gebhart/patrepeval huggingface dataset:
A novel hemagglutinin protein produced in bacteria protects chickens against H5N1 highly pathogenic avian influenza viruses by inducing H5 subtype-specific neutralizing antibodies (2017)

The highly pathogenic (HP) H5N1 avian influenza viruses (AIVs) cause a mortality rate of up to 100% in infected chickens and pose a permanent pandemic threat. Attempts to obtain effective vaccines against H5N1 HPAIVs have focused on hemagglutinin (HA), an immunodominant viral antigen capable of eliciting neutralizing antibodies. The vast majority of vaccine projects have been performed using eukaryotic expression systems. In contrast, we used a bacterial expression system to produce vaccine HA protein (bacterial HA) according to our own design. The HA protein with the sequence of the H5N1 HPAIV strain was efficiently expressed in Escherichia coli, recovered in the form of inclusion bodies and refolded by dilution between two chromatographic purification steps. Antigenicity studies showed that the resulting antigen, referred to as rH5-E. coli, preserves conformational epitopes targeted by antibodies specific for H5-subtype HAs, inhibiting hemagglutination and/or neutralizing influenza viruses in vitro. The proper conformation of this protein and its ability to form functional oligomers were confirmed by a hemagglutination test. Consistent with the biochemical characteristics, prime-boost immunizations with adjuvanted rH5-E. coli protected 100% and 70% of specific pathogen-free, layer-type chickens against challenge with homologous and heterologous H5N1 HPAIVs, respectively. The observed protection was related to the positivity in the FluAC H5 test (IDVet) but not to hemagglutination-inhibiting antibody titers. Due to full protection, the effective contact transmission of the homologous challenge virus did not occur. Survivors from both challenges did not or only transiently shed the viruses, as established by viral RNA detection in oropharyngeal and cloacal swabs. Our results demonstrate that vaccination with rH5-E. coli could confer control of H5N1 HPAIV infection and transmission rates in chicken flocks, accompanied by reduced virus shedding. Moreover, the role of H5 subtype-specific neutralizing antibodies in anti-influenza immunity and a novel correlate of protection are indicated.
Synthesis of Armchair Graphene Nanoribbons on Germanium-on-Silicon (2019)

The\nsynthesis of graphene nanoribbons on complementary metal–oxide–semiconductor-compatible\nsubstrates is a significant challenge hindering their integration\ninto commercial semiconductor electronics. Here, the bottom-up synthesis\nof armchair graphene nanoribbons on epilayers of Ge on Si(001) via\nchemical vapor deposition is demonstrated. The synthesis leverages\nthe previous discovery that graphene crystal growth can be driven\nwith an extreme shape anisotropy on Ge(001) surfaces to directly form\nnanoribbons. However, compared to nanoribbon synthesis on Ge(001),\nsynthesis on Ge/Si(001) is complicated by the possibility of Si diffusion\nto the Ge surface and the presence of threading dislocations. Herein,\nwe demonstrate that similar to Ge(001), armchair nanoribbons with\nfaceted edges and sub-10 nm widths can indeed be grown on Ge/Si(001).\nThe nanoribbon synthesis proceeds faster than the diffusion of Si\nto the Ge surface if a sufficiently thick Ge epilayer is used (e.g.,\n3 μm), thereby avoiding competing reactions that form SiC. Moreover,\nthreading dislocations in the Ge epilayer are not observed to affect\nthe nucleation or anisotropic growth kinetics of the nanoribbons.\nThese results demonstrate that previous successes in graphene nanoribbon\nsynthesis on Ge(001) can be extended to Si(001) by using epilayers\nof Ge, motivating the future exploration of this promising platform\nfor hybrid semiconducting graphene/Si electronics.
High-Throughput Characterization of Small and Large Molecules Using Only a Matrix and the Vacuum of a Mass Spectrometer (2015)

