gebhart/patrepeval huggingface dataset:
Chemokine receptors that mediate B cell homing to secondary lymphoid tissues are highly expressed in B cell chronic lymphocytic leukemia and non-Hodgkin lymphomas with widespread nodular dissemination (2004)

B cell neoplasms present heterogeneous patterns of lymphoid organ involvement, which may be a result of the differential expression of chemokine receptors. We found that chemokine receptor (CCR)7, CXC chemokine receptor (CXCR)4, or CXCR5, the main chemokine receptors that mediate B cell entry into secondary lymphoid tissues and their homing to T cell and B cell zones therein, were highly expressed in B malignancies with widespread involvement of lymph nodes. Conversely, those pathologies with little or no nodular dissemination showed no expression to very low levels of CCR7 and CXCR5 and low to moderate levels of CXCR4. These findings provide evidence for the role of CCR7, CXCR4, and CXCR5 in determining the pattern of lymphoid organ involvement of B tumors. Functional studies were performed on B malignancies expressing different levels of CCR7, CXCR5, and CXCR4. Multiple myeloma (MM) cells did not express CCR7 nor CXCR5 and did not migrate in response to their ligands; a moderate expression of CXCR4 on MM cells was accompanied by a migratory response to its ligand, CXCL12. By contrast, cells from B cell chronic lymphocytic leukemia (B-CLL) expressed the highest levels of these chemokine receptors and efficiently migrated in response to all ligands of CCR7, CXCR4, and CXCR5. In addition, the migration index of B-CLL cells in response to both of the CCR7 ligands correlated with the presence of clinical lymphadenopathy, thus indicating that the high expression of functional chemokine receptors justifies the widespread character of B-CLL, representing a clinical target for the control of tumor cell dissemination.
Indole-2-Carboxylic Acid: A Competitive Antagonist of Potentiation by Glycine at the NMDA Receptor (1989)

The N-methyl-D-aspartate (NMDA) class of excitatory amino acid receptors regulates the strength and stability of excitatory synapses and appears to play a major role in excitotoxic neuronal death associated with stroke and epilepsy. The conductance increase gated by NMDA is potentiated by the amino acid glycine, which acts at an allosteric site tightly coupled to the NMDA receptor. Indole-2-carboxylic acid (I2CA) specifically and competitively inhibits the potentiation by glycine of NMDA-gated current. In solutions containing low levels of glycine, I2CA completely blocks the response to NMDA, suggesting that NMDA alone is not sufficient for channel activation. I2CA will be useful for defining the interaction of glycine with NMDA receptors and for determining the in vivo role of glycine in excitotoxicity and synapse stabilization.
Kinetics of fetal cellular and cell‐free DNA in the maternal circulation during and after pregnancy: implications for noninvasive prenatal diagnosis (2001)

Fetal genetic material can be detected throughout pregnancy, and its quantity is a function of gestational age and of whether the plasma or cellular compartment is examined. Both the absolute quantity of fetal DNA and its ratio to total DNA (maternal + fetal) are greater in the plasma than in the cellular compartment. Fetal DNA is cleared rapidly from both compartments after parturition, which suggests that turnover is dynamic. Because they provide prospective and quantitative data concerning fetal DNA levels, these observations and kinetic PCR methods may have implications for noninvasive prenatal diagnosis. Further studies will be needed to determine the immunologic implications of fetal-maternal DNA exchange and cellular microchimerism.
Synthesis and Deposition of Egg Proteins (2019)

The regulation of egg protein synthesis has provided an exceptional model system for physiological and biochemical studies on developmental and hormonal regulation of gene expression. Some of the genes specifying major egg proteins have served as paradigms for detailed analyses of the molecular mechanisms involved. Egg-white proteins are secreted directly from the tubular gland cells into the lumen of the oviduct, while the yolk proteins, following secretion from the liver, are transported in the blood and then enter the oocyte via receptor-mediated mechanisms. All of the major yolk proteins are secreted from the liver as lipoprotein particles. The Msp1 site overlaps a sequence corresponding to a canonical estrogen response element (ERE). Based on short-term transfection studies carried out by Burch and colleagues, the canonical ERE acts synergistically with a second imperfect ERE located approximately 300 nucleotides closer to the gene.
High-Efficiency Gene Transfer Mediated by Adenovirus Coupled to DNA–Polylysine Complexes (1992)

