gebhart/patrepeval huggingface dataset:
Linear and Nonlinear Spectroscopy of a Porphyrin−Squaraine−Porphyrin Conjugated System (2009)

The linear and nonlinear absorption properties of a squaraine-bridged porphyrin dimer (POR-SQU-POR) are investigated using femto-, pico-, and nanosecond pulses to understand intramolecular processes, obtain molecular optical parameters, and perform modeling of the excited-state dynamics. The optical behavior of POR-SQU-POR is compared with its separate porphyrin and squaraine constituent moieties. Linear spectroscopic studies include absorption, fluorescence, excitation and emission anisotropy, and quantum yield measurements. Nonlinear spectroscopic studies are performed across a wide range (approximately 150 fs, approximately 25 ps, and approximately 5 ns) of pulsewidths and include two-photon absorption (2PA), single and double pump-probe, and Z-scan measurements with detailed analysis of excited-state absorption induced by both one- and two-photon absorption processes. The 2PA from the constituent moieties shows relatively small 2PA cross sections; below 10 GM (1 GM = 1 x 10(-50) cm4 s/photon) for the porphyrin constituent and below 100 GM for the squaraine constituent except near their one-photon resonances. In stark contrast, the composite POR-SQU-POR molecule shows 2PA cross sections greater than 10(3) GM over most of the spectral range from 850 to 1600 nm (the minimum value being 780 GM at 1600 nm). The maximum value is approximately 11,000 GM near the Nd:YAG laser wavelength of 1064 nm. This broad spectral range of large 2PA cross sections is unprecedented in any other molecular system and can be explained by intramolecular charge transfer. A theoretical quantum-chemical analysis in combination with different experimental techniques allows insight into the energy-level structure and origin of the nonlinear absorption behavior of POR-SQU-POR.
Analysis of IFN- κ Expression in Pathologic Skin Conditions: Downregulation in Psoriasis and Atopic Dermatitis (2006)

Interferon-kappa (IFN-kappa) is a type I IFN expressed by keratinocytes, monocytes and dendritic cells (DCs). In human keratinocytes, it is produced in response to double-stranded RNA (dsRNA) and other IFNs and protects from viral infections. In monocytes and DCs, IFN-kappa induces tumor necrosis factor-alpha (TNF-alpha) and interleukin-10 (IL-10) and inhibits lipopolysaccharide (LPS)-induced IL-12. In this study, we evaluated IFN-kappa expression in skin lesions of patients with common immune-mediated inflammatory disorders using immunohistochemical techniques. IFN-kappa was not detectable in healthy skin but was strongly expressed in allergic contact dermatitis and lichen planus-affected skin. IFN-kappa was localized mainly in basal and suprabasal keratinocytes and in some leukocytes infiltrating the dermis. In contrast, IFN-kappa expression in psoriatic or atopic dermatitis (AD) pidermis was weak and detectable in only 2 of 5 patients examined. Consistently, cultured keratinocytes and monocytes obtained from psoriatic and AD patients expressed null or low levels of IFN-kappa in response to IFN-gamma, which strongly upregulates IFN-kappa in normal keratinocytes. IFN-kappa accumulated in keratinocyte cytoplasm and plasma membrane, and only limited amounts were released extracellularly. Soluble IFN-kappa did not influence keratinocyte proliferation or chemokine and membrane molecule expression, and only its membrane-associated form activated IFN-stimulated response element (ISRE) signaling. Given the difference in IFN-kappa expression levels in the skin disorders examined, IFN-kappa presence or deficiency might have different pathogenetic consequences depending also on other disease-specific intrinsic alterations.
Statistics and Data Practices Overview (2007)

Author(s): Balzano, Laura; Hajj Chehade, Nabil; Chen, Gong; Mayernik, Matt; Nair, Sheela; Pepe, Alberto; Ramanathan, Nithya; Reddy, Sasank; Sharma, Abhishek; Yau, Nathan; Wallis, Jillian; Borgman, Christine; Estrin, Deborah; Golubchik, Leana; Govindan, Ramesh; Hansen, Mark; Kohler, Eddie; Pottie, Greg; Srivastava, Mani
Nearest-neighbour transition-state analysis for nucleic acid kinetics (2021)

