gebhart/patrepeval huggingface dataset:
Synthesis and Pharmacological Properties of Novel 8-Substituted Imidazobenzodiazepines:  High-Affinity, Selective Probes for α5-Containing GABAAReceptors (1996)

The synthesis and pharmacological properties of imidazobenzodiazepines with both high affinity and selectivity for alpha 5-containing GABAA receptors are described. Four of these compounds (5, 6, 8, and 9) inhibited [3H]flunitrazepam binding to recombinant alpha 5 beta 2 gamma 2 GABAA receptors with IC50 values between approximately 0.4 and 5 nM. These compounds were > or = 24-75-fold more selective for recombinant receptors containing alpha 5 subunits compared to other, "diazepam-sensitive" GABAA receptors containing either alpha 1, alpha 2, or alpha 3 subunits. Imidazobenzodiazepine 9 (used as the prototypical alpha 5 selective ligand) inhibited [3H]flunitrazepam binding to hippocampal membranes with high- and low-affinity components (IC50 0.6 +/- 0.2 and 85.6 +/- 13.1 nM, respectively), representing approximately 16% and approximately 84% of the receptor pool. Inhibition of [3H]flunitrazepam binding to cerebellar membranes with imidazobenzodiazepine 9 was best fitted to a single population of sites with an IC50 of 79.8 +/- 18.3 nM. These imidazobenzodiazepines behaved as GABA negative ligands in recombinant GABAA receptors expressed in Xenopus oocytes and were convulsant in mice after parenteral administration. The relative potencies of flumazenil and zolpidem in blocking convulsions induced by 9 and DMCM, respectively, indicated that occupation of alpha 5-containing GABAA receptors substantially contributed to the convulsant properties of acetylene analog 9. These 8-substituted imidazobenzodiazepines (5, 6, 8 and 9) should prove useful in examining the physiological roles of GABAA receptors bearing an alpha 5 subunit and may also lead to the development of novel, subtype selective therapeutic agents.
ChemInform Abstract: Synthesis of DNA Templates Containing the Fifth Base, 2‐Amino‐6‐(dimethylamino)purine, for Specific Transcription Involving Unnatural Base Pairs. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The transcriptional program of a human B cell line in response to Myc (2001)

The proto-oncogene c-myc (myc) encodes a transcription factor (Myc) that promotes growth, proliferation and apoptosis. Myc has been suggested to induce these effects by induction/repression of downstream genes. Here we report the identification of potential Myc target genes in a human B cell line that grows and proliferates depending on conditional myc expression. Oligonucleotide microarrays were applied to identify downstream genes of Myc at the level of cytoplasmic mRNA. In addition, we identified potential Myc target genes in nuclear run-on experiments by changes in their transcription rate. The identified genes belong to gene classes whose products are involved in amino acid/protein synthesis, lipid metabolism, protein turnover/folding, nucleotide/DNA synthesis, transport, nucleolus function/RNA binding, transcription and splicing, oxidative stress and signal transduction. The identified targets support our current view that myc acts as a master gene for growth control and increases transcription of a large variety of genes.
Applications of conducting polymers: robotic fins and other devices (2007)

Conducting polymers are becoming viable engineering materials and are gradually being integrated into a wide range of devices. Parallel efforts conducted to characterize their electromechanical behavior, understand the factors that affect actuation performance, mechanically process films, and address the engineering obstacles that must be overcome to generate the forces and displacements required in real-world applications have made it possible to begin using conducting polymers in devices that cannot be made optimal using traditional actuators and materials. The use of conducting polymers has allowed us to take better advantage of biological architectures for robotic applications and has enabled us to pursue the development of novel sensors, motors, and medical diagnostic technologies. This paper uses the application of conducting polymer actuators to a biorobotic fin for unmanned undersea vehicles (UUVs) as a vehicle for discussing the efforts in our laboratory to develop conducting polymers into a suite of useful actuators and engineering components.
Structure–Function Analysis of the Extended Conformation of a Polyketide Synthase Module (2018)

