gebhart/patrepeval huggingface dataset:
The physiology of germinal centers. (1996)

GCs contain Ag-induced rapidly proliferating B cell blasts called centroblasts and centrocytes and are located in primary follicles of peripheral lymphoid tissue. Their peak development is at 7 to 10 d after Ag. The generation of memory B cells occurs in GCs, accompanied by frequent Ig isotype switching, Ig gene V region somatic hypermutation, and/or (in rabbits) gene conversion. The nature and function of the cell types that make up the microenvironment of the GC B cells, the CD4+ T cells and FDCs, are discussed in detail. The high rate of apoptosis that occurs in GCs is thought to be the result of processes of positive and negative selection ongoing in different compartments of GCs. The rescue of cells through high-affinity interaction with Ag localized on FDCs and subsequent presentation of Ag by GC B cells to T cells may represent the positive selection with apoptosis as the default pathway. Negative selection may occur, aimed at the prevention of autoimmunity caused by cells with mutated sIg binding to autoAgs. Some aspects of GC-derived lymphomas in humans and mice are also reviewed.
Transient thermoreflectance from thin metal films (1986)

This report describes the first demonstration of thermal diffusivity measurements using picosecond transient thermoreflectance (TTR). Although previously reported methods of measuring thermal transport properties of thin films require precise knowledge of the thermal properties of the substrate, this technique allows measurements on films as thin as 100 nm without any evidence of substrate interaction. The TTR measurement is modeled with a one-dimensional heat flow equation using a two-parameter fitting routine to determine the thermal diffusivity. The validity of our approach is confirmed by the TTR measured thermal diffusivity of single crystal nickel. We have also measured the thermal diffusivity of sputtered and evaporated single element metal films. Preliminary results from TTR measurements on compositionally modulated structures are also presented.
Programmable RNA Binding Proteins for Imaging and Therapeutics (2017)

ADVERTISEMENT RETURN TO ISSUEViewpointNEXTProgrammable RNA Binding Proteins for Imaging and TherapeuticsSimone Rauch† and Bryan C. Dickinson*‡View Author Information† Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States‡ Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States*E-mail: [email protected]. Twitter: @chembioBryan.Cite this: Biochemistry 2018, 57, 4, 363–364Publication Date (Web):November 17, 2017Publication History Received31 October 2017Published online17 November 2017Published inissue 30 January 2018https://pubs.acs.org/doi/10.1021/acs.biochem.7b01101https://doi.org/10.1021/acs.biochem.7b01101editorialACS PublicationsCopyright © 2017 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views3270Altmetric-Citations7LEARN 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 PDF (189 KB) Get e-AlertscloseSUBJECTS:Fluorescence,Genetics,Nucleic acids,Peptides and proteins,Targeting Get e-Alerts
Identification of Key Odorants Related to the Typical Aroma of Oxidation-Spoiled White Wines (2003)

The oxidative degradation of white wines rapidly leads to a loss of their sensorial qualities. The identification of the most important descriptors related with oxidation-spoiled wine was performed by a trained sensory panel. The terms selected were "honey-like", "farm-feed", "hay", and "woody-like". By gas chromatography-olfactometry analysis three aromatic zones related to these descriptors in the oxidation-spoiled white wines could be determined. Comparison of the aroma extract dilution analysis aromagrams of oxidation-spoiled white wines and a nonspoiled wine showed the highest values of dilution factors were attributed to 3-(methylthio)propionaldehyde, phenylacetaldehyde, 1,1,6-trimethyl-1,2-dihydronaphthalene (TDN), and 4,5-dimethyl-3-hydroxy-2(5H)-furanone (sotolon). A "forced aging" experiment was implemented to simulate the typical oxidation-spoiled aroma. Samples rated with the highest score in the ranking test were also those that presented the highest concentration of these four molecules. To test the sensory impact of these substances, a normal wine (unspoiled) was spiked with these molecules (with the exception of TDN) singly and in combination, and the similarity value (SV) between samples and the oxidation-spoiled white wines was then determined. The highest value from the similarity tests was 5.4 when the three compounds were added simultaneously; 3-(methylthio)propionaldehyde alone was found to be responsible for 3.6, suggesting that, among the molecules studied, it is the most important contributor to the typical aroma of an oxidation-spoiled white wine.
Role of hepatic α- and β-adrenergic receptor stimulation on hepatic glucose production during heavy exercise (1997)

