gebhart/patrepeval huggingface dataset:
Spiking dynamic neural fields architectures on FPGA (2014)

Neuromorphic engineering is a very active field aiming to design dedicated hardware architectures to simulate the tremendous power and complexity of the brain at real time speed. Many high scaled generic projects are a success but we focus on decentralized embeddable implementations of dynamic neural fields (DNFs): a popular building blocks approach to simulate high level cognitive behaviors. The main difficulty of this approach is its mandatory all-to-all connectivity within the neural network which does not fit hardware constraints. Here we show that it is possible to decentralize the DNF computations using a cellular grid of spiking neurons with stochastic transmissions mapped onto a field programmable gate array (FPGA). The advantages of these randomly spiking dynamic neural fields (RSDNFs) are a dedicated 1-bit probabilistic XY broadcast routing network with inherent synaptic weights computations that provides hardware compatibility thanks to the 4-neighbor cellular connectivity. Moreover, this implementation strategy exhibits fault tolerance properties but it is more area greedy and time consuming than a standard implementation that broadcasts neuron addresses and coordinates using the address event representation (AER) on a centralized bus.
ChemInform Abstract: Design and Synthesis of Potent, Selective, and Orally Bioavailable Tetrasubstituted Imidazole Inhibitors of p38 Mitogen‐Activated Protein Kinase. (1999)

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.
Domino Aza‐Claisen/Mannich Cyclization Reaction from a Chiral α‐Alkoxy Enamine or Sequential Alkylation of an α‐Alkoxy Ester Enolate or Nitrile Anion, Followed by an Intramolecular Wittig Reaction: Two (3+2) Annulation Routes to Homochiral 4‐Alkyl‐4‐hydroxy‐2‐cyclopentenone Synthesis (2003)

Abstract A study on the enantioselective synthesis of 4‐alkyl‐4‐hydroxyalkylidene‐cyclopentenone prostaglandins is reported. Two (3+2) annulation processes allow the synthesis of homochiral 4‐alkyl‐4‐hydroxy‐2‐cyclopentenones 4−5 , 10−11 , and 17 . The first process involves a domino aza‐Claisen/Mannich cyclization reaction, resulting from the alkylation of an α‐alkoxy‐enamine, derived from chiral α‐alkoxy aldehydes 1 , 9 , or 16 with 3‐iodo‐2‐(methoxymethoxy)prop‐1‐ene ( 3 ) as the acetonyl equivalent. The second process is based on the sequential alkylation of esters 21 , 39 , or nitrile 20 with acetonyl equivalents 3 or 25 , followed by an intramolecular Wittig reaction. As an application, the synthesis of the naturally occurring alkylidene‐cyclopentenone prostaglandin clavulone II from the spiro[cyclopentene‐furan]one 5 and the formal total synthesis of (+/‐)‐untenone 19 has been carried out. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Photonic readout of superconducting nanowire single photon counting detectors (2023)

Scalable, low power, high speed data transfer between cryogenic and room temperature environments is essential for the realization of practical, large-scale systems based on superconducting technologies. Optical fiber presents a 100–1,000x lower heat load than conventional electrical wiring, relaxing the requirements for thermal anchoring, and allows for very high bandwidth densities by carrying multiple signals through the same physical fiber. By operating a CMOS modulator in the forward bias regime at a temperature of 3.6 K, we have demonstrated the optical readout of a superconducting nanowire single-photon detector (SNSPD) without the need for an interfacing device.
Broadband passive RLGC(f) modeling for on-chip interconnect design (2011)

To design state-of-the-art on-chip interconnect structures, efficient modeling tools are needed that accurately incorporate all substrate loss mechanisms and the finite conductivity and shape of the metallic interconnects. In this contribution, accurate broadband macromodels are conceived for the per unit length resistance (R), inductance (L), conductance (G) and capacitance (C) parameters of such on-chip interconnects. By means of adaptive frequency sampling (AFS) the simulation cost to obtain these models is small. Additionally, passivity can be assessed and enforced. The technique is applied to the analysis of an inverted embedded microstrip (IEM) line. Compared to commercial simulation software, both in frequency and time domain, excellent agreement and superior efficiency is observed, illustrating the method's applicability for on-chip design purposes.
Reply on RC2 (2022)

