gebhart/patrepeval huggingface dataset:
Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail (2023)

Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-COV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the AZD1061 (COV2-2130) mAb. Here, we show that this mutation remodels the receptor-binding site allosterically, thereby altering the epitopes recognized by these three mAbs and vaccine-elicited neutralizing antibodies while remaining functional. Our results demonstrate the spectacular structural and functional plasticity of the SARS-CoV-2 RBD, which is continuously evolving in emerging SARS-CoV-2 variants, including currently circulating strains that are accumulating mutations in the antigenic sites remodeled by the E406W substitution.
Supplementary Table 2 from Personalized Chemotherapy Profiling Using Cancer Cell Lines from Selectable Mice (2023)

&lt;p&gt;XLSX file - 165K, Response of Panc502 to 125 anti-neoplastic drugs.&lt;/p&gt;
Supplementary Table 7 from Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2023)

&lt;p&gt;Primer and probe list of genes used for quantitative Methylation Specific PCR.&lt;/p&gt;
Probabilistic Design of Optical Transmission Systems (2016)

Traditionally, optical fiber nonlinearity is considered a limiting factor for transmission systems. Nevertheless, from a system design perspective this nonlinearity can be exploited to minimize the impact of uncertainty on the system performance. A consequence of this is that it becomes beneficial to consider the uncertainty at the design stage, resulting in a probabilistic design, rather than conventional design approaches whereby uncertainty is added by way of system margins to a deterministic design. In this paper, we conduct extensive experimental measurements to quantify the impact of uncertainty for a multispan wavelength division multiplexed system transmitting 100 GbE or 200 GbE as dual polarization quadrature phase-shift keying (QPSK) or 16 quadrature amplitude modulation (16QAM), respectively. The impact of uncertainty in the power launched into a span is assessed for a 10 × 80 km link. For dual polarization (DP)-QPSK, the intralink power deviation with the probabilistic design with 100% reliability is ±1.3 dB falling to 99% reliability with ±1.6 dB. In contrast, for DP-16QAM maximum deviation for 100% reliability is ±0.5 dB falling to 99% for ±0.6 dB. Following this, we consider the interplay between polarization dependent loss (PDL) and fiber nonlinearity over an 8 × 80 km system again for both DP-QPSK and DP-16QAM. A system Q variation of less than 0.15 dB due to the interaction between PDL and fiber nonlinearity is observed for 99.9% of examined PDL values for DP-QPSK and DP-16QAM, thereby allowing the two effects to be considered separately.
RELAXATION OF VASCULAR SMOOTH MUSCLE INDUCED BY LOW‐POWER LASER RADIATION (1993)

The relaxation of rabbit aorta rings induced by low-power laser radiation was investigated in vitro to determine the location of the chromophore(s) responsible for this response and evaluate possible mechanisms. An action spectrum for relaxation was measured on rabbit thoracic aorta rings precontracted with norepinephrine. The decrease in isometric tension was measured during exposure to laser light (351-625 nm) delivered via a fiber optic to a small spot on the adventitial surface. The shortest UV wavelength (351 nm) was 35-fold more effective than 390 nm and 1700-fold more effective than 460 nm. Ultraviolet wavelengths also produced greater maximum relaxation (0.40-0.45) than visible wavelengths (0.20-0.25), suggesting that photovasorelaxation involves more than one chromophore. The adventitial layer was not necessary for photovasorelaxation, indicating that the light is absorbed by a chromophore in the medial layer. The same degree of relaxation was obtained on rings without adventitia when either one-half of the ring, or a small spot was irradiated indicating that communication between smooth muscle cells spreads a signal from the area illuminated to the entire ring. The mechanism for photovasorelaxation was investigated using potential inhibitors. N-monomethyl-L-arginine and N-amino-L-arginine, inhibitors of nitric oxide synthase, did not alter photovasorelaxation nor did indomethacin, an inhibitor of cyclooxygenase, and zinc protoporphyrin, an inhibitor of heme oxygenase.
The molecular mechanisms of insecticide resistance in aphid crop pests (2023)

Aphids are a group of hemipteran insects that include some of the world's most economically important agricultural pests. The control of pest aphids has relied heavily on the use of chemical insecticides, however, the evolution of resistance poses a serious threat to their sustainable control. Over 1000 cases of resistance have now been documented for aphids involving a remarkable diversity of mechanisms that, individually or in combination, allow the toxic effect of insecticides to be avoided or overcome. In addition to its applied importance as a growing threat to human food security, insecticide resistance in aphids also offers an exceptional opportunity to study evolution under strong selection and gain insight into the genetic variation fuelling rapid adaptation. In this review we summarise the biochemical and molecular mechanisms underlying resistance in the most economically important aphid pests worldwide and the insights study of this topic has provided on the genomic architecture of adaptive traits.
Minimum Cost Input/Output Design for Large Scale Linear Structural Systems (2014)

