gebhart/patrepeval huggingface dataset:
Retinoic acid-induced 1 gene haploinsufficiency alters lipid metabolism and causes autophagy defects in Smith-Magenis syndrome (2022)

Smith-Magenis syndrome (SMS) is a neurodevelopmental disorder characterized by cognitive and behavioral symptoms, obesity, and sleep disturbance, and no therapy has been developed to alleviate its symptoms or delay disease onset. SMS occurs due to haploinsufficiency of the retinoic acid-induced-1 (RAI1) gene caused by either chromosomal deletion (SMS-del) or RAI1 missense/nonsense mutation. The molecular mechanisms underlying SMS are unknown. Here, we generated and characterized primary cells derived from four SMS patients (two with SMS-del and two carrying RAI1 point mutations) and four control subjects to investigate the pathogenetic processes underlying SMS. By combining transcriptomic and lipidomic analyses, we found altered expression of lipid and lysosomal genes, deregulation of lipid metabolism, accumulation of lipid droplets, and blocked autophagic flux. We also found that SMS cells exhibited increased cell death associated with the mitochondrial pathology and the production of reactive oxygen species. Treatment with N-acetylcysteine reduced cell death and lipid accumulation, which suggests a causative link between metabolic dyshomeostasis and cell viability. Our results highlight the pathological processes in human SMS cells involving lipid metabolism, autophagy defects and mitochondrial dysfunction and suggest new potential therapeutic targets for patient treatment.
Airway epithelium expresses interleukin-18 (1999)

Interleukin (IL)-18 is an interferon (IFN)-gamma-inducing cytokine suggested to be important in regulating inflammatory responses. This study investigated the pulmonary expression of IL-18 under conditions characterized by T-helper (Th)1 (lipopolysaccharide (LPS) treatment/sarcoidosis) and Th2 (ovalbumin (OVA) challenge/asthma) cytokine production. In situ hybridization and immunocytochemistry were used to determine the number of cells expressing IL-18, IFN-gamma, IL-5 and major basic protein (MBP) within lung tissue from Balb/c mice stimulated with LPS, OVA and in normal control mice. Bronchial biopsies from patients with sarcoidosis, asthma and control individuals were also examined. IL-18 was localized primarily to airway epithelium and mononuclear cells. Constitutive expression was observed within the lungs of control mice. Animals challenged with LPS exhibited more IL-18 messenger ribonucleic acid (mRNA)-positive and IFN-gamma immunoreactive cells, compared to control mice (p<0.01). OVA-challenged mice had fewer IL-18 mRNA positive and more IL-5 and MBP immunoreactive cells, compared to control mice (p<0.01). Similarly, constitutive expression of IL-18 protein was observed within the airway epithelium of control individuals, with more positive cells found within sarcoidosis tissue (p<0.01) and fewer within asthmatic tissue (p<0.01), compared to controls. These results demonstrate the expression of interleukin-18 within airway epithelium and the regulation of this cytokine under conditions of both T-helper1 and T-helper2 cytokine production.
Research Update: Strategies for improving the stability of perovskite solar cells (2016)

The power-conversion efficiency of perovskite solar cells has soared up to 22.1% earlier this year. Within merely five years, the perovskite solar cell can now compete on efficiency with inorganic thin-film technologies, making it the most promising of the new, emerging photovoltaic solar cell technologies. The next grand challenge is now the aspect of stability. The hydrophilicity and volatility of the organic methylammonium makes the work-horse material methylammonium lead iodide vulnerable to degradation through humidity and heat. Additionally, ultraviolet radiation and oxygen constitute stressors which can deteriorate the device performance. There are two fundamental strategies to increasing the device stability: developing protective layers around the vulnerable perovskite absorber and developing a more resilient perovskite absorber. The most important reports in literature are summarized and analyzed here, letting us conclude that any long-term stability, on par with that of inorganic thin-film technologies, is only possible with a more resilient perovskite incorporated in a highly protective device design.
Surveillance for SARS-CoV-2 in Ohio’s wildlife, companion, and agricultural animals (2022)