<strong class="journal-contentHeaderColor">Abstract.</strong> NMR-based analysis of metabolite mixtures provides crucial information on biological systems but mostly relies on 1D <span class="inline-formula"><sup>1</sup></span>H experiments for maximizing sensitivity. However, strong peak overlap of <span class="inline-formula"><sup>1</sup></span>H spectra often is a limitation for the analysis of inherently complex biological mixtures. Dissolution dynamic nuclear polarization (d-DNP) improves NMR sensitivity by several orders of magnitude, which enables <span class="inline-formula"><sup>13</sup></span>C NMR-based analysis of metabolites at natural abundance. We have recently demonstrated the successful introduction of d-DNP into a full untargeted metabolomics workflow applied to the study of plant metabolism. Here we describe the systematic optimization of d-DNP experimental settings for experiments at natural <span class="inline-formula"><sup>13</sup></span>C abundance and show how the resolution, sensitivity, and ultimately the number of detectable signals improve as a result. We have systematically optimized the parameters involved (in a semi-automated prototype d-DNP system, from sample preparation to signal detection, aiming at providing an optimization guide for potential users of such a system, who may not be experts in instrumental development). The optimization procedure makes it possible to detect previously inaccessible protonated <span class="inline-formula"><sup>13</sup></span>C signals of metabolites at natural abundance with at least 4Â times improved line shape and a high repeatability compared to a previously reported d-DNP-enhanced untargeted metabolomic study. This extends the application scope of hyperpolarized <span class="inline-formula"><sup>13</sup></span>C NMR at natural abundance and paves the way to a more general use of DNP-hyperpolarized NMR in metabolomics studies.
Overhauser dynamic nuclear polarization (ODNP)-enhanced two-dimensional proton NMR spectroscopy at low magnetic fields (2021)

The majority of low-field Overhauser dynamic nuclear polarization (ODNP) experiments reported so far have been 1D NMR experiments to study molecular dynamics and in particular hydration dynamics. In this work, we demonstrate the application of ODNP-enhanced 2D J-resolved (JRES) spectroscopy to improve spectral resolution beyond the limit imposed by the line broadening introduced by the paramagnetic polarizing agent. Using this approach, we are able to separate the overlapping multiplets of ethyl crotonate into a second dimension and clearly identify each chemical site individually. Crucial to these experiments is interleaved spectral referencing, a method introduced to compensate for temperature-induced field drifts over the course of the NMR acquisition. This method does not require additional hardware such as a field-frequency lock, which is especially challenging when designing compact systems.
Faraday rotation in femtosecond laser micromachined waveguides (2007)

We demonstrate magneto-optic switching in femtosecond-laser micromachined waveguides written inside bulk terbium-doped Faraday glass. By measuring the polarization phase shift of the light as a function of the applied magnetic field, we find that there is a slight reduction in the effective Verdet constant of the waveguide compared to that of bulk Faraday glass. Electron Paramagnetic Resonance (EPR) measurements confirm that the micromachining leaves the concentration of the terbium ions that are responsible for the Faraday effect virtually unchanged.
BQ123, an ETA Receptor Antagonist, Inhibits Endothelin-1-mediated Proliferation of Human Pulmonary Artery Smooth Muscle Cells (1993)

