gebhart/patrepeval huggingface dataset:
Optical perfect-shuffle interconnection using a computer-generated hologram (1993)

We propose the use of a computer-generated hologram that combines a fanout and focusing element that can be used to perform an optical perfect-shuffle interconnection. The hologram is designed by calculation of the interference fringes between diverging waves from four point sources and a reference plane wave. With this element we show experimentally the resulting perfect-shuffle pattern. The use of the computer-generated hologram makes it easy to implement a planar optical perfect-shuffle interconnect, which is compact, has low aberration, and is easy to align. The planar optics configuration for a perfect-shuffle interconnection network is also discussed.
Control Lyapunov-Razumikhin functions for time delay systems (2003)

Motivated by control Lyapunov functions and Razumikhin theorems on stability of time delay systems, we introduce the concept of control Lyapunov-Razumikhin functions (CLRF). The main reason for considering CLRFs is construction of stabilizing control laws for time delay systems. Most existing formulas that apply to CLFs, are not applicable to CLRFs. However, it turns out that the domination redesign control law applies, achieving global practical stability and, under an additional assumption, global asymptotic stability. This additional assumption is satisfied in the practically important case when the quadratic part of a CLRF is itself a CLRF for the Jacobian linearization of the system.
Studies on Structure and Properties of HDPE Functionalized Through Ultraviolet Irradiation and Its Blends with CaCO 3 (2005)

Abstract The structure and properties of high-density polyethylene (HDPE) functionalized through ultraviolet irradiation in air and its blends with CaCO3 were studied by Fourier transfer infrared (FTIR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), contact angle measurement, Molau test, and mechanical properties test. The experimental results reveals that oxygen-containing groups such as C = O and C - O were introduced onto the molecular chains of HDPE through ultraviolet irradiation in air, and the groups' concentration increases with irradiation time. After irradiation, the water contact angle of HDPE becomes smaller, showing that the hydrophilicity of irradiated HDPE increases. Compared with those of HDPE/CaCO3 blend, the dispersion of CaCO3 particles in irradiated HDPE/CaCO3 blend, the interface interaction between CaCO3 particles and irradiated HDPE matrix, and the mechanical properties of irradiated HDPE/CaCO3 blend are improved due to the introduction of polar groups.
Identification of Residues Crucially Involved in the Binding of the Heme Moiety of Soluble Guanylate Cyclase (2004)

Soluble guanylate cyclase (sGC), a heterodimeric hemeprotein, is the only receptor for the biological messenger nitric oxide (NO) identified to date and is intimately involved in various signal transduction pathways. By using the recently discovered NO- and heme-independent sGC activator BAY 58-2667 and a novel cGMP reporter cell, we could distinguish between heme-containing and heme-free sGC in an intact cellular system. Using these novel tools, we identified the invariant amino acids tyrosine 135 and arginine 139 of the beta(1)-subunit as crucially important for both the binding of the heme moiety and the activation of sGC by BAY 58-2667. The heme is displaced by BAY 58-2667 due to a competition between the carboxylic groups of this compound and the heme propionic acids for the identified residues tyrosine 135 and arginine 139. This displacement results in the release of the axial heme ligand histidine 105 and to the observed activation of sGC. Based on these findings we postulate a signal transmission triad composed of histidine 105, tyrosine 135, and arginine 139 responsible for the enzyme activation by this compound and probably also for transducing changes in heme status and porphyrin geometry upon NO binding into alterations of sGC catalytic activity.
Gravitational anomaly of (3+1)-dimensional Z2 toric code with fermionic charges and fermionic loop self-statistics (2022)

Quasiparticle excitations in $3+1$ dimensions can be either bosons or fermions. In this work, we introduce the notion of fermionic loop excitations in $(3+1)$-dimensional $(3+1\text{d})$ topological phases. Specifically, we construct a new many-body lattice invariant of gapped Hamiltonians, the loop self-statistics $\ensuremath{\mu}=\ifmmode\pm\else\textpm\fi{}1$, that distinguishes two bosonic topological orders that both superficially resemble $3+1\mathrm{d}\phantom{\rule{4pt}{0ex}}{\mathbb{Z}}_{2}$ gauge theory coupled to fermionic charged matter. The first has fermionic charges and bosonic ${\mathbb{Z}}_{2}$ gauge flux loops (FcBl) and is just the ordinary fermionic toric code. The second has fermionic charges and fermionic loops (FcFl) and, as we argue, can only exist at the boundary of a nontrivial $(4+1)$-dimensional $(4+1\mathrm{d})$ invertible phase, stable without any symmetries, i.e., it possesses a gravitational anomaly. We substantiate these claims by constructing an explicit exactly solvable $4+1\mathrm{d}$ model using a method that bootstraps a boundary theory into a bulk Hamiltonian, analogous to that of Walker and Wang, and computing the loop self-statistics in the fermionic ${\mathbb{Z}}_{2}$ gauge theory hosted at its boundary. We also show that the FcFl phase has the same gravitational anomaly as all-fermion quantum electrodynamics. Our results are in agreement with the recent classification of nondegenerate braided fusion 2-categories by Johnson-Freyd, and with the cobordism prediction of a nontrivial ${\mathbb{Z}}_{2}$-classified $4+1\mathrm{d}$ invertible phase with action $S=\frac{1}{2}\ensuremath{\int}{w}_{2}{w}_{3}$.
Acceleration of GPU-based Krylov solvers via data transfer reduction (2015)

