gebhart/patrepeval huggingface dataset:
Bovine Serum Albumin-Protected Gold Nanoclusters for Sensing of SARS-CoV-2 Antibodies and Virus (2023)

An approach to assess severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (and past infection) was developed. For virus detection, the SARS-CoV-2 virus nucleocapsid protein (NP) was targeted. To detect the NP, antibodies were immobilized on magnetic beads to capture the NPs, which were subsequently detected using rabbit anti-SARS-CoV-2 nucleocapsid antibodies and alkaline phosphatase (AP)-conjugated anti-rabbit antibodies. A similar approach was used to assess SARS-CoV-2-neutralizing antibody levels by capturing spike receptor-binding domain (RBD)-specific antibodies utilizing RBD protein-modified magnetic beads and detecting them using AP-conjugated anti-human IgG antibodies. The sensing mechanism for both assays is based on cysteamine etching-induced fluorescence quenching of bovine serum albumin-protected gold nanoclusters where cysteamine is generated in proportion to the amount of either SARS-CoV-2 virus or anti-SARS-CoV-2 receptor-binding domain-specific immunoglobulin antibodies (anti-RBD IgG antibodies). High sensitivity can be achieved in 5 h 15 min for the anti-RBD IgG antibody detection and 6 h 15 min for virus detection, although the assay can be run in "rapid" mode, which takes 1 h 45 min for the anti-RBD IgG antibody detection and 3 h 15 min for the virus. By spiking the anti-RBD IgG antibodies and virus in serum and saliva, we demonstrate that the assay can detect the anti-RBD IgG antibodies with a limit of detection (LOD) of 4.0 and 2.0 ng/mL in serum and saliva, respectively. For the virus, we can achieve an LOD of 8.5 × 10<sup>5</sup> RNA copies/mL and 8.8 × 10<sup>5</sup> RNA copies/mL in serum and saliva, respectively. Interestingly, this assay can be easily modified to detect myriad analytes of interest.
TOPOCHEMISTRY OF SiO2 WOOD-INORGANIC COMPOSITES FOR ENHANCING WATER-REPELLENCY (1999)

Methyltrimethoxysilane (MTMOS) was used to prepare the SiO2 wood-inorganic composites. To enhance the properties of these composites, 2-heptadecafluorooctylethyltrimethoxysilane (HFOETMOS) as a property enhancer was added to this reaction system for SiO2 wood-inorganic composites. To elucidate the mechanism for enhancing the water-repellent property in the HFOETMOS-SiO2 wood-inorganic composites, the composites with various weight percent gains (WPGs) were prepared, and the prepared composites with the lower WPG revealed the better property in water-repellency, whereas those with the higher WPG could not attain the high water-repellent property. SEM-EDXA analysis on these composites revealed that the HFOETMOS-derived residues were concentrated on the boundary between the cell wall and cell lumen in both composites with the lower and higher WPGs, while SiO2 gels were almost uniformly distributed within the cell walls in the composites with lower WPG. SiO2 gels in the composites with higher WPG were distributed in a similar manner but slightly higher in its concentration at the boundary between the cell wall and cell lumen. From these results, it was assumed that for the composites with lower WPG, the cell wall would be covered with the long hydrophobic alkyl residue of the HFOETMOS, whereas for the composites with higher WPG, SiO2 gels formed in the cell lumen would have prevented HFOETMOS-derived residues from being exposed uniformly over the surface of cell wall. This may be why the different water-repellent properties were shown between the composites with higher and lower WPGs. These results suggest that the topochemical effects of the SiO2 gels and HFOETMOS-derived residues exist for the enhancement of water-repellent property.
Real-time kinematic positioning for unmanned air vehicles (2016)

Real-Time Kinematic (RTK) positioning with lowcost mass-market Global Navigation Satellite System (GNSS) receivers and antennas is attractive for precise landing of Unmanned Air Vehicles (UAV). Code multipath mitigation and a reliable resolution of the carrier phase integer ambiguities are two challenges. In this paper, we describe an RTK method which estimates a code multipath parameter for each double difference to fully exploit the temporal correlation of multipath and to prevent a mapping of the multipath into the baseline and ambiguities. The ambiguity fixing is performed in two phases: In the first phase, sets of integer candidate vectors are derived from the float solution at multiple epochs. We merge the sets of candidate vectors to increase the likelihood of including the correct candidate vector in the set of candidates. In the second phase, we track each candidate vector by determining a single epoch baseline estimate for each candidate vector. The respective measurement residuals are accumulated over time to increase the likelihood of selecting the correct candidate. The proposed method was applied to real measurements from two low-cost ANavS GPS modules and enabled a millimeterlevel positioning accuracy despite code multipath of up to 50 m.
Coupling of hydrodynamics and chemical reaction in gas‐lift reactors (1999)

