gebhart/patrepeval huggingface dataset:
Inspired by Nature: Isostere Concepts in Plant Hormone Chemistry (2023)

Chemical concepts such as isosteres and scaffold hopping have proven to be powerful tools in agrochemical innovation processes. They offer opportunities to modify known molecular lead structures with the aim to improve a range of parameters, including biological efficacy and spectrum, physicochemical properties, stability, and toxicity. While recent biochemical insights into plant-specific receptors and signaling pathways trigger the discovery of the first lead structures, the disclosure of such a new chemical structure sparks a broad range of synthesis activities giving rise to diverse chemical innovation and often a considerable boost in biological activity. Herein, recent examples of isostere concepts in plant-hormone chemistry will be discussed, outlining how synthetic creativity can broaden the scope of natural product chemistry and giving rise to new opportunities in research fields such as abiotic stress tolerance and growth promotion.
Decentralized Aggregation for Energy-Efficient Federated Learning via Overlapped Clustering and D2D Communications (2022)

&lt;p&gt;Federated learning (FL) has emerged as a distributed machine learning (ML) technique to train models without sharing users' private data. In this paper, we propose a decentralized FL scheme that is called \underline{f}ederated \underline{l}earning \underline{e}mpowered \underline{o}verlapped \underline{c}lustering for \underline{d}ecentralized aggregation (FL-EOCD). The introduced FL-EOCD leverages device-to-device (D2D) communications and overlapped clustering to enable decentralized aggregation, where a cluster is defined as a coverage zone of a typical device. The devices located on the overlapped clusters are called bridge devices (BDs). In the proposed FL-EOCD scheme, a clustering topology is envisioned where clusters are connected through BDs, so as the aggregated models of each cluster is disseminated to the other clusters in a decentralized manner without the need for a global aggregator or an additional hop of transmission. Unlike the star-based FL, the proposed FL-EOCD scheme involves a large number of local devices by reusing the RRBs in different non-adjacent clusters. To evaluate our proposed FL-EOCD scheme as opposed to baseline FL schemes, we consider minimizing the overall energy-consumption of devices while maintaining the convergence rate of FL subject to its time constraint. To this end, a joint optimization problem, considering scheduling the local devices/BDs to the CHs and computation frequency allocation, is formulated, where an iterative solution to this joint problem is devised. Extensive simulations are conducted to verify the effectiveness of the proposed FL-EOCD algorithm over FL conventional schemes in terms of energy consumption, latency, and convergence rate.&lt;/p&gt;
DNA Detection through Signal Amplification by Using NADH:Flavin Oxidoreductase and Oligonucleotide–Flavin Conjugates as Cofactors (2005)

Der Cofaktor ist entscheidend für den hier vorgestellten DNA-Nachweis mithilfe eines Enzyms. Wenn die Enzymfunktion nur eintritt, falls der an ein Oligonucleotid gebundene Cofaktor nicht hybridisiert ist, kann die fluoreszenzspektroskopisch verfolgte Substratumsetzung als Sonde für die Hybridisierung dienen (siehe Schema). Da zudem das Enzym viele Substratmoleküle umsetzt, wird das Signal erheblich verstärkt. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z461145_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Solute displacement in the aqueous phase of water–NaCl–organic ternary mixtures relevant to solvent-driven water treatment (2020)