Employment of recombinant viruses as gene transfer vectors is limited by constraints on the size and functional design of the genetic material to be transferred as well as potential safety hazards deriving from obligatory co-transfer of viral genetic elements. As an alternative strategy that capitalizes on the efficient cellular entry mechanisms of viruses, we have derived adenovirus-polylysine-DNA complexes whereby foreign DNA is transferred bound to the exterior of the virion. This linkage was accomplished utilizing an antibody bridge in which a monoclonal antibody was rendered competent to carry DNA by the attachment of a polylysine residue. Attachment of the antibody-polylysine to the virus was by virtue of the antibody's specificity for the virion. The resulting vector system mediates high-efficiency gene transfer to target cells in vitro. In addition, this vector design allows greatly enhanced flexibility in terms of the size and design of heterologous sequences that can be transferred. Since this strategy selectively exploits viral entry functions, which are independent of viral gene expression, the potential exists to derive vectors that avoid the hazards deriving from transfer of parent virus genome.
Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression (2015)

Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.
Gene Therapy Protocols (1996)

In Gene Therapy Protocols, leading researchers describe in detail all the essential molecular methods for developing gene transfer systems, along with the methods for introducing genes into specific tissue types either in vivo or ex vivo. These easily reproducible methods range from those for specific viral and nonviral delivery systems, to those concerned with gene delivery to particular tissues. Methods for applying specific therapeutic systems, such as ribozymes and tumor suppressor genes for the treatment of AIDS and cancer, are also included in this authoritative collection. Gene Therapy Protocols is the first major collection of the methods needed for successful gene delivery and subsequent in vivo gene expression, techniques at the center of the many and significant recent advances in the treatment of both genetic and acquired diseases. It will surely become today's indispensable standard reference source for all scientists working to realize the promises of gene therapy
Bipolar Molecules with High Triplet Energies: Synthesis, Photophysical, and Structural Properties (2011)

This article sheds new light on the interplay of electronic and conformational effects in luminescent bipolar molecules. A series of carbazole/1,3,4-oxadiazole hybrid molecules is described in which the optoelectronic properties are systematically varied by substituent effects which tune the intramolecular torsion angles. The synthesis, photophysical properties, cyclic voltammetric data, X-ray crystal structures, and DFT calculations are presented. Excited state intramolecular charge transfer (ICT) is observed from the donor carbazole/2,7-dimethoxycarbazole to the acceptor phenyl/diphenyloxadiazole moieties. Introducing more bulky substituents onto the diphenyloxadiazole fragment systematically increases the singlet and triplet energy levels (E(S) and E(T)) and blue shifts the absorption and emission bands. The triplet excited state is located mostly on the oxadiazole unit. The introduction of 2,7-dimethoxy substituents onto the carbazole moiety lowers the value of E(S), although E(T) is unaffected, which means that the singlet-triplet gap is reduced (for 7bE(S) - E(T) = 0.61 eV). A strategy has been established for achieving unusually high triplet levels for bipolar molecules (E(T) = 2.64-2.78 eV at 14 K) while at the same time limiting the increase in the singlet energy.
CLINICAL USE OF CYSTINE SUPERSATURATION MEASUREMENTS (2000)

Clinical management of cystinuria can be improved by direct measurement of cystine solubility because it varies widely at any given pH. Increasing 24-hour collection pH with sodium bicarbonate additionally improves accuracy of supersaturation measurement by recovering crystallized cystine.
The Spectrum of Mutations in Progranulin (2010)

Pathogenic mutations were found only in FTD-spectrum cases and not in other related neurodegenerative diseases. Haploinsufficiency of GRN is the predominant mechanism leading to FTD.
Chondrogenic differentiation of bovine bone marrow mesenchymal stem cells (MSCs) in different hydrogels: Influence of collagen type II extracellular matrix on MSC chondrogenesis (2006)