We used stopped-flow to monitor hypochromicity for 43 oligonucleotide duplexes to study nucleic acid kinetics and extract transition-state parameters for association and dissociation. Reactions were performed in 1.0 M NaCl (for literature comparisons) and 2.2 mM MgCl2 (PCR conditions). Dissociation kinetics depended on sequence, increased exponentially with temperature, and transition-state parameters inversely correlated to thermodynamic parameters (r = -0.99). Association had no consistent enthalpic component, varied little with temperature or sequence, and poorly correlated to thermodynamic parameters (r = 0.28). Average association rates decreased 78% in MgCl2 compared to NaCl while dissociation was relatively insensitive to ionic conditions. A nearest-neighbour kinetic model for dissociation predicted rate constants within 3-fold of literature values (n = 11). However, a nearest-neighbour model for association appeared overparameterized and inadequate for predictions. Kinetic predictions were used to simulate published high-speed (<1 min) melting analysis and extreme (<2 min) PCR experiments. Melting simulations predicted apparent melting temperatures increase on average 2.4°C when temperature ramp rates increased from 0.1 to 32°C/s, compared to 2.8°C reported in the literature. PCR simulations revealed that denaturation kinetics are dependent on the thermocycling profile. Simulations overestimated annealing efficiencies at shorter annealing times and suggested that polymerase interactions contribute to primer-template complex stability at extension temperatures.
Information Gathering in Networks via Active Exploration (2015)

How should we gather information in a network, where each node's visibility is limited to its local neighborhood? This problem arises in numerous real-world applications, such as surveying and task routing in social networks, team formation in collaborative networks and experimental design with dependency constraints. Often the informativeness of a set of nodes can be quantified via a submodular utility function. Existing approaches for submodular optimization, however, require that the set of all nodes that can be selected is known ahead of time, which is often unrealistic. In contrast, we propose a novel model where we start our exploration from an initial node, and new nodes become visible and available for selection only once one of their neighbors has been chosen. We then present a general algorithm NetExp for this problem, and provide theoretical bounds on its performance dependent on structural properties of the underlying network. We evaluate our methodology on various simulated problem instances as well as on data collected from social question answering system deployed within a large enterprise.
Diamine reagents in thermospray mass spectrometry (1992)

Determination of the molecular weight for an unknown by thermospray liquid chromatographic/mass spectrometric analysis using ammonium acetate mobile phase can be both confusing and misleading. This is due to the uncertainty of whether an ion is either a protonated species or an ammonium adduct or both. Deuterium oxide and ammonium acetate buffers have been used to elucidate molecular species of unknown compounds with some success. We have investigated an alternative method which utilizes diamine reagents. This method simplifies the identification of unknown molecular species in an inexpensive manner. Diamines form adduct ions readily with many substances. A comparison of spectra obtained for an unknown using ammonium acetate or diaminoethane in separate analyses is useful for identifying molecular species. Using ammonium acetate as a mobile phase, a molecule is often detected as a protonated molecular species. However, using diaminoethane mobile phase, this same molecule is most often detected as a diaminoethane adduct. Comparison of each spectrum reveals a mass difference of 60 for a molecule detected as a protonated species and a diaminoethane adduct. In addition, a mass difference of 43 will be obtained in a similar spectral comparison if a molecule forms ammonium adducts using ammonium acetate mobile phase and diaminoethane adducts using diaminoethane. An analysis of an unknown substance with several molecular species is presented as an example of the utility of diamine reagents in thermospray mass spectrometry. By observing mass spectral differences, molecular species can be identified as either a protonated ion or an adduct ion.
Pharmacokinetics, safety and tolerability of the orally administered receptor antagonist of cysteinyl-leukotrienes BAY x 7195 in single-dose escalation studies. (1995)