Twelve water miscible organic solvents (MOS): acetone, tetrahydrofuran, isopropanol, acetonitrile, dimethyl sulfoxide, 1,4-dioxane, dimethylacetamide, <i>N</i>-methyl-2-pyrrolidone, trifluoroethanol, isopropylamine, dimethylformamide, and dimethyl ether (DME) were used to produce ternary mixtures of water-NaCl-MOS relevant to MOS-driven fractional precipitation. The aqueous-phase composition of the ternary mixture at liquid-liquid equilibrium and liquid-solid endpoint was established through quantitative nuclear magnetic resonance and mass balance. The results highlight the importance of considering the hydrated concentrations of salts and suggest that at high salt concentrations and low MOS concentration, the salt concentration is governed by competition between the salt ions and MOS molecules. Under these conditions a LS phase boundary is established, over which one mole of salt is replaced by one mole of MOS (solute displacement). At higher MOS concentrations, MOS with higher water affinity deviate from the one-to-one solute exchange but maintain a LS boundary with a homogenous liquid phase, while MOS with lower water affinity form a liquid-liquid phase boundary. DME is found to function effectively as an MOS for fractional precipitation, precipitating 97.7% of the CaSO<sub>4</sub> from a saturated solution, a challenging scalant. DME-driven water softening recycles the DME within the system improving the atom-efficiency over existing seawater desalination pretreatments by avoiding chemical consumption.
Structure--Activity Relationships for Unsaturated Dialdehydes. 10. The Generation of Bioactive Products by Autoxidation of Isovelleral and Merulidial. (1995)

The autoxidation of the two mutagenic and antimicrobial sesquiterpenes merulidial (1a) and isovelleral (5) generates a number of bioactive products that are suggested to be partly responsible for the mutagenic and antimicrobial activities of the two compounds. The biological activities of the autoxidation products are, as far as has been possible to assay, of the same order as the parent compounds, and it is shown that they are formed in normal bioassay media. Merulidial (1a) is especially interesting, as its rate of autoxidation is considerably higher compared with non-mutagenic derivatives of 1a. In addition, natural isovelleral [(+/-)-5] was found to be twice as mutagenic as synthetic isovelleral [(+/-)-5], indicating that (-)-isovelleral is only weakly active or inactive, and supporting the suggestion that the interaction of isovelleral (5) and its derivatives with DNA depends on the absolute stereochemistry of the unsaturated dialdehyde moiety.
Perfluoroalkyl-thwarted Rearrangement of Quinol Esters. Formation of Catechol Derivatives via 1,3-Migration of Acyloxyl Group (1988)

Abstract Treatment of 4-perfluoroalkyl-4-quinols with acetic anhydride-sulfuric acid was found to lead to 1,2- and 1,3-migration of acetoxyl group in initially formed quinol acetates followed by aromatization to give a mixture of 4-perfluoroalkylresorcinol diacetate and 4-perfluoroalkylcatechol diacetate.
Efficient and Durable Oxygen Reduction Electrocatalyst Based on CoMn Alloy Oxide Nanoparticles Supported Over N-Doped Porous Graphene (2017)

Transition metal oxide derived materials are very important for various applications, such as electronics, magnetism, catalysis, electrochemical energy conversion, and storage. Development of efficient and durable catalysts for the oxygen reduction reaction (ORR), an important reaction in fuel cells and metal–air batteries, is highly desirable. Moreover, the futuristic catalysts for these applications need to be cost-effective in order to ensure a competitive edge for these devices in the energy market. This article describes the synthesis of a cost-effective and efficient electrocatalyst for ORR. It is based on supporting CoMn alloy oxide nanoparticles on N-doped porous graphene through a simple and scalable microwave irradiation method. Microwave irradiation was found to be very crucial for the fast creation of pores in the graphene framework with a concomitant formation of the CoMn alloy oxide nanoparticles. A series of catalysts have been synthesized by varying the Co:Mn ratio, among which, the one with the Co:Mn ratio of 2:1 [designated as CoMn/pNGr(2:1)] displayed remarkably higher ORR activity in 0.1 M KOH solution. It showed a ∼60 mV potential shift with a low Tafel slope of 74 mV/decade, which is comparable to that derived from the commercial Pt/C catalyst. This high activity of CoMn/pNGr(2:1) has been credited to the cooperative effect arising from the metal entities and the defects present in the N-doped porous graphene. Finally, real system-level validations of the use of CoMn/pNGr(2:1) as cathode catalyst could be performed by fabricating and testing single-cells of an anion-exchange membrane fuel cell (AEMFC) and a primary Zn–air battery, which successfully demonstrated the efficiency of the catalyst to facilitate ORR in real integrated systems of the single-cell assemblies.
Ultra-Low Profile Hybrid Switched Capacitor Converter with Matrix Multi-Tapped Autostransformer (2021)

