gebhart/patrepeval huggingface dataset:
Bladder hyperactivity and increased excitability of bladder afferent neurons associated with reduced expression of Kv1.4 α-subunit in rats with cystitis (2009)

Hyperexcitability of C-fiber bladder afferent pathways has been proposed to contribute to urinary frequency and bladder pain in chronic bladder inflammation including interstitial cystitis. However, the detailed mechanisms inducing afferent hyperexcitability after bladder inflammation are not fully understood. Thus, we investigated changes in the properties of bladder afferent neurons in rats with bladder inflammation induced by intravesical application of hydrochloric acid. Eight days after the treatment, bladder function and bladder sensation were analyzed using cystometry and an electrodiagnostic device of sensory function (Neurometer), respectively. Whole cell patch-clamp recordings and immunohistochemical staining were also performed in dissociated bladder afferent neurons identified by a retrograde tracing dye, Fast Blue, injected into the bladder wall. Cystitis rats showed urinary frequency that was inhibited by pretreatment with capsaicin and bladder hyperalgesia mediated by C-fibers. Capsaicin-sensitive bladder afferent neurons from sham rats exhibited high thresholds for spike activation and a phasic firing pattern, whereas those from cystitis rats showed lower thresholds for spike activation and a tonic firing pattern. Transient A-type K(+) current density in capsaicin-sensitive bladder afferent neurons was significantly smaller in cystitis rats than in sham rats, although sustained delayed-rectifier K(+) current density was not altered after cystitis. The expression of voltage-gated K(+) Kv1.4 alpha-subunits, which can form A-type K(+) channels, was reduced in bladder afferent neurons from cystitis rats. These data suggest that bladder inflammation increases bladder afferent neuron excitability by decreasing expression of Kv1.4 alpha-subunits. Similar changes in capsaicin-sensitive C-fiber afferent terminals may contribute to bladder hyperactivity and hyperalgesia due to acid-induced bladder inflammation.
β-Sheet Structure Formation within Binary Blends of Two Spider Silk Related Peptides (2023)

Intrinsically disordered proteins (IDPs) play an important role in molecular biology and medicine because their induced folding can lead to so-called conformational diseases, where β-amyloids play an important role. Still, the molecular folding process into the different substructures, such as parallel/antiparallel or extended β-sheet/crossed β-sheet is not fully understood. The recombinant spider silk protein eADF4(Cx) consisting of repeating modules C, which are composed of a crystalline (pep-c) and an amorphous peptide sequence (pep-a), can be used as a model system for IDP since it can assemble into similar structures. In this work, blend films of the pep-c and pep-a sequences were investigated to modulate the β-sheet formation by varying the molar fraction of pep-c and pep-a. Dichroic Fourier-transform infrared spectroscopy (FTIR), circular dichroism, spectroscopic ellipsometry, atomic force microscopy, and IR nanospectroscopy were used to examine the secondary structure, the formation of parallel and antiparallel β-sheets, their orientation, and the microscopic roughness and phase formation within peptide blend films upon methanol post-treatment. New insights into the formation of filament-like structures in these silk blend films were obtained. Filament-like structures could be locally assigned to β-sheet-rich structures. Further, the antiparallel or parallel character and the orientation of the formed β-sheets could be clearly determined. Finally, the ideal ratio of pep-a and pep-c sequences found in the fibroin 4 of the major ampullate silk of spiders could also be rationalized by comparing the blend and spider silk protein systems.
Tables S1 and S3 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer (2023)

&lt;p&gt;Table S1. Genetic characterization of patient-derived xenografts using the Illumina Trusight panel capturing frequent mutations in 94 genes and 284 SNPs associated with cancer Table S3. Triptolide-induced effects on the mRNA abundance was determined by Illumina HighSeq RNA sequencing of 001 cells treated with 100 nM triptolide in vitro for 6 hours.&lt;/p&gt;
Improved Saccharification of Wheat Straw for Biofuel Production Using an Engineered Secretome of Trichoderma reesei (2010)