Krylov subspace iterative solvers are often the method of choice when solving large sparse linear systems. At the same time, hardware accelerators such as graphics processing units continue to offer significant floating point performance gains for matrix and vector computations through easy-to-use libraries of computational kernels. However, as these libraries are usually composed of a well optimized but limited set of linear algebra operations, applications that use them often fail to reduce certain data communications, and hence fail to leverage the full potential of the accelerator. In this paper, we target the acceleration of Krylov subspace iterative methods for graphics processing units, and in particular the Biconjugate Gradient Stabilized solver that significant improvement can be achieved by reformulating the method to reduce data-communications through application-specific kernels instead of using the generic BLAS kernels, e.g. as provided by NVIDIA’s cuBLAS library, and by designing a graphics processing unit specific sparse matrix-vector product kernel that is able to more efficiently use the graphics processing unit’s computing power. Furthermore, we derive a model estimating the performance improvement, and use experimental data to validate the expected runtime savings. Considering that the derived implementation achieves significantly higher performance, we assert that similar optimizations addressing algorithm structure, as well as sparse matrix-vector, are crucial for the subsequent development of high-performance graphics processing units accelerated Krylov subspace iterative methods.
The discharge plasma in ion engine neutralizers: Numerical simulations and comparisons with laboratory data (2010)

Numerical simulations of neutralizer hollow cathodes at various operating conditions and orifice sizes are presented. The simulations were performed using a two-dimensional axisymmetric model that solves numerically an extensive system of conservation laws for the partially ionized gas in these devices. The results for the plasma are compared directly with Langmuir probe measurements. The computed keeper voltages are also compared with the observed values. Whenever model inputs and/or specific physics of the cathode discharge were uncertain or unknown additional sensitivity calculations have been performed to quantify the uncertainties. The model has also been employed to provide insight into recent ground test observations of the neutralizer cathode in NASA’s evolutionary xenon thruster. It is found that a likely cause of the observed keeper voltage drop in a long duration test of the engine is cathode orifice erosion.
Elucidation of the Biosynthesis and Degradation of Allantofuranone by Isotopic Labelling and Fermentation of Modified Precursors (2010)

Feeding experiments with the ascomycete Allantophomopsis lycopodina indicated that the potent fungistatic allantofuranone is biosynthesized from phenylalanine. Further experiments with synthetic precursors gave evidence that the naturally occurring polyporic acid serves as a key intermediate in the biosynthesis. In addition to the formation of allantofuranone, its abiotic and metabolic degradation were investigated.
Effect of the mGluR5-NAM Basimglurant on Behavior in Adolescents and Adults with Fragile X Syndrome in a Randomized, Double-Blind, Placebo-Controlled Trial: FragXis Phase 2 Results (2017)

Preclinical data suggest that inhibition of the metabotropic glutamate receptor 5 (mGluR5) receptor might hold therapeutic benefits in Fragile X syndrome (FXS). Treatment of Fmr1 knockout mice with mGluR5-negative allosteric modulators (NAMs) has been reported to correct a broad range of phenotypes related to FXS. The early short-term clinical trials with mGluR5 NAMs, including basimglurant, assessing the effects in individuals with FXS, were supportive of further exploration in larger, well-controlled trials. We evaluated basimglurant, a potent and selective mGluR5 NAM, in a 12-week, double-blind, parallel-group study of 183 adults and adolescents (aged 14-50, mean 23.4 years) with FXS. Individuals with an FMR1 full mutation were randomized to placebo or one of two doses of basimglurant. The primary efficacy endpoint was the change from baseline in behavioral symptoms using the Anxiety Depression and Mood Scale (ADAMS) total score. All treatment arms showed marked behavioral improvements from baseline to week 12 with less improvement in the basimglurant 1.5 mg arm than placebo; however, basimglurant 0.5 mg was inferior to placebo in the ADAMs total score. Treatment with basimglurant was overall well-tolerated. A higher incidence of adverse events classified as psychiatric disorders were reported in patients treated with basimglurant, including three patients with hallucinations or psychosis. In this phase 2 clinical trial, basimglurant did not demonstrate improvement over placebo. Evaluation of the overall risk-benefit in younger patient populations is an important consideration for the design of potential further investigations of efficacy with this class of medications.
Closed-loop adaptive feedback control of cavitation during high-intensity focussed ultrasound therapy. (2009)