In server AI application one of the biggest bottlenecks to keep up calculation capability is power management, hence high power density and high efficiency power supply are required. 48 V power-delivery architecture has been promoted to replace the 12 V power supply [1] where a two-stage approach is commonly adopted. First stage is typically implemented with an unregulated converter such as LLC or STC [2]. LLC converters with matrix transformer are suitable for these applications, however, where isolation is not needed a non-isolated resonant hybrid switched capacitor converter is a valuable candidate. In this paper a novel magnetic structure called matrix multi-tapped autotransformer is presented. This structure combines the benefit of matrix transformer with the advantages of hybrid switched capacitor structure. Experimental results for a 450 W prototype in 8th brick ultra-low profile factor achieving 1300 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> power density, are proving the effectiveness of the proposed approach.
GDNF and its receptors in the regulation of the ureteric branching (1999)

Recent transgenic and organ culture experiments have inevitably shown that glial cell line-derived neurotrophic factor (GDNF) is a mesenchyme-derived signal for ureteric budding and branching. The signalling receptor complex for GDNF includes a dimer of Ret receptor tyrosine kinase and two molecules of GDNF family receptor alpha1. Alpha-receptors are not only needed for the ligand binding and Ret activation, but they might mediate signals without Ret. While GDNF is clearly required for ureteric branching, tissue recombination studies have shown that it is not sufficient for the completion of ureteric morphogenesis, and other signalling molecules are needed. Different experimental models have resulted in somewhat contradictory results on their molecular identity, but transforming growth factor-beta1, -beta2, fibroblast growth factor-7 and hepatocyte growth factor form, obviously among others, a redundant set of growth factors in ureteric differentiation. Three other members of the GDNF family, neurturin, artemin and persephin, are also expressed in the developing kidney, and at least neurturin and persephin promote ureteric branching in vitro, but their true in vivo roles are still unclear.
B-spline registration of 3D images with Levenberg-Marquardt optimization (2004)

B-splines are a well-known approach for non-rigid image registration. Though successfully applied to various medical applications they exhibit a high computational complexity mainly because of the lack of dedicated optimization methods. In this work we focus on a Levenberg-Marquardt type optimization routine. As a similarity measure we use least-squares functionals such as the sum of squared differences, the cross-correlation and the local correlation measure, respectively. The latter is used for multi-modality registration tasks. The proposed registration algorithm consists of three main parts. In each iteration step one has to (a) build a linear system of equations, (b) solve this system and compute an update, (c) determine the step length for the following iteration step. Appropriate stopping criteria ensure the termination of the registration task. A standard approach for (c) and several modifications are investigated. Using a quadratic model we are able to avoid additional execution of (b) during the step length adaption. Several solvers (Cholesky, CG, pre-conditioning) for (b) have been evaluated. Also, modifications on the most time consuming task (a) are investigated, leading to a speed-up by a factor up to 30. Finally, the algorithm is embedded in a multi-scale framework (both on image and on parameter level) providing additional regularization, an increased capture range and speed-up. Convergence tests have been successfully applied for a priori known transformations. Feasibility of the proposed approach is also shown for clinical applications including PET-CT registrations (19 data sets) and MR mammography.
Transfer of long-chain fluorescent free fatty acids between unilamellar vesicles (1986)