BAY x 7195 is a novel receptor antagonist of cysteinyl-leukotrienes currently under development for the treatment of asthma. It is effective in antagonizing the leukotriene-D4 induced bronchoconstriction in healthy volunteers following oral administration. The pharmacokinetics, safety and tolerability of the drug were investigated in six partially placebo-controlled studies in healthy volunteers with single oral administration of a 50, 100, 250, 500 and 1000 mg dose as a tablet. The drug was well tolerated. The only remarkable adverse event was diarrhea in one volunteer receiving the highest dose of 1000 mg. There were no additional clinically relevant changes in any safety parameter including laboratory values. Concentrations of BAY x 7195 were determined in plasma and urine by high performance liquid chromatography with fluorescence detection and plasma-concentrations were further evaluated by compartmental and non-compartmental methods. The concentration vs time profiles of the drug were biphasic with a dominant t1/2 of 0.5-2 h and a terminal t1/2 of 5-10 h. Pharmacokinetics were linear in the investigated range of doses. In spite of substantial inter-subject variability intra-individual variability in AUC and Cmax was reasonable. In general, the concentration vs time profiles could be described with a 2-compartment body model. However, in some cases the occurrence of second and third concentration maxima necessitated the use of a multiple segment absorption model to accomplish a good fit to the data. Enterohepatic recirculation following glucuronidation of the drug is the likely reason for the multiple peaks. Urinary excretion of BAY x 7195 and its glucuronide metabolite was negligible the amount excreted into urine from 0 to 48 h being < 0.1% of the dose. The low renal clearance of BAY x 7195 (< or = 0.07 ml/min) is suggestive of significant reabsorption in the renal tubuli taking into account that the expected renal clearance for a drug with 99.5% protein binding is about 0.6 ml/min.
Using quantum dot photoluminescence for load detection (2016)

We propose a novel concept for an integrable and flexible sensor capable to visualize mechanical impacts on lightweight structures by quenching the photoluminescence (PL) of CdSe quantum dots. Considering the requirements such as visibility, storage time and high optical contrast of PL quenching with low power consumption, we have investigated a symmetrical and an asymmetrical layer stack consisting of semiconductor organic N,N,N′,N′-Tetrakis(3-methylphenyl)-3,3′-dimethylbenzidine (HMTPD) and CdSe quantum dots with elongated CdS shell. Time-resolved series of PL spectra from layer stacks with applied voltages of different polarity and simultaneous observation of power consumption have shown that a variety of mechanisms such as photo-induced charge separation and charge injection, cause PL quenching. However, mechanisms such as screening of external field as well as Auger-assisted charge ejection is working contrary to that. Investigations regarding the influence of illumination revealed that the positive biased asymmetrical layer stack is the preferred sensor configuration, due to a charge carrier injection at voltages of 10 V without the need of coincident illumination.
Physical Parameter Extraction and Modeling of Metallized Deeply-Etched Vertical Mirrors (2021)

In this work, vertical micromirrors that are fabricated using deep etching of silicon followed by metal sputtering are studied. Physical parameter extraction methodology, image processing, machine learning and discrete element analysis are used to extend the easy-to-take scanning electron microscope images into 3-D topographical information, that are usually obtained using atomic force microscope and transmission electron microscope. The experimental results show that vertical micromirrors surface quality has a granular nature showing degraded performance and a different optical response with respect to the bulk metal. A physical model is developed and validated by comparing the measured reflectivity of the fabricated micromirrors with a multi-layer reflectivity optical model based on the effective medium theory fed by the extracted physical parameters. In agreement with the experimental results, the model predicts a reflectivity of about 60 % for a sputtered aluminum thickness of 50 nm, compared to 97.5% reflectivity predicted by the bulk metal model. [2021-0154]
Modeling of electronic charge transport in smectic liquid crystals (2003)