Abstract A model was developed to study the strong coupling between hydrodynamics and chemical reaction that occurs in external‐loop gas‐lift reactors. The model predicts the liquid circulation rate, as well as the axial profiles of gas holdup, pressure, gas and liquid velocity, and reactant conversion in the riser. The study on the first‐order, irreversible, isothermal reaction in the gas phase nA→B with a change in the number of moles on reaction shows that for n&gt;1, the gas holdup decreases along the riser, the liquid circulation rate is lower than that in the absence of reaction, and liquid circulation decreases as n and k increase. The bubble radius at the sparger and the inlet gas composition can have important effects on reactor performance. Scale‐up strategies that involve increasing the reactor length result in higher reactant conversion, but a lower ratio of liquid circulation rate to gas feed rate.
Solving the α-Conotoxin Folding Problem: Efficient Selenium-Directed On-Resin Generation of More Potent and Stable Nicotinic Acetylcholine Receptor Antagonists (2010)

Alpha-conotoxins are tightly folded miniproteins that antagonize nicotinic acetylcholine receptors (nAChR) with high specificity for diverse subtypes. Here we report the use of selenocysteine in a supported phase method to direct native folding and produce alpha-conotoxins efficiently with improved biophysical properties. By replacing complementary cysteine pairs with selenocysteine pairs on an amphiphilic resin, we were able to chemically direct all five structural subclasses of alpha-conotoxins exclusively into their native folds. X-ray analysis at 1.4 A resolution of alpha-selenoconotoxin PnIA confirmed the isosteric character of the diselenide bond and the integrity of the alpha-conotoxin fold. The alpha-selenoconotoxins exhibited similar or improved potency at rat diaphragm muscle and alpha3beta4, alpha7, and alpha1beta1 deltagamma nAChRs expressed in Xenopus oocytes plus improved disulfide bond scrambling stability in plasma. Together, these results underpin the development of more stable and potent nicotinic antagonists suitable for new drug therapies, and highlight the application of selenocysteine technology more broadly to disulfide-bonded peptides and proteins.
An economic view on mobile and fixed broadband networks in Germany (2015)

Broadband markets are subjected to competition of different fixed (copper, coax, fiber) and mobile technologies (4G/LTE, 5G). In the case of internet-access, fixed broadband connections reach currently higher connections speeds than mobile connections. Due to new technologies as LTE Advanced and 5G, mobile accesses get a bandwidth boost and reach a stronger position in terms of broadband speed. This paper discusses mobile radio technologies' influence on broadband markets in the world and especially in Germany. We will answer the question: Will mobile infrastructures dominate broadband markets in terms of market share, access speed, distribution and number of subscribers? First we will give an overview of the current mobile and fixed broadband developments in the world and particularly in Germany, focusing on the number of subscribers, data traffic and revenues. In the second part of the paper, we discuss the field of competition and in which fields mobile and fixed infrastructures are in a direct competition. Furthermore, we will present the effect of the different technical characteristics of the mobile and fixed technologies and their impact on the broadband markets. Finally, we try to figure out how broadband technologies will develop in the short and long run.
Sequence of αPD-1 relative to local tumor irradiation determines the induction of abscopal antitumor immune responses (2021)