Catalytic modules of assembly-line polyketide synthases (PKSs) have previously been observed in two very different conformations-an "extended" architecture and an "arch-shaped" architecture-although the catalytic relevance of neither has been directly established. By the use of a fully human naïve antigen-binding fragment (F<sub>ab</sub>) library, a high-affinity antibody was identified that bound to the extended conformation of a PKS module, as verified by X-ray crystallography and tandem size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS). Kinetic analysis proved that this antibody-stabilized module conformation was fully competent for catalysis of intermodular polyketide chain translocation as well as intramodular polyketide chain elongation and functional group modification of a growing polyketide chain. Thus, the extended conformation of a PKS module is fully competent for all of its essential catalytic functions.
Investigation of Co UBM for direct bumping on Cu/LowK dies (2004)

When changing to lead-free solders, also the under hump metallurgy (UBM) needs to be re-investigated and possibly redefined. In this paper, CO is investigated on its applicability as under bump metal for CUnow K dies. The interaction of CO in combination with SnPb and pure Sn humps is studied. Since during annealing a meta-stable Sn - Co(Cu) phase forms, CO cannot act as diffusion barrier for Cu. Nevertheless, the use of CO as UBM with Sn-solder is successful. No signs of degradation of Cu-Co-Sn bumps are noticed till 15M)h at 150
Optical Networks in Edge Clouds: Energy and Application Dimensions (2019)

Optical networks provide capacity and low latency that can enable new edge cloud computing based applications, including 5G baseband processing, personal computing, and connected vehicles. The role of optical networks in these applications is examined and the efficiency of the associated networks is reviewed.
Highly Parallel Translation of DNA Sequences into Small Molecules (2012)

A large body of in vitro evolution work establishes the utility of biopolymer libraries comprising 10(10) to 10(15) distinct molecules for the discovery of nanomolar-affinity ligands to proteins. Small-molecule libraries of comparable complexity will likely provide nanomolar-affinity small-molecule ligands. Unlike biopolymers, small molecules can offer the advantages of cell permeability, low immunogenicity, metabolic stability, rapid diffusion and inexpensive mass production. It is thought that such desirable in vivo behavior is correlated with the physical properties of small molecules, specifically a limited number of hydrogen bond donors and acceptors, a defined range of hydrophobicity, and most importantly, molecular weights less than 500 Daltons. Creating a collection of 10(10) to 10(15) small molecules that meet these criteria requires the use of hundreds to thousands of diversity elements per step in a combinatorial synthesis of three to five steps. With this goal in mind, we have reported a set of mesofluidic devices that enable DNA-programmed combinatorial chemistry in a highly parallel 384-well plate format. Here, we demonstrate that these devices can translate DNA genes encoding 384 diversity elements per coding position into corresponding small-molecule gene products. This robust and efficient procedure yields small molecule-DNA conjugates suitable for in vitro evolution experiments.
Supplementary Figure Legend from Enhancement of Human Cancer Cell Motility and Invasiveness by Anaphylatoxin C5a via Aberrantly Expressed C5a Receptor (CD88) (2023)

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Two-Layered Oscillatory Neural Networks with Analog Feedforward Majority Gate for Image Edge Detection Application (2023)

The increasing volume of smart edge devices, like smart cameras, and the growing amount of data to treat incited the development of light edge Artificial Intelligence (AI) solutions with neuromorphic computing. Oscillatory Neural Network (ONN) is a promising neuromorphic computing approach which uses networks of coupled oscillators, and their inherent parallel synchronization to compute. Also, ONN phase computing allows to limit voltage amplitude and reduce power consumption. Low-power, fast, and parallel computation properties make ONN attractive for edge AI. In state-of-the-art, ONN is built with a fully-connected architecture, with coupling defined from unsupervised learning to perform auto-associative memory tasks, like with Hopfield Networks. However, to allow ONN to solve beyond associative memory applications, there is a need to explore further ONN architectures. In this work, we propose a novel architecture of cascaded analog fully-connected ONNs interconnected with an analog feedforward majority gate layer. In particular, we show this architecture can solve image edge detection task using two fully-connected ONN layers. This is, to our best knowledge, a first analog-based solution to cascade two fully-connected ONNs.
The effects of temperature on the characteristics of the focal region in high-intensity focused ultrasound (1999)

