gebhart/patrepeval huggingface dataset:
A cellular mechanism for targeting newly synthesized mRNAs to synaptic sites on dendrites (2001)

Long-lasting forms of activity-dependent synaptic plasticity involve molecular modifications that require gene expression. Here, we describe a cellular mechanism that mediates the targeting newly synthesized gene transcripts to individual synapses where they are locally translated. The features of this mechanism have been revealed through studies of the intracellular transport and synaptic targeting of the mRNA for a recently identified immediate early gene called activity-regulated cytoskeleton-associated protein Arc. Arc is strongly induced by patterns of synaptic activity that also induce long-term potentiation, and Arc mRNA is then rapidly delivered into dendrites after episodes of neuronal activation. The newly synthesized Arc mRNA localizes selectively at synapses that recently have been activated, and the encoded protein is assembled into the synaptic junctional complex. The dynamics of trafficking of Arc mRNA reveal key features of the mechanism through which synaptic activity can both induce gene expression and target particular mRNA transcripts to the active synapses.
Androgen Receptor Assay with [3H]Methyltrienolone (R1881) in the Presence of Progesterone Receptors* (1979)

The synthetic radiolabeled androgen methyltrienolone-17βhiydroxy-17α-methyl-estra-4,9,ll-trien-3-one (R1881) is superior to the native ligand 5α-dihydrotestosterone (DHT) in the measurement of androgen receptor (AR), especially in tissues where radiolabeled DHT binds with high affinity to plasma proteins in addition to receptor or is rapidly metabolized to inactive derivatives. However, R1881 also binds progesterone receptor (PgR), as shown by its ability to complete for [3]-promestone-17α,21-dimethyl-19-nor-pregna-4,9-diene-3,20-dione (R5020) binding to 8S PgR on sucrose density gradients, resulting in an overestimation of AR if PgR is present. Therefore, we have devised a method by which PgR binding of R1881 can be blocked without interfering with AR binding. The glucocorticoid triamcinolone acetonide (TA) was found to bind PgR (competition for 8S [3]R5020 binding) but not AR (no competition for 8S [3H]DHT binding). In cytosols containing both receptors, a 500-fold excess of unlabeled TA was sufficient to eliminate [3H]R1881 binding to PgR, leaving only [3H]R1881 binding to AR, which was not affected even by larger TA doses. Scatchard plots of [3H]R1881 binding in such cytosols were reduced by TA to agree with [3H]DHT binding to AR. In rat prostate, which contains little if any PgR, [3H]R1881 binding was slightly greater than that of [3H]DHT, and neither was affected by a 500-fold excess of TA. In a human prostate tumor, however, [3H]R1881 revealed a substantial 8S peak, shown to be AR by the failure of TA to compete, even though [3H]DHT was unable to show 8S binding in the same cytosol. The use of TA to selectively block [3H]R1881 binding to PgR in AR assays has been validated using a variety of methods (sucrose gradient, protamine sulfate, and dextran charcoal) and systems (MCF-7 human breast cancer cells, rat uterus, and human prostate cancer).
Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. (2007)

Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10a(T), 11c and 12B, can tolerate 5 % (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria-Bertani agar medium. The optimum temperature for growth was 37 degrees C (range 16-45 degrees C) and the optimum pH was 7.0-8.0 (range pH 5.5-9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related to Bacillus fusiformis DSM 2898(T) (97.2 % similarity) and Bacillus sphaericus DSM 28(T) (96.9 %). DNA-DNA relatedness was greater than 97 % among the isolated strains and 61.1 % with B. fusiformis DSM 2898(T) and 43.2 % with B. sphaericus IAM 13420(T). The phylogenetic and phenotypic analyses and DNA-DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5-37.9 mol%, MK-7 as the predominant menaquinone system and iso-C(15 : 0) (32 % of the total) as a major cellular fatty acid. In contrast to the type species of the genus Bacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the name Lysinibacillus boronitolerans gen. nov., sp. nov. is proposed. The type strain of Lysinibacillus boronitolerans is strain 10a(T) (=DSM 17140(T)=IAM 15262(T)=ATCC BAA-1146(T)). It is also proposed that Bacillus fusiformis and Bacillus sphaericus be transferred to this genus as Lysinibacillus fusiformis comb. nov. and Lysinibacillus sphaericus comb. nov., respectively.
The Risks of Key Recovery, Key Escrow, and Trusted Third-Party Encryption (1997)

A variety of "key recovery," "key escrow," and "trusted third-party" encryption requirements have been suggested in recent years by government agencies seeking to conduct covert surveillance within the changing environments brought about by new technologies. This report examines the fundamental properties of these requirements and attempts to outline the technical risks, costs, and implications of deploying systems that provide government access to encryption keys.
Generating Graph Snapshots from Streaming Edge Data (2016)