The role of catecholamines in the control of hepatic glucose production was studied during heavy exercise in dogs, using a technique to selectively block hepatic alpha- and beta-adrenergic receptors. Surgery was done > 16 days before the study, at which time catheters were implanted in the carotid artery, portal vein, and hepatic vein for sampling and the portal vein and vena cava for infusions. In addition, flow probes were implanted on the portal vein and hepatic artery. Each study consisted of a 100-min equilibration, a 30-min basal, a 20-min heavy exercise (approximately 85% of maximum heart rate), a 30-min recovery, and a 30-min adrenergic blockade test period. Either saline (control; n = 7) or alpha (phentolamine)- and beta (propranolol)-adrenergic blockers (Blk; n = 6) were infused in the portal vein. In both groups, epinephrine (Epi) and norepinephrine (NE) were infused in the portal vein during the blockade test period to create supraphysiological levels at the liver. Isotope ([3-3H]glucose) dilution and arteriovenous differences were used to assess hepatic function. Arterial Epi, NE, glucagon, and insulin levels were similar during exercise in both groups. Endogenous glucose production (Ra) rose similarly during exercise to 7.9 +/- 1.2 and 7.5 +/- 2.0 mg.kg-1.min-1 in control and Blk groups at time = 20 min. Net hepatic glucose output also rose to a similar rate in control and Blk groups with exercise. During the blockade test period, arterial plasma glucose and Ra rose to 164 +/- 5 mg/dl and 12.0 +/- 1.4 mg.kg-1.min-1, respectively, but were essentially unchanged in Blk. The attenuated response to catecholamine infusion in Blk substantiates the effectiveness of the hepatic adrenergic blockade. In conclusion, these results show that direct hepatic adrenergic stimulation does not participate in the increase in Ra, even during the exaggerated sympathetic response to heavy exercise.
The complexity of NF-κB signaling in inflammation and cancer (2013)

The NF-κB family of transcription factors has an essential role in inflammation and innate immunity. Furthermore, NF-κB is increasingly recognized as a crucial player in many steps of cancer initiation and progression. During these latter processes NF-κB cooperates with multiple other signaling molecules and pathways. Prominent nodes of crosstalk are mediated by other transcription factors such as STAT3 and p53 or the ETS related gene ERG. These transcription factors either directly interact with NF-κB subunits or affect NF-κB target genes. Crosstalk can also occur through different kinases, such as GSK3-β, p38, or PI3K, which modulate NF-κB transcriptional activity or affect upstream signaling pathways. Other classes of molecules that act as nodes of crosstalk are reactive oxygen species and miRNAs. In this review, we provide an overview of the most relevant modes of crosstalk and cooperativity between NF-κB and other signaling molecules during inflammation and cancer.
Biochemical analysis of human breast tissues using Fourier-transform Raman spectroscopy (2006)

We employ Fourier-transform Raman spectroscopy to study normal and tumoral human breast tissues, including several subtypes of cancers. We analyzed 194 Raman spectra from breast tissues that were separated into 9 groups according to their corresponding histopathological diagnosis. The assignment of the relevant Raman bands enabled us to connect the several kinds of breast tissues (normal and pathological) to their corresponding biochemical moieties alterations and distinguish among 7 groups: normal breast, fibrocystic condition, duct carcinoma in situ, duct carcinoma in situ with necrosis, infiltrating duct carcinoma not otherwise specified, colloid infiltrating duct carcinoma, and invasive lobular carcinomas. We were able to establish the biochemical basis for each spectrum, relating the observed peaks to specific biomolecules that play a special role in the carcinogenesis process. This work is very useful for the premature optical diagnosis of a broad range of breast pathologies. We noticed that we were not able to differentiate inflammatory and medullary duct carcinomas from infiltrating duct carcinoma not otherwise specified.
Phase Control Of Coherent Diode Laser Arrays Using Liquid Crystals (1989)