In this paper, we provide optimal solutions to two different (but related) input/output design problems involving large-scale linear dynamical systems, where the cost associated to each directly actuated/measured state variable can take different values, but is independent of the labeled input/output variable. Under these conditions, we first aim to determine and characterize the input/output placement that incurs in the minimum cost while ensuring that the resulting placement achieves structural controllability/observability. Further, we address a constrained variant of the above problem, in which we seek to determine the minimum cost placement configuration, among all possible input/output placement configurations that ensures structural controllability/observability, with the lowest number of directly actuated/measured state variables. We show that both problems can be solved efficiently, i.e., using algorithms with polynomial time complexity in the number of the state variables. Finally, we illustrate the obtained results with an example.
Estimation of Long Term Gas Condensate Well Productivity Using Pressure Transient Data (SPE94065) (2005)

SPE 94065 Estimation of Long Term Gas Condensate Well Productivity Using Pressure Transient Data R. Osorio G. Stewart A. Danesh D. Therani and M. Jamiolahmady Inst.of Petroleum Engineering Heriot-Watt U. Copyright 2005 Society of Petroleum Engineers This paper was prepared for presentation at the SPE Europec/EAGE Annual Conference held in Madrid Spain 13-16 June 2005. This paper was selected for presentation by an SPE Program Committee following review of information contained in an abstract submitted by the author(s). Contents of the paper as presented have not been reviewed by the Society of Petroleum Engineers and are subject to correction by
ChemInform Abstract: Caledonin, a Natural Peptide Bolaphile with ZnII and CuI Complexing Properties from the Tunicate Didemnun rodriguesi. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An Optimal PID Controller for a Bidirectional Inductive Power Transfer System Using Multiobjective Genetic Algorithm (2013)

Bidirectional inductive power transfer (IPT) systems are suitable for applications that require wireless and two-way power transfer. However, these systems are high-order resonant networks in nature and, hence, design and implementation of an optimum proportional–integral–derivative (PID) controller using various conventional methods is an onerous exercise. Further, the design of a PID controller, meeting various and demanding specifications, is a multiobjective problem and direct optimization of the PID gains often lead to a nonconvex problem. To overcome the difficulties associated with the traditional PID tuning methods, this paper, therefore, proposes a derivative-free optimization technique, based on genetic algorithm (GA), to determine the optimal parameters of PID controllers used in bidirectional IPT systems. The GA determines the optimal gains at a reasonable computational cost and often does not get trapped in a local optimum. The performance of the GA-tuned controller is investigated using several objective functions and under various operating conditions in comparison to other traditional tuning methods. It was observed that the performance of the GA-based PID controller is dependent on the nature of the objective function and therefore an objective function, which is a weighted combination of rise time, settling time, and peak overshoot, is used in determining the parameters of the PID controller using multiobjective GA. Simulated and experimental results of a 1-kW prototype bidirectional IPT system are presented to demonstrate the effectiveness of the GA-tuned controller as well as to show that gain selection through multiobjective GA using the weighted objective function yields the best performance of the PID controller.
Reply by Authors - Impact of Resection Technique on Perioperative Outcomes and Surgical Margins after Partial Nephrectomy for Localized Renal Masses (2020)

Contains fulltext : 219890.pdf (Publisher’s version ) (Open Access)
Electroabsorption optical modulator (2023)

An electroabsorption modulator that operates based on electroabsorption of a surface plasmon polariton mode is improved by various structural changes and/or selection of different materials. For example, at least a portion of the waveguide may be made to be conductive, e.g., by doping. Also, layers that make up the modulator structure may be placed along sides of waveguides in addition to or instead of simply on the top thereof. High permittivity gate dielectric materials may be employed. Also, materials other than ITO may be employed as a transparent conductor. Such an improved plasmonic electroabsorption modulator can be fabricated using standard semiconductor processing techniques and may be integrated with standard photonic integrated circuits, including silicon photonics and compound semiconductor-based platforms. Advantageously, high-speed, low-voltage operation over a wide spectrum of wavelengths may be achieved.
GEOGRAPHIC RANGES, POPULATION STRUCTURE, AND AGES OF SEXUAL AND PARTHENOGENETIC SNAIL LINEAGES (2006)

