gebhart/patrepeval huggingface dataset:
Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity (2022)

In this article, we describe a set of subsequent five-steps chemical reactions to synthesize a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>). Structural characterization of <b>10</b> and its intermediate products was also performed and reported to attest to their formation. A molecular docking study was performed to propose the novel synthesized ferrocene derivative (<b>10</b>) as a potential antitumor candidate targeting the mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The computed docking score of (<b>10</b>) at -9.50 kcal/mol compared to the native anticancer staurosporine at -8.72 kcal/mol postulated a promising anticancer activity. Also, molecular dynamics (MD) simulations were carried out for 500 ns followed by MM-GBSA-binding free energy calculations for both the docked complexes of ferrocene and staurosporine to give more deep insights into their dynamic behavior in physiological conditions. Furthermore, DFT calculations were performed to unravel some of the physiochemical characteristics of the ferrocene derivative (<b>10</b>). The quantum mechanics calculations shed the light on some of the structural and electrochemical configurations of (<b>10</b>) which would open the horizon for further investigation. HighlightsThe synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described.Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed.DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out.Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1.Communicated by Ramaswamy H. Sarma.
Stady‐state and Dynamical Simulation of an Autothermal Gasoline Reformer (2003)

Abstract Detailed numerical simulation is an important tool for the analysis, development and optimization of new reactor systems. In this contribution results of steady‐state and dynamic simulations of a hydrogen production system for mobile applications based on gasoline are presented. The system consists of an autothermal reformer, a high temperature shift reactor and a countercurrent heat exchanger for heat integration. The simulations are based on 1‐D, multiphase, dynamic models, which are solved with the simulation tool PDEX‐Pack. Firstly steady‐state and dynamic simulations of the autothermal reformer alone are presented. Concentration and temperature profiles in the reformer under different operation conditions are discussed and possibilities to improve the performance are assessed. Dynamic simulations of load change and cold start show the fast dynamic response of the reformer due to its low thermal mass. Simulations of the coupled system underline the impact of the heat exchanger design for the system performance, especially under dynamic conditions. Finally dynamic simulations of a possible cold start strategy for the system are discussed.
Supplementary Figure 1 from Gain of Glucose-Independent Growth upon Metastasis of Breast Cancer Cells to the Brain (2023)

&lt;p&gt;Supplementary Figure S1. Western blot characterization of antibodies against BCKDH-E1 and BCKDH-pSer-E1&lt;/p&gt;
ChemInform Abstract: High‐Density Yttria for Practical Ceramic Applications. (1992)

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.
Distributed Signal Processing Algorithms for the Physical Layer of Large‐Scale Sensor Networks (2005)

The ability to move the sensed data out of the network (the reachback communication) is one of the basic communication primitives that must be supported by every sensor network. This is most commonly achieved by routing of information through the network to some central data collection point that will act on the sensed information. Authors propose an approach to this problem by developing a method to allow all nodes in the network to cooperatively generate a strong information bearing signal to communicate with a distant data collection point. Such a solution would be extremely robust to the failure of nodes in the network and would allow for the deployment of a homogeneous network of extremely small, low-power nodes for a variety of applications. This approach to the sensor reachback problem is called cooperative reachback. In this chapter two aspects of the cooperative reachback problem are considered: time synchronization and reachback modulation schemes. Time synchronization facilitates the design of cooperative reachback modulation schemes. A system model that will apply to both the time synchronization problem and reachback communication is described. Authors then study the properties of waveforms generated by asymptotically dense networks and then move into the development of a time synchronization mechanism for dense networks using these waveform properties. In the asymptotic regime, this time synchronization framework can keep the synchronization mean squared error from increasing with distance from the ideal time source. Next, authors study the performance of this asymptotically optimal scheme for networks of finite size. They then develop a modulation scheme for reachback communication again using these waveform properties and study its performance using simulations.
<title>Thin-film silica sol-gels doped with ion-responsive fluorescent lipid bilayers</title> (1999)

A metal ion sensitive, fluorescent lipid-bilayer material (5% PSIDA/DSPC) was successfully immobilized in a silica matrix using a tetramethoxysilane (TMOS) sol-gel procedure. The sol- gel immobilization method was quantitative in the entrapment of self-assembled lipid-bilayers and yielded thin films for facile configuration to optical fiber platforms. The silica matrix was compatible with the solvent sensitive lipid bilayers and provided physical stabilization as well as biological protection. Immobilization in the silica sol-gel produced an added benefit of improving the bilayer's metal ion sensitivity by up to two orders of magnitude. This enhanced performance was attributed to a preconcentrator effect from the anionic surface of the silica matrix. Thin gels (193 micron thickness) were coupled to a bifurcated fiber optic bundle to produce a metal ion sensor probe. Response times of 10 - 15 minutes to 0.1 M CuCl<SUB>2</SUB> were realized with complete regeneration of the sensor using an ethylenediaminetetraacetic acid (EDTA) solution.
Ethylenediamine and piperazine sensitivity. (1983)

