gebhart/patrepeval huggingface dataset:
Facet-Dependent Thermal Instability in LiCoO2 (2017)

Thermal runaways triggered by the oxygen release from oxide cathode materials pose a major safety concern for widespread application of lithium ion batteries. Utilizing in situ aberration-corrected scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) at high temperatures, we show that oxygen release from LixCoO2 cathode crystals is occurring at the surface of particles. We correlated this local oxygen evolution from the LixCoO2 structure with local phase transitions spanning from layered to spinel and then to rock salt structure upon exposure to elevated temperatures. Ab initio molecular dynamics simulations (AIMD) results show that oxygen release is highly dependent on LixCoO2 facet orientation. While the [001] facets are stable at 300 °C, oxygen release is observed from the [012] and [104] facets, where under-coordinated oxygen atoms from the delithiated structures can combine and eventually evolve as O2. The novel understanding that emerges from the present study provides in-depth insights into the thermal runaway mechanism of Li-ion batteries and can assist the design and fabrication of cathode crystals with the most thermally stable facets.
Investigation of the interaction of iron(iii) complexes with dAMP by ESI-MS, MALDI-MS and potentiometric titration: insights into synthetic nuclease behavior (2010)

We report herein the characterization by electrospray ionization (ESI) mass spectrometry (MS), matrix assisted laser desorption ionization (MALDI-MS) and potentiometric titration of three iron(III) compounds: [Fe(III)(HPClNOL)Cl2]·NO3 (1), [Cl(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)Cl]·Cl2·H2O (2) and [(SO4)(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)(SO4)]·6H2O (3), where HPClNOL= 1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol). Despite the fact that the compounds have distinct structures in solid state and non-buffered solution, all compounds present similar ESI and MALDI mass spectra in a buffered medium (pH 7.0). At this pH, the species [(PClNOL)Fe(III)-(μ-O)-Fe(III)(PClNOL)](2+) (m/z 354) was observed for all the compounds under investigation. Potentiometric titration confirms a similar behavior for all compounds, indicating that the dihydroxo form [(OH)(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)(OH)](2+) is the major species at pH 7.0, for all the compounds. The products of the interaction between compounds (1), (2) and (3) and dAMP (2'-deoxyadenosine-5'-monophosphate) in a buffered medium (pH 7.0) were identified by MALDI-MS/MS. The fragmentation data obtained by MS/MS allow one to identify the nature of the interaction between the iron(III) compounds and dAMP, revealing the direct interaction between the iron center and phosphate groups.
Effects of Salt, Polyethylene Glycol, and Water Content on Dough Rheology for Two Red Spring Wheat Varieties (2017)

In this research, the relationship between dough rheology and water behavior was investigated in response to two osmotic regulators, salt (NaCl) and polyethylene glycol (PEG), using two Canadian Western Red Spring (CWRS) wheat varieties (Harvest and Pembina). The effects of NaCl (0.5, 1.0, and 1.5 g/100 g of flour) and PEG 400 (2.5, 5.0, and 7.5 g/100 g of flour) on dough rheology (oscillatory and creep) were estimated by using a central composite design. Variation of NaCl showed a significant effect on the phase angle δ, indicating that increasing the NaCl resulted in a more elastic dough. The opposite trend was observed with the addition of PEG. PEG 400 exerted a softening effect owing to plasticization, so that a more compliant liquid‐like dough was produced. The effects of water content (±10% of farinograph absorption) and PEG molar mass on dough rheology and freezable water content were estimated by using a full factorial design. PEGs with different molar mass (400, ≈1,600, and 3,350 g/mol) were added at a concentration of 1 g/100 g of flour. The water content significantly affected all dough rheological attributes, whereas PEG molar mass had no effect. The complex shear modulus ( G* ) decreased with increasing water content, and dough creep compliance ( J max ) increased. The elastic response of dough, determined as the relative elastic part ( J el ) decreased with increasing water content. A high correlation was found between the freezable water content and dough rheological attributes.
Designing New Forms of Digital Autopoietic Machines (2022)

The general theory of information (GTI) tells us that information is represented, processed and communicated using physical structures. The physical universe is made up of structures combining matter and energy. According to GTI, &ldquo;information is related to knowledge as energy is related to matter.&rdquo; GTI also provides tools to deal with transformation of information and knowledge. We present here the application of these tools for the design of digital autopoietic machines with higher efficiency, resiliency and scalability than the information processing systems based on the Turing machines. We discuss the utilization of these machines for building autopoietic and cognitive applications in a multi-cloud infrastructure.
Interlayer Structure and Bonding in Nonswelling Primary Amine Intercalated Clays (2005)

