gebhart/patrepeval huggingface dataset:
Photocatalytic Water Oxidation by a Mixed‐Valent MnIII3MnIVO3 Manganese Oxo Core that Mimics the Natural Oxygen‐Evolving Center (2014)

The functional core of oxygenic photosynthesis is in charge of catalytic water oxidation by a multi-redox Mn(III)/Mn(IV) manifold that evolves through five electronic states (S(i), where i=0-4). The synthetic model system of this catalytic cycle and of its S0→S4 intermediates is the expected turning point for artificial photosynthesis. The tetramanganese-substituted tungstosilicate [Mn(III)3Mn(IV)O3(CH3COO)3(A-α-SiW9O34)](6-)(Mn4POM) offers an unprecedented mimicry of the natural system in its reduced S0 state; it features a hybrid organic-inorganic coordination sphere and is anchored on a polyoxotungstate. Evidence for its photosynthetic properties when combined with [Ru(bpy)3](2+) and S2O8(2-) is obtained by nanosecond laser flash photolysis; its S0→S1 transition within milliseconds and multiple-hole-accumulating properties were studied. Photocatalytic oxygen evolution is achieved in a buffered medium (pH 5) with a quantum efficiency of 1.7%.
Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine (2014)

Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine.
Human transcription factor YY1 could upregulate the HIV-1 gene expression (2020)

Gene expression in HIV-1 is regulated by the promoters in 5' long-terminal repeat (LTR) element, which contain multiple DNA regulatory elements that serve as binding sites for cellular transcription factors. YY1 could repress HIV-1 gene expression and latent infection. Here, however, we observed that virus production can be increased by YY1 over-expression and decreased under YY1 depleted condition by siRNA treatment. To identify functional domain(s) of YY1 activation, we constructed a number of YY1 truncated mutants. Our data show that full-length YY1 enhances the viral transcription both through U3 and U3RU5 promoters. Moreover, the C-terminal region (296-414 residues) of YY1 is responsible for the transcriptional upregulation, which could be enhanced further in the presence of the viral Tat protein. The central domain of YY1 (155-295 residues) does not affect LTR activity but has a negative effect on HIV-1 gene expression. Taken together, our study shows that YY1 could act as a transcriptional activator in HIV-1 replication, at least in the early stages of infection. [BMB Reports 2020; 53(5): 248-253].
Three-Dimensional Periodic Structures via Pattern-Integrated Interference Lithography (2014)

Simulation results predicting the single-exposure fabrication of custom-modified 3D periodic microstructures by pattern-integrated interference lithography (PIIL) are presented. These results indicate PIIL is a viable method of making versatile 3D microstructures rapidly.
Neuronal Network Morphology and Electrophysiologyof Hippocampal Neurons Cultured on Surface-Treated Multielectrode Arrays (2007)

Toward the development of biocompatible surfaces for implantable electrode arrays and the creation of patterned neuronal networks, the impact of select biochemical substrates [poly-D-lysine (PDL), polyornithine (PO), polyethylenimine (PEI), and a basement membrane extract (BM)] on network morphology and spontaneous electrophysiological activity of dissociated hippocampal neurons was investigated. Cultured in serum-free Neurobasal medium at 100 000 cells/cm(2), neurons attached to each substrate. PDL, PO, and PEI induced little or no neuronal clustering and process fasciculation, whereas the addition of BM promoted these features. The ratios of somas to processes, and axons to dendrites, as determined by immunohistochemical staining and image analysis were comparable across all substrates. Spontaneous firing was recorded using planar multielectrode arrays (MEAs) at the third week in vitro for the two most divergent morphologies according to Euclidian cluster analysis, namely those induced by PO + BM and PEI. Mean spike amplitude, mean firing rate, median interspike interval (ISI), mean burst rate, and correlation index were analyzed and compared to morphological features. Synchronized bursting was highly correlated with neuronal clustering and process fasciculation. Spike amplitude was negatively correlated with thin branching which was most evident in neurons grown on PEI. These data indicate that factors, which influence adherence of neurons to surfaces, can profoundly impact both neuronal network morphology and electrophysiological activity in vitro.
Learning-Based Distributed Detection-Estimation in Sensor Networks with Unknown Sensor Defects (2015)