Matrix assisted ionization vacuum (MAIV) rapidly generates gas-phase analyte ions from subliming solid-phase matrix:analyte crystals for analysis by mass spectrometry (MS). Ionization from the solid-phase allows the use of a variety of surfaces for introducing matrix:analyte samples to the vacuum of a mass spectrometer, including common laboratory materials, such as disposable pipet tips, filter paper, tooth picks, and nylon mesh. MAIV is shown here to be capable of analyses as fast as 3 s per sample with achievable sensitivities in the low femtomole range. MAIV-MS coupled with ion mobility spectrometry (IMS)-MS and tandem mass spectrometry (MS/MS) is shown to be especially powerful for analysis and characterization of a wide range of molecules ranging from small molecules such as drugs and metabolites (∼300 Da) to intact proteins (25.6 kDa). Automated sample introduction is demonstrated on two different commercial mass spectrometers using a programmable XYZ stage. A MAIV high-throughput nontargeted MS(E) approach is also demonstrated utilizing IMS for rapid characterization of small molecules and peptides from standard solutions, as well as drug spiked human urine.
Microstructure of the High-Strength Magnesium Alloy on Cylinder Upsetting (2012)

Magnesium alloys are known for its light weight. Due to the desirable properties,magnesium is required in the fields such as transportation from the point of significant energy savings.Magnesium alloys are also being expected as an alternative for the next generation materials in fieldsof variety. At present, casting and thixomolding process are the main manufacturing methods formagnesium alloy parts. The major problem for forging of magnesium alloy is the lack of basicprocess data, such as strength and ductility.Mg96Zn2Y2 is a high strength magnesium alloy material newly developed by Dr. Y. Kawamurain Japan. It has attracted much attention recently. The name of this alloy is called as 'Kumadai Goukin'.'Kumadai Goukin' of high strength magnesium alloy material is expected as forged parts of theautomobile and materials for aerospace applications. It is necessary to clarify forging processcharacteristics of this material.The purpose of the present study is to evaluate the processing property of Mg96Zn2Y2 material.In this study, cylinder upsetting tests were performed under various deformation temperatures andspeeds for 'Kumadai Goukin'. Furthermore, the dependence of flow stress and ductility of thesematerials to processing temperature and speed was evaluated. We performed microstructureobservation to examine mechanism. We were analyzed that ductility of this material had improved.
Determining topological charge of an optical beam using a wedged optical flat (2017)

The topological charge of a beam carrying an optical vortex is an important parameter that specifies the amount of orbital angular momentum carried by the beam and the azimuthal order of the beam mode. We present an experimental method to determine the sign and magnitude of the topological charge using a wedged optical flat as a lateral shearing interferometer. When the curvature of the wavefront is adjusted to be planar, the fringe pattern generated by the shearing interferometer consists of two conjoined forks that unambiguously identify the topological charge of the beam. We also investigated the changes in the pattern when the wedged flat is rotated.
Discovery of Novel Triazole-Based Opioid Receptor Antagonists (2006)

We report the computer-aided design, chemical synthesis, and biological evaluation of a novel family of delta opioid receptor (DOR) antagonists containing a 1,2,4-triazole core structure that are structurally distinct from other known opioid receptor active ligands. Among those delta antagonists sharing this core structure, 8 exhibited strong binding affinity (K(i) = 50 nM) for the DOR and appreciable selectivity for delta over mu and kappa opioid receptors (delta/mu = 80; delta/kappa > 200).
Lead Iodide Thin Film Crystallization Control for High-Performance and Stable Solution-Processed Perovskite Solar Cells (2015)

PbI2 thin film crystallization control is a prerequisite of high-quality perovskite thin film for sequentially solution-processed perovskite solar cells. An efficient and simple method has been developed by adding HCl to improve perovskite thin film quality, and an efficiency of 15.2% is obtained. This approach improves coverage, uniformity, and stability of pervoskite thin film.
Random walk of coherently amplified solitons in optical fiber transmission (1986)

In an optical-communications system using soliton pulse transmission, periodic amplification is needed to maintain the energy of the solitons. We show that amplifier noise causes a soliton's group velocity to undergo a random-walk process. The resultant timing errors at the receiver limit the system's product of length times bit rate, in one example, to about 24 000 GHz-km.
Volumetric BOLD fMRI simulation: from neurovascular coupling to multivoxel imaging (2012)

