordinating decentralized autonomous agents is presented and applied within a smart energy grid. The framework brings together the concept of policy-based computing and market-based coordination. In this context, agents can be seen as self-interested entities that are governed by their local policies. Efficient coordination between these self-interested agents is realized through a market mechanism that incentivizes the agents to reveal their policies to the market. By knowing the agent’s policies, an efficient solution for the overall system can be determined. Leveraging a declarative, policy-based approach facilities the specification of highly customizable strategies that can be easily adapted to various resources and markets. As an example for a realworld application, the framework is used for efficient balancing of decentralized energy supply (e.g. photovoltaic, wind power, CHP) and demand (e.g. households, businesses) in a power grid. 1
P037: High breadth whole exome sequencing of circulating tumor DNA identifies novel recurrent genetic alterations in Hodgkin lymphoma (2022)

Hodgkin lymphoma (HL) is a B-cell lymphoma with a generally favorable prognosis. However, side effects of aggressive front-line treatment and difficult-to-treat relapsed/refractory disease are still a clinical challenge. A better understanding of the biological diversity of HL at baseline might help to further individualize the treatment of patients and thus ultimately improve outcome. A broad characterization of the genetic drivers of HL is highly important to improve our understanding of the biological diversity of HL. Here, we present the results of our study using whole-exome sequencing of circulating tumor (ct)DNA to broadly characterize the HL oncogenome in 165 patients. After extraction of germline and cell-free DNA, WES was performed, targeting 37 Mb of the human genome. An in-house customized bioinformatic pipeline including twofold error reduction using unique molecular identifiers (UMIs) and digital error suppression was used as previously described by us (Sobesky et. al., Med, 2021). The median ctDNA concentration per patient was 2.26 log haploid genome equivalents per milliliter (log hGE/ml) (range: 1.41–4.18 log hGE/ml) without significant correlation with clinical parameters such as sex, international prognostic score (IPS) or clinical stage. In addition to the detection of several genetic aberrations involved in the pathogenesis of HL (such as B2M, CSF2RB, GNA13, SOCS1), we were able to detect several novel, recurrently mutated potential oncogenes and tumor suppressor genes. Among the most frequently mutated genes not previously described in HL were olfactory receptor family 10 subfamily G member 7 (OR10G7) (11.5%), Apolipoprotein B (APOB) (10.3%) and Filaggrin 2 (FLG2) (9.7%). Furthermore, several previously undescribed copy number variations (CNV) were detected (losses: 13q13.1, 1p36.13a, 6p21.33; gains: 19q13.42, 9p24, 12q12). To decipher the detected genes’ and CNVs’ contribution to the biological diversity of HL, we performed non-negative matrix factorization. Furthermore, neoantigen load was assessed through human-leukocyte antigen (HLA) sequencing. Detailed results will be presented at the meeting. In conclusion, our ctDNA based WES approach provides sufficient sensitivity to both perform genotyping in HL and detecting novel genomic aberrations potentially involved in the pathogenesis of HL.
Microplastics Originating from Polymer Blends: An Emerging Threat? (2021)

No one can have missed the growing global environmental problems with plastics ending up as microplastics in food, water, and soil, and the associated effects on nature, wildlife, and humans. A hitherto not specifically investigated source of microplastics is polymer blends. A 1 g polymer blend can contain millions to billions of micrometer-sized species of the dispersed phase and therefore aging-induced fragmentation of the polymer blends can lead to the release of an enormous amount of microplastics. Especially if the stability of the dispersed material is higher than that of the surrounding matrix, the risk of microplastic migration is notable, for instance, if the matrix material is biodegradable and the dispersed material is not. The release can also be much faster if the matrix polymer is biodegradable. The purpose of writing this feature article is to arise public and academic attention to the large microplastic risk from polymer blends during their development, production, use, and waste handling.
Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq (2016)

In this study, we provided novel transcriptomic information on Phlebia sp. MG-60, and these RNA-seq data were useful in targeting genes involved in ethanol production for future genetic engineering.
MR1-restricted mucosal-associated invariant T (MAIT) cells respond to mycobacterial vaccination and infection in nonhuman primates (2016)