Endothelin (ET-1) has been shown to be co-mitogenic for vascular smooth muscle cells (SMC) from human systemic arteries. A more modest growth-promoting effect has also been described in SMC from the bovine and porcine pulmonary circulation. Whether ET-1 has mitogenic properties in the human pulmonary circulation, and which ET receptor subtype mediates this response, is unknown. We first examined the effects of ET-1, ET-3, and the selective ETB agonist, Sarafotoxin 6c, on human pulmonary artery SMC growth. Cells were harvested from normal lung transplant donors. Growth was assessed by change in cell number 3 days after stimulation of quiescent cells. ET-1 in the presence of 0.3% serum produced a dose-dependent increase (82 +/- 1.5%) in cell number (threshold, 10(-11) M; maximal, 10(-7) M). ET-3 also stimulated growth (36 +/- 3.8%) but was less potent than ET-1 (threshold, 10(-9) M; maximal, 10(-7) M). The ETB selective agonist Sarafotoxin 6c had no proliferative effect. The effects of BQ123, a selective ETA receptor antagonist, on ET-1-induced growth were then assessed. BQ123 inhibited (threshold, 1.5 x 10(-7) M; maximal, 1.5 x 10(-5) M) ET-1-induced growth but had no effect on proliferation stimulated by the non-ET receptor-mediated growth factors, platelet-derived growth factor BB and 5-hydroxytryptamine. These results suggest that ET-1 is a potent co-mitogen for human proximal pulmonary artery SMC and that this effect is transduced by selective activation of the ETA receptor.
Obtencao de mesalazina (5-asa) por carboxilacao de p-aminofenol (1995)

The 5-aminosalicylic acid is usually prepared: 1. by the reduction of the azodye from diazotized aniline and salicylic acid and the posterior reduction of the formed compound; 2. for carboxylation with carbon dioxide under high pressure of p-aminophenol. Both do not present high yield, but the carboxylation process of p-aminophenol can easily be used and can reduce the obtainment process of 3 steps to only 2. Another advantage of this process is the fact that the product is produced without contaminants, because only one solid reagent (p-aminophenol) and the agent of carboxylation (CO2) is used.
OR05-5 AZP-3404, a 9-Amino Acid Peptide Analog of Insulin-Like Growth Factor-Binding Protein 2, Reverses Insulin Resistance in Leptin-Deficient ob/ob Mice (2019)

Insulin-like growth factor-binding protein-2 (IGFBP-2), one of six highly-conserved binding proteins that modulate circulating IGF1, has significant regulatory actions on carbohydrate, lipid and bone metabolism that are independent of its IGF-1 binding role. The metabolic activity of IGFBP-2 has been localized to a short peptide sequence within its unique heparin-binding domain, HBD-1, that is able to reproduce the metabolic actions of the full IGFBP-2 on bone and fat. Through structure-activity studies of this sequence, an acylated 9-amino acid peptide, AZP-3404, with enhanced stability and pharmacokinetics, has been developed that retains the activity of IGFBP-2 on fat and bone metabolism. As IGFBP-2 treatment has also been demonstrated to improve glucose homeostasis in animal models of severe insulin resistance, including the leptin-deficient ob/ob mouse, the present study was undertaken to determine whether AZP-3404 is able to reverse insulin resistance and improve glucose homeostasis in the ob/ob mouse. Male B6.Cg-Lepob/J mice were implanted with HD-XG telemetric devices (Data Sciences International), which allows continuous, wireless monitoring of carotid blood glucose under awake, unrestrained conditions. Animals were randomly assigned to groups (n=8) receiving either saline or AZP-3404 at 1 or 3 mg/kg, b.i.d. for four weeks. The mean daily blood glucose level prior to study initiation was 507 ± 102 mg/dL. Treatment with AZP-3404 dose-dependently decreased the average daily glucose concentration, such that by day 27, glucose levels were reduced by 64 ± 29 and 100 ± 16 mg/dL in the 1 and 3 mg/kg AZP-3404-treated groups, respectively, while slightly increased by 14 ± 29 mg/dL in the vehicle-treated group. On days 7, 14, 21 and 28, following a 24-hour fast, the mice were given an intraperitoneal glucose tolerance test (IPGTT: 1g glucose/kg) to evaluate the impact of AZP-3404 on glucose disposal which is impaired in ob/ob mice. By day 28, the fasting glucose level was reduced by 8% and 20% in the 1 and 3 mg/kg AZP-3404-treated groups, respectively, as compared with fasting levels on day 7. The IPGTTs revealed a progressive, dose-dependent reduction in glucose excursion that reached a decrease of 40% after 4 weeks of treatment with 3mg/kg AZP-3404. In related studies, we have observed that AZP-3404, both alone and in an additive manner with insulin, stimulates glucose transport in mouse C2C12 differentiated myotubes through activation of AMP-activated protein kinase (AMPK). These findings suggest that AZP- 3404 stimulates glucose uptake by muscle tissue in ob/ob mice thereby improving glucose homeostasis. The results from these studies confirm that AZP-3404 retains the ability of IGFBP-2 to restore glucose homeostasis and support the development of AZP-3404 as a novel therapeutic approach for syndromes of severe insulin resistance.
A methodology for the verification of a “system on chip” (1999)