We consider the problem of distributed estimation of an unknown deterministic scalar parameter (the target signal) in a wireless sensor network (WSN), where each sensor receives a single snapshot of the field. We assume that the observation at each node randomly falls into one of two modes: a valid or an invalid observation mode. Specifically, mode one corresponds to the desired signal plus noise observation mode (\emph{valid}), and mode two corresponds to the pure noise mode (\emph{invalid}) due to node defect or damage. With no prior information on such local sensing modes, we introduce a learning-based distributed procedure, called the mixed detection-estimation (MDE) algorithm, based on iterative closed-loop interactions between mode learning (detection) and target estimation. The online learning step re-assesses the validity of the local observations at each iteration, thus refining the ongoing estimation update process. The convergence of the MDE algorithm is established analytically. Asymptotic analysis shows that, in the high signal-to-noise ratio (SNR) regime, the MDE estimation error converges to that of an ideal (centralized) estimator with perfect information about the node sensing modes. This is in contrast to the estimation performance of a naive average consensus based distributed estimator (without mode learning), whose estimation error blows up with an increasing SNR.
Narrow track dual magnetoresistive heads for tape (1997)

An experimental investigation of a dual magnetoresistive head tested on a Metrum tape test stand, is presented. The dual magnetoresistive (DMR) head has a trackwidth of 4 μm and a gap length of 0.1 μm. Metal particle tape, with a Mrδ of 16 memu/cm2 and a coercivity of 1.8 kOe, was used. A square wave was recorded with an FeAlN thin film inductive head, with a trackwidth of 33 μm and a gap of 1.9 μm. A shielded shunt biased MR head used in quarter inch cartridge drives (QIC), with a trackwidth of 19 μm and a shield to element gap of 0.25 μm was used as a benchmark. The DMR head showed a larger signal to dc erased noise per unit trackwidth than the QIC MR head, at linear densities of 20 to 100 kfci. Isolated transitions and dibits with a bit spacing of 0.3 μm were recorded for time domain measurements. The dibit response of the DMR head, characterized by a unipolar pulse with small side over/undershoots demonstrated the differential character of the DMR head. The QIC MR head PW50, measured directly from the isolated transition response and indirectly from the dibit response, was 1.4 μm. This large PW50 value was essentially write process limited, to first order independent of the read head gap length.
Water as a Reagent for Soil Remediation (2003)

SRI International conducted experiments in a two-year, two-phase process to develop and evaluate hydrothermal extraction technology, also known as hot water extraction (HWE) technology, for remediating petroleum-contaminated soils. The bench-scale demonstration of the process has shown great promise, and the implementation of this technology will revolutionize the conventional use of water in soil remediation technologies and provide a standalone technology for removal of both volatile and heavy components from contaminated soil.
Named Entity Recognition on Code-Switched Data: Overview of the CALCS 2018 Shared Task (2019)

In the third shared task of the Computational Approaches to Linguistic Code-Switching (CALCS) workshop, we focus on Named Entity Recognition (NER) on code-switched social-media data. We divide the shared task into two competitions based on the English-Spanish (ENG-SPA) and Modern Standard Arabic-Egyptian (MSA-EGY) language pairs. We use Twitter data and 9 entity types to establish a new dataset for code-switched NER benchmarks. In addition to the CS phenomenon, the diversity of the entities and the social media challenges make the task considerably hard to process. As a result, the best scores of the competitions are 63.76% and 71.61% for ENG-SPA and MSA-EGY, respectively. We present the scores of 9 participants and discuss the most common challenges among submissions.
Application of hybrid blocking layers in solid-state dye-sensitized solar cells (2015)

A hybrid blocking layer consisting of a conducting TiO2 network embedded in a ceramic matrix is implemented in a solid-state dye-sensitized solar cell. This novel type of blocking layer is thinner than the classical blocking layer films as shown with SEM and XRR measurements, and thereby the conductivity of the hybrid film is increased by 110%. A percolating TiO2 network, proven by TEM/ESI and GISAXS measurements, allows for the charge transport. Although being thinner, the hybrid film completely separates the rough electrode material from the hole-transport medium in solar cells to avoid the recombination of charge carriers at this interface. In total, the power conversion efficiency of solar cells is improved: the application in photovoltaics shows that the efficiency of devices with the hybrid blocking layer is increased by 6% compared to identical solar cells employing the conventional blocking layer.
Comparison of sound field measurements and predictions in coupled volumes between numerical methods and scale model measurements (2013)

