gebhart/patrepeval huggingface dataset:
Single-molecule diffusion in a periodic potential at a solid–liquid interface (2013)

We used single-molecule tracking experiments to observe the motion of small hydrophobic fluorescent molecules at the interface between water and a solid surface that exhibited periodic chemical patterns. The dynamics were characterized by non-ergodic, continuous time random walk statistics. The step-size distributions displayed enhanced probability of steps to periodic distances, consistent with theoretical predictions for diffusion in an atomic/molecular scale periodic potential. Surprisingly, this general behavior was observed here for surfaces exhibiting characteristic length scales three orders of magnitude larger than atomic/molecular dimensions, and may provide a new way to understand and control solid-liquid interfacial diffusion for molecular targeting applications.
EXCHANGE POLARIZATION AND THE MAGNETIC BEHAVIOR OF TRANSITION METAL AND RARE EARTH IONS (1962)

Investigations were carried out for the contribution of paired electrons to the magnetic properties of solids utilizing the spin or exchange polarizatnon mechanism in the Hartree-Fock formalism. Three different physical properties were studied, each distinguished by the particular region in which the spin density predominates: the magnetic interaction of a rare earth ion with its neighbors and with its own conduction electrons. The contribution of the core polarization to the effective magnetic fields observed by Mossbauer, NMR, EPR and specific heat measurements and to the observed Knight shifts for systems with unpaired s and d (or f) electrons. The contribution of the paired electrons to the magnetic scattering of neutrons by transition metal and rare earth ions. (auth)
A MODEL FOR THE DYNAMICAL BEHAVIOR OF PATTERNED THIN FILM STRUCTURES ON SILICON (2010)

Metrology of metal‐dielectric thin film structures fabricated on silicon wafers has emerged as a major application area of laser ultrasonics. The measurements are oftentimes performed on structures comprised of periodic line arrays, which as regards their dynamical behavior, form a distinct class of phononic crystals. Recently reported measurements of laser‐generated surface acoustic modes in Cu‐SiO2 line arrays on silicon have uncovered a number of interesting phenomena. The goal of this paper is to provide a simple theoretical model capturing the salient features of the experiment and leading to a better understanding of the physical nature of the observed phenomena. The structure is simulated by a uniform layer on a substrate with periodic mass loading applied to its upper surface, and is treated by the plane wave expansion method. We establish that the large bandgap observed inside the Brillouin zone originates from the hybridization of the Rayleigh and Sezawa modes of the film‐substrate structure. The displacement pattern in the Rayleigh and Sezawa waves explains their strong interaction, leading to a larger bandgap than the ones formed at the zone boundary. Unexpectedly low radiation loss of the hybridized Rayleigh‐Sezawa mode in the “supersonic” domain, is also reproduced by the model.
Interaction of TNF and TNFR2 stabilizes the phenotype and function of CD4+FoxP3+ regulatory T cells in the inflammatory environment (179.16) (2012)

Abstract Our previous results showed that TNF-TNFR2 signaling promotes activation and expansion of Tregs. Thus we hypothesize that TNF-TNFR2 signaling may play a critical role in maintaining phenotypic and functional stability of Tregs during an inflammatory response. We were able to confirm that, in colitis model induced by transfer of naïve CD4 cells into Rag KO mice, the disease could be inhibited by co-transfer of WT Tregs, but not by co-transfer of TNFR2-deficient Tregs. Furthermore, in the colon lamina propria of the colitis model, the majority of WT Tregs maintained FoxP3 expression. In contrast, increased number of TNFR2-deficient Tregs lost FoxP3 expression. In vitro, FoxP3 expression by highly purified Tregs was reduced to almost undetectable levels after potent TCR-stimulation, which was partially abrogated by TNF. This effect of TNF was blocked by anti-TNFR2 Ab, but not by anti-TNFR1 Ab. In addition, TNF was not able to increase FoxP3 expression by TNFR2-deficient Tregs undergoing TCR-stimulation. A full mouse genome array study revealed that, as compared with TNFR2- Tregs, TNFR2+ Tregs from normal mice expressed 4-fold lower levels of a gene encoding SATB1, in line with a recent study show that the repression of this genome organizer play a crucial role in maintenance of Treg phenotype and function. Thus, our data clearly show that the TNF-TNFR2 signaling is critical for the phenotypic and functional stability of Treg in the inflammatory environment.
Immunomodulation of Melanoma by Chemo-Thermo-Immunotherapy Using Conjugates of Melanogenesis Substrate NPrCAP and Magnetite Nanoparticles: A Review (2022)