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in humans in late 2019 and spread rapidly to become a global pandemic. A zoonotic spillover event from animal to human was identified as the presumed origin. Subsequently, reports began emerging regarding spillback events resulting in SARS-CoV-2 infections in multiple animal species. These events highlighted critical links between animal and human health while also raising concerns about the development of new reservoir hosts and potential viral mutations that could alter virulence and transmission or evade immune responses. Characterizing susceptibility, prevalence, and transmission between animal species became a priority to help protect animal and human health. In this study, we coalesced a large team of investigators and community partners to surveil for SARS-CoV-2 in domestic and free-ranging animals around Ohio between May 2020 and August 2021. We focused on species with known or predicted susceptibility to SARS-CoV-2 infection, highly congregated or medically compromised animals (e.g. shelters, barns, veterinary hospitals), and animals that had frequent contact with humans (e.g. pets, agricultural animals, zoo animals, or animals in wildlife hospitals). This included free-ranging deer (n=76), mink (n=57), multiple species of bats (n=65), and other wildlife in addition to domestic cats (n=275) and pigs (n= 184). In total, we tested 800 animals (34 species) via rRT-PCR for SARS-CoV-2 RNA. SARS-CoV-2 viral RNA was not detected in any of the tested animals despite a major peak in human SARS-CoV-2 cases that occurred in Ohio subsequent to the peak of animal samplings. Importantly, due to lack of validated tests for animals, we did not test for SARS-CoV-2 antibodies in this study, which limited our ability to assess exposure. While the results of this study were negative, the surveillance effort was critical and remains key to understanding, predicting, and preventing re-emergence of SARS-CoV-2 in humans or animals.
Plane-wave scattering by self-complementary metasurfaces in terms of electromagnetic duality and Babinet's principle (2013)

We investigate theoretically electromagnetic plane-wave scattering by self-complementary metasurfaces. By using Babinet's principle extended to metasurfaces with resistive elements, we show that the frequency-independent transmission and reflection are realized for normal incidence of a circularly polarized plane wave onto a self-complementary metasurface, even if there is diffraction. Next, we consider two special classes of self-complementary metasurfaces. We show that self-complementary metasurfaces with rotational symmetry can act as coherent perfect absorbers, and those with translational symmetry compatible with their self-complementarity can split the incident power equally, even for oblique incidences.
Fluoroquinolone supersusceptibility mediated by outer membrane protein OprH overexpression in Pseudomonas aeruginosa: evidence for involvement of a nonporin pathway (1992)

Overexpression of Pseudomonas aeruginosa outer membrane protein OprH led to an 8- to 32-fold increase in susceptibility to chloramphenicol and the quinolones nalidixic acid, norfloxacin, ciprofloxacin, and fleroxacin in comparison with the susceptibility of the wild-type strain H103 grown on Mg(2+)-sufficient medium. This was true regardless of whether OprH overexpression was induced by growth of strain H103 on Mg(2+)-deficient medium, the addition of 5 mM m-toluate to cells containing the cloned oprH gene behind the inducible tol promoter in plasmid pGB25, or mutation in the polymyxin-resistant derivative strain H181. In contrast, OprH overexpression failed to reverse the quinolone resistance phenotype of a nalB mutant. OprH was purified to homogeneity by selective detergent solubilization and fast protein liquid chromatography. The addition of OprH to the solution bathing a black lipid bilayer membrane failed to give rise to an increase in membrane conductance. This suggests that OprH is not a porin but, instead, may cause increased uptake of quinolones and chloramphenicol via a non-porin pathway.
A Comparison Study of Validity Indices on Swarm-Intelligence-Based Clustering (2012)

Swarm intelligence has emerged as a worthwhile class of clustering methods due to its convenient implementation, parallel capability, ability to avoid local minima, and other advantages. In such applications, clustering validity indices usually operate as fitness functions to evaluate the qualities of the obtained clusters. However, as the validity indices are usually data dependent and are designed to address certain types of data, the selection of different indices as the fitness functions may critically affect cluster quality. Here, we compare the performances of eight well-known and widely used clustering validity indices, namely, the Caliński-Harabasz index, the CS index, the Davies-Bouldin index, the Dunn index with two of its generalized versions, the I index, and the silhouette statistic index, on both synthetic and real data sets in the framework of differential-evolution-particle-swarm-optimization (DEPSO)-based clustering. DEPSO is a hybrid evolutionary algorithm of the stochastic optimization approach (differential evolution) and the swarm intelligence method (particle swarm optimization) that further increases the search capability and achieves higher flexibility in exploring the problem space. According to the experimental results, we find that the silhouette statistic index stands out in most of the data sets that we examined. Meanwhile, we suggest that users reach their conclusions not just based on only one index, but after considering the results of several indices to achieve reliable clustering structures.
Involvement of phospholipase C-gamma2 in activation of mitogen-activated protein kinase and phospholipase A2 by zooxanthellatoxin-A in rabbit platelets. (1997)