The on-axis fields from separate elements of a coherent laser array can interfere either constructively or destructively, depending upon the relative phases. We describe thin film transistor (TFT) and direct-drive controlled arrays of liquid crystal phase shifters, which provide both phase matching and fine beamsteering. The transmissive liquid crystal devices contain homogeneously aligned layers of nematic liquid crystals sandwiched between two glass plates. The devices impart electrically controllable analog phase delays to laser beams passing through the cells. The devices are divided into arrays of individually controlled elements using separate transparent electrodes.
Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing (2005)

After reconsideration of the spectral data and syntheses/characterization of model compounds, it has come to our attention that the structures of compounds 6, 14a, and 14t should be as illustrated below.1 The misassignment occurred in the alkylation steps. With the benzylic-bromide-derived reagents (but not the chlorocarbonates), these alkylations occurred on the nucleobases and not on the 3’-O as originally supposed. Consequently, the structures of intermediates 3–5 and 11–13 should be revised accordingly. We thank Dr’s W. Wu (LaserGen) and G. Lu (Texas A & M) for valuable discussions.
Petroleum Expulsion Part 2. Organic Matter Type and Maturity Effects on Kerogen Swelling by Solvents and Thermodynamic Parameters for Kerogen from Regular Solution Theory (2006)

The swelling of kerogen in several well-defined solvents was measured to derive thermodynamic parameters specified by an extended Flory−Rehner and Regular Solution Theory framework. These parameters are needed to assess the importance of the selective solubility of individual petroleum compounds into kerogen as a mechanism for the chemical fractionation that occurs during expulsion. The swelling of kerogen by a set of organic solvents was quantified following exposure to 30, 90, and 150 °C temperatures for 24 h in a closed system. The organic solvents were selected to reflect the prevalent hydrocarbon and heteroatom structures in petroleum. A total of 13 different, well-characterized Type II and Type IIIC kerogens were studied that included a maturity suite for each kerogen type. The swelling results were pooled and analyzed using an analysis of variance (ANOVA) statistical method to determine if swelling differences were related to the temperature, solvent, kerogen type, and level of kerogen maturity. There was no statistical difference in the mean volumetric swelling ratio (Qv) at 30 and 90 °C (2.1%) and only a slight increase in the mean Qv at 150 °C (3.0%) after exposing kerogen for 24 h to the solvents used in this study. The weak temperature dependence indicates that these kerogen−solvent systems have nearly equilibrated after 24 h at 30 °C. Statistically significant differences in the mean Qv were found among different kerogens and nonpolar/slightly polar solvents with varying solubility parameter (δ) values. Average swelling data for Type II and Type IIIC kerogens were interpreted to derive thermodynamic parameters (solubility parameter, cross-link density, and the volume fraction of the kerogen network Veq that minimizes its elastic strain energy, termed “native swelling”) by optimizing the match between the experimental data and theoretical predictions. These parameters enable general predictions of swelling behavior of these kerogen types in other solvents and complex solvent mixtures. To verify the model, the swelling of kerogen by 50:50 n-hexadecane/solvent mixtures was calculated and compared to experimental data. Good agreement was observed between the Qv and compositionally based swelling ratio (Qc) for all kerogens.
Small-molecule inhibition of STAT3 in radioresistant head and neck squamous cell carcinoma (2016)