A major advance in drug discovery and targeted therapy directed at cancer cells may be achieved by the exploitation and immunomodulation of their unique biological properties. This review summarizes our efforts to develop novel chemo-thermo-immunotherapy (CTI therapy) by conjugating a melanogenesis substrate, <i>N</i>-propionyl cysteaminylphenol (NPrCAP: amine analog of tyrosine), with magnetite nanoparticles (MNP). In our approach, NPrCAP provides a unique drug delivery system (DDS) because of its selective incorporation into melanoma cells. It also functions as a melanoma-targeted therapeutic drug because of its production of highly reactive free radicals (melanoma-targeted chemotherapy). Moreover, the utilization of MNP is a platform to develop thermo-immunotherapy because of heat shock protein (HSP) expression upon heat generation in MNP by exposure to an alternating magnetic field (AMF). This comprehensive review covers experimental in vivo and in vitro mouse melanoma models and preliminary clinical trials with a limited number of advanced melanoma patients. We also discuss the future directions of CTI therapy.
Metabolomics as a tool for target identification in strain improvement: the influence of phenotype definition (2010)

For the optimization of microbial production processes, the choice of the quantitative phenotype to be optimized is crucial. For instance, for the optimization of product formation, either product concentration or productivity can be pursued, potentially resulting in different targets for strain improvement. The choice of a quantitative phenotype is highly relevant for classical improvement approaches, and even more so for modern systems biology approaches. In this study, the information content of a metabolomics dataset was determined with respect to different quantitative phenotypes related to the formation of specific products. To this end, the production of two industrially relevant products by Aspergillus niger was evaluated: (i) the enzyme glucoamylase, and (ii) the more complex product group of secreted proteases, consisting of multiple enzymes. For both products, six quantitative phenotypes associated with activity and productivity were defined, also taking into account different time points of sampling during the fermentation. Both linear and nonlinear relationships between the metabolome data and the different quantitative phenotypes were considered. The multivariate data analysis tool partial least-squares (PLS) was used to evaluate the information content of the datasets for all the different quantitative phenotypes defined. Depending on the product studied, different quantitative phenotypes were found to have the highest information content in specific metabolomics datasets. A detailed analysis of the metabolites that showed strong correlation with these quantitative phenotypes revealed that various sugar derivatives correlated with glucoamylase activity. For the reduction of protease activity, mainly as-yet-unidentified compounds correlated.
REACTIONS OF NITROPARAFFINS.<sup>*</sup> III. DERIVATIVES OF 3-METHYL-3-NITRO-1,2-BUTANEDICARBOXYLIC ACID<sup>1</sup> (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTREACTIONS OF NITROPARAFFINS.* III. DERIVATIVES OF 3-METHYL-3-NITRO-1,2-BUTANEDICARBOXYLIC ACID1PHILIP S. MAGEE and MILTON C. KLOETZELCite this: J. Org. Chem. 1954, 19, 2, 168–175Publication Date (Print):February 1, 1954Publication History Published online1 May 2002Published inissue 1 February 1954https://doi.org/10.1021/jo01367a004Request reuse permissionsArticle Views93Altmetric-Citations-LEARN 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 InReddit PDF (488 KB) Get e-Alertsclose Get e-Alerts
Protein Phosphatase 2A Catalytic Subunit α Plays a MyD88-Dependent, Central Role in the Gene-Specific Regulation of Endotoxin Tolerance (2013)