Prediction of sound fields in closed spaces can be achieved by various methods, either physical or numerical, based on different theoretical features. While the benefits and limitations of many methods have been examined for single volume spaces, there has been little effort in examining these effects for coupled volume situations. The present study presents a case study comparing theoretical, experimentally physical measurements on a scale model, and various numerical methods, namely boundary element method (BEM), finite-difference time-domain (FDTD), and ray-tracing through the commercial software CATT-Acoustic and ODEON. Although these numerical methods all use 3D numerical models of the architecture, each is different. Ray-tracing is more suitable to geometries with larger planes; BEM requires a more regular finer surface mesh; and FDTD requires a volumetric mesh of the propagation medium. A simple common geometry based on the scale model is used as a basis to compare these different approaches. Application to coupled spaces raises issues linked to later parts in the decay due to multi-slope decay rates, as well as diffraction phenomenon due to acoustic energy traveling between coupling surfaces from one volume to another. The ability of these numerical methods to adequately model these effects is the question under study.
Fundamental mode emission in tapered quantum cascade lasers for high brightness (2019)

Currently, the highest power quantum cascade lasers (QCLs) profit from (i) the efficient active region design, minimizing the energy fraction transferred into heat, (ii) relatively high number (40) of cascades, increasing the mode confinement factor, &Gamma;, and (iii) narrow buried-heterostructure (BH) waveguides, which cool efficiently the active region due to the high lateral heat ow. This combination allows Watt-level continuous wave (cw) emission powers at room temperature. Moreover, narrow waveguides often support the fundamental TM<sub>00</sub> lateral mode, resulting into a nearly Gaussian laser beam. Power scaling is possible in this configuration only by laser length, which is limited by the needs for robust construction and transparent anti-reflection coatings. Broad-area (BA) QCLs with a small number of cascades can also deliver a Watt-level cw powers at room temperature, profiting from the enhanced vertical heat flow. Power can also be scaled for these lasers via the laser width, and is nearly unlimited. The usual drawback of the BA lasers is poor beam quality. In this paper we report on the first demonstration of the room temperature cw operation of the BA QCL at the fundamental TM<sub>00</sub> mode. The stable and reproducible transverse mode selection is achieved by the double-taper waveguide geometry. The laser emits at 4.6 &mu;m and has demonstrated room-temperature cw power of 100 mW.
A mutation in integrase can compensate for mutations in the simian immunodeficiency virus att site (1997)

Sequences at the left terminus of U3 in the left long terminal repeat (LTR) and at the right terminus of U5 in the right LTR are important for integration of retroviral DNA. In the infectious pathogenic molecular clone of simian immunodeficiency virus strain mac239 (SIVmac239), 10 of the 12 terminal base pairs form an imperfect inverted repeat structure (5' TGGAAGGGATTT 3' [nucleotides 1 to 12] and 3' ACGATCCCTAAA 5' [nucleotides 10279 to 10268]). Nineteen different mutant forms of SIVmac239 proviral DNA with changes at one or more of the positions in each of the 12-terminal-base-pair regions were constructed. Viral replication was severely or completely compromised with nine of these mutants. Revertants appeared 40 to 50 days after transfection in two independent experiments with mutant 7, which contained changes of AGG to TAC at positions 5 to 7 in U3 and TCC to GAA at positions 10275 to 10273 in U5. Virus produced at these times from mutant 7 transfection replicated upon reinfection with only a slight delay when compared to the wild type. Sequence analysis of the LTR and integrase regions from infected cultures revealed two predominant changes: G to A at position 10275 in U5 and Glu to Lys at position 136 in integrase. Derivatives of clone 7 in which these changes were introduced individually and together were constructed by site-specific mutagenesis. Each change individually restored replication capacity only partially. However, the combination of both mutations restored replicative capacity to that of the original revertants. These results indicate that changes in integrase can compensate for mutations in the terminal nucleotides of the SIV LTR. The results further indicate that resistance to integrase inhibitors may include both integrase and LTR mutations.
Amoscanate as a Topically Applied Chemical for Prophylaxis against Schistosoma Mansoni Infections in Mice (1983)

Amoscanate (0.1% w/v) in methanol solution applied to skin by tail immersion 1 day prior to cercarial exposure provided mice with better than 90% protection against mature Schistosoma mansoni infections. Cercariae penetrated and schistosomula migrated from treated skins as readily as in control skins. Lung incubation assays, however, indicated that day 7 lung worm burdens were only about half those of control values. By day 20, worm burdens were reduced further to approximately 15% of those for control mice. The delayed prophylactic activity was apparently not due to percutaneously absorbed compound. Wipe application of amoscanate to the skin was nearly as effective as immersion.
A 38 GHz on-chip antenna in 28-nm CMOS using artificial magnetic conductor for 5G wireless systems (2016)

