gebhart/patrepeval huggingface dataset:
Layered inorganic–organic frameworks based on the 2,2-dimethylsuccinate ligand: structural diversity and its effect on nanosheet exfoliation and magnetic properties (2012)

The structures of four new 2,2-dimethylsuccinate frameworks suitable for exfoliation into nanosheets using ultrasonication are reported. These hybrid compounds contain either monovalent (Li(+)) or divalent (Co(2+) and Zn(2+)) cations, and they all feature hydrophobically capped covalently bonded layers that only interact with each other via weak van der Waals forces. Critically this shows that the use of this dicarboxylate ligand generally yields two dimensional compounds suitable for simple and affordable nanosheet exfoliation. This extends the range of frameworks that can be exfoliated and highlights the 2,2-dimethylsuccinate ligand as an excellent versatile platform for the production of nanosheets. The topologies of the layers in each framework were found to vary significantly and this appears to have a significant effect on the relative size of the nanosheets produced; increased space between methyl groups and more extensive inorganic connectivity appears to favour the formation of thin nanosheets with larger lateral dimensions. Additionally the magnetic properties of two of these frameworks were examined, and it was found that both exhibit strong low dimensional antiferromagnetic coupling despite their well-separated layers preventing three dimensional magnetic order.
A framework for implementing cooperative motion on industrial controllers. (2004)

The use of two or more robots jointly manipulating a common object, termed cooperative control, has many advantages in industrial applications. Much of the previous work on cooperative control, however, has emphasized capabilities, such as joint torque control, not generally present on industrial robots. This paper applies the concept of cooperative control to industrial robots by taking advantage of those capabilities that do exist on industrial robots. Specifically, a design approach that makes use of tool-based coordinate systems, trajectory generation, real-time modification, and distributed control of multiple robots is presented. These concepts are implemented on a system of two industrial robots using an adaptive fuzzy controller, and the results are discussed.
Cystatin C, Alias Post-γ-Globulin: A Marker for Multiple Sclerosis? (1987)

Cystatin C, alias post-gamma-globulin or gamma-trace protein, has been shown to be a potent inhibitor of cysteine proteinases; this protein is normally present in different biological fluids, but particularly so in cerebrospinal fluid. The concentration of cystatin C was determined by radial immunodiffusion in cerebrospinal fluid from patients affected with multiple sclerosis, patients affected with various neurological diseases and in controls; it was also determined in brain tissue from 2 patients affected with multiple sclerosis and 3 control brains. Cystatin C cerebrospinal fluid levels were undetectable or depressed in many multiple sclerosis cases and the median value differed significantly from the control one. Its low concentration in multiple sclerosis suggests that the regulation of cysteine proteinases is impaired in this disease; hence enhanced activity of cysteine proteinases could initiate, or increase the breakdown of myelin. Although it is perhaps a little premature to consider cystatin C as a marker for multiple sclerosis, this protein is nevertheless associated to demyelination; consequently its biochemical assay in cerebrospinal fluid is recommended as a complementary diagnostic tool.
Gleipnir: toward practical error analysis for Quantum programs (2021)

Practical error analysis is essential for the design, optimization, and evaluation of Noisy Intermediate-Scale Quantum(NISQ) computing. However, bounding errors in quantum programs is a grand challenge, because the effects of quantum errors depend on exponentially large quantum states. In this work, we present Gleipnir, a novel methodology toward practically computing verified error bounds in quantum programs. Gleipnir introduces the (ρ,δ)-diamond norm, an error metric constrained by a quantum predicate consisting of the approximate state ρ and its distance δ to the ideal state ρ. This predicate (ρ,δ) can be computed adaptively using tensor networks based on the Matrix Product States. Gleipnir features a lightweight logic for reasoning about error bounds in noisy quantum programs, based on the (ρ,δ)-diamond norm metric. Our experimental results show that Gleipnir is able to efficiently generate tight error bounds for real-world quantum programs with 10 to 100 qubits, and can be used to evaluate the error mitigation performance of quantum compiler transformations.
Packet scheduling in broadcast WDM networks with arbitrary transceiver tuning latencies (1997)