We study the problem of determining the proper aggregation granularity for a stream of time-stamped edges. Such streams are used to build time-evolving networks, which are subsequently used to study topics such as network growth. Currently, aggregation lengths are chosen arbitrarily, based on intuition or convenience. We describe ADAGE, which detects the appropriate aggregation intervals from streaming edges and outputs a sequence of structurally mature graphs. We demonstrate the value of ADAGE in automatically finding the appropriate aggregation intervals on edge streams for belief propagation to detect malicious files and machines.
Autoantibodies Recognizing the Amino Terminal 1-17 Segment of CENP-A Display Unique Specificities in Systemic Sclerosis (2013)

Centromere-associated protein A (CENP-A), a common autoimmune target in a subset of systemic sclerosis patients, appears to have no role to explain why its corresponding auto-antibodies are more frequently found in the limited than the diffuse form of systemic sclerosis. Therefore, we investigated the fine specificity of anti-CENP-A antibodies as a first step to understanding their role in systemic sclerosis pathology. We focused on the amino-terminal portion of CENP-A spanning amino acids 1 to 17 (Ap(1-17)), which represents, along with Ap(17-30), an immunodominant epitope of the protein. Peptide Ap(1-17) was used to purify antibodies from 8 patients with systemic sclerosis. Anti-Ap(1-17) antibodies specifically reacted with human CENP-A but did not cross-react with CENP-B or Ap(17-30). Panning of a phage display peptide library with anti-Ap(1-17) antibodies from 2 patients identified two novel, partially overlapping motifs, <(5)Rx(st)xKP(10)> and <(9)KPxxPxR(15)> as the result of the alignment of specific phage clone insert sequences. Anti-Ap(1-17) IgG from the 8 patients had different reactivities to isolated phage clone insert sequences. Scanning the Swiss-Prot database revealed a large number of different types of proteins containing the two Ap(1-17) antigenic motifs. These data show that anti-CENP-A(1-17) antibodies are generated independently from anti-CENP-B antibodies and display great heterogeneity in their specificity by recognizing different motifs within that peptide sequence. This finding, along with the widespread interspecies and human tissue distribution of the two motifs, suggests that the number of motif-expressing proteins which can be the potential target of these antibodies is markedly higher than that estimated from the peptide-based epitope spreading model.
Targeting CB2 cannabinoid receptors as a novel therapy to treat malignant lymphoblastic disease (2002)

In the current study, we examined whether ligation of CB2 receptors would lead to induction of apoptosis in tumors of immune origin and whether CB2 agonist could be used to treat such cancers. Exposure of murine tumors EL-4, LSA, and P815 to delta-9-tetrahydrocannabinol (THC) in vitro led to a significant reduction in cell viability and an increase in apoptosis. Exposure of EL-4 tumor cells to the synthetic cannabinoid HU-210 and the endogenous cannabinoid anandamide led to significant induction of apoptosis, whereas exposure to WIN55212 was not effective. Treatment of EL-4 tumor-bearing mice with THC in vivo led to a significant reduction in tumor load, increase in tumor-cell apoptosis, and increase in survival of tumor-bearing mice. Examination of a number of human leukemia and lymphoma cell lines, including Jurkat, Molt-4, and Sup-T1, revealed that they expressed CB2 receptors but not CB1. These human tumor cells were also susceptible to apoptosis induced by THC, HU-210, anandamide, and the CB2-selective agonist JWH-015. This effect was mediated at least in part through the CB2 receptors because pretreatment with the CB2 antagonist SR144528 partially reversed the THC-induced apoptosis. Culture of primary acute lymphoblastic leukemia cells with THC in vitro reduced cell viability and induced apoptosis. Together, the current data demonstrate that CB2 cannabinoid receptors expressed on malignancies of the immune system may serve as potential targets for the induction of apoptosis. Also, because CB2 agonists lack psychotropic effects, they may serve as novel anticancer agents to selectively target and kill tumors of immune origin.
Topographic localization of the heparin-binding domain of the neural cell adhesion molecule N-CAM. (1986)