Prior experimental evidence indicates that the occurrence of inertial cavitation at the HIFU focus enhances the local rate of heat deposition, due to increased absorption of the broadband emissions associated with collapsing bubbles. However, initiating and sustaining cavitation activity throughout HIFU exposure remain a major challenge. Previous open-loop attempts at maintaining cavitation activity by varying the HIFU pulse duration have necessitated the use of duty cycles on the order of 20%, which are too low to achieve ablative temperatures. The present work presents the design, validation, and testing of a real-time closed-loop adaptive controller for sustaining thermally relevant cavitation within the HIFU focal region at duty cycles in excess of 95%. During 1.067 MHz HIFU exposure of an agar tissue-mimicking material, cavitation activity is continuously monitored and quantified using a single-element broadband passive cavitation detector (PCD) positioned coaxially with the HIFU transducer. The HIFU amplitude is adaptively modulated in direct response to the PCD signal, making it possible to maintain cavitation activity and a temperature rise in excess of 30 °C for more than 30 s. Most importantly, the acoustic energy needed to achieve such focal heating is only a fraction of that required in the absence of cavitation control.
Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait (2019)

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic genetic variation underlying a <i>Saccharomyces cerevisiae</i> colony phenotype that is typically suppressed in a cross of the laboratory strain BY4716 (BY) and a derivative of the clinical isolate 322134S (3S). To do this, we comprehensively dissect the trait's genetic basis in the BYx3S cross in the presence of three different genetic perturbations that enable its expression. This allows us to detect and compare the specific loci that interact with each perturbation to produce the trait. In total, we identify 21 loci, all but one of which interact with just a subset of the perturbations. Beyond impacting which loci contribute to the trait, the genetic perturbations also alter the extent of additivity, epistasis, and genotype-environment interaction among the detected loci. Additionally, we show that the single locus interacting with all three perturbations corresponds to the coding region of the cell surface gene <i>FLO11</i> While nearly all of the other remaining loci influence <i>FLO11</i> transcription in <i>cis</i> or <i>trans</i>, the perturbations tend to interact with loci in different pathways and subpathways. Our work shows how layers of cryptic genetic variation can influence complex traits. Here, these layers mainly represent different regulatory inputs into the transcription of a single key gene.
Multicellular immune hubs and their organization in MMRd and MMRp colorectal cancer (2021)

Abstract Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd patients. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across patient tumors and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage, and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T-cell-attracting chemokines. By identifying interacting cellular programs, we thus reveal the logic underlying spatially organized immune-malignant cell networks.
A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic cell turnover (2002)

Hematopoietic stem cells from different strains of mice vary widely with respect to their cell cycle activity. In the present study we used complementary genetic and genomic approaches to identify molecular pathways affecting this complex trait. We identified a major quantitative trait locus (QTL) associated with variation in cell proliferation in C57BL/6 and DBA/2 mice to a 10 centimorgan (cM) region on chromosome 11. A congenic mouse model confirmed that a genomic interval on chromosome 11 in isolation confers the proliferation phenotype. To detect candidate genes we performed subtractive hybridizations and gene arrays using cDNA from highly enriched stem cells from parental strains. Intriguingly, a disproportionate number of differentially expressed genes mapped to chromosome 11 and, more specifically, these transcripts occurred in 3 distinct clusters. The largest cluster colocalized exactly with the cell cycling QTL. Such clustering suggested the involvement of genetic variation that affects higher-order chromosomal organization. This hypothesis was reinforced by the fact that differentially expressed genes mapped to recombination "coldspots," as a consequence of which clustered genes are collectively inherited. These findings suggest the functional interdependence of these closely linked genes. Our data are consistent with the hypothesis that this isolated cell cycle QTL does not result from a mutation in a single gene but rather is a consequence of variable expression of a collection of highly linked genes.
Photochemically Mediated Polymerization of Molecular Furan and Pyridine: Synthesis of Nanothreads at Reduced Pressures (2022)