Preparation of industrially useful clay−polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine−clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.
Alternative strategies for the study and treatment of clinical bacterial biofilms (2017)

Biofilms represent an adaptive lifestyle where microbes grow as structured aggregates in many different environments, e.g. on body surfaces and medical devices. They are a profound threat in medical (and industrial) settings and cause two-thirds of all infections. Biofilm bacteria are especially recalcitrant to common antibiotic treatments, demonstrating adaptive multidrug resistance. For this reason, novel methods to eradicate or prevent biofilm infections are greatly needed. Recent advances have been made in exploring alternative strategies that affect biofilm lifestyle, inhibit biofilm formation, degrade biofilm components and/or cause dispersal. As such, naturally derived compounds, molecules that interfere with bacterial signaling systems, anti-biofilm peptides and phages show great promise. Their implementation as either stand-alone drugs or complementary therapies has the potential to eradicate resilient biofilm infections. Additionally, altering the surface properties of indwelling medical devices through bioengineering approaches has been examined as a method for preventing biofilm formation. There is also a need for improving current biofilm detection methods since in vitro methods often do not accurately measure live bacteria in biofilms or mimic in vivo conditions. We propose that the design and development of novel compounds will be enabled by the improvement and use of appropriate in vitro and in vivo models.
Analytical characterization of the MPDR-based power estimators in snapshot scarce regime (2012)

The Minimum Power Distortionless Response (MPDR) beamformer processes the input signal such that the output power is minimized and the signal arriving from a look direction is undistorted. The sample spatial correlation matrix, estimated from snapshots of the received signal, plays a central role in the calculation of MPDR array weights and the estimate of the received signal power from the desired look direction. When the number of available snapshots and the number of array sensors are of similar order, the true and estimated correlation matrices might differ significantly. This paper presents analytical characterization of the MPDR-based power estimators in the snapshot scarce regime and when diagonal loading is used. In this effort, some results from the theory of large dimensional random matrices are exploited. The derived characterizations are validated via simulations.
An Assessment of Computational Fluid Dynamics Cavitation Models Using Bubble Growth Theory and Bubble Transport Modeling (2019)

This effort investigates advancing cavitation modeling relevant to computational fluid dynamics (CFD) through two strategies. The first aims to reformulate the cavitation models and the second explores adding liquid–vapor slippage effects. The first aspect of the paper revisits cavitation model formulations with respect to the Rayleigh–Plesset equation (RPE). The present approach reformulates the cavitation model using analytic solutions to the RPE. The benefit of this reformulation is displayed by maintaining model sensitivities similar to RPE, whereas the standard models fail these tests. In addition, the model approach is extended beyond standard homogeneous models, to a two-fluid modeling framework that explicitly models the slippage between cavitation bubbles and the liquid. The results indicate a significant impact of slip on the predicted cavitation solution, suggesting that the inclusion of such modeling can potentially improve CFD cavitation models. Overall, the results of this effort point to various aspects that may be considered in future CFD-modeling efforts with the goal of improving the model accuracy and reducing computational time.
Perhexiline promotes HER3 ablation through receptor internalization and inhibits tumor growth (2015)

This is the first demonstration that HER3 can be targeted with small molecules by eliminating it from the cell membrane. The novel approach used here led to the discovery that perhexiline ablates HER3 expression, and offers an opportunity to identify HER3 ablation modulators as innovative therapeutics to improve survival in breast cancer patients.
Condensation methodologies for two-dimensional non-uniform constellations (2017)

Two-dimensional non-uniform constellations (2D-NUC) have been adopted for the most recent terrestrial broadcasting system called ATSC 3.0. They are known for being more efficient than one-dimensional non uniform constellations (1D-NUC) and uniform constellations (UC). They can be used in any communication system with the bit-interleaved coded modulation (BICM) structure. However, one of the main challenges of such constellations is their design for optimal behaviour in a wide range of cases and the design of a demapper that exploits their advantages. This paper presents two different condensation methodologies to design efficient 2D-NUCs simple in design and with limited demapping complexity. The proposal provides a complexity reduction of the design and demapping processes in the range from 13% to 94%. The demapping stage provides performance losses less than 0.1 dB if compared with standard 2D-NUC demapping.
Protocol to identify and monitor key mutations of broadly neutralizing antibody lineages following sequential immunization of Ig-humanized mice (2022)