In this preliminary study we assessed the efficiency of glucagon given intranasally in raising blood glucose concentrations in normal subjects. Subjects and methodsSeven normal adult subjects, all doctors or undergraduate medical students at this hospital, volunteered for the study.They were studied while in bed in the morning, after fasting overnight, and not smoking.After 30 minutes to ensure steady blood glucose and plasma glucagon concentrations drops of solutions containing glucagon (1 mg/subject) were inserted in both nostrils and the subjects were asked to take a deep breath.In four subjects control experiments were performed on a different occasion and distilled water was substituted for glucagon, the subjects being unaware of the contents of the drops.Finally, in two of the above subjects glucagon 1 mg was given intramuscularly.Solutions to form nasal drops were obtained from porcine glucagon (Novo, Copenhagen, Denmark) diluted with sodium glycocholate 10 or 15 mg as a surfactant.5 Blood samples were obtained at the times indicated in the figure; placed in tubes containing heparin and aprotinin (10 000 KIU/ml), and centrifuged at 4'C.Blood glucose concentrations were estimated by an enzymatic method.Plasma was stored at -20'C until assayed for immuno- reactive insulin and immunoreactive glucagon.Immunoreactive glucagon was assayed using the antibody R-78, C-terminus directed.Incubation lasted 48 h at 4°C and free immunoreactive glucagon was separated from bound immunoreactive glucagon by centrifugation at 2000 g for 20 minutes.Kits for immunoreactive insulin and immunoreactive glucagon were supplied by Serono Biodata (Rome, Italy).Statistical analyses were performed by Student's t test for paired data and confirmed by the non-parametric Wilcoxon's test.1500
Methods for phase noise mitigation for DFT-S-OFDM waveforms (2016)

This paper addresses the problem of phase noise mitigation in communications links utilizing DFT-S-OFDM waveforms. The paper discusses use of two different pilot configurations to do the compensation of the common phase error part of the phase noise. The pilot configurations are inserting pilots as logical symbols before the DFT spreading and inserting frequency domain pilots as subcarriers as in OFDM waveforms. Then, based on the former pilot configuration, a computationally efficient intercarrier interference compensation algorithm is proposed. The pilot configurations and techniques are evaluated in terms of peak-to-average power ratio and phase noise mitigation performance with realistic numerology in numerical simulations.
A 33-mpixel 120-fps CMOS image sensor using 0.11-μm CIS process (2014)

We have been researching and developing a CMOS image sensor that has 2.8 &mu;m x 2.8 &mu;m pixel, 33-Mpixel resolution (7680 horizontal pixels x 4320 vertical pixels), 120-fps frame rate, and 12-bit analog-to-digital converter for “8K Super Hi-Vision.” In order to improve its sensitivity, we used a 0.11-&mu;m nanofabricated process and attempted to increase the conversion gain from an electron charge to a voltage in the pixel. The prototyped image sensor shows a sensitivity of 2.4 V/lx&bull;s, which is 1.6 times higher than that of a conventional image sensor. This image sensor also realized the input-referred random noise as low as 2.1 e<sup>-</sup><sub>rms.</sub>
Intrasplenic trafficking of natural killer cells is redirected by chemokines upon inflammation (2008)

The spleen is a major homing site for NK cells. How they traffic to and within this site in homeostatic or inflammatory conditions is, however, mostly unknown. Here we show that NK cells enter the spleen through the marginal sinus and home to the red pulp via a pertussis toxin-insensitive mechanism. Upon inflammation induced by poly(I:C) injection or mouse cytomegalovirus infection, many NK cells left the red pulp while others transiently entered the white pulp, predominantly the T cell area. This migration was dependent on both CXCR3 and CCL5, suggesting a synergy between CXCR3 and CCR5, and followed the path lined by fibroblastic reticular cells. Thus, the entry of NK cells in the white pulp is limited by the expression of pro-inflammatory chemokines. This phenomenon ensures the segregation of NK cells outside of the white pulp and might contribute to the control of immunopathology.
Biochemical and behavioral studies of the 5‐HT1B receptor agonist, CP‐94,253 (1992)