Studies on mucosal-associated invariant T cells (MAITs) in nonhuman primates (NHP), a physiologically relevant model of human immunity, are handicapped due to a lack of macaque MAIT-specific reagents. Here we show that while MR1 ligand-contact residues are conserved between human and multiple NHP species, three T-cell receptor contact-residue mutations in NHP MR1 diminish binding of human MR1 tetramers to macaque MAITs. Construction of naturally loaded macaque MR1 tetramers facilitated identification and characterization of macaque MR1-binding ligands and MAITs, both of which mirrored their human counterparts. Using the macaque MR1 tetramer we show that NHP MAITs activated in vivo in response to both Bacillus Calmette-Guerin vaccination and Mycobacterium tuberculosis infection. These results demonstrate that NHP and human MR1 and MAITs function analogously, and establish a preclinical animal model to test MAIT-targeted vaccines and therapeutics for human infectious and autoimmune disease.
Hybrid storage designs for continuous operation of solar-powered LiBr-water absorption air-conditioning (2016)

The design of the energy storage serving solar-powered LiBr–water absorption air-conditioning systems to meet 24-h a day operation is an important parameter that determines the performance of the system and optimizes its components. Introducing hybrid storage designs can improve system performance, reduce collector size, lower storage tank capacity, and hence make 24-h a day operating solar-powered LiBr–water absorption air-conditioning systems more feasible. Moreover, hybrid storage designs will ensure uninterrupted operation in case of maintenance for one of the storage tanks. This paper investigates four hybrid storage designs (heat and refrigerant storage, cold and refrigerant stfsorage, heat and cold storage, and heat, cold, and refrigerant storage) for a continuous operation (24 h a day) of solar-powered LiBr–water absorption air-conditioning. The study includes system description, features, and selection analysis for a constant cooling load of 5 kW in a typical family house in Dhahran City, Saudi Arabia. The results indicate that the hybrid cold and refrigerant storage system is the most suitable design for 24-h a day supply of the cooling effect. Copyright © 2016 John Wiley & Sons, Ltd.
Optimal interleaving angle determination in multi paralleled converters considering the DC current ripple and grid Current THD (2015)

A typical application for parallel connected converters is in multi megawatt wind turbine systems. Manipulating the interleaving angle between the Pulse Width Modulated (PWM) carrier waves of each converter can result in reduced grid and DC link current ripple, thus the passive components from the DC link and grid filter can be minimized. In previous studies the optimization of the interleaving angle for either the grid current Total Harmonic Distortion (THD) or the DC link current ripple has been made. In this study a compromise is made in order to maintain a THD of the grid current in a level that complies with the standards, while in the DC link the current ripple is reduced. The dependency of the grid current THD and the DC link current ripple on the interleaving angle were determined by simulations. The results were also validated on a hardware setup.
Magnetically engineered spintronic sensors and memory (2003)

The discovery of enhanced magnetoresistance and oscillatory interlayer exchange coupling in transition metal multilayers just over a decade ago has enabled the development of new classes of magnetically engineered magnetic thin-film materials suitable for advanced magnetic sensors and magnetic random access memories. Magnetic sensors based on spin-valve giant magnetoresistive (GMR) sandwiches with artificial antiferromagnetic reference layers have resulted in enormous increases in the storage capacity of magnetic hard disk drives. The unique properties of magnetic tunnel junction (MTJ) devices has led to the development of an advanced high performance nonvolatile magnet random access memory with density approaching that of dynamic random-access memory (RAM) and read-write speeds comparable to static RAM. Both GMR and MTJ devices are examples of spintronic materials in which the flow of spin-polarized electrons is manipulated by controlling, via magnetic fields, the orientation of magnetic moments in inhomogeneous magnetic thin film systems. More complex devices, including three-terminal hot electron magnetic tunnel transistors, suggest that there are many other applications of spintronic materials.
Design, Synthesis, and Pharmacological Evaluation of Fluorinated Tetrahydrouridine Derivatives as Inhibitors of Cytidine Deaminase (2014)