While STAT3 has been validated as a target for treatment of many cancers, including head and neck squamous cell carcinoma (HNSCC), a STAT3 inhibitor is yet to enter the clinic. We used the scaffold of C188, a small-molecule STAT3 inhibitor previously identified by us, in a hit-to-lead program to identify C188-9. C188-9 binds to STAT3 with high affinity and represents a substantial improvement over C188 in its ability to inhibit STAT3 binding to its pY-peptide ligand, to inhibit cytokine-stimulated pSTAT3, to reduce constitutive pSTAT3 activity in multiple HNSCC cell lines, and to inhibit anchorage dependent and independent growth of these cells. In addition, treatment of nude mice bearing xenografts of UM-SCC-17B, a radioresistant HNSCC line, with C188-9, but not C188, prevented tumor xenograft growth. C188-9 treatment modulated many STAT3-regulated genes involved in oncogenesis and radioresistance, as well as radioresistance genes regulated by STAT1, due to its potent activity against STAT1, in addition to STAT3. C188-9 was well tolerated in mice, showed good oral bioavailability, and was concentrated in tumors. Thus, C188-9, either alone or in combination with radiotherapy, has potential for use in treating HNSCC tumors that demonstrate increased STAT3 and/or STAT1 activation.
Synthesis and Structure-Activity Relationships of Substituted 2-((2-Imidazolylsulfinyl)methyl)anilines as a New Class of Gastric H+/K+ -ATPase Inhibitors. II. (1992)

A series of N-substituted 2-[(2-imidazolylsulfinyl)methyl]anilines (3) was synthesized and evaluated for its biological activity against gastric H+/K(+)-ATPase prepared from rabbit stomach and gastric acid secretions in Heidenhain pouch dogs. Monoalkyl substituents on the nitrogen atom of the aniline moiety markedly inhibited the enzyme activity to the same degree as omeprazole, a representative H+/K(+)-ATPase inhibitor. Most of these compounds, administered at 3 mg/kg i.v. inhibited histamine-stimulated gastric acid secretion. The inhibitory activity of these derivatives on the enzymes at pH 6.0 was more potent than that at pH 7.4, and was distinctly correlated to stability in aqueous solution at pH 5.0.
Cysteinyl-tRNA synthetase: determination of the lastE.coliaminoacyl-tRNA synthetase primary structure (1991)

The gene coding for E. coli cysteinyl-tRNA synthetase (cysS) was isolated by complementation of a strain deficient in cysteinyl-tRNA synthetase activity at high temperature (43 degrees C). Sequencing of a 2.1 kbp DNA fragment revealed an open reading frame of 1383 bp coding for a protein of 461 amino acid residues with a Mr of 52,280, a value in close agreement with that observed for the purified protein, which behaves as a monomer. The sequence of CysRS bears the canonical His-Ile- Gly -His (HIGH) and Lys-Met-Ser-Lys-Ser (KMSKS) motifs characteristic of the group of enzymes containing a Rossmann fold; furthermore, it shows striking homologies with MetRS (an homodimer of 677 residues) and to a lesser extent with Ile-, Leu-, and ValRS (monomers of 939, 860, and 951 residues respectively). With its monomeric state and smaller size, CysRS is probably more closely related to the primordial aminoacyl-tRNA synthetase from which all have diverged.
A Novel Sulindac Derivative That Does Not Inhibit Cyclooxygenases but Potently Inhibits Colon Tumor Cell Growth and Induces Apoptosis with Antitumor Activity (2009)