Using the VRC01-class of anti-HIV-1 broadly neutralizing antibodies (bnAbs) elicited in sequentially immunized Ig-humanized mice as an example, we describe a protocol to identify key mutations for bnAb function by point mutagenesis and antibody binding and neutralization assays. We also describe steps to monitor how the key mutations arise in response to specific immunogens, which is critical for vaccine evaluation and design, via longitudinal antibody mutation profiling. This protocol can be customized for other V-gene-specific bnAbs and animal models. For complete details on the use and execution of this profile, please refer to Chen et al. (2021).
Some experimental techniques in the study of flame stabilization (1964)

The purpose of this note is to describe one or two techniques&#13;\nwhich are currently being used at Cranfield in various investigations&#13;\ninto the effects of flameholder geometry and flow parameters on the&#13;\nprocess of flame stabilization. Much of the report is concerned with a&#13;\ndescription of the nitrogen dilution technique as a means of simulating&#13;\nlow combustion pressures, and a comparison is made between this and the&#13;\nnow established water injection technique. It is shown that many&#13;\naspects of flame stability can be effectively studied by local injection&#13;\nof nitrogen directly into the combustion zone, with appreciable economies&#13;\nin the amounts of nitrogen required. A further application of this local&#13;\ninjection method is also described which has proved useful in an&#13;\ninvestigation of the factors governing the amount of air entrained in the&#13;\nrecirculation zone.
Advanced biomolecular materials based on membrane-protein/polymer complexation (1998)

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The goal of this project was to apply neutron reflectometry and atomic force microscopy to the study of lipid membranes containing proteins. Standard sample preparation techniques were used to produce thin films of these materials appropriate for these techniques. However, these films were not stable, and a new sample preparation technique was required. Toward this goal, the authors have developed a new capability to produce large, freely suspended films of lipid multi-bilayers appropriate for these studies. This system includes a controlled temperature/humidity oven in which the films 5-cm x 5-cm are remotely drawn. The first neutron scattering experiments were then performed using this oven.
ChemInform Abstract: SYNTHESIS AND ANTITUMOR ACTIVITY OF STRUCTURAL ANALOGS OF THE ANTICANCER BENZOPHENANTHRIDINE ALKALOID FAGARONINE CHLORIDE (1985)

Abstract Die Analoga (VI), (IX) und (XII) von Fagaroninchlorid (I) erhält man gemäß Formelschema.
Interphase composition profile in SB/SBS block copolymers, measured with electron microscopy, and microstructural implications (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInterphase composition profile in SB/SBS block copolymers, measured with electron microscopy, and microstructural implicationsRichard J. Spontak, Michael C. Williams, and David A. AgardCite this: Macromolecules 1988, 21, 5, 1377–1387Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/ma00183a033https://doi.org/10.1021/ma00183a033research-articleACS PublicationsRequest reuse permissionsArticle Views195Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ChemInform Abstract: A Novel Synthesis of Benzothiazoles. (1988)

Abstract 2‐Aminothiophenol (I) undergoes cyclocondensation with the 2‐phenyloxazol‐5‐ones (II) in acetic acid, yielding the benzoylaminoalkylbenzothiazoles (III).
Understanding Chemokine Biology Through Mouse Genetics (1999)

Beginning in the 1980s, investigators began to uncover a mammalian system of cell—cell communication that has developed into an entire field of research with implications for immunology, virology, neurobiology, developmental biology, and oncology. What began as a small number of inducible monocyte/macrophage and neutrophil chemo-attractants has grown to include molecules that may signal virtually all cells of the lymphoid and myeloid lineage, as well as endothelial cells, neurons, fibroblasts, and epithelial cells. In simplistic terms, it appears that nature operated on a protein motif that served as a template for the evolution of an entire gene family of ligands and receptors through gene duplication; the very organization of the ligands and receptors in the genome bears witness to this. It has been presumed that the selective advantage for the evolution of the chemokine/receptor system lies in the realm of host defense. However, the obviously critical role of several alpha chemokines and their receptors in developmental biology may lead to other interpretations, as will be discussed in a following section.KeywordsChemokine ReceptorLymphoid FollicleHigh Endothelial VenuleExtramedullary HematopoiesisMouse NeutrophilThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Localization of Adrenergic Receptors in Guinea Pig Ileum and Rabbit Jejunum to Cholinergic Neurons and to Smooth Muscle Cells (1977)