Article A methodology for the verification of a "system on chip" Share on Authors: Daniel Geist IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Giora Biran IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Tamara Arons IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Michael Slavkin IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Yvgeny Nustov IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Monica Farkas IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Karen Holtz IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, Israel IBM Haifa Research Lab, MATAM Advanced Technology Center, Haifa, IsraelView Profile , Andy Long IBM Field Design Center, Essex Junction, VT IBM Field Design Center, Essex Junction, VTView Profile , Dave King IBM Field Design Center, Essex Junction, VT IBM Field Design Center, Essex Junction, VTView Profile , Steve Barret IBM Field Design Center, Essex Junction, VT IBM Field Design Center, Essex Junction, VTView Profile Authors Info & Claims DAC '99: Proceedings of the 36th annual ACM/IEEE Design Automation ConferenceJune 1999 Pages 574–579https://doi.org/10.1145/309847.310001Online:01 June 1999Publication History 8citation442DownloadsMetricsTotal Citations8Total Downloads442Last 12 Months6Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Effects of Functional Groups in Redox-Active Organic Molecules: A High-Throughput Screening Approach (2016)

Nonaqueous redox flow batteries have attracted recent attention with their potential for high electrochemical storage capacity, with organic electrolytes serving as solvents with a wide electrochemical stability window. Organic molecules can also serve as electroactive species, where molecules with low reduction potentials or high oxidation potentials can provide substantial chemical energy. To identify promising electrolytes in a vast chemical space, high-throughput screening (HTS) of candidate molecules plays an important role, where HTS is used to calculate properties of thousands of molecules and identify a few organic molecules worthy of further attention in battery research. Here, we present reduction and oxidation potentials obtained from HTS of 4178 molecules. The molecules are composed of base groups of five- or six-membered rings with one or two functional groups attached, with the set of possible functional groups including both electron-withdrawing and electron-donating groups. In addition to observing the trends in potentials that result from differences in organic base groups and functional groups, we analyze the effects of molecular characteristics such as multiple bonds, Hammett parameters, and functional group position. This work provides useful guidance in determining how the identities of the base groups and functional groups are correlated with desirable reduction and oxidation potentials.
Midbody assembly and its regulation during cytokinesis (2012)

The midbody is a transient structure that connects two daughter cells at the end of cytokinesis, with the principal function being to localize the site of abscission, which physically separates two daughter cells. Despite its importance, understanding of midbody assembly and its regulation is still limited. Here we describe how the structural composition of the midbody changes during progression throughout cytokinesis and explore the functional implications of these changes. Deriving from midzones, midbodies are organized by a set of microtubule interacting proteins that colocalize to a zone of microtubule overlap in the center. We found that these proteins split into three subgroups that relocalize to different parts of the midbody: the bulge, the dark zone, and the flanking zone. We characterized these relocalizations and defined domain requirements for three key proteins: MKLP1, KIF4, and PRC1. Two cortical proteins-anillin and RhoA-localized to presumptive abscission sites in mature midbodies, where they may regulate the endosomal sorting complex required for transport machinery. Finally, we characterized the role of Plk1, a key regulator of cytokinesis, in midbody assembly. Our findings represent the most detailed description of midbody assembly and maturation to date and may help elucidate how abscission sites are positioned and regulated.
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes (2017)