Nonsteroidal anti-inflammatory drugs such as sulindac have shown promising antineoplastic activity, although toxicity from cyclooxygenase (COX) inhibition and the suppression of prostaglandin synthesis limits their use for chemoprevention. Previous studies have concluded that the mechanism responsible for their antineoplastic activity may be COX independent. To selectively design out the COX inhibitory activity of sulindac sulfide (SS), in silico modeling studies were done that revealed the crucial role of the carboxylate moiety for COX-1 and COX-2 binding. These studies prompted the synthesis of a series of SS derivatives with carboxylate modifications that were screened for tumor cell growth and COX inhibitory activity. A SS amide (SSA) with a N,N-dimethylethyl amine substitution was found to lack COX-1 and COX-2 inhibitory activity, yet potently inhibit the growth of human colon tumor cell lines, HT-29, SW480, and HCT116 with IC(50) values of 2 to 5 micromol/L compared with 73 to 85 micromol/L for SS. The mechanism of growth inhibition involved the suppression of DNA synthesis and apoptosis induction. Oral administration of SSA was well-tolerated in mice and generated plasma levels that exceeded its in vitro IC(50) for tumor growth inhibition. In the human HT-29 colon tumor xenograft mouse model, SSA significantly inhibited tumor growth at a dosage of 250 mg/kg. Combined treatment of SSA with the chemotherapeutic drug, Camptosar, caused a more sustained suppression of tumor growth compared with Camptosar treatment alone. These results indicate that SSA has potential safety and efficacy advantages for colon cancer chemoprevention as well as utility for treating malignant disease if combined with chemotherapy.
Thermal conductivity of porous catalysts (1965)

Abstract A random pore model of catalytic pore structure is applied to the determination of the thermal conductivity of porous catalytic solids. The low thermal conductivities reported for such materials are explained by considering the microporous particles to consist of a packed bedlike assembly of smaller particles; heat transfer through the solid fraction occurs by conduction through individual small particles in contact with other particles. An expression for the effective thermal conductivity of a gas in the region between ordinary thermal conduction and free molecule conduction is used in determination of heat conduction through the void volume. Agreement of the theory with experimental data on alumina and silver catalysts over a wide range of conditions is good.
Submicroscopic contact imaging with visible light by energy transfer (1982)

The resolution of contact imaging with light is limited by the distance between object and image and not by the wavelength. Contact imaging with visible light at submicroscopic resolution (100 nm) is demonstrated using the concept of imaging by energy transfer. The bleaching of a dye is inhibited by energy transfer to a metal in close proximity. This mechanism is exploited for imaging a planar metal pattern onto a film of a cyanine dye.
9(10 .fwdarw. 19)-Abeo steroids. Total synthesis abeo-estradiol, abeo-estradiol 3-methyl ether, and 17.alpha.-ethynyl abeo-estradiol 3-methyl ether (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT9(10 .fwdarw. 19)-Abeo steroids. Total synthesis abeo-estradiol, abeo-estradiol 3-methyl ether, and 17.alpha.-ethynyl abeo-estradiol 3-methyl etherElie Abushanab, Daw-Yuan Lee, William A. Meresak, and William L. DuaxCite this: J. Org. Chem. 1976, 41, 9, 1601–1603Publication Date (Print):April 1, 1976Publication History Published online1 May 2002Published inissue 1 April 1976https://doi.org/10.1021/jo00871a026Request reuse permissionsArticle Views164Altmetric-Citations5LEARN 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 (418 KB) Get e-Alertsclose Get e-Alerts
Unsupervised Learning of Human Action Categories Using Spatial-Temporal Words (2006)

We present a novel unsupervised learning method for human action categories. A video sequence is represented as a collection of spatial-temporal words by extracting space-time interest points. The algorithm automatically learns the probability distributions of the spatial-temporal words and the intermediate topics corresponding to human action categories. This is achieved by using latent topic models such as the probabilistic Latent Semantic Analysis (pLSA) model and Latent Dirichlet Allocation (LDA). Our approach can handle noisy feature points arisen from dynamic background and moving cameras due to the application of the probabilistic models. Given a novel video sequence, the algorithm can categorize and localize the human action(s) contained in the video. We test our algorithm on three challenging datasets: the KTH human motion dataset, the Weizmann human action dataset, and a recent dataset of figure skating actions. Our results reflect the promise of such a simple approach. In addition, our algorithm can recognize and localize multiple actions in long and complex video sequences containing multiple motions.