Movement of free fatty acids (ffa) between small unilamellar vesicles (SUV) was studied by measuring the transfer of fluorescent n-(9-anthroyloxy)-labeled analogues (AOffa) between donor and acceptor vesicles. Donors were composed of egg phosphatidylcholine (PC) loaded with 1-2 mol % AOffa, and acceptors were egg PC containing 10-12 mol % N-(7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylethanolamine (NBD-PE). The fluorescence of AO added directly to acceptor SUV was greater than 98% quenched by energy transfer to NBD. Thus, AOffa movement from donor to acceptor was monitored by the time-dependent decrease in AO fluorescence. The transfer of the short-chain AOffa, although too fast to be resolved by the methods used here, is consistent with studies that find transfer rates on the order of milliseconds and kinetics which are first order. In contrast, transfer rates for the long-chain AOffa are more than 2 orders of magnitude slower, and the kinetics of the transfer process are best described by the sum of two exponentials plus a constant. The ffa ionization state was also found to be an important determinant of transfer rate. The charged species transferred an average of 10-fold faster than the protonated ffa. The ffa pKa in the membrane is 9, as calculated from the pH dependence of transfer. Similar to results found for other lipids, long-chain AOffa are transferred via water rather than a collision-mediated process. The aqueous phase route of AOffa intermembrane transfer is indicated by the lack of effect on transfer of large alterations in the product of donor and acceptor phospholipid concentrations. Moreover, the transfer rate is decreased as [NaCl] is increased from 0.1 to 4 M. This effect of ionic strength is probably due not only to a decrease in the aqueous phase partition of the AOffa but also to an alteration in bilayer structure, as measured by fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene. The observed kinetics are consistent with a model in which the transfer involves two steps: transbilayer movement between the inner and outer bilayer leaflets, followed by transfer from the outer leaflet to the aqueous phase (off rate). Within the framework of this model, the observed slow rate is primarily determined by the rate of transbilayer movement, and the observed fast rate is approximately equal to the off rate. The off rate is about 10-fold faster than the rate of transbilayer movement.
Supplementary Figure 1 from Universal Marker and Detection Tool for Human Sarcoma Circulating Tumor Cells (2023)

&lt;p&gt;PDF file - 3630KB, Detection of cell surface vimentin using western blotting, flow cytometry. Determination of specificity and sensitivity of 84-1 antibody.&lt;/p&gt;
A robust decoder for distributed turbo codes in relay channel (2010)

In this paper, a decoder based on log-MAP (maximum a-priori) algorithm for distributed turbo codes in relay channel is designed. The structure of the proposed turbo decoder is similar to the standard turbo iterative decoder with two soft-input soft-output (SISO) modules. However, the inputs to the decoder as well as the extrinsic signals between the two SISO modules are differently calculated. The principle of the proposed decoder is to get inputs to each SISO module that comes from one specific transmitter. Simulation results show that the proposed decoder has faster convergence and better BER performance than the standard decoder when the input from source and relay are with mismatched signal strength. The proposed decoder is also robust against this signal quality mismatch.
Pulmonary Artery Catheter Use in Acute Myocardial Infarction-Cardiogenic Shock (2020)

In AMI-CS, there was a 75% decrease in PAC use between 2000 and 2014. Admissions receiving a PAC were a higher risk cohort with worse clinical outcomes.
TopoAL: An Adversarial Learning Approach for Topology-Aware Road\n Segmentation (2020)

Most state-of-the-art approaches to road extraction from aerial images rely\non a CNN trained to label road pixels as foreground and remainder of the image\nas background. The CNN is usually trained by minimizing pixel-wise losses,\nwhich is less than ideal to produce binary masks that preserve the road\nnetwork's global connectivity. To address this issue, we introduce an\nAdversarial Learning (AL) strategy tailored for our purposes. A naive one would\ntreat the segmentation network as a generator and would feed its output along\nwith ground-truth segmentations to a discriminator. It would then train the\ngenerator and discriminator jointly. We will show that this is not enough\nbecause it does not capture the fact that most errors are local and need to be\ntreated as such. Instead, we use a more sophisticated discriminator that\nreturns a label pyramid describing what portions of the road network are\ncorrect at several different scales. This discriminator and the structured\nlabels it returns are what gives our approach its edge and we will show that it\noutperforms state-of-the-art ones on the challenging RoadTracer dataset.\n
Addition of Maraviroc Versus Placebo to Standard Antiretroviral Therapy for Initial Treatment of Advanced HIV Infection (2020)

INSERM-ANRS (French National Agency for Research on AIDS).
Abstract 2197: p53-dependent expression of the fluorouracil (5-FU) catabolic enzyme dihydropyrimidine dehydrogenase (DPD) in mouse liver. (2013)