MyD88, the intracellular adaptor of most TLRs, mediates either proinflammatory or immunosuppressive signaling that contributes to chronic inflammation-associated diseases. Although gene-specific chromatin modifications regulate inflammation, the role of MyD88 signaling in establishing such epigenetic landscapes under different inflammatory states remains elusive. Using quantitative proteomics to enumerate the inflammation-phenotypic constituents of the MyD88 interactome, we found that in endotoxin-tolerant macrophages, protein phosphatase 2A catalytic subunit α (PP2Ac) enhances its association with MyD88 and is constitutively activated. Knockdown of PP2Ac prevents suppression of proinflammatory genes and resistance to apoptosis. Through site-specific dephosphorylation, constitutively active PP2Ac disrupts the signal-promoting TLR4-MyD88 complex and broadly suppresses the activities of multiple proinflammatory/proapoptotic pathways as well, shifting proinflammatory MyD88 signaling to a prosurvival mode. Constitutively active PP2Ac translocated with MyD88 into the nuclei of tolerant macrophages establishes the immunosuppressive pattern of chromatin modifications and represses chromatin remodeling to selectively silence proinflammatory genes, coordinating the MyD88-dependent inflammation control at both signaling and epigenetic levels under endotoxin-tolerant conditions.
Bis-allylic Deuterated DHA Alleviates Oxidative Stress in Retinal Epithelial Cells (2019)

Oxidative stress plays a crucial role in developing and accelerating retinal diseases including age-related macular degeneration (AMD). Docosahexaenoic acid (DHA, C22:6, n-3), the main lipid constituent of retinal epithelial cell membranes, is highly prone to radical and enzymatic oxidation leading to deleterious or beneficial metabolites for retinal tissue. To inhibit radical oxidation while preserving enzymatic metabolism, deuterium was incorporated at specific positions of DHA, resulting in D<sub>2</sub>-DHA when incorporated at position 6 and D<sub>4</sub>-DHA when incorporated at the 6,9 <i>bis</i>-allylic positions. Both derivatives were able to decrease DHAs' toxicity and free radical processes involved in lipid peroxidation, in ARPE-19 cells (Adult Retinal Pigment Epithelial cell line), under pro-oxidant conditions. Our positive results encouraged us to prepare lipophenolic-deuterated-DHA conjugates as possible drug candidates for AMD treatment. These novel derivatives proved efficient in limiting lipid peroxidation in ARPE-19 cells. Finally, we evaluated the underlying mechanisms and the enzymatic conversion of both deuterated DHA. While radical abstraction was affected at the deuterium incorporation sites, enzymatic conversion by the lipoxygenase 15s-LOX was not impacted. Our results suggest that site-specifically deuterated DHA could be used in the development of DHA conjugates for treatment of oxidative stress driven diseases, or as biological tools to study the roles, activities and mechanisms of DHA metabolites.
A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis (2014)

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.
Model independent peak fitting and uncertainty assignment for high-precision time-of-flight mass spectrometry (2020)

A procedure is introduced to extract the time-of-flight probability density distribution for ions of one type using an accumulated ion peak as a template for use in the fitting of time-of-flight peaks of co-accumulated ions. We demonstrate the use of logarithmic splines and discuss the statistical criteria for the selection of the spline smoothing parameter to obtain a smooth function for approximating such an ion peak. Furthermore, a "Bootstrap" method is proposed to determine the uncertainty of the fitted time-of-flight values, which is calculated using the extracted peak shape via a repeated statistical experiment. The developed procedure is validated against time-of-flight data obtained in a previously reported experiment. It is shown that atomic masses derived from our newly proposed methodology are in good agreement with those from the 2016 Atomic Mass Evaluation and the values determined using an analytically defined function (exponential-Gaussian hybrid), approximately matching the observed peak shape. In contrast to the previously used approach, our newly proposed methodology is a much more flexible, robust, and universal method for peak shape approximation, which can be applied to any peak shape.
P4‐056: The Role of Aquaporin‐4 (AQP4) Single Nucleotide Polymorphisms in Cognitive Decline (2016)