We have investigated the hole transport in smectic mesophases by Monte Carlo simulation based on a 2D hopping transport in Gaussian-distributed density of states and time-of-flight experiments. We found that their unique carrier transport properties such as non-Poole-Frenkel type of behavior i.e., field-and-temperature independent mobility, is well explained by the 2D disorder model with a small Gaussian width of 50-60 meV. Furthermore, we found the Pool-Frenkel type of behavior in a biphenyl derivatives and at a low temperaure range below ambient temperature in a therthiphene derviative and determined the Gaussian width to be 100-120meV and 50 meV, respectively. We came to a conclusion that the charge carrier transport in smectic mesophases can be explained by a 2D disorder model with a small Gaussian width of the density of states &sigma;, where a value of &sigma;/kT plays important role to determien its behavior at a given temperature.
Template based parallel checkpointing in a massively parallel computer system (2023)

A method and apparatus for a template based parallel checkpoint save for a massively parallel super computer system using a parallel variation of the rsync protocol, and network broadcast. In preferred embodiments, the checkpoint data for each node is compared to a template checkpoint file that resides in the storage and that was previously produced. Embodiments herein greatly decrease the amount of data that must be transmitted and stored for faster checkpointing and increased efficiency of the computer system. Embodiments are directed to a parallel computer system with nodes arranged in a cluster with a high speed interconnect that can perform broadcast communication. The checkpoint contains a set of actual small data blocks with their corresponding checksums from all nodes in the system. The data blocks may be compressed using conventional non-lossy data compression algorithms to further reduce the overall checkpoint size.
Evaluating the Robustness of Metal–Organic Frameworks for Synthetic Chemistry (2021)

Metal-organic frameworks (MOFs) are emerging as sustainable reagents and catalysts with promising applications in synthetic chemistry. Although the hydrothermal stabilities of MOFs have been well studied, their robustness toward various reagents, including acids, bases, nucleophiles, electrophiles, oxidants, and reductants, remains poorly characterized. As such, heterogeneous platforms for promising catalysts are generally identified on an <i>ad hoc</i> basis and have largely been limited to carboxylate frameworks to date. To address these limitations, here we systematically characterize the robustness of 17 representative carboxylate, salicylate, and azolate MOFs toward 30 conditions representing the scope of synthetic organic chemistry. Specifically, analysis of the full width at half-maximum of powder X-ray diffraction patterns, as well as infrared spectroscopy, 77 K N<sub>2</sub> adsorption measurements, and scanning electron microscopy in select cases are employed to appraise framework degradation and dissolution under a range of representative conditions. Our studies demonstrate that azolate MOFs, such as Fe<sub>2</sub>(bdp)<sub>3</sub> (bdp<sup>2-</sup> = 4,4'-(1,4-phenylene)bis(pyrazolate)), generally possess excellent chemical stabilities under myriad conditions. In addition, we find that carboxylate and salicylate frameworks possess complementary stabilities, with carboxylate MOFs possessing superior robustness toward acids, electrophiles, and oxidants, and salicylate MOFs demonstrating improved robustness toward bases, nucleophiles, and reductants. The guidelines provided herein should facilitate the rational design of robust frameworks for applications in synthetic chemistry and guide the development of new strategies for the postsynthetic modification of MOFs as well.
Oral fluid matrix metalloproteinase (MMP)-8 as a diagnostic tool in chronic periodontitis (2016)

Abstract: Periodontal diseases that affect the marginal and apical periodontium result from the interaction between bacterial biofilm and the host response. Oral fluid biomarkers might aid clinical diagnosis. Matrix metalloproteinases (MMPs) are a family of 24 proteases that act in physiological and pathological conditions. They can degrade almost all extracellular matrix constituents and regulate inflammatory processes. They are mainly inhibited by tissue inhibitors of metalloproteinases. The aim of this study was to perform a current literature review with a special reference on the diagnostic and clinical utility of oral fluid MMPs, especially MMP-8, and their inhibitors in periodontal and oral diseases. MMP-8 is the main collagenolytic MMP detected in oral fluids, such as saliva, oral mouthrinse, gingival crevicular fluid, and peri-implant fluid. MMP-8, and potentially MMP-9, in oral fluids represent strong biomarker candidates associated especially with periodontal disease diagnosis, severity, progression, and follow-up. Additionally, they show diagnostic potential for systemic conditions, such as pregnancy, myocardial infarction, and smoking. A commercially available mouthrinse, active MMP-8 chair-side/point-of-care lateral flow immunoassay, shows enough sensitivity and specificity to detect clinical signs of periodontitis. The current literature supports that high MMP-8 levels reflect the loss of periodontal supporting tissues rather than inflammation, representing a potentially useful side-diagnostic point-of-care oral disease biomarker, especially in periodontal diseases. Keywords: gingival crevicular fluid, saliva, biomarkers
Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium (2018)