Although radiotherapy has been used for over a century to locally control tumor growth, alone it rarely induces an abscopal response or systemic antitumor immunity capable of inhibiting distal tumors outside of the irradiation field. Results from recent studies suggest that combining immune checkpoint blockades to radiotherapy may enhance abscopal activity. However, the treatment conditions and underlying immune mechanisms that consistently drive an abscopal response during radiation therapy combinations remain unknown. Here, we analyzed the antitumor responses at primary and distal tumor sites, demonstrating that the timing of αPD-1 antibody administration relative to radiotherapy determined the potency of the induced abscopal response. Blockade of the PD-1 pathway after local tumor irradiation resulted in the expansion of polyfunctional intratumoral CD8<sup>+</sup> T cells, a decrease in intratumoral dysfunctional CD8<sup>+</sup> T cells, expansion of reprogrammable CD8<sup>+</sup> T cells, and induction of potent abscopal responses. However, administration of αPD-1 before irradiation almost completely abrogated systemic immunity, which associated with increased radiosensitivity and death of CD8<sup>+</sup> T cells. The subsequent reduction of polyfunctional effector CD8<sup>+</sup> T cells at the irradiated tumor site generated a suboptimal systemic antitumor response and the loss of abscopal responses. Therefore, this report maximizes the potential synergy between radiotherapy and αPD-1 immunotherapy, information that will benefit clinical combinations of radiotherapy and immune checkpoint blockade.
Enhanced Conversion of DNA Radical Damage to Double Strand Breaks by 1,2,4-Benzotriazine 1,4-Dioxides Linked to a DNA Binder Compared to Tirapazamine (2003)

Targeting the anticancer compound tirapazamine (3-amino-1,2,4-benzotriazine 1,4-dioxide; TPZ) to DNA by appended binding units has been found to greatly increase the free radical-induced production of both single and double strand breaks under hypoxia compared to TPZ itself. The (*)OH radical, produced upon the radiolysis of aqueous solutions, was used to damage plasmid DNA, and both types of strand breaks were quantified in the absence and presence of TPZ and analogues. Targeted analogues of TPZ show increases of 12-18-fold in single strand breaks, and 60-110-fold in double strand breaks, as compared with TPZ itself. The observed increased formation of double strand breaks under hypoxia is the likely mechanism for the large increase in potency previously demonstrated for a similarly targeted analogue of TPZ as a bioreductive drug (Delahoussaye et al. (2003) Biochem. Pharmacol. 65, 1807-1815). The one-electron reduction potential of the two-electron reduced metabolite of TPZ (the 1-oxide, SR 4317) has been measured as -568 +/- 9 mV, which is sufficiently high to oxidize carbon-centered radicals such as those formed on the sugar moiety of DNA. Targeting the 1-oxide moiety to DNA resulted in a ca. 50% increase in single strand breaks over that seen for TPZ without the dramatic increase in double strand breaks seen for the similarly targeted benzotriazine 1,4-dioxides. These studies support the mechanism by which the reduction of TPZ to an oxidizing radical leads to free radical damage on DNA that can be further oxidized by TPZ or SR4317 (and especially well by DNA-targeted analogues) to yield lesions resulting in strand breakage. The targeting of benzotriazine 1,4-dioxide analogues to DNA by appending binding units to the compounds thus represents an efficient system for inducing strand breaks in DNA.
Paradoxical sex-specific patterns of autoantibody response to SARS-CoV-2 infection (2021)

Background. Amidst the millions of individuals affected directly by the pandemic, pronounced sex differences in the susceptibility and response to SARS-CoV-2 infection remain poorly understood. Emerging evidence has highlighted the potential importance of autoimmune activation in modulating not only the acute response but also recovery trajectories following SARS-CoV-2 exposure. Given that immune-inflammatory activity can be sex-biased in the setting of severe COVID-19 illness, we deliberately examined sex-specific autoimmune reactivity to SARS-CoV-2 in the absence of extreme clinical disease. 
Methods. We used a bead-based array containing over 90 autoantigens previously linked to a range of classic autoimmune diseases to assess autoantibody (AAB) titers in 177 participants. All participants had confirmed evidence of prior SARS-CoV-2 infection based on presence of positive anti-nucleocapsid IgG serology results (Abbott Diagnostics, Abbott Park, Illinois). We used multivariate analysis to determine whether sex-bias was associated with increased rates of AABs reactivity and symptom burden after SARS-CoV2 infection. 
Results. 82.4% of AABs reactivity was associated with being male compared to 17.6% with female. We found a diversity of AABs responses that exhibited sex-specific patterns of frequency distribution as well as associations with symptomatology and symptom burden. 
Conclusion. Our results reveal a remarkable sex-specific prevalence and selectivity of AAB responses to SARS-CoV-2. Further understanding of the nature of triggered and persistent AAB activation among men and women exposed to SARS-CoV-2 will be essential for developing effective interventions against immune-mediated sequelae of COVID-19.
Outcomes of patients with POEMS syndrome treated initially with radiation (2013)