The glymphatic system is a brain-wide perivascular network that facilitates clearance of proteins, including amyloid beta, from the brain interstitium. The astrocytic water channel aquaporin-4 (AQP4) is required for glymphatic system function, yet whether changes in AQP4 function influence development of age-related cognitive decline or Alzheimer's disease (AD) is not known. We identified five noncoding single nucleotide polymorphisms (SNPs) in the human AQP4 gene that were associated with altered cognitive decline after AD diagnosis. Using genetic and longitudinal neurocognitive data from 794 elderly participants from the NIA - Oregon Alzheimer's Disease Center cohorts (512 cognitively intact, 124 mild cognitive impairment, and 158 AD at first visit) the association between five human AQP4 SNPs and rate of cognitive decline (using the Mini Mental State Examination (MMSE)) and dementia progression (using the Clinical Dementia Rating (CDR)) scale was evaluated. Data analysis was carried out using linear mixed-modeling to evaluate the associations of minor SNP alleles with altered longitudinal rates of cognitive decline. Of the five SNPs, three were associated with slower cognitive decline or dementia progression after AD diagnosis, and two were associated with faster cognitive decline or dementia progression after AD diagnosis. Heterozygous or homozygous possession of the minor allele at position rs9951307 (genotype TC or TT) was associated with slower increase in CDR sum of the boxes score (t=-4.31, p<0.001), while rs335929 (genotype CA or CC) was associated with slower decline in MMSE score (t=3.46, p<0.001), and rs387509 (genotype TC or CC) was associated with both slower decline in MMSE score (t=2.66, p=0.008) and slower increase in CDR score (t=-4.80, p<0.001). rs3763043 (genotype GA or GG) was associated with faster decline in MMSE (t=-3.29, p<0.001) and faster increase in CDR score (t=4.00, p<0.001). rs3763040 (genotype AG or AA) was also associated with faster decline in MMSE (t=-5.28, p<0.001) and faster increase in CDR score (t=3.70, p<0.001). These results suggest that variations in the AQP4 gene, which plays a vital role in the glymphatic pathway, may modulate the progression of cognitive decline and dementia in AD. This may provide a novel therapeutic target for the prevention or treatment of AD.
Cooperative research in coal liquefaction infratechnology and generic technology development: Quarterly report, July 1-October 1, 1987. [Kentucky coal deposits] (1987)

Research programs in coal liquefaction continued in the following areas: (1) catalytic coal liquefaction using Mo catalysts; (2) coprocessing experiments, using Maya topper long resid as a solvent for Illinois No. 6 coal using a variety of both unimodal and bimodal catalysts. The effect of agitation rate on conversion in a horizontally aligned tubing bond experiment was investigated; (3) the effect of tetrabutyltin and FeSO/sub 4/ . 7H/sub 2/O catalysts on coprocessing. A mathematical model was used to determine critical coprocessing rate constants; (4) a study of the bond cleavage reactions of benzl phenyl ethers was completed. Similar bond cleavages may be induced in coal and lead to liquid products under low severity conditions. EPR studies of Cr(V) model compounds established an unusual lineshape. Solvent extraction using N-methyl-2-pyrrolidone on a high resinite coal from Utah. New NMP experimets are in progress on oil shales and tar sands. New experimental apparatus has been devised for investigating the kinetics of the extraction process; (5) collection and analysis of the eastern Kentucky coals was completed. Chemical and petrographic analyses were placed in the KECL coal data base; (6) liquefaction screening of the eastern Kentucky coals was completed. Liquefaction data is being correlated withmore » the coal properties; (7) a new /sup 13/C NMR technique, variable angle sample spinning (VASS), show great promise for determining the average cluster size in coal. Sink/float methods are being developed to obtain gram quantities of maceral enriched (> 90%) specimens on which liquefaction studies can be made. Pyrolysis and mass spectrometry studies are being made on raw Elkhorn coal; (8) biological desulfurization studies emphasized experiments with Sulfolobus brierleyi. The growth of Sulfolobus solfataricus on casamino acids and yeast extract was investigated; (9) the CFFLS computer network/liquefaction database became operational. 4 refs., 13 figs., 18 tabs.« less
MICROBIOLOGICAL HYDROXYLATION OF STEROIDS (1958)