We consider the problem of scheduling packet transmissions in a broadcast, single-hop wavelength-division multiplexing (WDM) network, with tunability provided only at one end. Our objective is to design schedules of minimum length to satisfy a set of traffic requirements given in the form of a demand matrix. We address a fairly general version of the problem as we allow arbitrary traffic demands and arbitrary transmitter tuning latencies. The contribution of our work is twofold, First we define a special class of schedules which permit an intuitive formulation of the scheduling problem. Based on this formulation we present algorithms which construct schedules of length equal to the lower bound provided that the traffic requirements satisfy certain optimality conditions. We also develop heuristics which, in the general case, give schedules of length equal or very close to the lower bound. Secondly, we identify two distinct regions of network operation. The first region is such that the schedule length is determined by the tuning requirements of transmitters; when the network operates within the second region however, the length of the schedule is determined by the traffic demands, not the tuning latency. The point at which the network switches between the two regions is identified in terms of system parameters such as the number of nodes and channels and the tuning latency. Accordingly, we show that it is possible to appropriately dimension the network to minimize the effects of even large values of the tuning latency.
Renal Tubular Cell Ferroptosis: A New Player in Pathogenesis of Lupus Nephritis (2022)

Abstract Background New research indicates that the injury to the renal tubular epithelial cells is a better predictor of renal outcomes in lupus nephritis (LN) as compared to glomerular injury. Iron accumulates mostly in the renal tubular cells of LN patients and murine models of LN. Ferroptosis is an incompletely understood form of cell death involving iron mediated lipid peroxidation, but its role in LN is not well established. Experiment LN and control patient biopsies were stained for markers of ferroptosis. Kidneys of female (MRL/lpr) and male (NZW X BXSB) F1, lupus mice were analyzed for markers of ferroptosis. Human proximal tubular cells (PTEC) were treated with LN serum with or without Liporxstatin-2, a novel ferroptosis inhibitor. Results Compared to controls, LN patients expressed higher levels of ACSL4 and 4HNE, the ferroptosis core proteins in the renal tubules. Compared to non-nephritic mice, nephritic mice had significantly higher gene expression of Aifm2, Acsl4, and Gpx1 as well as protein levels of Acsl4. Nephritic mice had an impaired renal glutathione synthesis pathway. Glutathione is an essential positive regulator of glutathione peroxidase 4 (Gpx4: ferroptosis inhibitor) which resulted in lower protein expression of Gpx4. Collectively, LN kidneys displayed a ferroptosis signature and was associated with an increase in Ngal and Kim1, PTEC injury markers. LN patients’ serum induced PTEC ferroptosis and associated pathology were significantly reduced by Liproxstatin-2. Conclusion Our data identify occurrence ferroptosis in renal tubular cell which can contribute to the pathogenesis of LN. Liproxstatin-2 mitigates human LN serum induced PTEC pathology and holds promise as an adjunct therapy to alleviate LN severity. Supported by grants from Vifor Pharma
Iterative Detection and Decoding for Wireless Communications (1999)

Turbo codes are a class of forward error correction (FEC) codes that offer energy efficiencies close to the limits predicted by information theory. The features of turbo codes include parallel code concatenation, recursive convolutional encoding, nonuniform interleaving, and an associated iterative decoding algorithm. Although the iterative decoding algorithm has been primarily used for the decoding of turbo codes, it represents a solution to a more general class of estimation problems that can be described as follows: a data set directly or indirectly drives the state transitions of two or more Markov processes; the output of one or more of the Markov processes is observed through noise; based on the observations, the original data set is estimated. This dissertation specifically describes the process of encoding and decoding turbo codes. In addition, a more general discussion of iterative decoding is presented. Then, several new applications of iterative decoding are proposed and investigated through computer simulation. The new applications solve two categories of problems: the detection of turbo codes over time-varying channels, and the distributed detection of coded multiple-access signals. Because turbo codes operate at low signal-to-noise ratios, the process of phase estimation and tracking becomes difficult to perform. Additionally, the turbo decoding algorithm requires precise estimates of the channel gain and noise variance. The first significant contribution of this dissertation is a study of several methods of channel estimation suitable specifically for turbo coded systems. The second significant contribution of this dissertation is a proposed method for jointly detecting coded multiple-access signals using observations from several locations, such as spatially separated base stations. The proposed system architecture draws from the concepts of macrodiversity combining, multiuser detection, and iterative decoding. Simulation results show that when the system is applied to the time division multiple-access cellular uplink, a significant improvement in system capacity results.
New CsI:Na-selenium x-ray detector (2004)