POEMS syndrome is a rare plasma cell dyscrasia presenting with polyneuropathy and other systemic findings. Patients with 1 to 3 bone lesions and negative bone marrows are often treated with involved field radiation therapy as the initial and potentially definitive therapy. Long-term outcomes of patients treated with this approach have not been systematically studied. Of the 146 patients with POEMS syndrome seen at the Mayo Clinic between January 1999 and September 2011, 38 (26%) were given targeted radiation as their initial primary therapy and are the ones studied here. The median number of bone lesions was 1 (range: 1-6). The median dose of radiation administered was 45 Gy (range: 35-54 Gy). Complete or partial hematologic, vascular endothelial growth factor, fluorodeoxyglucose-positron emission tomography, and clinical responses were documented in 31%, 14%, 22%, and 47%, respectively. With median follow-up of 43 months, the 4-year overall survival is 97% and event-free survival is 52%. Risk factors for needing salvage therapy included reduced pulmonary diffusing capacity of carbon monoxide and increased urinary total protein. The presence of 3 lesions compared with 1 or 2 did not increase risk for treatment failure. Among selected patients with POEMS syndrome, radiation produces durable, meaningful responses.
Buckyball Nucleation of HiPco Tubes (2012)

The purpose of this innovation is to enhance nucleation of single-wall nanotubes (SWNTs) in the HiPco process, selectively producing 10,10 tubes, something which until now has not been thought possible. This is accomplished by injecting C60, or a derivative of C60, solubilized in supercritical CO2 together with a transition metal carboneal cocatalyst into the HiPco reactor. This is a variant on the supercritical disclosure. C60 has never been used to nucleate carbon nanotubes in the gas phase. C60 itself may not have adequate solubility in supercritical CO2. However, fluorinated C60, e.g., C60F36, is easy to make cheaply and should have much enhanced solubility.
Multicore multimode fibers with high spatial density (2016)

Multicore multimode fiber is a promising candidate for achieving high spatial density SDM systems, since it can increase the spatial channel count in a fiber using the multiplicity of the core and mode. In this presentation, recent progress of multicore multimode fibers is reviewed.
Characterization and Serologic Analysis of theTreponema pallidumProteome (2010)

Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease characterized by widespread tissue dissemination and chronic infection. In this study, we analyzed the proteome of T. pallidum by the isoelectric focusing (IEF) and nonequilibrating pH gel electrophoresis (NEPHGE) forms of two-dimensional gel electrophoresis (2DGE), coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis. We determined the identity of 148 T. pallidum protein spots, representing 88 T. pallidum polypeptides; 63 of these polypeptides had not been identified previously at the protein level. To examine which of these proteins are important in the antibody response to syphilis, we performed immunoblot analysis using infected rabbit sera or human sera from patients at different stages of syphilis infection. Twenty-nine previously described antigens (predominantly lipoproteins) were detected, as were a number of previously unidentified antigens. The reactivity patterns obtained with sera from infected rabbits and humans were similar; these patterns included a subset of antigens reactive with all serum samples tested, including CfpA, MglB-2, TmpA, TmpB, flagellins, and the 47-kDa, 17-kDa, and 15-kDa lipoproteins. A unique group of antigens specifically reactive with infected human serum was also identified and included the previously described antigen TpF1 and the hypothetical proteins TP0584, TP0608, and TP0965. This combined proteomic and serologic analysis further delineates the antigens potentially useful as vaccine candidates or diagnostic markers and may provide insight into the host-pathogen interactions that occur during T. pallidum infection.
Dynamic manipulation of particles via transformative optofluidic waveguides (2015)