Asexual reproduction is thought to doom organisms to extinction due to mutation accumulation and parasite exploitation. Theoretical models suggest that parthenogens may escape the negative effects of conspecifics and biological enemies through escape in space. Through intensive sequencing of a mitochondrial DNA (mtDNA) and a nuclear intron locus in sexual and parthenogenetic freshwater snails (Campeloma), I examine three questions: (1) Are sexual mtDNA lineages more restricted geographically than parthenogenetic mtDNA lineages? (2) Are independent parthenogenetic lineages shorter lived than sexual lineages? and (3) Do parthenogens have higher intraindividual nuclear sequence diversity and form well-differentiated monophyletic groups as expected under the Meselson effect? Geographic ranges of parthenogenetic lineages are significantly larger than geographic ranges of sexual lineages. Based on coalescence times under different demographic assumptions, asexual lineages are short lived, but there is variation in clonal ages. Although alternative explanations exist, these results suggest that asexual lineages may persist in the short term through dispersal, and that various constraints may cause geographic restriction of sexual lineages. Both allotriploid and diploid Campeloma parthenogens have significantly higher allelic divergence within individuals, but show limited nuclear sequence divergence from sexual ancestors. In contrast to previous allozyme evidence for nonhybrid origins of diploid Campeloma parthenogens, cryptic hybridization may account for elevated heterozygosity.
C-band 340-W and X-band 100-W GaN power amplifiers with over 50-% PAE (2009)

In this paper, we report a C-band power amplifier with over 340-W output power using 0.8-mum GaN-HEMTs and an X-band power amplifier with over 100-W output power using 0.25-mum GaN-HEMTs. We used two-chip configurations and the three-stage impedance transformers to extend the bandwidth for both circuits. The input and output lines adjacent to each chip are divided by four to suppress the non-uniform heat distribution in a chip at high frequencies. As a result, we obtained 343-W output power and 53-% power added efficiency (PAE) at 4.8 GHz. This is the highest output power ever reported C-band power amplifiers. We also obtained 101-W output power and 53-% PAE at 9.8 GHz. This is also the highest PAE ever reported X-band power amplifiers with over 50-W output power.
Hierarchical, Vertically‐Oriented Carbon Nanowall Foam Supercapacitor using Room Temperature Ionic Liquid Mixture for AC Line Filtering with Ultrahigh Energy Density (2019)

Abstract Supercapacitors have been considered as a promising alternative of aluminum electrolytic capacitors (AECs) for AC line filtering applications. However, realizing supercapacitors with fast frequency response and superior energy density still remains an open issue. Herein, we demonstrate a hierarchical, vertically‐oriented carbon nanowall foam (CWF) supercapacitor using mixed room temperature ionic liquids (RTILs) for high‐performance AC line filtering. Hierarchical CWF exhibits macrospores as electrolyte reservoirs to shorten ion transport distance, vertically‐oriented, open channels to enable fast ion diffusion and consecutive scaffolds to promote electron transfer. CWF supercapacitor using RTIL mixture realizes a recorded‐high areal energy density of 1.23 μWh cm −2 at 120 Hz (almost ∼2.0 times/∼10.0 times larger than those of organic/aqueous electrolytes, respectively) and fast frequency response (RC time constant=∼1.3 ms). More importantly, CWF supercapacitor achieves a capacitance advantage over commercial AECs up to 1,000 V, substantially larger than those reported in state‐of‐the‐art literatures (maximum of ∼250 V).
Amplification in the full 1.2 to 1.7 µm communication bandwidth using OPA in electric-field poled LiNbO3 waveguides (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. Galvanauskas, K. K. Wong, K. El Hadi, M. Hofer, M. E. Fermann, D. Harter, M. H. Chou, and M. M. Fejer, "Amplification in the full 1.2 to 1.7 µm communication bandwidth using OPA in electric-field poled LiNbO3 waveguides," in Ultrafast Electronics and Optoelectronics, J. Bowers and W. Knox, eds., Vol. 28 of OSA Trends in Optics and Photonics (Optica Publishing Group, 1999), paper PD1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Mixed-Initiative for Big Data: The Intersection of Human + Visual Analytics + Prediction (2016)

Existing surveys in visual analytics focus on the importance of the topic. However, many do not discuss the increasingly critical area of mixed-initiative systems. In this survey we discuss the importance of research in mixed-initiative systems and how it is different from visual analytics and other research fields. We present the conceptual architecture of a mixed-initiative visual analytics system (MIVAS) and the five key components that make up MIVASs (data wrangling, alternative discovery and comparison, parametric interaction, history tracking and exploration, and system agency and adaptation), which forms our main contribution. We compare and contrast different research that claims to be mixed-initiative against MIVASs and show how there is still a considerable amount of work that needs to be accomplished before any system can truly be mixed-initiative.
Crystallization and preliminary X-ray diffraction analysis of ribosomal protein L11 methyltransferase fromThermus thermophilusHB8 (2003)