Digital x-ray imager known to flat-panel detector has been studied for the application of a various medical modalities. Currently, two types of detection methods have been realized in digital radiography. One is an indirect conversion method and the other is a direct conversion method. we have been developing a new x-ray detector that combines a columnar CsI:Na scintillation layer with a photosensitive a-Se with dielectric thin film. In this structure, an x-ray is converted to visible light in a CsI:Na scintillation layer and visible light is then converted to electric charges in a-Se layer. The electron-hole pairs can be also generated from x-ray interaction in the a-Se photoconductor, which can improve the detection efficiency of electric charge. We designed the thickness of CsI:Na scintillator by using computer simulation. MCNP is a general-purpose, continuous-energy, generalized-geometry, time-dependent, coupled neutron / photon / electron Monte Carlo transport code. The spectra of x-ray absorption was simulated by using MCNP 4C code. The morphology of the vacuum deposited CsI:Na scintillator and the parylene film were analyzed. Photoluminescence characterization of CsI:Na showed a light emission peak centered at 420nm as expected, which matched the absorption spectrum of amorphous selenium(a-Se). For an electric field of 10V/&mu;m, the dark currents of our detector were below 370 pA/cm<sup>2</sup> and the SNR of CsI:Na coupled a-Se detector with a dielectric layer was 1.8 times greater than that without CsI:Na layer.
Photoresponsive Switches at Surfaces Based on Supramolecular Functionalization with Azobenzene–Oligoglycerol Conjugates (2014)

The synthesis, supramolecular complexation, and switching of new bifunctional azobenzene-oligoglycerol conjugates in different environments is reported. Through the formation of host-guest complexes with surface immobilized β-cyclodextrin receptors, the bifunctional switches were coupled to gold surfaces. The isomerization of the amphiphilic azobenzene derivatives was examined in solution, on gold nanoparticles, and on planar gold surfaces. The wettability of functionalized gold surfaces can be reversibly switched under light-illumination with two different wavelengths. Besides the photoisomerization processes and concomitant effects on functionality, the thermal cis to trans isomerization of the conjugates and their complexes was monitored. Thermal half-lives of the cis isomers were calculated for different environments. Surprisingly, the half-lives on gold nanoparticles were significantly smaller compared to planar gold surfaces.
The PAS Superfamily: Sensors of Environmental and Developmental Signals (2000)

Over the past decade, PAS domains have been identified in dozens of signal transduction molecules and various forms have been found in animals, plants, and prokaryotes. In this review, we summarize this rapidly expanding research area by providing a detailed description of three signal transduction pathways that utilize PAS protein heterodimers to drive their transcriptional output. It is hoped that these model pathways can provide a framework for use in understanding the biology of the less well-understood members of this emerging superfamily, as well as of those to be characterized in the days to come. We use this review to develop the idea that most eukaryotic PAS proteins can be classified by functional similarities, as well as by predicted phylogenetic relationships. We focus on the alpha-class proteins, which often act as sensors of environmental signals, and the beta-class proteins, which typically act as broad-spectrum partners that target these heterodimers to their genomic targets.
Gene Expression Profile Assessment in Zebrafish (Danio rerio) (2007)