Abstract CP‐94,253, 3‐(1,2,5,6‐tetrahydro‐4‐pyridyl)‐5‐propoxypyrrolo[3,2‐ b ]pyridine, a new serotonergic ligand, was found to exhibit significantly greater binding affinity at 5‐HT 1B receptors than at 5‐HT 1A or 5‐HT 1C receptors. Saturation studies showed CP‐94,253 to be a competitive inhibitor of [ 125 l]iodocyanopindolol binding to 5‐HT 1B sites. Its competition curve with this radioligand was shifted to the right (decreased affinity) in the presence of Gpp(NH)p, indicating an agonist function for CP‐94,253. Oral administration of CP‐94,253 to rats caused inhibition of food intake, decrease in body weight gain, and hyperlocomotion, effects apparently elicited via activation of 5‐HT 1B receptors. © 1992 Wiley‐Liss, Inc.
Data format standard for sharing light source measurements (2013)

Optical design requires accurate characterization of light sources for computer aided design (CAD) software. Various methods have been used to model sources, from accurate physical models to measurement of light output. It has become common practice for designers to include measured source data for design simulations. Typically, a measured source will contain rays which sample the output distribution of the source. The ray data must then be exported to various formats suitable for import into optical analysis or design software. Source manufacturers are also making measurements of their products and supplying CAD models along with ray data sets for designers. The increasing availability of data has been beneficial to the design community but has caused a large expansion in storage needs for the source manufacturers since each software program uses a unique format to describe the source distribution. In 2012, the Illuminating Engineering Society (IES) formed a working group to understand the data requirements for ray data and recommend a standard file format. The working group included representatives from software companies supplying the analysis and design tools, source measurement companies providing metrology, source manufacturers creating the data and users from the design community. Within one year the working group proposed a file format which was recently approved by the IES for publication as TM-25. This paper will discuss the process used to define the proposed format, highlight some of the significant decisions leading to the format and list the data to be included in the first version of the standard.
An automated computational image analysis pipeline for histological grading of cardiac allograft rejection (2021)

These results show that the CACHE-grader pipeline, derived using intuitive morphological features, can provide expert-quality rejection grading, performing within the range of inter-grader variability seen among human pathologists.
Vicinal Amino Alcohols as Organocatalysts in Asymmetric Cross-Aldol Reaction of Ketones:  Application in the Synthesis of Convolutamydine A (2007)

Leucinol and valinol have been identified as efficient organocatalysts for the aldol reaction of isatin and its derivatives (as examples of activated, non-enolizable ketones) with acetone. Uncommon mechanistic features were observed and used in the formulation of the transition state of the reaction.
Learning to predict code-switching points (2008)

Predicting possible code-switching points can help develop more accurate methods for automatically processing mixed-language text, such as multilingual language models for speech recognition systems and syntactic analyzers. We present in this paper exploratory results on learning to predict potential code-switching points in Spanish-English. We trained different learning algorithms using a transcription of code-switched discourse. To evaluate the performance of the classifiers, we used two different criteria: 1) measuring precision, recall, and F-measure of the predictions against the reference in the transcription, and 2) rating the naturalness of artificially generated code-switched sentences. Average scores for the code-switched sentences generated by our machine learning approach were close to the scores of those generated by humans.
Synthesis and structure of microporous layered tin(IV) sulfide materials (1998)

Synthetic methods have been developed which yield large single crystals and highly crystalline phase-pure microporous layered SnS-n materials. This allows study of the structure–property–function relations of these materials. The tin sulfide layer of the SnS-1 structure type contains hexagonally shaped 24-atom rings which are constituted by six Sn3S4 broken-cube cluster building units, linked together by double bridge Sn(µ-S)2Sn sulfur bonds. The SnS-3 structure type contains elliptically shaped 32-atom rings which are also constructed from six Sn3S4 broken-cube clusters. However, they are linked by double bridge Sn(µ-S)2Sn sulfur bonds as well as tetrahedral edge-bridging Sn(µ-S2SnS2)Sn spacer units. The SnS-1 structure type [A2Sn3S7 ] was obtained in the presence of A+=Et4N+ , DABCOH+ (protonated 1,8-diazabicyclooctane), and a mixed template system of NH4+ /Et4N+ , while the SnS-3 structure type [A2Sn4S9 ] emerged in the presence of A+=Prn4N+ and Bun4N+ . Various SnS-1 and SnS-3 structures are examined and compared in relation to the size/shape of constituent template cations. A particular kind of structure-directing function was observed, that is, larger template molecules create larger void spaces within and between the tin sulfide sheets. Unique framework flexibility was discovered for both structure types. In order to accommodate the size/shape changes of templates, the flexible porous tin(iv) sulfide layers are able to undergo a certain degree of elastic deformation to alter the architecture of void spaces within and between the layers, rather than forming a completely new porous structure type. This is believed to be responsible for the relatively small number of structure types so far discovered for tin(iv) sulfide-based microporous layered materials compared to the myriad of three-dimensional open-framework structure types found for the zeolites and aluminophosphates. The observed differences among the various SnS-1 or SnS-3 structures is significant and has resulted in distinct adsorption behavior towards guest molecules. The TPA-SnS-3 framework is also found to be pressure sensitive. This all bodes well for envisaged chemical sensor applications for this class of porous materials.
ChemInform Abstract: N‐ALKYL‐4‐(N′,N′‐DIALKYLAMINO)PYRIDINIUM SALTS: THERMALLY STABLE PHASE‐TRANSFER CATALYSTS FOR NUCLEOPHILIC AROMATIC DISPLACEMENT (1985)