For the purpose of a industrial process of cellulosic ethanol production, an efficient β-glucosidase was evolved by L-Shuffling starting from three parental genes (i.e., Chaetomium globosum glucosidase putative gene, Trichoderma reesei bgl1 gene, and Neurospora crassa glucosidase putative gene, named genes A, B, and C, respectively) originating from microbial biodiversity and showing 70% of identity at the amino acid level. Enzyme B (encoded by bgl1 gene) was chosen as a reference so that the backbone of the evolved enzymes would be based on this enzyme. Two rounds of L-Shuffling and colonies screening (20,000 colonies per round) on chromogenic glucose substrate were performed. Compared with native β-glucosidase, the most evolved enzyme has a 242-fold increased kcat for the pNPGlc substrate. After expression of this improved β-glucosidase in T. reesei, a new efficient enzymatic cocktail was secreted by the strain allowing for a 4-fold decrease in cellulase loading without any loss in hydrolysis performance of degradation of a steam-exploded wheat straw compared to the untransformed parental strain.
Self-hosted placement for massively parallel processor arrays (2009)

We consider the placement problem as part of the CAD flow for a massively parallel processor arrays (MPPAs). In contrast to traditional placers, which operate on a workstation with one or several cores and are able to take advantage of parallelism to a limited degree, we investigate running the placer on the target architecture itself. As the number of processor elements (PEs) in such a device scale, so too does the computational power available to the placer. This natural scaling helps avoid the long runtimes that afflict FPGA flows. In this paper, we propose a distributed placer suitable to run on a MPPA. This placer takes advantage of local interconnect fabric, and may be efficiently coded on a simple, RISC-like core. We investigate the performance of this placer and compare it to traditional, simulated annealing-based placers using both unrealistic (but nearly optimal) and realistic (but suboptimal) annealing schedules. On a simulated 32 × 32 = 1024-core MPPA, the proposed algorithm furnishes placements within 5 % of the optimal placement quality a level competetive with the realistic, traditional placer. To do so, the distributed placer requires each PE to consider 1/256 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> as many swaps as the traditional placer, a computational advantage which scales favourably as the number of cores on the MPPA increases.
Tuning OER Electrocatalysts toward LOM Pathway through the Lens of Multi-Descriptor Feature Selection by Artificial Intelligence-Based Approach (2022)

From the thermodynamic and kinetic viewpoints, the oxygen evolution reaction (OER) is central to the production of hydrogen through electrocatalytic water splitting process. As a result, extensive research is carried out with an aim to develop (preferably low cost) electrocatalysts for efficient OER reaction. Two main mechanisms, the lattice oxygen mediated mechanism (LOM) and the adsorbate evolution mechanism (AEM), are proposed for the OER process, but the former seems to be favored as the latter is surrounded by a number of discrepancies. The LOM is based on the oxidation and reduction chemistry of lattice oxygen anions. Both from fundamental and application perspectives, identification and selection of crucial electronic and structural features to rationally tune the LOM for OER process and determine the rate of the OER reaction are essential but remain a challenge. As yet, this has largely been attempted by trial and error (synthesis and performance evaluation) approaches and, hence, has been tied up by tediousness and inefficiency. Considering the availability of large chemical space and huge probabilities in fine-tuning of electronic and structural attributes, the use of artificial intelligence (AI) can be efficacious. To predict promising material features that enable rational design of OER electrocatalysts, electrocatalytic performance maps have been developed based on reactivity multiple descriptors. The reactivity multiple descriptors are numerous and are classified into several families. Therefore, modern materials informatics technique is urgently required to enable large-scale data mining to rapidly screen and select the best physical features from multiple descriptors for a rational design of LOM-induced OER electrocatalysts. In this context, feature selection by artificial intelligence-based approach can be a solution to such challenge. Yet to the best of our knowledge, no attempt has been made before to tune electrocatalysts for the OER through LOM reaction mechanism following feature selection by artificial intelligence-based approach.
The antiviral activity of the CXCR4 antagonist AMD3100 is independent of the cytokine-induced CXCR4/HIV coreceptor expression level (2003)