The localization of adrenergic receptors mediating a relaxing action was investigated in innervated and denervated longitudinal muscle strips from guinea pig ileum and rabbit jejunum. Denervated preparations were contracted by drugs that had a direct effect on smooth muscle cells, such as acetylcholine and histamine, but not by stimuli acting on cholinergic neurons, such as electrical field stimulation or nicotine. After blockade of beta-adrenoceptors, norepinephrine relaxed the innervated guinea pig ileum contracted by electrical field stimulation, by stimulating alpha-adrenoceptors. Norepinephrine in low concentrations did not relax denervated preparations contracted by agents acting directly on smooth muscle. In high concentrations, it relaxed denervated preparations by a nonadrenergic mechanism, resistant to alpha- and/or beta-receptor blockade, but which was also activated by 1-(3,4-dihydroxyphenyl) ethanol. Phenylephrine only had a weak agonistic effect on the electrically stimulated innervated preparation and did not relax the denervated one. The denervated rabbit intestine contracted by acetylcholine was relaxed by norepinephrine and phenylephrine by stimulation of alpha-adrenoceptors. In the innervated preparations both drugs were more effective in inhibiting contractions induced by electrical field stimulation or eserine than those induced by exogenous acetylcholine. Both the denervated guinea pig and rabbit intestine were relaxed by stimulation of beta-adrenoceptors. It is suggested that in the guinea pig ileum alpha-adrenoceptors mediating relaxation are located only in cholinergic neurons, whereas in rabbit jejunum they are located both in these neurons and in the smooth muscle cells. Beta-adrenoceptors are located in the smooth muscle cells of both organs.
Synthesis and Structure—Activity Relationships of Novel Poly(ADP‐Ribose) Polymerase‐1 Inhibitors. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
A screen for inducers of bHLH activity identifies pitavastatin as a regulator of p21, Rb phosphorylation and E2F target gene expression in pancreatic cancer (2017)

// Nicholas Villarino 1 , Lia Signaevskaia 1 , Jaco van Niekerk 1 , Rachel Medal 1 , Heejung Kim 1 , Reyhaneh Lahmy 1 , Kathleen Scully 1 , Anthony Pinkerton 2 , Sangwun Kim 3 , Andrew Lowy 4 and Pamela Itkin-Ansari 1, 5 1 Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA 2 Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA 3 Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea 4 Departments of Pathology and Surgery, Division of Surgical Oncology, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA 5 Department of Pediatrics, University of California San Diego, La Jolla, CA, USA Correspondence to: Pamela Itkin-Ansari, email: pitkin@sbpdiscovery.org Keywords: bHLH proteins, pancreatic cancer, high throughput screening, drug discovery, statins Received: March 15, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Accepted: May 23, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Published: June 21, 2017 ABSTRACT The average survival for patients with Pancreatic Ductal Adenocarcinoma (PDA) is merely 6 months, underscoring the need for new therapeutic approaches. During PDA progression, pancreatic acinar cells lose activity of the ClassI/II bHLH factors that regulate quiescence. We previously found that promoting transcriptional activity of the Class I bHLH factor E47 in highly aggressive PDA cells induced stable growth arrest in vitro and in vivo . To translate these findings for clinical utility, we developed a high throughput screening platform to identify small molecule inducers of Class I/II bHLH activity. A screen of 4,375 known drugs identified 70 bHLH activators. Prominent among the hits were members of the statin class of HMG-CoA reductase inhibitors, cholesterol lowering drugs that are also being evaluated in cancer. Studies with pitavastatin in primary patient derived tumor cells and established PDA lines, revealed dose dependent growth inhibition. At the molecular level, pitavastatin induced expression of the cyclin dependent kinase (CDK) inhibitor p21 in a cholesterol independent manner, blocked repressive phosphorylation of the Retinoblastoma tumor suppressor protein at CDK targeted sites, and reduced expression of E2F target genes required for progression through the G1/S boundary. Together, the data provide new insight into mechanisms by which statins constrain proliferation in cancer and establish the effectiveness of a novel screening platform to identify small molecules of clinical relevance in pancreatic cancer.
40 GHz optical pulse generation using sinusoidally-driven travelling-wave electroabsorption modulator (2002)

Optical pulse generation at a 40 GHz repetition rate using a sinusoidally-driven high-modulation-efficiency travelling-wave electroabsorption modulator is reported. Travelling-wave behaviour is demonstrated by comparing the pulse generation in the co- and counter-propagation configurations and confirmed by a theoretical model.