Several 2'-fluorinated tetrahydrouridine derivatives were synthesized as inhibitors of cytidine deaminase (CDA). (4R)-2'-Deoxy-2',2'-difluoro-3,4,5,6-tetrahydrouridine (7a) showed enhanced acid stability over tetrahydrouridine (THU) 5 at its N-glycosyl bond. As a result, compound 7a showed an improved oral pharmacokinetic profile with a higher and more reproducible plasma exposure in rhesus monkeys compared to 5. Co-administration of 7a with decitabine, a CDA substrate, boosted the plasma levels of decitabine in rhesus monkeys. These results demonstrate that compound 7a can serve as an acid-stable alternative to 5 as a pharmacoenhancer of drugs subject to CDA-mediated metabolism.
Directional neighbor discovery in dual-band systems (2015)

The neighbor discovery process is a key component of Device-to-Device (D2D) communication. This paper considers the problem of directional neighbor discovery in dual-band systems, where wireless devices operate in both mm-wave and microwave frequency bands and employ antenna arrays. Due to the propagation loss, the set of neighbors in a direction at mm-wave frequencies is a subset of the neighbors at microwaves. Consequently, the knowledge of neighbors in one of the bands allows to greatly accelerate the neighbor discovery process. We propose a distributed random discovery algorithm for the mm-wave band, where each device finds the relevant algorithm parameters, i.e., transmission and beam steering probabilities, given only local information at the microwave band. Because each node knows only its own local information, imposition of a fairness condition prevents selfish behavior that would deteriorate network performance. Optimum algorithm parameters are obtained as solutions of a linear program. Simulations show that the proposed scheme outperforms the optimum single-band random scheme and significantly reduces the average discovery time, especially for small numbers of neighbors per beam.
536 Approach of weight reduction for the formula racing vehicle (2006)

In the recent years, the development of an analysis technology enabled a high-accuracy forecast of the vehicle performance. The analysis requires various data. However those data are indeterminacy in early stage. In this article, we researched the technique for forecasting the vehicle performance with a little detailed data in concept stage of development to promote weight reduction and controlling center of gravity.
Platelet factor 4 binds to low-density lipoprotein receptors and disrupts the endocytic itinerary, resulting in retention of low-density lipoprotein on the cell surface (2002)

The influence of platelets on the cellular metabolism of atherogenic lipoproteins has not been characterized in detail. Therefore, we investigated the effect of platelet factor 4 (PF4), a cationic protein released in high concentration by activated platelets, on the uptake and degradation of low-density lipoprotein (LDL) via the LDL receptor (LDL-R). LDL-R-dependent binding, internalization, and degradation of LDL by cultured cells were inhibited 50%, 80%, and 80%, respectively, on addition of PF4. PF4 bound specifically to the ligand-binding domain of recombinant soluble LDL-R (half-maximal binding 0.5 microg/mL PF4) and partially (approximately 50%) inhibited the binding of LDL. Inhibition of internalization and degradation by PF4 required the presence of cell-associated proteoglycans, primarily those rich in chondroitin sulfate. PF4 variants with impaired heparin binding lacked the capacity to inhibit LDL. PF4, soluble LDL-R, and LDL formed ternary complexes with cell-surface proteoglycans. PF4 induced the retention of LDL/LDL-R complexes on the surface of human fibroblasts in multimolecular clusters unassociated with coated pits, as assessed by immuno-electron microscopy. These studies demonstrate that PF4 inhibits the catabolism of LDL in vitro in part by competing for binding to LDL-R, by promoting interactions with cell-associated chondroitin sulfate proteoglycans, and by disrupting the normal endocytic trafficking of LDL/LDL-R complexes. Retention of LDL on cell surfaces may facilitate proatherogenic modifications and support an expanded role for platelets in the pathogenesis of atherosclerosis.
Subpicosecond stable infrared pulses from mode-locked semiconductor lasers (1988)

Mode-locked semiconductor lasers are important sources for many applications because (1) they are compact, which is important for use as sources for commercial electrooptic samplers; (2) they operate at the important wavelengths of 0.82, 1.3, and 1.55 μm rather than visible wavelengths and are thus suitable for ultrafast experiments on semiconductor materials; (3) they are tunable, so excitation at various wavelengths above and below the band gap can be made; (4) they have very tow amplitude and phase noise, particularly when compared to compressed YAG laser pulses; and (5) several subpicosecond sources can be synchronized together by driving several actively mode- locked lasers off the same microwave oscillator.