This paper presents the first-ever millimeter wave on-chip antenna (AoC) in 28 nm CMOS technology. The addition of artificial magnetic conductor (AMC) can increase the antenna's power gain and radiation efficiency to -1.75 dBi and 22%, respectively, with an occupied area of 0.95 mm×4.75 mm at 38 GHz. This structure is intended for fully integrated single-chip nanometer CMOS transceivers for 5G communication systems.
Progesterone androstenedione testosterone and clinical characteristics in endometrial carcinoma. (1992)

Serum concentrations of progesterone (P), androstenedione (A) and testosterone (T) were measured in 128 postmenopausal women with endometrial adenocarcinoma. The correlations between these hormones were studied and related to such clinical parameters as: stage, histopathology, age, gynaecological history, body mass index and related diseases. In previous studies we have shown the relations between oestron (E1) and oestradiol (E2) serum concentration and clinical parameters. A clear correlation was seen between E1 and E2. Both E1 and E2 also strongly correlated with BMI. In this study androstenedione is found to correlate with E1 and E2, p less than 0.03 and p less than 0.02 resp. Progesterone and E1 were correlated, p less than 0.01, but not P and E2. Testosterone correlated with E1, p less than 0.002, E2, p less than 0.003 and A, p less than 0.02. None of the hormones P, A or T correlate with BMI. Androstenedione and age, and A and menopausal years showed a negative correlation, p less than 0.01 for both. Testosterone correlated with menopausal years, p less than 0.03; and correlated negatively with years of menstruation, p less than 0.03. These results do not support the hypothesis that A is the exclusive precursor for conversion to E1 in fat tissue. The correlation between P and E1 could indicate a relation to steroids higher up in the synthesis chain. The influence of P, A and T on the investigated clinical factors can not be strong, since correlations are virtually missing.
Synthesis of Polysiloxane-Bound (Ether−phosphine)palladium Complexes. Stoichiometric and Catalytic Reactions in Interphases1 (1996)

The reaction of two equiv of the monomeric ether-phosphine O,P ligand (MeO)(3)Si(CH(2))(3)(Ph)PCH(2)-Do [1a(T(0)()), 1b(T(0)())] {Do = CH(2)OCH(3) [1a(T(0)())], CHCH(2)CH(2)CH(2)O [1b(T(0)())]} with PdCl(2)(COD) yields the monomeric palladium(II) complexes Cl(2)Pd(P approximately O)(2) [2a(T(0)())(2)(), 2b(T(0)())(2)()]. The compounds 2a(T(0)())(2)() and 2b(T(0)())(2)() are sol-gel processed with variable amounts (y) of Si(OEt)(4) (Q(0)()) to give the polysiloxane-bound complexes 2a(T(n)())(2)()(Q(k)())(y)(), 2b(T(n)())(2)()(Q(k)())(y)() (Table 1) {P approximately O = eta(1)-P-coordinated ether-phosphine ligand; for T(n)() and Q(k)(), y = number of condensed T type (three oxygen neighbors), Q type (four oxygen neighbors) silicon atoms; n and k = number of Si-O-Si bonds; n = 0-3; k = 0-4; 2a(T(n)())(2)()(Q(k)())(y)(), 2b(T(n)())(2)()(Q(k)())(y)() = {[M]-SiO(n)()(/2)(OX)(3)(-)(n)()}(2)[SiO(k)()(/2)(OX)(4)(-)(k)()](y)(), [M] = (Cl(2)Pd)(1/2)(Ph)P(CH(2)Do)(CH(2))(3)-, X = H, Me, Et}. The complexes 2b(T(n)())(2)()(Q(k)())(y)() (y = 4, 12, 36) show high activity and selectivity in the hydrogenation of 1-hexyne and tolan. The dicationic complexes [Pd(P&arcraise;O)(2)][SbF(6)](2) [3a(T(0)())(2)(), 3b(T(0)())(2)()] are formed by reacting Cl(2)Pd(P approximately O)(2) with 2 equiv of a silver salt {P&arcraise;O = eta(2)-O&arcraise;P-coordinated ether-phosphine ligand; 3a(T(0)())(2)(), 3b(T(0)())(2)() = [M]-SiOMe(3); [M] = {[Pd(2+)](1/)(2)P(Ph)(CH(2)CH(2)OCH(3))(CH(2))(3)-}{SbF(6)} (a), {[Pd(2+)](1/)(2)P(Ph)(CH(2)CHCH(2)CH(2)CH(2)O)(CH(2))(3)-}{SbF(6)} (b)}. Their polysiloxane-bound congeners 3a(T(n)())(2)(), 3b(T(n)())(2)() {[M]-SiO(n)()(/2)(OX)(3)(-)(n)} are obtained if a volatile, reversible bound ligand like acetonitrile is employed during the sol-gel process. The bis(chelate)palladium(II) complexes 3a(T(n)())(2)(), 3b(T(n)())(2)() are catalytic active in the solvent-free CO-ethene copolymerization, producing polyketones with chain lengths comparable to those obtained with chelating diphosphine ligands. The polysiloxane-bound palladium(0) complexes 5a(T(n)())(2)()(Q(k)())(4)(), 5b(T(n)())(2)()(Q(k)())(4)() {[M]-SiO(n)()(/)(2)(OX)(3)(-)(n)}(2)[SiO(k)()(/2)(OX)(4)(-)(k)](4), [M] = [(dba)Pd](1/)(2)P(Ph)(CH(2)Do)(CH(2))(3)-} undergo an oxidative addition reaction with iodobenzene in an interphase with formation of the complexes PhPd(I)(P approximately O)(2).4SiO(2) [6a(T(n)())(2)()(Q(k)())(4)(), 6b(T(n)())(2)()(Q(k)())(4)()] {[M]-SiO(n)()(/)(2)(OX)(3)(-)(n)](2)[SiO(k)()(/2)(OX)(4)(-)(k)](4), [M] = [PhPd(I)](1/2)P(Ph)(CH(2)Do)(CH(2))(3)-}, which insert carbon monoxide into the palladium-aryl bond even in the solid state.
Glucagon regulates gluconeogenesis through KAT2B- and WDR5-mediated epigenetic effects (2013)