Quorum sensing (QS) allows many common bacterial pathogens to coordinate group behaviors such as virulence factor production, host colonization, and biofilm formation at high population densities. This cell-cell signaling process is regulated by <i>N</i> <b>-</b>acyl L-homoserine lactone (AHL) signals, or autoinducers, and LuxR-type receptors in Gram<b>-</b>negative bacteria. SdiA is an orphan LuxR-type receptor found in <i>Escherichia, Salmonella, Klebsiella, and Enterobacter</i> genera that responds to AHL signals produced by other species and regulates genes involved in several aspects of host colonization. The inhibition of QS using non-native small molecules that target LuxR-type receptors offers a non-biocidal approach for studying, and potentially controlling, virulence in these bacteria. To date, few studies have characterized the features of AHLs and other small molecules capable of SdiA agonism, and no SdiA antagonists have been reported. Herein, we report the screening of a set of AHL analogs to both uncover agonists and antagonists of SdiA and to start to delineate structure-activity relationships (SARs) for SdiA:AHL interactions. Using a cell-based reporter of SdiA in <i>Salmonella enterica</i> serovar Typhimurium, several non-natural SdiA agonists and the first set of SdiA antagonists were identified and characterized. These compounds represent new chemical probes for exploring the mechanisms by which SdiA functions during infection and its role in interspecies interactions. Moreover, as SdiA is highly stable when produced in vitro, these compounds could advance fundamental studies of LuxR-type receptor:ligand interactions that engender both agonism and antagonism.
Surface Modification of Porous Titanium Composites Obtained by Different Processing Methods (2009)

Numerous application areas for titanium alloys reqiure not only specific bulk material properties but are rather dominated by the surface properties of the device. Therefore different processing methods for a multi-scale adjustment of surface microstructure and composition of porous titanium composites have been investigated. Starting from the generation of macro porous coatings, serveral hundreds of microns thick, by a PM method, through deposition of micrometer scale ceramic layers and void filling by an electro chemical method down to sub micron scale surface changes by application of laser or plasma processing a differentiated functionality of the surface can be achieved. In particular, laser processing can be used for smoothening or selective oxidation of the surface, and nanoscaled substructures can be generated by low preassure laser processing in order to change the surface energy of the material. An overview of the different processing methods is presented, with emphasis on the influence certain process conditions have on biocompatibility or bioactivity of Ti based implants.
Chemical consequences of orbital interactions. 14. Ab initio molecular orbital study of the geometries, properties, and protonation of simple organofluorides (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical consequences of orbital interactions. 14. Ab initio molecular orbital study of the geometries, properties, and protonation of simple organofluoridesWilliam L. Jorgensen and Michael E. CournoyerCite this: J. Am. Chem. Soc. 1978, 100, 17, 5278–5285Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/ja00485a006https://doi.org/10.1021/ja00485a006research-articleACS PublicationsRequest reuse permissionsArticle Views81Altmetric-Citations20LEARN 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
A parallel permeability assay of peptides across artificial membranes and cell monolayers using a fluorogenic reaction (2019)

Here, we report a facile permeability assay to quantitatively evaluate the membrane permeability of multiple peptides in parallel. With a fluorogenic click reaction between azidocoumarin and a terminal alkyne tag introduced on a peptide, the peptide that crossed an artificial membrane or a cell monolayer was quantitatively detected. The method allows a rapid measurement of the permeability of multiple compounds on a plate reader even in the presence of a complex mixture of biological molecules.