The chemokine receptor CXCR4 is the main coreceptor used by T-tropic X4 HIV-1 strains to infect its target T cells. It has been proven that the CXCR4 expression level in T cells is strongly up-regulated by interleukin (IL)-4, a Th2-type cytokine that is secreted preferentially in HIV-infected patients in a later stage of disease. This results in an enhancement of HIV-1 replication in CD4+ T-lymphocytes. We have now evaluated the potency of the CXCR4 antagonist AMD3100 in phytohemagglutinin (PHA)/IL-2- versus PHA/IL-4-activated T cells in order to determine whether the compound has comparable CXCR4-antagonistic and anti-HIV-1 effects under these different cytokine treatments. We analyzed the CXCR4 expression level and the dose-dependent inhibition of CXCR4 expression by AMD3100, by monitoring the binding of an anti-CXCR4 monoclonal antibody (clone 12G5). We also determined stromal cell-derived factor (SDF)-1-induced intracellular calcium signaling and HIV-1 replication in these cells in the absence and pre...
Abstract 16905: Evaluation of Immediate Procedural Outcome After MitraClip Using Automated Quantitaive Real-time Volume Color Flow Doppler Transesophageal Echocardiography (2015)

Background: Current echocardiographic evaluation of residual MR after Mitra-Clip is based on a semi-quantitative scale (trace to 4+). We evaluated a previously validated quantitative approach using automated real-time volume color flow Doppler (3D-RTVCFD). Methods: 30 patients (age 82 ± 5) underwent Mitra-Clip implantation guided by 3D-RTVCFD TEE (Siemens SC2000, CA). In 10 patients, data to automatically quantify 3-D regurgitant volume (RV, ml) and fraction (RF, %) and anatomic regurgitant orifice area (AROA) was available (Figure, upper panel). All patients had conventional 2-D Echo data for assessment of MR severity using the standard integrated approach. Results: MR was severe (4+) in 8, and moderately severe (3+) in 2 patients at baseline. MR post Mitra-Clip was mild or trace in 6 (≤1+, Group 1), and moderate in 4 (Group 2) patients. At baseline, the (mean±SD) 3-D RV/RF was 54.5±19.9 ml/60.6±10.2% and the AROA was 0.6±0.2 cm2 for the whole group. Post Mitra-Clip, the 3-D RV/RF was 23.6±10.3 ml/37.0±13.9% (p&lt;0.01/p&lt;0.001 vs. baseline) and the AROA was 0.3±0.1 cm2 (p&lt;0.05). Both Group 1 and Group 2 had similar baseline RF, and both demonstrated a 39% and 38% decrease in RF post Mitra-clip, respectively (Figure, bottom graph). The decrease in AROA in both groups post Mitra-Clip was also significant (~53% in Group 1 and ~59% in Group 2). Thus, despite “moderate” residual MR using the semi-quantitative scale in Group 2, there was significant decreases in both RF and AROA. Conversely, in Group 1 some of the residual MR assessed as “mild” indeed had 3-D RF and AROA in the moderate range, post Mitra-clip. Conclusion: Automated quantitative 3-D real-time volume color flow Doppler TEE offers a quantitative assessment of residual MR post Mitra-clip immediately after the procedure. This may refine decision-making with regard to number of clips. Both accuracy of 3D RTVCFD TEE to quantify MR and it’s predictive value for mid- to long term procedural success need further studies.
A multi-fpga 10x-real-time high-speed search engine for a 5000-word vocabulary speech recognizer (2009)

Today's best quality speech recognition systems are implemented in software. These systems fully occupy the resources of a high-end server to deliver results at real-time speed: each hour of audio requires a significant fraction of an hour of computation for recognition. This is profoundly limiting for applications that require extreme recognition speed, for example, high-volume tasks such as video indexing (e.g., YouTube), or high-speed tasks such as triage of homeland security intelligence. We describe the architecture and implementation of one critical component -- the backend search stage -- of a high-speed, large-vocabulary recognizer. Implemented on a multi-FPGA Berkeley Emulation Engine 2 (BEE2) platform, we handle a standard 5000-word Wall Street Journal speech benchmark. Our backend search engine can decode on average 10 times faster than real-time running at 100 MHz, i.e, 10x faster than real-time, with negligible degradation in accuracy, running at a clock rate ~ 30x slower than a conventional server. To the best of our knowledge, this is both the most complex, and the fastest recognizer ever to be realized in a hardware form.
Hydrogenation of CO2 to Formic Acid with a Highly Active Ruthenium Acriphos Complex in DMSO and DMSO/Water (2016)