Nanothreads are emerging one-dimensional sp<sup>3</sup>-hybridized materials with high predicted tensile strength and a tunable band gap. They can be synthesized by compressing aromatic or nonaromatic small molecules to pressures ranging from 15-30 GPa. Recently, new avenues are being sought that reduce the pressure required to afford nanothreads; the focus has been placed on the polymerization of molecules with reduced aromaticity, favorable stacking, and/or the use of higher reaction temperatures. Herein, we report the photochemically mediated polymerization of pyridine and furan aromatic precursors, which achieves nanothread formation at reduced pressures. In the case of pyridine, it was found that a combination of slow compression/decompression with broadband UV light exposure yielded a crystalline product featuring a six-fold diffraction pattern with similar interplanar spacings to previously synthesized pyridine-derived nanothreads at a reduced pressure. When furan is compressed to 8 GPa and exposed to broadband UV light, a crystalline solid is recovered that similarly demonstrates X-ray diffraction with an interplanar spacing akin to that of the high-pressure synthesized furan-derived nanothreads. Our method realizes a 1.9-fold reduction in the maximum pressure required to afford furan-derived nanothreads and a 1.4-fold reduction in pressure required for pyridine-derived nanothreads. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions. The reduction of the onset pressure is caused by an initial [4+4] cycloaddition followed by increasingly facile thermal [4+2]-cycloadditions during polymerization.
Optimal Design of a Switched Reluctance Motor With Magnetically Disconnected Rotor Modules Using a Design of Experiments – Differential Evolution (DOE-DE) Finite Element Analysis (FEA) Based Method (2018)

Switched reluctance (SR) machines are attractive because they present relatively high efficiencies and torque densities but have no permanent magnets. Their limitations include high torque ripple, mitigated in large inertia applications such as electric vehicles. This digest focuses on the multi-objective optimization of an external rotor switched reluctance motor. The stator has concentrated coils and the rotor is configured with magnetically isolated modules. The experimental methodology tries to identify the variables affecting the objectives of loss and active mass. After this, differential evolution is used for optimization. The digest illustrates the optimal design process associated with the development of a prototype machine and its systematic comparison with a conventional SR motor design. Improvements with respect to the chosen objectives over a reference machine are quantified through finite element analysis. Further, a method for comparing the different designs on the Pareto front and identify the best compromise designs is proposed.
The role of earthworms as biological indicators of soil contamination. (2009)

Earthworms are important components of the soil system. mainly because of their favorable effects on soil structure and function. In addition. earthworms help to increase soil fertility by formation of an organic matter layer in topsoil. These features. among others. have led to the popularity of earthworms as excellent biological indicators of soil pollution. Thus. earthworms are appropriate sentinel organisms to evaluate the impact of human activities to soil. The most widely studied earthworm species are Eisenia fetida. Eisenia andrei. Lumbricus terrestris and Lumbricus rubellus. Internationally standardized or academically not standardized test are described in the present article such as the nematode maturity index. the earthworm reproduction test. the lysosomal membrane stability test. immune system tests. enzymatic methods. heat-shock protein response assessment and DNA damage and alterations analyses
Toward A Method For Measuring Instantaneous Fungal Growth Rates In Field Samples (1991)

Methods are available in the literature for the measurement of instantaneous growth rates in field samples of photosynthetic microbes and procaryotic saprotrophic microbes, but there has been no such method for eucaryotic saprotrophic microbes (members of the kingdom Fungi). We have devised a technique for estimating instantaneous growth rates for ergosterol—containing fungi in field material, and preliminarily applied the technique to estimation of fungal productivities and throughputs in two types of standing—dead grass (one saltwater, one freshwater), obtaining plausible values (e.g., conversion efficiencies, total fungal production ° leaf mass loss, were calculated to be 36—64%). This method is based on measuring rates of radiolabeled acetate incorporation into ergosterol. We examined several potential problem areas for use of radiolabeled precursors in measurement of microbial molecular syntheses, and its extrapolation to microbial productivity. Key findings were: (a)5 mmol/L added acetate (required for maximization of detection of change in rates) had positive or neutral impact on 48—h fungal growth, and no shift—up (sudden upward change in rate) or lag in incorporation of acetate into ergosterol occurred between 0.25 and 1.25 h of incubation of naturally decaying leaf (Spartina alteriflora) samples with 5 mmol/L acetate; (b) bacterial assemblages on leaves did not contribute radioactivity to the ergosterol fraction after incubation with radioacetate (as opposed to &gt; 30 Bq per centimetre length of leaf containing fungal mycelium); (c) the average empirical factor for conversion from nanomoles 1 4 C—acetate incorporated to micrograms organic fungal mass produced was 8.2 mg/nmol (coefficient of variation, 27%). We tentatively conclude that the acetate—to—ergosterol method is tenable for measurement of natural fungal productivity.