The application of high-intensity focused ultrasound uses the transformation of ultrasonic energy into thermal energy to raise the temperature of tissue rapidly and induce necrosis of tumor cells. Targeting and control of the heated region and the amount of energy delivered are important issues. These numerical simulations couple sound propagation with the bio-heat equation to investigate tissue heating over time. The temperature rise affects both sound speed and attenuation. These, in turn, influence the spatial boundaries and magnitude of the ultrasonic time average intensity which, in turn, drives the temperature. In this model, the dependence of the sound speed and tissue attenuation on temperature is based on experimental results obtained in pig liver [Bloch et al., Proc. 16th Intl. Cong. Acoust., Seattle, WA, 1065–1066 (1998)]. The results show a spatial shifting of the focal region toward the transducer accompanied by a reduction in the magnitude of the ultrasonic time average intensity depending upon the on-time of the transducer and the initial pressures at which it is driven. The temperature response follows the same behavior, with a spatial shift of the hottest spot and a decrease in its peak value, although thermal conduction tends to counteract the process. [Work supported by DARPA.]
p27 Kip1 and p21 Cip1 Are Not Required for the Formation of Active D Cyclin-cdk4 Complexes (2003)

Our studies address questions pertaining to the regulation of D cyclin-cdk4 activity, and the following results were obtained. Conditions that increased the abundance of the D cyclins also increased the abundance of enzymatically active D cyclin-cdk4 complexes in mouse embryo fibroblasts (MEFs) lacking both p27(Kip1) and p21(Cip1) (p27/p21(-/-)). Such conditions included ectopic expression of cyclin D1 and inhibition of D cyclin degradation by the proteasome inhibitor MG132. However, as determined by treatment of wild-type MEFs with MG132, maximal accumulation of D cyclin-cdk4 complexes required p27(Kip1) and p21(Cip1) and coincided with the formation of inactive D cyclin-cdk4-p27(Kip1) or -p21(Cip1) complexes. p27(Kip1) or p21(Cip1) also increased the abundance of D cyclin-cdk4 complexes and reduced amounts of cdk4 activity when ectopically expressed in p27/p21(-/-) MEFs. Lastly, increases in the stability of the D cyclins accounted for their greater abundance in wild-type MEFs than in p27/p21(-/-) MEFs. We conclude that (i) D cyclin-cdk4 complexes are formed and become active in the absence of p27(Kip1) and p21(Cip1) and (ii) p27(Kip1) and p21(Cip1) maximize the accumulation but inhibit the activity of D cyclin-cdk4 complexes. We suggest that D cyclin-cdk4 complexes are more stable when bound to p27(Kip1) or p21(Cip1) and that formation of ternary complexes also stabilizes the D cyclins.
Transistor Device Optimization for RF Power Amplifier Employing Rapid Envelope Load-Pull System (2010)

This paper reports mathematical explanation and the application domain of rapid envelope load-pull system. It is demonstrated that this novel load-pull technique finds immediate use in the optimization of transistor devices for the design of microwave power amplifiers. The limitations of the existing load-pull systems severely affect the overall performance optimization of transistor devices. The envelope load-pull improves on the limitations of the existing systems and thus provides a very effective methodology for the design and investigation of the RF power amplifiers. Initially the paper describes the mathematical foundation of the envelope load- pull concept and then the rapid, accurate and reliable measurement capability of the system is presented. It clearly vindicates the potential areas of application of the system in improving the measurement throughput and yield optimization of the microwave devices. Finally, the harmonic envelope load-pull is utilized on a commercially available 1W GaAs FET that demonstrates the rapid RF power amplifier design, investigation and optimization strategy.
Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability (2013)