Abstract Durch Alkylierung werden die Ammoniumsalze (I)‐(IV) hergestellt, die bei PhasenTransfer‐Reaktionen als Katalysatoren wesentlich höhere Stabilitäten als z.B. Tetrabutylammoniumbromid besitzen.
ChemInform Abstract: Regiospecific 4‐O‐Alkylation to Tetronic Acids with Isoureas. (2000)

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.
Influence of temporal regularization and radial undersampling factor on compressed sensing reconstruction in dynamic contrast enhanced MRI of the breast (2015)

This study demonstrates objective spatial and temporal similarity measures can be used to assess the influence of sparsity constraint and undersampling in compressed sensing DCE-MRI and also shows that the iGRASP method provides the flexibility of optimizing these reconstruction parameters in the postprocessing stage using the same acquired data.
Pioglitazone reduces the incidence of Alzheimer’s disease: From genetics to population‐based validation (2021)

Background Genome-wide association studies (GWAS) have identified numerous susceptibility loci for Alzheimer’s disease (AD). However, utilizing GWAS to identify high-confidence AD risk genes (ARGs) that can guide development of new therapeutics for patients suffering from AD has heretofore not been successful. Method To address this critical problem in the field, we have developed a genotype-informed, network-based methodology that interrogates pathogenesis to identify new therapeutics. When applied to AD, this approach integrates GWAS findings, multi-omics data from brain samples of AD patients and AD transgenic animal models, drug-target networks, and the human protein-protein interactome, along with large-scale patient database validation and in vitro mechanistic observations in human microglia cells. Result Through this approach, we identified 103 ARGs validated by various levels of pathobiological evidence in AD. Via network-based prediction and population-based validation, we then showed that three drugs are significantly associated with decreased risk of AD compared with matched control populations: pioglitazone (P = 0.005, hazard ratio (HR) = 0.916, 95% confidence interval [CI] 0.861-0.974), febuxostat (HR = 0.815, 95% CI 0.710-0.936, P = 0.004), and atenolol (HR = 0.949, 95% CI 0.923-0.976, P = 2.8 x 10-4). Pioglitazone is a peroxisome proliferator-activated receptor (PPAR) agonist used to treat type 2 diabetes, and propensity score matching cohort studies confirmed its association with reduced risk of AD in comparison to glipizide (HR =0.921, 95% CI 0.862-0.984, P = 0.0159), an insulin secretagogue that is also used to treat type 2 diabetes. In vitro experiments showed that pioglitazone downregulated glycogen synthase kinase 3 beta (GSK3β) and cyclin-dependent kinase (CDK5) in human microglia cells, supporting a possible mechanism-of-action for its beneficial effect in AD. Conclusion In summary, we present an integrated, network-based methodology to rapidly translate GWAS findings and multi-omics data to genotype-informed therapeutic discovery in AD.
From bench to bedside: Improving the clinical safety of GalNAc–siRNA conjugates using seed-pairing destabilization (2022)

Preclinical mechanistic studies have pointed towards RNA interference-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here, we demonstrate that a single glycol nucleic acid or 2'-5'-RNA modification can substantially reduce small interfering RNA (siRNA) seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established hepatotoxicity driven by off-target effects, these novel designs with seed-pairing destabilization, termed enhanced stabilization chemistry plus (ESC+), demonstrated a substantially improved therapeutic window in rats. In contrast, siRNAs thermally destabilized to a similar extent by the incorporation of multiple DNA nucleotides in the seed region showed little to no improvement in rat safety suggesting that factors in addition to global thermodynamics play a role in off-target mitigation. We utilized the ESC+ strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient and asymptomatic alanine aminotransferase elevations in healthy volunteers. The redesigned ALN-HBV02 (VIR-2218) showed improved specificity with comparable on-target activity and the program was reintroduced into clinical development.
ChemInform Abstract: Preparation and Determination of the Absolute Configuration of Optically Active 9‐Hydroxy‐7‐oxabicyclo(4.3.0)non‐4‐en‐8‐ones. (1995)

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.