Zooxanthellatoxin-A (ZT-A), a polyhydroxypolyene isolated from a symbiotic dinoflagellate Symbiodinium sp., caused thromboxane A2-(TXA2) dependent and genistein-sensitive aggregation in rabbit platelets. Our study was performed to clarify the mechanism of the action of ZT-A. ZT-A caused an increase in tyrosine phosphorylation of 42-kDa protein, which is defined as p42 mitogen-activated protein kinase (MAPK) by immunoprecipitation. Although indomethacin (10 microM) completely inhibited ZT-A-induced TXB2 release, it partially inhibited the MAPK activation. The remained MAPK activation was completely inhibited by genistein (50 microM). Genistein (50 microM), by itself, abolished TXB2 release induced by ZT-A. ZT-A (2 microM) stimulated liberation of arachidonic acid and the subsequent metabolites such as TXB2 and 12-hydroperoxyeicosatetraenoic acid. However, ZT-A-stimulated phosphoinositide hydrolysis which was due to an increase in tyrosine phosphorylation of phospholipase C-(PLC)gamma2. The phosphorylation of PLC-gamma2 and the phosphoinositide hydrolysis were also partially inhibited by indomethacin (10 microM), and were abolished by a combined treatment of indomethacin (10 microM) and genistein (50 microM). ZT-A- (2 microM) induced MAPK activation in the presence of indomethacin (10 microM) was concentration-dependently inhibited by staurosporine and calphostin C, protein kinase C inhibitors. PD98059 (50 microM), a MAPK kinase inhibitor, also inhibited ZT-A-induced TXB2 release. Depletion of external Ca++ abolished ZT-A- (2 microM) induced MAPK activation, phosphoinositide hydrolysis, arachidonic acid liberation and TXB2 release. These results suggest that ZT-A stimulates a protein tyrosine kinase in the presence of external Ca++, resulting in the activation of MAPK probably via PLC-gamma2 and protein kinase C. The MAPK stimulated a liberation of arachidonic acid that is rapidly converted to TXA2. The released TXA2 causes aggregation accompanied with second stimulation of MAPK cascade.
Hypergraph Modelization of a Syntactically Annotated English Wikipedia Dump (2016)

International audience
Cover Picture: Functionalized Gold Nanoparticles Mimic Catalytic Activity of a Polysiloxane‐Synthesizing Enzyme (Adv. Mater. 10/2005) (2005)

Abstract A system that acts as a biomimetic of the silica‐synthesizing enzyme found in a marine sponge is reported by Morse and co‐workers on p. 1234. Gold nanoparticles (GNPs) are functionalized with the same organic moieties that are found in the enzyme's catalytic site. Interaction between the nucleophilic (OH‐terminated) and hydrogen‐bonding (imidazole‐terminated) GNPs, as shown on the cover, is required for the hydrolysis of a silicon alkoxide precursor and subsequent polycondensation to form silica at a low temperature and near‐neutral pH. Replacement of either of the required functional groups by a non‐reactive methyl group abolishes catalysis in this synthetic system, as it does in the biological enzyme. Cover art provided by Peter Allen.
Delta-Sleep-Inducing Peptide Reduces CRF-Induced Corticosterone Release (1985)

It has been reported that delta-sleep-inducing peptide (DSIP) can affect several activities other than sleep, including reduction of stress. We studied the effects of this nonapeptide on corticotropin releasing factor (CRF)-stimulated release of corticosterone in rats treated with chlorpromazine-morphine-pentobarbital. Significant reduction of corticosterone levels were observed after intravenous injection of 5-30 micrograms/kg DSIP. No effect of DSIP was found on the corticosterone release elicited by injection of adrenocorticotropic hormone. The results suggest that DSIP attenuates the effects of CRF at the level of the pituitary.
High-Performance Wrap-Gated InGaAs Nanowire Field-Effect Transistors with Sputtered Dielectrics (2015)