Our simulation results show that the MR magnitude image is not an exact replica of the magnetic susceptibility source (spatial correlation ≈ 0.90), and that the MR phase image conforms closely with the susceptibility-induced fieldmap (spatial correlation ≈ 1.00).
Space-time tradeoffs in software-based deep Packet Inspection (2011)

Deep Packet Inspection (DPI) lies at the core of contemporary Network Intrusion Detection/Prevention Systems and Web Application Firewalls. DPI aims to identify various malware (including spam and viruses) by inspecting both the header and the payload of each packet and comparing it to a known set of patterns. DPI is often performed on the critical path of the packet processing, thus the overall performance of the security tools is dominated by the speed of DPI. The seminal algorithm of Aho-Corasick (AC) is the de facto standard for pattern matching in network intrusion detection systems (NIDS). Basically, the AC algorithm constructs a Deterministic Finite Automaton (DFA) for detecting all occurrences of a given set of patterns by processing the input in a single pass. The input is inspected symbol by symbol (usually each symbol is a byte), such that each symbol results in a state transition. Thus, in principle, the AC algorithm has deterministic performance, which does not depend on specific input and therefore is not vulnerable to algorithmic complexity attacks, making it very attractive to NIDS systems. In this paper we show that, when implementing the AC algorithm in software, this property does not hold, due to the fact that contemporary pattern sets induce very large DFAs that cannot be stored entirely in cache. We then propose a novel technique to compress the representation of the Aho-Corasick automaton, so it can fit in modern cache. We compare both the performance and the memory footprint of our technique to previously-proposed implementation, under various settings and pattern sets. Our results reveal the space-time tradeoffs of DPI. Specifically, we show that our compression technique reduces the memory footprint of the best prior-art algorithm by approximately 60%, while achieving comparable throughput.
WIND MEASUREMENTS WITH HIGH-ENERGY DOPPLER LIDAR (2006)

Coherent lidars at 2-micron wavelengths from holmium or thulium solid-state lasers have been in use to measure wind for applications in meteorology, aircraft wake vortex tracking, and turbulence detection [1,2,3] These field-deployed lidars, however, have generally been of a pulse energy of a few millijoules, limiting their range capability or restricting operation to regions of high aerosol concentration such as the atmospheric boundary layer. Technology improvements in the form of high-energy pulsed lasers, low noise detectors, and high optical quality telescopes are being evaluated to make wind measurements to long ranges or low aerosol concentrations. This research is aimed at developing lidar technology for satellite-based observation of wind on a global scale. The VALIDAR project was initiated to demonstrate a high pulse energy coherent Doppler lidar. VALIDAR gets its name from the concept of validation lidar, in that it can serve as a calibration and validation source for future airborne and spaceborne lidar missions. VALIDAR is housed within a mobile trailer for field measurements.
Parallel beamformer design under response equalization constraints (2004)

In some applications, it may be desirable to design a certain number of fixed beamformers that have different look directions but the same response to a certain predetermined signal, referred to as the equalization signal. In this article we present a method to accomplish this task, and show that it is optimal for a natural directivity criterion. We then demonstrate the effectiveness of this method with an application to an audio conference telephone where the equalization signal is the direct-path loudspeaker coupling signal.
Synthesis of Methacrylic Acid by Catalytic Decarboxylation and Dehydration of Carboxylic Acids Using a Solid Base and Subcritical Water (2016)

Methacrylic acid was synthesized from the biobased substrates citric acid, itaconic acid, and 2-hydroxyisobutyric acid (2-HIBA). Hydrotalcite, a solid base catalyst, was employed to form methacrylic acid (MAA) through decarboxylation of itaconic acid and citric acid. The effect of temperature, catalyst mass, residence time, substrate concentration, and fermentation media, on carboxylic acid conversion and methacrylic acid yield was determined. Optimum MAA yields occurred at a substrate to catalyst mass ratio of 9.6 g-substrate/g-catalyst and 21% for citric acid and 6.4 g/g and 23% for itaconic acid (250 °C, 15 min). Catalyst reusability experiments resulted in higher methacrylic acid yields for both citric and itaconic acid. Methacrylic acid was also formed from 2-hydroxyisobutyric acid in a single-step dehydration reaction. Among these three substrates, the highest yield of methacrylic acid (71.5%) was achieved at 275 °C (1 min) using 2-HIBA and subcritical water. Finally, we tested conversion of these three acids in a simulated residual fermentation broth (0.1 M NaOH, 0.04 M Na2SO4, 0.04 M Na2HPO4, 0.06 M glucose, 0.12 wt % albumin) and MAA yields from itaconic acid and citric acid using hydrotalcite increased in the presence of these fermentation “impurities” and decreased slightly from 2-HIBA.
Proteomic and microarray characterization of the AggR regulon identifies a <i>pheU</i> pathogenicity island in enteroaggregative <i>Escherichia coli</i> (2006)