Oxidizability of progesterone was examined with 284 strains of Rhizopus sp. preserved in this Institute. Among these, 21 strains were found to have such ability. Mass culture of five of these strains was carried out and the oxidation product was identified as 11α-hydroxyprogesterone. The yield obtained was approximately 50%, using Rh. Chinensis SAITO 10-10.
Condensation of Atmospheric Moisture from Tropical Maritime Air Masses as a Freshwater Resource (1967)

A method is proposed whereby potable water may be obtained by condensing moisture from the atmosphere in suitable seashore or island areas. Deep, cold, offshore seawater is used as a source of cold and is pumped to condensers set up on shore to intercept the flow of highly humid, tropical, maritime air masses. This air, when cooled, condenses moisture, which is conducted away and stored for use as a water supply. Windmill-driven generators would supply low-cost power for the operation. Side benefits are derived by using the nutritious deep water to support aquiculture in nearby lagoons or to enhance the productivity of the outfall area. Additional benefits are derived from the condenser as an air-conditioning device for nearby residents. The islands of the Caribbean are used as an example of a location in the trade-winds belt where nearly optimum conditions for the operation of this system can be found.
Human Activity Recognition Using a Single Wrist IMU Sensor via Deep Learning Convolutional and Recurrent Neural Nets (2017)

In this paper, the authors aimed to propose novel deep learning-based HAR systems with a single wrist IMU sensor. This research used time-series activity data from only one IMU sensor at a wrist to build two deep learning algorithm-based HAR systems: one is based on Convolutional Neural Nets (CNN) and the other Recurrent Neural Nets (RNN). Our two HAR systems are evaluated by 5-fold cross-validation tests to compare the performance of both systems. Five primary daily activities, including standing, walking, running, walking downstairs, and walking upstairs, were recognized. Our results show that the CNN-based HAR system achieved an average accuracy of 95.43% and the RNN-based HAR system accuracy of 96.95%. This result presents the feasibility of HAR for some macro human activities with only a single wearable IMU device.
Physical and tribological properties of a-Si<sub>1-x</sub>C<sub>x</sub> : H coatings prepared by r.f. plama-assisted chemical vapour deposition (1993)

a-Si1-xCx : H films deposited by r.f. plasma-assisted chemical vapour deposition were studied as a function of their composition. The friction and wear properties were investigated with the help of a conventional ball-on-disc apparatus. These results are correlated with chemical (Si/C atomic ratio) and structural (Raman and infrared spectroscopy) properties. The friction coefficient in a humid ambient atmosphere changes markedly with the carbon fraction and reaches a value as low as 0.05 for coatings with 70 to 90 at.% C. The carbon-rich films consist of diamond-like carbon with silicon.
Fluoropyrimidine biochemical modulation in colon cancer: pharmacology relevant in both the laboratory and the clinic. (1991)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1991.9.3.365 Journal of Clinical Oncology - published online before print September 22, 2016 PMID: 1999704 Fluoropyrimidine biochemical modulation in colon cancer: pharmacology relevant in both the laboratory and the clinic. J H DoroshowxJ H DoroshowSearch for articles by this author , E M NewmanxE M NewmanSearch for articles by this author https://doi.org/10.1200/JCO.1991.9.3.365 First Page PDF © 1991 by American Society of Clinical Oncology