Bone marrow mesenchymal stem cells (MSCs) are candidate cells for cartilage tissue engineering. This is due to their ability to undergo chondrogenic differentiation after extensive expansion in vitro and stimulation with various biomaterials in three-dimensional (3-D) systems. Collagen type II is one of the major components of the hyaline cartilage and plays a key role in maintaining chondrocyte function. This study aimed at analyzing the MSC chondrogenic response during culture in different types of extracellular matrix (ECM) with a focus on the influence of collagen type II on MSC chondrogenesis. Bovine MSCs were cultured in monolayer as well as in alginate and collagen type I and II hydrogels, in both serum free medium and medium supplemented with transforming growth factor (TGF) beta1. Chondrogenic differentiation was detected after 3 days of culture in 3-D hydrogels, by examining the presence of glycosaminoglycan and newly synthesized collagen type II in the ECM. Differentiation was most prominent in cells cultured in collagen type II hydrogel, and it increased in a time-dependent manner. The expression levels of the of chondrocyte specific genes: sox9, collagen type II, aggrecan, and COMP were measured by quantitative "Real Time" RT-PCR, and genes distribution in the hydrogel beads were localized by in situ hybridization. All genes were upregulated by the presence of collagen, particularly type II, in the ECM. Additionally, the chondrogenic influence of TGF beta1 on MSCs cultured in collagen-incorporated ECM was analyzed. TGF beta1 and dexamethasone treatment in the presence of collagen type II provided more favorable conditions for expression of the chondrogenic phenotype. In this study, we demonstrated that collagen type II alone has the potential to induce and maintain MSC chondrogenesis, and prior interaction with TGF beta1 to enhance the differentiation.
One NY-ESO-1-Derived Epitope That Promiscuously Binds to Multiple HLA-DR and HLA-DP4 Molecules and Stimulates Autologous CD4+ T Cells from Patients with NY-ESO-1-Expressing Melanoma (2005)

Abstract NY-ESO-1 is expressed by a broad range of human tumors and is often recognized by Abs in the sera of cancer patients with NY-ESO-1-expressing tumors. The NY-ESO-1 gene also encodes several MHC class I- and class II-restricted tumor epitopes recognized by T lymphocytes. In this study we report one novel pan-MHC class II-restricted peptide sequence, NY-ESO-1 87–111, that is capable of binding to multiple HLA-DR and HLA-DP4 molecules, including HLA-DRB1*0101, 0401, 0701, and 1101 and HLA-DPB1*0401 and 0402 molecules. We also demonstrate that peptide NY-ESO-1 87–111 stimulates Th1-type and Th-2/Th0-type CD4+ T cells and clones when presented in the context of these HLA-DR and HLA-DP4 molecules. Both bulk CD4+ T cells and CD4+ T cell clones were capable of recognizing not only peptide-pulsed APCs, but also autologous dendritic cells, either loaded with the NY-ESO-1 protein or transfected with NY-ESO-1 cDNAs. Using IFN-γ and IL-5 ELISPOT assays and PBL from patients with NY-ESO-1-expressing tumors, we observed the existence of Th1-type circulating CD4+ T cells recognizing peptide NY-ESO-1 87–111 in the context of HLA-DP4 molecules. Taken together, these data represent the first report of an HLA-DR- and HLA-DP-restricted epitope from a tumor Ag. They also support the relevance of cancer vaccine trials with peptides NY-ESO-1 87–111 in the large number of cancer patients with NY-ESO-1-expressing tumors.
Toward the Development of New Textile/Plastic Electrochromic Cells Using Triphenylamine-Based Copolymers (2006)