Although wrap-gated nanowire field-effect-transistors (NWFETs) have been explored as an ideal electronic device geometry for low-power and high-frequency applications, further performance enhancement and practical implementation are still suffering from electron scattering on nanowire surface/interface traps between the nanowire channel and gate dielectric as well as the complicated device fabrication scheme. Here, we report the development of high-performance wrap-gated InGaAs NWFETs using conventional sputtered Al2O3 layers as gate dielectrics, instead of the typically employed atomic layer deposited counterparts. Importantly, the surface chemical passivation of NW channels performed right before the dielectric deposition is found to significantly alleviate plasma induced defect traps on the NW channel. Utilizing this passivation, the wrap-gated device exhibits superior electrical performances: a high ION/IOFF ratio of ~ 2 × 10(6), an extremely low sub-threshold slope of 80 mV/decade and a peak field-effect electron mobility of ~ 1600 cm(2)/(Vs) at VDS = 0.1 V at room temperature, in which these values are even better than the ones of state-of-the-art NWFETs reported so far. By combining sputtering and pre-deposition chemical passivation to achieve high-quality gate dielectrics for wrap-gated NWFETs, the superior gate coupling and electrical performances have been achieved, confirming the effectiveness of our hybrid approach for future advanced electronic devices.
Dynamic Branch Prediction for a VLIW Processor (2000)

This paper describes the design of a dynamic branch predictor for a VLIW processor. The developed branch predictor predicts the direction of a branch, i.e., taken or not taken, and in the case of taken prediction it also predicts the issue-slot that contains the taken branch. This information is used to perform the BTB lookup. We compare this method against a typical superscalar branch predictor and against a branch predictor developed for VLIWs by Intel and HP. For a 2K entry BHT, 512 entry BTB, gshare branch predictor we obtain a next pc misprediction rate of 7.83%, while a traditional superscalar-type branch predictor of comparable costs achieves 10.3% and the Intel/HP predictor achieves 9.31%. In addition, we propose to have both predicted and delayed branches in the ISA and let the compiler select which type to apply. Simulations show performance improvements of 2-7% for benchmarks that are well-known for their high misprediction rates. This paper also contributes an experiment to determine whether speculative update in the fetch stage and correction of mispredictions is really necessary for VLIWs, instead of updating when branches are resolved. Experiments show that the performance advantage of speculative updating is small.
Mehrfachbindungen zwischen Hauptgruppenelementen und Übergangsmetallen, LIX. Brückenständige Zinn‐Atome in Organomangan‐Komplexen: Aufbau, Strukturchemie und Reaktivität von Mangan–Zinn‐Mehrfachbindungen (1989)

Abstract Linear und trigonal‐planar konfigurierte Zinn‐Atome aufweisende Organomangan‐Komplexe sind nach zwei Methoden darstellbar: Schrittweise Behandlung des Komplexes (η 5 ‐C 5 H 4 CH 3 )‐Mn(CO) 2 (THF) ( 1a ) mit Zinn(II)‐chlorid und Zink‐Staub führt ebenso zum Zinn‐Komplex (μ 3 ‐Sn)[(η 5 ‐C 5 H 4 CH 3 )Mn(CO) 2 ] 3 ( 2a ) wie die Umsetzung von 1a mit Monostannan, SnH 4 . Der Pentamethylcyclopentadienyl‐Komplex 1b ergibt analog die Derivate (μ 3 ‐Sn)[(η 5 ‐C 5 Me 5 )(CO) 2 ] 3 ( 2b ) und (μ‐Sn)[(η 5 ‐C 5 Me 5 )Mn‐(CO) 2 ] 2 ( 3b ). Formal weist der μ 3 ‐Sn‐Komplex 2a zwei MnSn‐Einfachbindungen und eine MnSn‐Doppelbindung auf (Einkristall‐Röntgenstrukturanalyse).
Degenerate four-wave mixing in solutions of diphenyl polyenes (1991)

Recently, optical limiting has been demonstrated in solutions of diphenyl polyenes, and χ (3) values an order of magnitude larger than CS 2 have been measured. 1 In this report, degenerate four-wave mixing (DFWM) has been used to investigate the origin of the nonlinear response in solutions of diphenyl polyenes. The DFWM measurements were made using a frequency doubled Q -switched Nd: YAG laser producing 7 nsec pulses at 532 nm. The temporal profile of the phase-conjugate signal observed contains two features separated by ~5 ns. These results indicate that the nonlinear response of these materials contains both a fast and a slow component. The fast component is attributed to intrinsic nonlinearities. The slow component is attributed to slowly responding processes such as thermal effects and has been studied using polarization and time delay experiments. The results of these experiments indicate that the slow component is not simply explained and may consist of more than one nonlinear response. The molecules are known to have two-photon absorption near the laser wavelength that may be contributing to the slow component that is observed.
Towards inferring neural circuits from population calcium imaging (2009)