The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary significantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete understanding of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as translation, being more robust than those linked to regulation. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression.
Performance of solvent resistant nanofiltration membranes for purification of residual solvent in the pharmaceutical industry: experiments and simulation (2011)

This study explores the possibility of developing a sustainable extraction method for use in pharmaceutical production, based on purification with membrane processes. Two types of commercial polymeric organic solvent nanofiltration membranes (StarMem122 and DuraMem150) were selected and tested for their abilities to recover the solvent from a pharmaceutical/solvent mixture (5, 10, 50 mg L−1). Five different pharmaceutical compounds have been selected in this work, namely: Imatinib mesylate, Riluzole, Donepezil HCl, Atenolol and Alprazolam. Solvents tested in the experiment were those used in the manufacturing process, i.e., methanol, ethanol, iso-propanol and ethyl acetate. An acceptable performance (rejection over 90%) was obtained for DuraMem150 in all tested pharmaceutical and solvent mixtures except for iso-propanol. No flux was observed for iso-propanol over the DuraMem150 due to its high viscosity. No separation was observed by using StarMem122 for Imatinib mesylate in iso-propanol (over 80%). Commercially available solvent resistant nanofiltration (SRNF) membranes (StarMem™122 and DuraMem™150) show promising performances as alternative tools to traditional separation units such as distillation columns for the recovery of solvents. Furthermore, to evaluate the potential of SRNF as a substitution for traditional solvent recovery, a model was developed for nanofiltration membrane units and implemented in a common process simulation software (Aspen Plus). These models were based on the pore flow mechanism and describe a single membrane module. A membrane module is not available in Aspen Plus and in its Model Library. In this study, this shortcoming was overcome through implementation of the NF membrane module within the Aspen Custom Modeler link to Aspen Plus. The model has been tested for two model solutes (Disperse orange 3 and Disperse red 19) since the pharmaceutical physical properties are not included in the Aspen Properties Database. The results presented here confirm the value of the Aspen Custom Modeler as a simulation tool for the use of NF as a novel and sustainable tool in pharmaceutical manufacturing.
L'instrumentation de l'action publique (2014)

Comment s’organise l’action collective ? Comment les acteurs coopèrent-ils ? Centré sur les aspects concrets et les supports matériels de l’action collective, ce chapitre introductif dresse un bilan des débats et controverses sur l’instrumentation et la manière dont cette notion est mobilisée par différentes disciplines (sciences de gestion, sociologie des sciences et des techniques, économie) et divers courants de la science politique pour analyser les formes d’action collective des marchés, du capitalisme, des entreprises et de l’autorité publique.
[High-dose ifosfamide in patients with stage IV non-small cell lung cancer: phase II trial from the Groupe français de pneumo-cancérologie (GFPC)]. (1999)

This modality of high dose ifosfamide is as effective as standard monotherapy schedules in stage IV NSCLC. Unexpected toxicities particularly hematological ones could be due to a short duration of fractionated treatment. Results in term of survival leads us to further evaluate ifosfamide monotherapy treatment on a 5-day schedule basis.
ChemInform Abstract: Catalytic Effect of Nickel(II) Chloride and Palladium(II) Acetate on Chromium(II)‐Mediated Coupling Reaction of Iodo Olefins with Aldehydes. (1987)

Abstract The CrCl 2 ‐catalyzed condensation of the aldehyde (I) with the iodo olefins (II) works well only if contaminated Cr(II) reagent is used, and it is found that the addition of NiCl 2 or Pd(O‐Ac)2 to the reaction mixture has a dramatic effect (see conditions (B), (C)).
Lateral adsorption geometry and site-specific electronic structure of a large organic chemisorbate on a metal surface (2006)

A combined study of scanning tunneling microscopy (STM) and density functional theory (DFT) reveals that 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) adsorbs on $\mathrm{Ag}(111)$ at bridge sites in two nonequivalent orientations, one nearly aligned with the $[10\overline{1}]$ substrate axis and the other $18\ifmmode^\circ\else\textdegree\fi{}$ misaligned. Site-specific spectroscopy reveals that molecules in the two configurations exhibit subtle differences in their electronic structure. DFT-based STM simulations trace these back to the influence of distinct local adsorption geometries on the chemical molecule-substrate and molecule-molecule interactions.
High-Q terahertz Fano resonance with extraordinary transmission in concentric ring apertures (2014)