The Zebrafish Danio rerio, in the last decade, has been recognized as the best model among the vertebrate model organisms. The exquisite features and the high homology with the mammalian system have facilitated its application in many field e.g. eco-toxicology, biomedicine, genetics and physiology. The complete sequencing of the genome provided enormous value giving the possibility to develop a DNA microarray for gene expression analysis. Gene expression represents a unique way of characterizing how cells and organisms adapt to changes in the external environment (Lettieri, EHP, 2006). The measurements of gene expression levels, upon exposure to a chemical, can be used both to provide information about the mechanism of action of the toxicant, and also to form a sort of ¿genetic signature¿ for the identification of toxic products. Benzo[a]pyrene (BaP) is a well-known chemical pollutant, which belongs to the family of polycyclic aromatic hydrocarbons (PAHs) which are formed during combustion processes. Extensive studies have been published on the metabolism and the toxicity of PAHs, as well as epidemiologic studies which suggest a role of the PAHs in carcinogenetic and mutagenic effects in many species. \nBaP as well as other PAHs is included in the Priority Hazardous Substances adopted in November 2001 by the new Water Framework Directive (2000).\nOur studies focused on the analysis of gene expression changes in a liver cell line of Zebrafish upon exposure to BaP concentrations close to environmental level using DNA Microarrays.\nIn our gene expression analysis, we identified nine genes, among them the cyctochrome P450 CYP1A involved in the xenobiotic response and the cyb5 whose role in the activation of human CYP1A2 was recently reported in the literature.
Effect of hypothalamic surgery on prolactin release induced by 5-hydroxytryptophan (5-HTP) in rats. (1976)

Intravenous injections of varying doses of 5-HTP (1, 3 and 5 mg/100 g body wt), a precursor of serotonin, caused a significant and dose-related increase in plasma prolactin concentrations in urethane-anesthetized rats. Increases in plasma prolactin concentrations caused by 5-HTP (1 mg/100 g body wt iv) were abolished by the concomitant administration of L-DOPA (2 mg/100 g body wt iv). Plasma prolactin levels were also significantly elevated following the injection of 5-HTP in rats with complete hypothalamic deafferentation, whereas 5-HTP had no significant effect on plasma prolactin levels in rats with extensive hypothalamic ablation. These results suggest that 5-HTP causes prolactin secretion by stimulating the serotoninergic mechanism in the hypothalamus.
Effects of Ni Content on Particle Size of Secondary Phase in Cu-Based Alloys with Liquid Immiscibility by Laser-Melting (2022)

A secondary liquid phase with a droplet shape is separated from the primary liquid phase in Cu-Ni-Fe-Mo-Si alloy during Laser Metal Deposition process. In the subsequent quenching process, the secondary liquid phase solidifies into hard particles that are dispersed in the primary matrix phase. The increase in Ni content suppresses the coarsening of the hard particles, but the mechanism of the phenomenon has not been clarified. In this study, we investigated the effects of Ni content on the hard particle sizes, mainly focusing on Marangoni effect controlled by the temperature variation of interfacial energy. The effects of Ni content on the hard particle size were analyzed based on the change in the start temperature of the separation of two liquid phases (L1 and L2) and the temperature dependence of interfacial energy with Ni content calculated by thermodynamic calculations. The results showed that Ni content had little effect on the temperature variation of interfacial energy. On the other hand, an increase in Ni content decreases the temperature of L2 droplet formation and shortens the time to solidification, resulting in reduced moving distance of the droplet. Therefore, the collision frequency of L2 droplets caused by the Marangoni effect was reduced and coarsening of the droplets was suppressed.
Peroxidation of n-3 Polyunsaturated Fatty Acids Inhibits the Induction of iNOS Gene Expression in Proinflammatory Cytokine-Stimulated Hepatocytes (2011)

Eicosapentaenoic acid and docosahexaenoic acid (EPA/DHA), n-3 polyunsaturated fatty acids (PUFAs), have a variety of biological activities including anti-inflammatory and anticancer effects. We hypothesized that their peroxidized products contributed in part to anti-inflammatory effects. In the liver, the production of nitric oxide (NO) by inducible nitric oxide synthase (iNOS) has been implicated as one of the factors in hepatic inflammation and injury. We examined whether the peroxidation of EPA/DHA influences the induction of iNOS and NO production in proinflammatory cytokine-stimulated cultured hepatocytes, which is in vitro liver inflammation model. Peroxidized EPA/DHA inhibited the induction of iNOS and NO production in parallel with the increased levels of their peroxidation, whereas unoxidized EPA/DHA had no effects at all. Peroxidized EPA/DHA reduced the activation of transcription factor, NF-κB, and the expression of the iNOS antisense transcript, which are involved in iNOS promoter transactivation (mRNA synthesis) and its mRNA stabilization, respectively. These findings demonstrated that peroxidized products of EPA/DHA suppressed the induction of iNOS gene expression through both of the transcriptional and posttranscriptional steps, leading to the prevention of hepatic inflammation.
A diode-end-pumped frequency-tunable THz source with very low threshold (2012)