Enteroaggregative Escherichia coli (EAEC) is defined by aggregative adherence (AA) to HEp-2 cells, where bacteria display adherence to cell surfaces and also to the intervening substratum in a stacked-brick configuration. We previously showed that an AraC homologue designated AggR is required for the expression of plasmid-encoded genes that mediate AA of EAEC strain 042. In this study, we hypothesized that AggR also controls the expression of other virulence determinants in EAEC 042. Using proteomic and microarray analysis, we identified for the first time that AggR activates the expression of chromosomal genes, including 25 contiguous genes (aaiA-Y), which are localized to a 117 kb pathogenicity island (PAI) inserted at pheU. Many of these genes have homologues in other Gram-negative bacteria and were recently proposed to constitute a type VI secretion system (T6SS). AaiC was identified as a secreted protein that has no apparent homologues within GenBank. EAEC strains carrying in-frame deletions of aaiB, aaiG, aaiO or aaiP still synthesized AaiC; however, AaiC secretion was abolished. Cloning of aai genes into E. coli HB101 suggested that aaiA-P are sufficient for AaiC secretion. A second T6SS was identified within the pheU PAI that secretes a protein unrelated by sequence identity to AaiC. Distribution studies indicated that aaiA and aaiC are commonly found in EAEC isolates worldwide, particularly in strains defined as typical EAEC. These data support the hypothesis that AggR is a global regulator of EAEC virulence determinants, and builds on the hypothesis that T6SS is an importance mediator of pathogenesis.
Photonic integration for Phased Array Systems (2015)

This talk describes how high-performance ultra-wideband Phased Array Systems can be enabled through silicon photonics based photonic integrated circuits. Component technologies including heterogeneous integration of III-V materials and ultra-low-loss silicon nitride waveguides, plus laser, modulator, filter and true-time-delay devices and sub-systems will be described.
Automatic breath and snore sounds classification from tracheal and ambient sounds recordings (2010)

In this study respiratory sound signals were recorded from 23 patients suspect of obstructive sleep apnea, who were referred for the full-night sleep lab study. The sounds were recorded with two microphones simultaneously: one placed over trachea and one hung in the air in the vicinity of the patient. During recording the sound signals, patients' Polysomnography (PSG) data were also recorded simultaneously. An automatic method was developed to classify breath and snore sound segments based on their energy, zero crossing rate and formants of the sound signals. For every sound segment, the number of zero crossings, logarithm of the signal's energy and the first formant were calculated. Fischer Linear Discriminant was implemented to transform the 3-dimensional (3D) feature set to a 1-dimensional (1D) space and the Bayesian threshold was applied on the transformed features to classify the sound segments into either snore or breath classes. Three sets of experiments were implemented to investigate the method's performance for different training and test data sets extracted from different neck positions. The overall accuracy of all experiments for tracheal recordings were found to be more than 90% in classifying breath and snore sounds segments regardless of the neck position. This implies the method's accuracy is insensitive to patient's position; hence, simplifying data analysis for an entire night recording. The classification was also performed on sounds signals recorded simultaneously with an ambient microphone and the results were compared with those of the tracheal recording.
Protein Quantity and Source, Fasting-Mimicking Diets, and Longevity (2019)