We report the preparation and characterization of new electrochromic polymers containing a 4-butyltriphenylamine (BuTPA) unit on the main chain. All polymers were obtained through the Suzuki−Miyaura cross-coupling reaction between 4-butyl-N,N-bis((4,4,5,5-tetramethyl-1,3,2-dioxaborolan-4-phenyl)aniline) and several aryl dibromide molecules to modulate the electronic properties of the resulting copolymers. 2,5-Dibromothiophene, 2,5-dibromo(3,4-ethylenedioxythiophene), 3,6-dibromo-N-octylcarbazole, bis(6-bromo-N-octylcarbazol-3-yl), and 2,7-dibromo-3,6-dimethoxy-9,9-dihexylfluorene were used as comonomers and led to five new copolymers, PT(BuTPA), PE(BuTPA), PC(BuTPA), PCC(BuTPA), and PF(BuTPA). These polymers are readily soluble in many common organic solvents, which make them suitable for spray-coating film deposition. Electrochromic cells with the following configuration were assembled: ITO-coated glass or plastic/electrochromic polymer/gel electrolyte/ITO-coated glass or plastic or conducting textile. These copolymers exhibit good optical and electrochemical properties for military camouflage needs with color transition from pale yellow to green, transparent to khaki, or pale green to reddish-brown. Electrochemistry, spectroelectrochemistry, and colorimetric measurements of the devices were examined.
Solubility of xenon in liquid n-alkanes: Temperature dependence and thermodynamic functions (1982)

Measurements of the Ostwald solubility as a function of temperature L(T) are reported for 133Xe gas in liquid n-alkanes. All the alkanes from n-C5H12 through n-C20H42 were investigated and the temperatures ranged from 10.0 to 50.0 °C. The experimental method is recently developed and has some unique aspects. From the temperature dependent results the chemical potential Δμ20(T), the enthalpy ΔH̄20, and the entropy ΔS̄20 of solution were determined. Values for Δμ20(T) ranged from 2546 cal/mol for n-C7H16 at 50.0 °C to 1811 cal/mol for n-C14H30 at 10.0 °C. The range of ΔH̄20 was from −2818 cal/mol for n-C5H12 to −2117 cal/mol for n-C20H42, and the corresponding range in ΔS̄20 was −16.90 to −13.58 cal/mol K. A Barclay–Butler plot of the thermodynamic functions and a plot of the dependence of solubility on the Hildebrand solubility parameter for this system are displayed. All of the data obtained in this experiment may be given to better than 0.8% by the empirical relation Δμ20=−RT ln x2=−0.0637nT+2.575×10−2T2, in which x2 is the mole fraction of solute in the solvent at 1 atm partial pressure and T is the absolute temperature. Because the solute is an inert monatomic gas and the solvents are a single homologous series of nonpolar liquids, the results show some interesting simple physical interpretation.
THE EFFECT OF NEUTRAL SALTS ON HYDROLYSIS BY WATER. (1909)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE EFFECT OF NEUTRAL SALTS ON HYDROLYSIS BY WATER.David R. KellogCite this: J. Am. Chem. Soc. 1909, 31, 8, 886–900Publication Date (Print):August 1, 1909Publication History Published online1 May 2002Published inissue 1 August 1909https://pubs.acs.org/doi/10.1021/ja01938a004https://doi.org/10.1021/ja01938a004research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Preparation, antibacterial effects and enzymatic degradation of 5-fluorouracil nucleosides (1980)

Reaction of perbenzoylated aldopentafuranosyl derivatives of uracil with fluorine in acetic acid afforded perbenzoylated 5-fluorouracil nucleosides. Their methanolysis gave the following free nucleosides of 5-fluorouracil: β-D-ribofuranoside ( Id ), 2-deoxy-β-D-ribofuranoside ( IId ), their enantiomers VIII and IX , α-D-ribofuranoside ( XIII ), 2-deoxy-α-D-ribofuranoside ( XV ), β-D-arabinofuranoside ( IV ) and its L-enantiomer X , β-D-xylofuranoside ( V ) and its α-D-anomer XI , α-L-lyxofuranoside ( VI ) and 2-deoxy-α-L-lyxofuranoside ( VII ) and the enantiomers of the latter two compounds, XII and XIV , respectively. Analogously were obtained 5-deoxy-β-D-ribofuranoside ( III ), β-D-ribopyranoside ( XVI ) and 1-( S )-(2,3-dihydroxypropyl)-5-fluorouracil ( XVIIc ). 1-Allyl-5-fluorouracil ( XVIII ) was prepared by reaction of allyl bromide with 2,4-bis(trimethylsilyloxy)-5-fluoropyrimidine. The cell-free extract from Escherichia coli cleaves all the 5-fluorouracil nucleosides in which the nucleoside carbon atom has the R -configuration and the 3'-hydroxyl of the sugar moiety is in trans -relation to the base. Compounds which have not these structural features are resistant. Besides nucleosides which on enzymatic cleavage afford 5-fluorouracil, also the non-cleavable 1-(2-deoxy-β-L-ribofuranosyl)-5-fluorouracil ( IX ), 1-(2-deoxy-α-D-ribofuranosyl)-5-fluorouracil ( XV ) and 1-(2-deoxy-α-D-lyxofuranosyl)-5-fluorouracil ( XIV ) exhibit an antibacterial effect towards E. coli (ID 50 1.0-2.5 . 10 -5 M). This effect can be reversed by 2'-deoxyuridine but not by thymidine.
The Nucleotide-binding Leucine-rich Repeat (NLR) Family Member NLRX1 Mediates Protection against Experimental Autoimmune Encephalomyelitis and Represses Macrophage/Microglia-induced Inflammation (2013)