We report a very compact, laser diode-pumped, frequency-tunable THz source (1.65 - 2.65 THz) based on Stimulated Polariton Scattering in Mg:LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> . The system operates with very low threshold (~ 2.5 W diode pump power) and outputs a maximum average power of 6.45 μW at 2 THz, at a pulse repetition frequency of 3 kHz.
SARS-CoV-2 infection and adverse outcomes in users of ACE inhibitors and angiotensin-receptor blockers: a nationwide case-control and cohort analysis (2020)

EUPAS34887.
On the Mechanism of Cu-Catalyzed Enantioselective Extended Conjugate Additions: A Structure-Based Approach (2014)

The enantioselective 1,6-addition to unsaturated carbonyl compounds offers unique opportunities to study the range of selectivities one can obtain using Cu catalysis. Here, a substrate–reagent approach to obtain structural information on the mechanism of extended conjugate additions is reported. By studying the influence of several halides in the Grignard reagent and in the Cu source on the enantioselective 1,6-addition, it was shown that it is advantageous to use a combination of EtMgBr as Grignard reagent and CuI as Cu source. Furthermore, exploring substrates bearing several alkyl esters revealed that tBu-ester substrates enhance the enantiodiscrimination in the 1,6-addition and allow the addition of BnCH2MgBr. Substrates with a variety of electron-withdrawing groups were investigated as well, identifying that ester substrates are optimal for the 1,6-addition. Two other investigations feature Me-substituted olefin substrates and substrates with all possible olefin geometries. These studies show unprecedented high enantioselectivity in the 1,6-addition when α-Me substrates are used and give relevant insight into the 1,6-addition mechanism. Finally, substrates with three or four olefins in conjugation with the electron-withdrawing groups were studied. Here, a 1,8-addition is reported that gives the corresponding products in reasonable yield, regio- and stereoselectivity. With the combined results of these studies, elucidating key substrate and reagent parameters, an adapted mechanism for the enantioselective 1,6-addition is proposed. This mechanism features the activation of a dimeric precatalyst by an equivalent of Grignard reagent, active catalyst coordination to the internal olefin of the substrate in a CuI-π-complex, followed by coordination of the catalyst to the remote olefin forming another CuI-π-complex. From the latter CuI-complex, an oxidative addition gives a CuIII-σ-complex at the δ-carbon, followed by transfer of the alkyl moiety to the δ-position. This reductive elimination yields the product and reforms the active CuI catalyst via transmetalation with another molecule of Grignard reagent.
The genome sequence of the popular hexose-transport-deficient Saccharomyces cerevisiae strain EBY.VW4000 reveals LoxP/Cre-induced translocations and gene loss (2015)

Saccharomyces cerevisiae harbours a large group of tightly controlled hexose transporters with different characteristics. Construction and characterization of S. cerevisiae EBY.VW4000, a strain devoid of glucose import, was a milestone in hexose-transporter research. This strain has become a widely used platform for discovery and characterization of transporters from a wide range of organisms. To abolish glucose uptake, 21 genes were knocked out, involving 16 successive deletion rounds with the LoxP/Cre system. Although such intensive modifications are known to increase the risk of genome alterations, the genome of EBY.VW4000 has hitherto not been characterized. Based on a combination of whole genome sequencing, karyotyping and molecular confirmation, the present study reveals that construction of EBY.VW4000 resulted in gene losses and chromosomal rearrangements. Recombinations between the LoxP scars have led to the assembly of four neo-chromosomes, truncation of two chromosomes and loss of two subtelomeric regions. Furthermore, sporulation and spore germination are severely impaired in EBY.VW4000. Karyotyping of the EBY.VW4000 lineage retraced its current chromosomal architecture to four translocations events occurred between the 6th and the 12th rounds of deletion. The presented data facilitate further studies on EBY.VW4000 and highlight the risks of genome alterations associated with repeated use of the LoxP/Cre system.