Dietary modifications, including caloric restriction, dietary restriction, various intervals of fasting, and even limiting the time when food is consumed can have a pronounced impact on longevity. In addition, dietary modifications are powerful interventions to delay, prevent, or treat many aging-related diseases such as cancer and diabetes. Restricting amino acid and protein intake generally decreases aging-related comorbidities and thereby increases health and longevity. However, chronic dietary interventions are likely not feasible for most people due to low adherence to dietary protocols or resistance to drastic changes to lifestyle, and might even cause detrimental effects, possibly by negatively affecting the immune system and wound healing. The periodic use of low-protein, low-calorie fasting-mimicking diets (FMDs) has the potential to promote health benefits, while minimizing the burden of chronic restriction. Protein restriction and FMDs together have the potential to play an important complementary role in medicine by promoting disease prevention and treatment, and by delaying the aging process at least in part by stimulating stem cell-based regeneration in periods of normal food intake after periodic FMD cycles. The aim of this narrative review is to summarize research on the impact of protein restriction on health and longevity in model organisms and to discuss the implementation of an FMD in mice and in human clinical trials and its effects on biomarkers of healthy aging. Taking into account the importance of sex on aging and diet, we include this information in all discussed studies. Whereas for some model organisms of aging, such as rodents, many studies are available, results are more limited for primates and/or humans.
E-QED: Electrical Bug Localization During Post-Silicon Validation Enabled by Quick Error Detection and Formal Methods (2017)

During post-silicon validation, manufactured integrated circuits are extensively tested in actual system environments to detect design bugs. Bug localization involves identification of a bug trace (a sequence of inputs that activates and detects the bug) and a hardware design block where the bug is located. Existing bug localization practices during post-silicon validation are mostly manual and ad hoc, and, hence, extremely expensive and time consuming. This is particularly true for subtle electrical bugs caused by unexpected interactions between a design and its electrical state. We present E-QED, a new approach that automatically localizes electrical bugs during post-silicon validation. Our results on the OpenSPARC T2, an open-source 500-million-transistor multicore chip design, demonstrate the effectiveness and practicality of E-QED: starting with a failed post-silicon test, in a few hours (9 hours on average) we can automatically narrow the location of the bug to (the fan-in logic cone of) a handful of candidate flip-flops (18 flip-flops on average for a design with ~ 1 Million flip-flops) and also obtain the corresponding bug trace. The area impact of E-QED is ~2.5%. In contrast, deter-mining this same information might take weeks (or even months) of mostly manual work using traditional approaches.
Regeneration of the Corneal Endothelium (2019)

Penetrating keratoplasty was the only therapeutic choice for the treatment of corneal endothelial decompensation until the introduction of evolutional endothelial keratoplasties, namely Descemet's stripping automated endothelial keratoplasty (DSAEK) and Descemet's membrane endothelial keratoplasty (DMEK). Although now in widespread use, DSAEK and DMEK still have associated problems, such as difficulty of the surgical technique, acute and chronic cell loss, and shortage of donor corneas. Therefore, regeneration of the corneal endothelium by tissue engineering techniques is being researched to overcome these problems. The concept of transplantation of cultured corneal endothelial cells (CECs) was proposed in the 1970s. However, cultivation of human CECs (HCECs) in sufficient quantity and with acceptable quality for clinical use has proven surprisingly difficult, and the development of methods for transplanting cultured HCECs has been necessary. Numerous research groups have developed culture protocols and techniques that are now bringing corneal endothelial regeneration closer to real-world therapy. For instance, we started a clinical trial in 2013 involving the injection of cultured HCECs into the anterior chamber of patients with corneal endothelial decompensation. This review outlines the rapid progression of this research field, including clinical trial results, and is also intended to identify topics that still require further research or discussion.
First-Principles Density Functional Theory Calculation of Metal-Substituted Lead Halide Perovskite (2017)

We investigated the optoelectronic properties of 3 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</i> metal-substituted lead halide perovskite by performing first-principles density functional theory calculations to examine whether the materials can be used for intermediate band solar cells. We found that Co substitution for Pb does not change the lattice constant significantly. Co substitution is able to induce intermediate bands that can absorb light, consistent with experiment results. In our calculations, Fe substitution for Pb also can induce intermediate bands, however, it is less energetically favored as compared to Co substitution, and experimentally such extra absorption was not observed.