Abstract Fluorouracil (5-FU) a commonly used drug in the treatment of cancer is hampered by a short unpredictable plasma half-life, which complicates dose modulation to minimize toxicity and improve efficacy of 5-FU treatment. Strategies to improve on the unfavorable pharmacokinetic properties of 5-FU, currently under clinical trial, involve targeting of the catabolic enzyme dihydropyrmidine dehydrogenase (DPD).This requires understanding the mechanisms regulating the expression of DPD and the inducibility of 5-FU catabolism, which is inadequately investigated. By performing in silico analysis we were able to identify putative p53 binding sites in the proximity of the dihydropyrimidine dehydrogenase gene (DPYD) and confirm by chromatin immunoprecipitation (ChIP) that p53 increasingly locates to a binding site (about 1.8 ± 0.05 fold over untreated control) downstream of DPYD (P53DBS) following a single IV bolus of 5-FU (150 mg/kg bw) in mouse liver. Indeed, DPYD mRNA increased by 1.8 fold and protein by 1.8 fold (P&amp;lt; 0.0005) respectively in a time- and p53-dependent manner in the liver of treated with 5-FU. Our ongoing studies are focused on assessing p53-dependent regulation of DPD-activity and the resulting change in 5-FU bioavailability We suggest that p53 can regulate an important step of pyrimidine-catabolism and targeting p53 in the context of 5-FU therapy of malignancies carrying p53 mutations may be another strategy to improve treatment efficacy. Citation Format: Prashanth R. Gokare, Niklas Finnberg, Joshua Allen, Jenny Dai, Wafik El-Deiry. p53-dependent expression of the fluorouracil (5-FU) catabolic enzyme dihydropyrimidine dehydrogenase (DPD) in mouse liver. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2197. doi:10.1158/1538-7445.AM2013-2197
Dynamic Multiple Reaction Monitoring of amphipod Gammarus fossarum caeca expands molecular information for understanding the impact of contaminants (2023)

Mass spectrometry in multiple reaction monitoring (MRM) mode is a powerful technique that can provide highly selective, multiplexed, and reproducible quantification of peptides derived from proteins. Ideal for the application of molecular biomarkers in biomonitoring surveys, MRM tools have been recently developed to quantify sets of pre-selected biomarkers in freshwater sentinel species. Still limited to the validation and application phase of biomarkers, dynamic MRM (dMRM) acquisition mode has increased the multiplexing capacity of mass spectrometers, expanding opportunities to explore proteome modulations in sentinel species. This study evaluated the feasibility to propose dMRM tools for investigating sentinel species proteomes at the organ level and demonstrated its potential for screening contaminant effects and discovering new protein biomarkers. As a proof of concept, a dMRM assay was developed to comprehensively capture the functional proteome of the caeca of Gammarus fossarum, a freshwater crustacean, commonly used as a sentinel species in environmental biomonitoring. The assay was then used to assess the effects of sub-lethal concentrations of cadmium, silver, and zinc on gammarid caeca. Results showed dose-response and specific metal effects on caecal proteomes, with a slight effect of zinc compared to the two non-essential metals. Functional analyses indicated that cadmium affected proteins involved in carbohydrate metabolism, digestive and immune processes, while silver affected proteins related to oxidative stress response, chaperonin complexes and fatty acid metabolism. Based on these metal-specific signatures, several proteins modulated in a dose-dependent manner were proposed as candidate biomarkers for tracking the level of these metals in freshwater ecosystems. Overall, this study highlights the potential of dMRM to decipher the specific modulations of proteome expression induced by contaminant exposure and pinpoints specific response signatures, offering new perspectives for the de novo identification and development of biomarkers in sentinel species.
ChemInform Abstract: Synthesis of 7α‐Methoxy‐2‐(1,3‐dithiolan‐2‐ylidene)cephem Sulfones. A New Series of Human Leukocyte Elastase Inhibitors. (1996)

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.