The novel [Ru(Acriphos)(PPh3 )(Cl)(PhCO2 )] [1; Acriphos=4,5-bis(diphenylphosphino)acridine] is an excellent precatalyst for the hydrogenation of CO2 to give formic acid in dimethyl sulfoxide (DMSO) and DMSO/H2 O without the need for amine bases as co-reagents. Turnover numbers (TONs) of up to 4200 and turnover frequencies (TOFs) of up to 260 h(-1) were achieved, thus rendering 1 one of the most active catalysts for CO2 hydrogenations under additive-free conditions reported to date. The thermodynamic stabilization of the reaction product by the reaction medium, through hydrogen bonds between formic acid and clusters of solvent or water, were rationalized by DFT calculations. The relatively low final concentration of formic acid obtained experimentally under catalytic conditions (0.33 mol L(-1) ) was shown to be limited by product-dependent catalyst inhibition rather than thermodynamic limits, and could be overcome by addition of small amounts of acetate buffer, thus leading to a maximum concentration of free formic acid of 1.27 mol L(-1) , which corresponds to optimized values of TON=16×10(3) and TOFavg ≈10(3) h(-1) .
Interlayer coupling and the thermopower of cuprate superconductors (1996)

A review of the extant literature on the thermopower (TEP) of the cuprate superconductors reveals a transition from polaronic to homogeneous itinerant electron behavior with increasing hole concentration in the ${\mathrm{CuO}}_{2}$ sheets. Superconductivity appears at the compositions of crossover from one regime to the other, and the normal state of the superconductors retains a heterogeneous electronic structure of mobile hole-rich and hole-poor domains, which introduces both a statistical and a transport component to the Seebeck coefficient. A primary manifestation of the transport component is an enhancement term \ensuremath{\delta}\ensuremath{\alpha}(T) having a maximum at a ${\mathit{T}}_{\mathrm{max}}$=100--140 K, which is characteristic of a strong coupling of the charge carriers to optical rather than acoustic phonons. Comparison of the TEP for ${\mathrm{La}}_{1.85}$${\mathrm{Sr}}_{0.15}$${\mathrm{CuO}}_{4}$ vs ${\mathrm{La}}_{0.85}$${\mathrm{Sr}}_{1.15}$${\mathrm{GaCuO}}_{5}$ and ${\mathrm{La}}_{1.8}$${\mathrm{Sr}}_{0.2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{6+\mathrm{\ensuremath{\delta}}}$ vs ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ indicates that an increase in the c-axis coupling between neighboring ${\mathrm{CuO}}_{2}$ sheets increases the size of the polaron or hole-rich domains in the underdoped compositions, thereby lowering the room-temperature value of the Seebeck coefficient \ensuremath{\alpha}(300 K) and increasing the magnitude of \ensuremath{\delta}\ensuremath{\alpha}(T). These observations implicate a strong elastic component, enhanced by electron-lattice interactions, in the c-axis coupling as well as in the formation of larger nonadiabatic polarons and their interactions within the ${\mathrm{CuO}}_{2}$ planes. They also signal that caution must be exercised in any application of a ``universal plot'' of \ensuremath{\alpha}(300 K) versus hole concentration p per Cu atom in a ${\mathrm{CuO}}_{2}$ plane to obtain a value of p from TEP data. \textcopyright{} 1996 The American Physical Society.
A Fortunate Story of an Unusual AK-47 Bullet Trajectory: Always Keep a Smartphone in Your Pocket (2016)

This is a report of a fortunate story of an unusual AK-47 bullet trajectory which took place during the Paris (France) attack of November 13th, 2015. A young man, trying to protect his girlfriend, interfered between her and a shooter. He had been wounded in the posterior compartment of the thigh. The bullet penetrated him and, instead of exiting, rebound against his Smartphone, which was in the front pocket of his pants. Thanks to that, the missile bullet did not injure his girlfriend but ended its trajectory in the fat tissue of his thigh. Thabouillot O , Perrier P , Roche NC , Agard D , Barbier O , Martin G , Viant E , Leclere JB . A fortunate story of an unusual AK-47 bullet trajectory: always keep a Smartphone in your pocket. Prehosp Disaster Med, 2016;31(3):343-345.
Fluids and Stress in Fractured Rocks: A Case Study with Applications to Hydrodynamic Modelling (Lodeve basin, South France): ABSTRACT (1995)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Early stages of the M-Inp (M=Ni,Pd) reaction: Solid-state amorphization and subsequent crystallization (1987)