Abstract Discovery of cancer drivers has traditionally focused on the identification of protein-coding genes. Here we present a comprehensive analysis of putative cancer driver mutations in both protein-coding and non-coding genomic regions across &gt;2,500 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We developed a statistically rigorous strategy for combining significance levels from multiple driver discovery methods and demonstrate that the integrated results overcome limitations of individual methods. We combined this strategy with careful filtering and applied it to protein-coding genes, promoters, untranslated regions (UTRs), distal enhancers and non-coding RNAs. These analyses redefine the landscape of non-coding driver mutations in cancer genomes, confirming a few previously reported elements and raising doubts about others, while identifying novel candidate elements across 27 cancer types. Novel recurrent events were found in the promoters or 5’UTRs of TP53, RFTN1, RNF34, and MTG2, in the 3’UTRs of NFKBIZ and TOB1, and in the non-coding RNA RMRP. We provide evidence that the previously reported non-coding RNAs NEAT1 and MALAT1 may be subject to a localized mutational process. Perhaps the most striking finding is the relative paucity of point mutations driving cancer in non-coding genes and regulatory elements. Though we have limited power to discover infrequent non-coding drivers in individual cohorts, combined analysis of promoters of known cancer genes show little excess of mutations beyond TERT .
Public History in the Age of Insurrection (2022)

Public historians have struggled to take a hard line against neo-Confederate groups in theory as well as practice. This article proposes a methodological shift that can clarify the work and obligations of the public historian following the insurrection on January 6, 2021. The frame of action research positions historians as public-facing actors and advocates. The frame of restorative justice clarifies the stakes of, and stakeholders within, historical harm. We apply these frameworks to two contested sites for public history in Florence, Alabama, that revolve around the Confederacy. Finally, we use our experiences from the field to distinguish communities from counter-communities and provide strategies for making cultural institutions inhospitable to cultural insurrectionists.
Phase-selective route to high T c superconducting Tl2Ba2Can−1CunO2n+4 films: Combined metalorganic chemical vapor deposition using an improved barium precursor and stoichiometry-controlled thallium vapor diffusion (1991)

Films of the Tl2Ba2Can−1CunO2n+4 high Tc superconductors (n=2 or 3) can be prepared with a high degree of phase selectivity using a combination of metalorganic chemical vapor deposition (MOCVD) and vapor diffusion. Ba-Ca-Cu-O films are first prepared by MOCVD using the volatile metalorganic precursors Ba(hexafluoroacetyl- acetonate)2(tetraglyme), Ca(dipivaloylmethanate)2, and Cu(acetylacetonate)2. The ‘‘second-generation’’ barium precursor exhibits significantly improved thermal stability and volatility over previously used compounds. Thallium is then incorporated into these films by vapor diffusion using a Tl-Ba-Ca-Cu oxide mixture of controlled composition as the source of volatile thallium oxides. Phase control is achieved by a combination of improved stoichiometry of the deposited film, a result of the new Ba source, and annealing with the appropriate oxide mixture. The resultant films consist predominantly of the Tl2Ba2Ca2Cu3Ox or Tl2Ba2CaCu2Ox phase, each having preferential orientation of the crystallite Cu-O planes parallel to the substrate surface. The films exhibit superconducting onset temperatures of ∼115 K with zero resistance by 93 and 85 K, respectively. Critical current densities for a number of films, estimated by the Bean method, are in the range 104–105 A/cm2 at 5 K.&amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt; &amp;lt;lz&amp;gt;