Optofluidics is one of the most remarkable areas in the field of microfluidic research. Particle manipulation with optofluidic platforms has become central to optical chromatography, biotechnology, and μ-total analysis systems. Optical manipulation of particles depends on their sizes and refractive indices (n), which occasionally leads to undesirable separation consequences when their optical mobilities are identical. Here, we demonstrate rapid and dynamic particle manipulation according to n, regardless of size. Integrated liquid-core/solid-cladding (LS) and liquid-core/liquid-cladding (L(2)) waveguides were fabricated and their characteristics were experimentally and theoretically determined. The high and low n particles showed the opposite behaviors by controlling the contrast of their n values to those of the working fluids. The LS waveguide was found to successfully manipulate particles according to n, and the L(2) waveguide was found to provide additional system stability and flexibility, compared to the LS system.
High performance technique for database applications using a hybrid GPU/CPU platform (2011)

Many database applications, such as sequence comparing, sequence searching, and sequence matching, etc, process large database sequences. we introduce a novel and efficient technique to improve the performance of database applications by using a Hybrid GPU/CPU platform. In particular, our technique solves the problem of the low efficiency resulting from running short-length sequences in a database on a GPU. To verify our technique, we applied it to the widely used Smith-Waterman algorithm. The experimental results show that our Hybrid GPU/CPU technique improves the average performance by a factor of 2.2, and improves the peak performance by a factor of 2.8 when compared to earlier implementations.
Optimal pre- and post-filtering in noisy sampled-data systems (1986)

In this thesis we consider the problem of jointly optimizing the pre- and post-filters in a communications or storage system, with optimality considered in a weighted mean-square error sense. We adopt a system model that is general enough to be applicable to a wide variety of problems, such as broadcasting, tape recording, telemetry, and signal coding, among others. Our fundamental assumptions throughout this work are that the pre- and post-filters are linear and that all signal and noise spectra of interest are known. We derive the optimal pre- and post-filters for three basic classes of systems, characterized by infinite impulse response (IIR), finite impulse response (FIR), and block filters. Whenever appropriate, we present filters with nearly optimal performance that can be efficiently implemented. We also derive analytic forms and a fast version for a recently introduced class of pre- and post-filters for block processing with overlapping basis functions, namely, &amp;quot;Lapped Orthogonal Transforms &amp;quot; (LOT&amp;apos;s). In all of these classes, for typical image processing and coding applications, we obtain improvements in the weighted
Studies directed toward the synthesis of (+)-mycotrienin I. Asymmetric synthesis of the C9N21 aromatic synthon (1995)

The asymmetric synthesis of the C9N21 fragment of (+)-mycotrienin I is described employing chiral allylsilane bond construction methodology for the installation of the C12C13 absolute stereochemical relationships. In this convergent synthesis the construction of the C9C16 and C17N21 aromatic synthon subunits and their coupling through a lithio dithiane alkylation strategy are detailed.
Use of topical mineral powder as monotherapy for treatment of active peptic ulcer bleeding (2022)

Hemospray is an effective initial treatment for patients with active peptic ulcer bleeding, but care should be taken to monitor for recurrent bleeding. (Clinical trial registration number: NCT01306864.).
Supplementary Figure 4 from Sangivamycin-like Molecule 6 Exhibits Potent Anti-Multiple Myeloma Activity through Inhibition of Cyclin-Dependent Kinase-9 (2023)

&lt;p&gt;PDF file, 66K, SLM6 does not inhibit PKC signaling at drug concentrations that induce death of MM cells.&lt;/p&gt;
Solid-phase synthesis of oligo(2'-deoxyxylonucleotides) and PCR amplification of base-modified DNA fragments. (1991)

1-(2'-Deoxy-beta-D-threo-pentofuranosyl)thymine (xTd) and -adenine (xAd) were converted into their appropriately protected 3'-phosphonates 1a, 2a as well as their 2-cyanoethyl phosphoramidites 1b, 2b. These compounds were used for solid-phase syntheses of the oligo(2'-deoxy-beta-D-xylonucleotides) 5-8. Structural properties and behavior against nucleases is described. Apart from oligo(2'-deoxyxylonucleotides) the PCR-amplification of a pUC18 DNA fragment with Taq polymerase was studied in the presence of the 7-deazapurine derivatives of dGTP, dATP, and dITP. The incorporation efficiency of the modified compounds was compared with those of the parent nucleotides. 7-Deaza-2'-deoxyguanosine protected the DNA-fragment from hydrolysis by the restriction endodeoxyribonuclease Eco RI, Pst I, Bam HI, and Sma I if the nucleoside was located within the recognition site.