The nucleotide binding domain and leucine-rich repeat-containing (NLR) family of proteins is known to activate innate immunity, and the inflammasome-associated NLRs are prime examples. In contrast, the concept that NLRs can inhibit innate immunity is still debated, and the impact of such inhibitory NLRs in diseases shaped by adaptive immune responses is entirely unexplored. This study demonstrates that, in contrast to other NLRs that activate immunity, NLRX1 plays a protective role in experimental autoimmune encephalomyelitis (EAE), a mouse model for multiple sclerosis. When compared with wild-type controls, Nlrx1(-/-) mice have significantly worsened clinical scores and heightened CNS tissue damage during EAE. NLRX1 does not alter the production of encephalitogenic T cells in the peripheral lymphatic tissue, but Nlrx1(-/-) mice are more susceptible to adoptively transferred myelin-reactive T cells. Analysis of the macrophage and microglial populations indicates that NLRX1 reduces activation during both active and passive EAE models. This work represents the first case of an NLR that attenuates microglia inflammatory activities and protects against a neurodegenerative disease model caused by autoreactive T cells.
Identifying critical regions in small-world marine metapopulations (2011)

The precarious state of many nearshore marine ecosystems has prompted the use of marine protected areas as a tool for management and conservation. However, there remains substantial debate over their design and, in particular, how to best account for the spatial dynamics of nearshore marine species. Many commercially important nearshore marine species are sedentary as adults, with limited home ranges. It is as larvae that they disperse greater distances, traveling with ocean currents sometimes hundreds of kilometers. As a result, these species exist in spatially complex systems of connected subpopulations. Here, we explicitly account for the mutual dependence of subpopulations and approach protected area design in terms of network robustness. Our goal is to characterize the topology of nearshore metapopulation networks and their response to perturbation, and to identify critical subpopulations whose protection would reduce the risk for stock collapse. We define metapopulation networks using realistic estimates of larval dispersal generated from ocean circulation simulations and spatially explicit metapopulation models, and we then explore their robustness using node-removal simulation experiments. Nearshore metapopulations show small-world network properties, and we identify a set of highly connected hub subpopulations whose removal maximally disrupts the metapopulation network. Protecting these subpopulations reduces the risk for systemic failure and stock collapse. Our focus on catastrophe avoidance provides a unique perspective for spatial marine planning and the design of marine protected areas.
THE POWER LINE TRANSMISSION CHARACTERISTICS FOR AN OFDM SIGNAL (2006)

In this paper, we measured what influence the sinusoidal transmission characteristics of the electric power line with various forms gave to the transmission characteristic of OFDM (Orthogonal Frequency Division Multiplexing) signal through PLC (power line communication system) modem. The electric power line transmission line with various forms in a real environment is classified into two basic elements, which are an outlet type branch and a switch type branch. Next, PHY rate (Physical rate) is measured for each basic element connected with the PLC modem. At this time, the transmission characteristics of the electric power line are simulated from measured data. OFDM sending and receiving systems are composed on the computer, and the PHY rate is simulated. By comparing with measured and calculated values, it is revealed that PHY rate of PLC modem is most affected in the case of the power line transmission characteristics having broad band and high level attenuation and is not affected in the case of that having narrow band group delay variation.