We experimentally demonstrate a polarization-independent terahertz Fano resonance with extraordinary transmission when light passes through two concentric subwavelength ring apertures in the metal film. The Fano resonance is enabled by the coupling between a high-Q dark mode and a low-Q bright mode. We find the Q factor of the dark mode ranges from 23 to 40, which is 3~6 times higher than Q of bright mode. We show the Fano resonance can be tuned by varying the geometry and dimension of the structures. We also demonstrate a polarization dependent Fano resonance in a modified structure of concentric ring apertures.
Accelerated First-order Methods on the Wasserstein Space for Bayesian Inference. (2018)

We consider doing Bayesian inference by minimizing the KL divergence on the 2-Wasserstein space $\mathcal{P}_2$. By exploring the Riemannian structure of $\mathcal{P}_2$, we develop two inference methods by simulating the gradient flow on $\mathcal{P}_2$ via updating particles, and an acceleration method that speeds up all such particle-simulation-based inference methods. Moreover we analyze the approximation flexibility of such methods, and conceive a novel bandwidth selection method for the kernel that they use. We note that $\mathcal{P}_2$ is quite abstract and general so that our methods can make closer approximation, while it still has a rich structure that enables practical implementation. Experiments show the effectiveness of the two proposed methods and the improvement of convergence by the acceleration method.
Retinal Vessel Tortuosity and Its Relation to Traditional and Novel Vascular Risk Markers in Persons with Diabetes (2015)

Increased retinal arteriolar tortuosity was related to longer diabetes duration and reduced flicker-light induced vasodilatory response, suggesting that retinal vascular tortuosity in adults with diabetes may be influenced by multiple diabetes-related physio-pathological changes.
Medial Collateral Ligament Reconstruction for Anteromedial Instability of the Knee: A Biomechanical Study In Vitro (2022)

Many MCL injuries occur in combination with ACL injuries, causing AMRI. These injuries may rupture the AM capsule and dMCL. Unaddressed MCL deficiency leads to an increased ACL reconstruction failure rate. A dMCL construct oriented anterodistally across the medial joint line, along with an sMCL graft, can restore native knee ER laxity. PMC/POL lesions did not contribute to AMRI.
Microwave Enhanced Green Synthesis of 2-Pyrazolines, Isoxazolines and Cyclohexenones (2013)

Hydroxy chalcones undergo simple cyclizations with phenylhydrazine to afford 2-pyrazolines under microwave irradiation in the presence of glacial AcOH as cyclizing agent, also undergo simple cyclizations with hydroxylamine to afford 2-isoxazolines under microwave irradiation in the presence of KOH, and new cyclohexenone derivatives. Some valuable intermediates in the synthesis of fused heterocycles, have been prepared through K2CO3 which activate the cyclocondensation of hydroxychalcones with ethyl acetoacetate. The obtained results indicate that the microwave irradiation give shorter reaction times and cleaner reactions for synthesis of biologically important compounds.
Extended x-ray absorption fine structure of copper in cytochrome c oxidase: Direct evidence for copper—sulfur ligation (1981)

The copper x-ray fluorescence excitation spectrum of cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) has been recorded in the 245-270 K range. The beat pattern observed in the extended x-ray absorption fine structure can be accounted for only by postulating a combination of sulfur and nitrogen (or oxygen) ligands to the copper. The average Cu-S distance is 2.27 +/- 0.02 A and the average Cu-N (or Cu-O) distance is 1.97 +/- 0.02 A. The amplitudes require ca, 1-1.5 sulfurs and 2 nitrogens (or oxygens) per copper. The distribution of sulfur ligands between Cu(A) and Cu(B) sites is not known, although there is some evidence that two sulfur atoms are bound to Cu(A).