The fabrication and reproducibility of stable metal (M) contacts to compound semiconductor (AB) devices are largely dependent on the knowledge or ability to predict both the phase formation sequence and the phases that are finally in thermodynamic equilibrium within the substrate at any given temperature. In addition to forming stable and metastable ternary phases, these M-AB reactions (particularly the Ni-InP and Pd-InP systems) are prime candidates for solid-state amorphization reactions. Hence, thermodynamic data from the binary M-A and M-B systems are insufficient to predict the compounds that will form during these M-AB reactions. In this paper, the formation of the initial products of the M-AB (M=Ni, Pd) reactions were characterized by TEM, energy dispersive x-ray microanalysis and in-situ heating experiments.
Reversible Methane Storage in a Polymer-Supported Semi-Clathrate Hydrate at Ambient Temperature and Pressure (2009)

A key issue regarding the use of clathrates and semi-clathrate hydrates for practical gas storage is the pressure−temperature stability of the material. For many practical applications, the avoidance of cooling, gas overpressure, and mechanical mixing would be very desirable. Here, we show that porous emulsion-templated polymer supports greatly enhance methane uptake kinetics in tetra-iso-amylammonium bromide semi-clathrate hydrates without introducing complex mixing technologies. These systems show unprecedented thermal stability and can be decomposed upon demand to release the gas. Single crystal X-ray structure analysis of the semi-clathrates loaded with methane or krypton were obtained, confirming that the gases are stored in the dodecahedral A′ and A′′ cages.
Visible light photopolymerization employing 2,4-diiodo-6-butoxy-3-fluorone and tetraorganylborate salts as photoinitiators (1996)

Several new tetraorganylborate salts have been synthesized and tested as coinitiators with 2,4-diiodo-6-butoxy-3-fluorone (DIBF) for the photopolymerization of acrylic monomer mixtures. The rate of photopolymerization has been found to be a function of chemical structure of the borates. Stability, solubility, and reactivity of these borates as coinitiators for photopolymerization have been investigated. Diphenyldialkylborates have been found to be the best among the tested coinitiators. © 1996 John Wiley & Sons, Inc.
Induction of apoptosis by piceatannol in human leukemic U937 cells through down-regulation of Bcl-2 and activation of caspases (2008)

Piceatannol is a polyphenol that is found in abundant quantities in grapes and wine. Although recent experimental data revealed the proapoptotic potency of piceatannol, the molecular mechanisms underlying the anti-leukemic activity have not yet been studied in detail. This study examined the effects of piceatannol on the growth of the human leukemia cell line U937. The results showed that piceatannol inhibits the viability of U937 cells by inducing apoptosis, as evidenced by the formation of apoptotic bodies, DNA fragmentation and the accumulation of the sub-G1 phase. RT-PCR and immunoblotting data showed that treating the cells with piceatannol caused the down-regulation of anti-apoptotic Bcl-2 and cIAP-2 expression. Piceatannol-induced apoptosis was also associated with the proteolytic activation of caspase-3, and the degradation/cleavage of poly (ADP-ribose) polymerase protein. z-DEVD-fmk, a caspase-3-specific inhibitor, blocked the activation of caspase-3 and increased the survival of the piceatannol-treated U937 cells, suggesting that caspase-3 activation is essential for piceatannol-induced apoptosis.
Light: The Essential Ingredient (2012)

From experience we know that our pictures turn out well when a scene is brightly illuminated. Simply stated, light provides the energy necessary to record an image, so we need good lighting. Lousy lighting makes lousy pictures. Just as we find it hard to do good work when we feel low on energy, the camera has a hard time making a good picture without enough light energy. We need to make sure that the light comes together just right, or else the picture will still be lousy, even if the scene is sufficiently lit. Another important consideration is the behavior of light. To design a camera that can form the best image possible, camera designers need to understand how light behaves as it propagates to the camera, through the camera, and finally onto the imaging sensor.