Ribosomal proteins are subjected to a variety of post-translational modifications, of which methylation is the most frequently found in all three kingdoms of life. PrmA is the only bacterial enzyme identified to date that catalyzes the methylation of a ribosomal protein. It is responsible for the introduction of nine methyl groups into the N-terminal domain of ribosomal protein L11. The PrmA protein from Thermus thermophilus HB8 was crystallized and a preliminary X-ray diffraction analysis was performed. A cryocooled crystal diffracted X-rays beyond 1.9 A using synchrotron radiation.
Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers Is Suppressed by a MicroRNA (2016)

BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for the regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3' UTR of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.
Hysteresis effects in the two-mode dye ring laser (1989)

By inserting an optical diode consisting of Faraday and quartz rotators into the cavity of a dye ring laser and by applying a sinusoidal current at 10 Hz to the Faraday rotator, we have been able to observe hysteresis in the intensity of each counterpropagating laser mode. The hysteresis results from the laser’s attempts to switch among metastable states in response to the external stimulus. We have studied the hysteresis as a function of laser pump parameter a and find that it starts when a exceeds about 25, reaches a peak when a is about 60, and becomes small when a exceeds about 70. At this stage the laser is unable to respond because of the high potential barrier between metastable states. The results are in general agreement with computer solutions of the equations of motion and are related to recent work on stochastic resonance in a dye ring laser.
Secreted Lymphotoxin-α Is Essential for the Control of an Intracellular Bacterial Infection (2001)

Although the essential role of tumor necrosis factor (TNF) in the control of intracellular bacterial infection is well established, it is uncertain whether the related cytokines lymphotoxin-alpha (LTalpha3) and lymphotoxin-beta (LTbeta) have independent roles in this process. Using C57Bl/6 mice in which the genes for these cytokines have been disrupted, we have examined the relative contribution of secreted LTalpha3 and membrane-bound LTbeta in the host response to aerosol Mycobacterium tuberculosis infection. To overcome the lack of peripheral lymph nodes in LTalpha-/- and LTbeta-/- mice, bone marrow chimeric mice were constructed. LT-/- chimeras, which lack both secreted LTalpha3 and membrane-bound LTbeta (LT1beta2 and LT2beta1), were highly susceptible and succumbed 5 wk after infection. LTbeta-/- chimeras, which lack only the membrane-bound LTbeta, controlled the infection in a comparable manner to wild-type (WT) chimeric mice. T cell responses to mycobacterial antigens and macrophage responses in LTalpha-/- chimeras were equivalent to those of WT chimeras, but in LTalpha-/- chimeras, granuloma formation was abnormal. LTalpha-/- chimeras recruited normal numbers of T cells into their lungs, but the lymphocytes were restricted to perivascular and peribronchial areas and were not colocated with macrophages in granulomas. Therefore, LTalpha3is essential for the control of pulmonary tuberculosis, and its critical role lies not in the activation of T cells and macrophages per se but in the local organization of the granulomatous response.
3D printing of high‐purity silicon carbide (2019)

Abstract A method for advanced manufacturing of silicon carbide offering complete freedom in geometric complexity in the three‐dimensional space is described. The method combines binder jet printing and chemical vapor infiltration in a process capable of yielding a high‐purity, fully crystalline ceramic—attributes essential for ideal performance in very high‐temperature applications or in the presence of displacement damage. Thermal conductivity and characteristic equibiaxial flexural strength of the resulting monolithic SiC at room temperature are 37 W·(m·K) −1 and 297 MPa, respectively.
Theoretical modeling of shielding for plasma flow and electron beam heating (2016)

Electron beam appears to be a good instrument for the simulation of heat loads because of low pressure to material and large depth of shielding layer, allowing for the application of higher loads. This work is focused on theoretical and numerical modeling of heating tungsten by plasma flow and electron beam heating to clarify differences in the heating process. The time necessary for vapor shielding development is found for both of them. Essential time differences between electron beams with various energies were found. It was explained by significant cooling by evaporation at one of the heating stages. The surface temperature is almost stabilized and the maximal temperature location shifts under the surface at this stage.
Ridge waveguide AlGaAs/GaAs distributed feedback lasers with multiple quantum well structure (1986)

Ridge waveguide AlGaAs/GaAs distributed feedback lasers with multiple quantum well structure were fabricated for the first time. The threshold current of 28 mA, which is the lowest ever reported among AlGaAs/GaAs distributed feedback lasers, was obtained at room temperature. Stable single longitudinal and transverse mode oscillation was observed over the wide temperature range. The dynamic linewidth was also measured and it was five to six times smaller than that of a double heterostructure distributed feedback laser.