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Differential branching fraction and angular analysis of the decay B 0 → K ∗0 μ + μ − (2013)

A bstract The angular distribution and differential branching fraction of the decay B 0 → K ∗0 μ + μ − are studied using a data sample, collected by the LHCb experiment in pp collisions at $ \sqrt{s}=7 $ TeV, corresponding to an integrated luminosity of 1 . 0 fb −1 . Several angular observables are measured in bins of the dimuon invariant mass squared, q 2 . A first measurement of the zero-crossing point of the forward-backward asymmetry of the dimuon system is also presented. The zero-crossing point is measured to be $ q_0^2={{{4.9\pm 0.9\;\mathrm{Ge}{{\mathrm{V}}^2}}} \left/ {{{c^4}}} \right.} $ , where the uncertainty is the sum of statistical and systematic uncertainties. The results are consistent with the Standard Model predictions.
Myocardial Infarction with Aortic Banding. A Combined Rat Model of Heart Failure. (1997)

The effect of additional abdominal aortic banding on parameters of heart failure was studied in male Wistar rats with myocardial infarction. Contractile function was studied 8-9 weeks after operation, with an isoprenaline dose response protocol, in a retrograde Langendorff perfusion. Also, plasma noradrenaline concentration, infarct size and morphology were determined. Compared with controls, myocardial infarction/aortic banding animals showed a decreased contractile function, both at baseline and after maximal isoprenaline stimulation, and elevated noradrenaline levels (1316 +/- 94) vs 1909 +/- 174 pg/ml, both p < 0.05). In myocardial infarction rats, baseline values, but not those after inotropic stimulation were decreased, when compared with controls, while the calculated Emax was significantly decreased. In aortic banding rats, contractile parameters were not significantly impaired, compared with controls. Both myocardial infarction and the myocardial infarction/aortic banding animals, but not aortic banding rats, had a significantly increased heart weight (1.4 +/- 0.04 g for controls vs 1.7 +/- 0.08 g for myocardial infarction and 2.0 +/- 0.12 g for myocardial infarction/aortic banding), and left ventricular cavity volume (19 +/- 1.4 mm3 for controls vs 49 +/- 5.5 mm3 for myocardial infarction and 48 +/- 4.3 mm3 for myocardial infarction/aortic banding) compared to control animals. Infarct size was 36.0% and 39.4% for the myocardial infarction and myocardial infarction/aortic banding animals, respectively. We conclude that myocardial infarction/aortic banding provides a new experimental model, which may yield important information and pathophysiology which allow evaluation of changes that may mimic clinical myocardial infarction with concomitant hypertension.
Investigating Eyes-away Mid-air Typing in Virtual Reality using Squeeze haptics-based Postural Reinforcement (2023)

In this paper, we investigate postural reinforcement haptics for mid-air typing using squeeze actuation on the wrist. We propose and validate eye-tracking based objective metrics that capture the impact of haptics on the user’s experience, which traditional performance metrics like speed and accuracy are not able to capture. To this end, we design four wrist-based haptic feedback conditions: no haptics, vibrations on keypress, squeeze+vibrations on keypress, and squeeze posture reinforcement + vibrations on keypress. We conduct a text input study with 48 participants to compare the four conditions on typing and gaze metrics. Our results show that for expert qwerty users, posture reinforcement haptics significantly benefit typing by reducing the visual attention on the keyboard by up to 44% relative to no haptics, thus enabling eyes-away behaviors.
Supplementary Figure from <i>Escherichia coli</i>–Specific CXCL13-Producing T<sub>FH</sub> Are Associated with Clinical Efficacy of Neoadjuvant PD-1 Blockade against Muscle-Invasive Bladder Cancer (2023)

Supplementary Figure from &lt;i&gt;Escherichia coli&lt;/i&gt;–Specific CXCL13-Producing T&lt;sub&gt;FH&lt;/sub&gt; Are Associated with Clinical Efficacy of Neoadjuvant PD-1 Blockade against Muscle-Invasive Bladder Cancer