Circulating pancreatic glucagon is increased during fasting and maintains glucose balance by stimulating hepatic gluconeogenesis. Glucagon triggering of the cAMP pathway upregulates the gluconeogenic program through the phosphorylation of cAMP response element-binding protein (CREB) and the dephosphorylation of the CREB coactivator CRTC2. Hormonal and nutrient signals are also thought to modulate gluconeogenic gene expression by promoting epigenetic changes that facilitate assembly of the transcriptional machinery. However, the nature of these modifications is unclear. Using mouse models and in vitro assays, we show that histone H3 acetylation at Lys 9 (H3K9Ac) was elevated over gluconeogenic genes and contributed to increased hepatic glucose production during fasting and in diabetes. Dephosphorylation of CRTC2 promoted increased H3K9Ac through recruitment of the lysine acetyltransferase 2B (KAT2B) and WD repeat-containing protein 5 (WDR5), a core subunit of histone methyltransferase (HMT) complexes. KAT2B and WDR5 stimulated the gluconeogenic program through a self-reinforcing cycle, whereby increases in H3K9Ac further potentiated CRTC2 occupancy at CREB binding sites. Depletion of KAT2B or WDR5 decreased gluconeogenic gene expression, consequently breaking the cycle. Administration of a small-molecule KAT2B antagonist lowered circulating blood glucose concentrations in insulin resistance, suggesting that this enzyme may be a useful target for diabetes treatment.
Design, synthesis and biological evaluation of new small molecules with anti-inflammatory activity (2015)

Per lipossigenasi (nota più comunemente con l'abbreviazione di LOX o LO) si intende una famiglia eterogenea di enzimi in grado di perossidare i lipidi e di causare l'ossigenazione di acidi grassi polinsaturi trasformandoli, così, nei corrispettivi derivati idroperossidici. Nello specifico, la 5-LO rappresenta l'enzima chiave nell'ossidazione dell'acido arachidonico (AA) in LTA4, intermedio indispensabile per la sintesi dei leucotrieni, potenti mediatori flogistici coinvolti in una serie di differenti processi patologici. Va da sé che l'inibizione, dell'attività di tale enzima, induce la diretta riduzione di LT, definendo la LOX come valido drug-target per la farmacoterapia di disturbi infiammatori quali asma, rinite allergica, aterosclerosi e alcune forme neoplastiche. [a cura dell'autore]