Previous studies have reported that the cell-binding region of the neural cell adhesion molecule (N-CAM) resides in a 65,000-D amino-terminal fragment designated Frl (Cunningham, B. A., S. Hoffman, U. Rutishauser, J. J. Hemperly, and G. M. Edelman, 1983, Proc. Natl. Acad. Sci. USA, 80:3116-3120). We have reported the presence of two functional domains in N-CAM, each identified by a specific mAb, that are required for cell-cell or cell-substratum adhesion (Cole, G. J., and L. Glaser, 1986, J. Cell Biol., 102:403-412). One of these domains is a heparin (heparan sulfate)-binding domain. In the present study we have determined the topographic localization of the heparin-binding fragment from N-CAM, which has been identified by our laboratory. The B1A3 mAb recognizes a 25,000-D heparin-binding fragment derived from chicken N-CAM, and also binds to a 65,000-D fragment, presumably Frl, produced by digestion of N-CAM with Staphylococcus aureus V8 protease. Amino-terminal sequence analysis of the isolated 25,000-D heparin-binding domain of N-CAM yielded the sequence: Leu-Gln-Val-Asp-Ile-Val-Pro-Ser-Gln-Gly. This sequence is identical to the previously reported amino-terminal sequence for murine and bovine N-CAM. Thus, the 25,000-D polypeptide fragment is the amino-terminal region of the N-CAM molecule. We have also shown that the B1A3 mAb recognizes not only chicken N-CAM but also rat and mouse N-CAM, indicating that the heparin-binding domain of N-CAM is evolutionarily conserved among different N-CAM forms. Additional peptide-mapping studies indicate that the second cell-binding site of N-CAM is located in a polypeptide region at least 65,000 D from the amino-terminal region. We conclude that the adhesion domains on N-CAM identified by these antibodies are physically distinct, and that the previously identified cell-binding domain on Frl is the heparin-binding domain.
Retinoid X Receptor Agonists Modulate Foxp3+ Regulatory T Cell and Th17 Cell Differentiation with Differential Dependence on Retinoic Acid Receptor Activation (2013)

Retinoic acid (RA) enhances TGF-β-dependent differentiation of Foxp3(+) inducible regulatory T cells (iTregs) and inhibits Th17 differentiation by binding to the RA receptor (RAR)/retinoid X receptor (RXR) heterodimer. The major physiologic RA, all-trans-RA, binds to RAR but not to RXR at physiological concentrations. It remained unclear whether RXR-mediated stimulation affected the iTregs and Th17 differentiation. We found in this study that the RXR agonists, PA024 and tributyltin, augmented the ability of all-trans-RA or the RAR agonist Am80 to enhance CD4(+)CD25(-) T cells to acquire Foxp3 expression and suppressive function. However, they failed to enhance Foxp3 expression in the presence of the RAR antagonist LE540, suggesting that the effect depends on RAR-mediated signals. They exerted the effect largely by augmenting the ability of all-trans-RA to suppress the production of IL-4, IL-21, and IFN-γ that inhibited Foxp3 expression. Agonists of peroxisome proliferator-activated receptors and liver X receptors (LXRs), permissive partners of RXR, failed to enhance Foxp3 expression. In contrast, RXR agonists and LXR agonists suppressed IL-17 expression. The RXR-mediated suppression was not canceled by blocking RAR stimulation but was likely to involve permissive activation of LXRs. All-trans-RA and an agonist of RXR or LXR additively suppressed IL-17 expression when the all-trans-RA concentration was low. RXR agonists also suppressed Ccr6 expression that is essential for Th17 cells to enter the CNS. Accordingly, tributyltin treatment of mice ameliorated experimental autoimmune encephalomyelitis through regulating Th17 cell activities. These results suggest that RXR stimulation modulates Foxp3(+) iTreg and Th17 differentiation with differential dependence on RAR-mediated stimulation.
An EM-like algorithm for color-histogram-based object tracking (2004)

The iterative procedure called 'mean-shift' is a simple robust method for finding the position of a local mode (local maximum) of a kernel-based estimate of a density function. A new robust algorithm is given here that presents a natural extension of the 'mean-shift' procedure. The new algorithm simultaneously estimates the position of the local mode and the covariance matrix that describes the approximate shape of the local mode. We apply the new method to develop a new 5-degrees of freedom (DOF) color histogram based non-rigid object tracking algorithm.
The Quantitative Significance of the Transsulfuration Enzymes for H 2 S Production in Murine Tissues (2011)

The enzymes of the transsulfuration pathway, cystathionine β-synthase (CBS) and cystathionine γ-lyase (CSE), are important for the endogenous production of hydrogen sulfide (H2S), a gaseous signaling molecule. The relative contributions of CBS and CSE to H2S generation in different tissues are not known. In this study, we report quantification of CBS and CSE in murine liver and kidney and their contribution to H2S generation in these tissues and in brain at saturating substrate concentrations. We show that CBS protein levels are significantly lower than those of CSE; 60-fold and 20-fold in liver and kidney, respectively. Each enzyme is more abundant in liver compared with kidney, twofold and sixfold for CBS and CSE, respectively. At high substrate concentrations (20 mM each cysteine and homocysteine), the capacity for liver H2S production is approximately equal for CBS and CSE, whereas in kidney and brain, CBS constitutes the major source of H2S, accounting for ∼80% and ∼95%, respectively, of the total output. At physiologically relevant concentrations of substrate, and adjusting for the differences in CBS versus CSE levels, we estimate that CBS accounts for only 3% of H2S production by the transsulfuration pathway enzymes in liver. Antioxid. Redox Signal. 15, 363–372.
A System for the Simultaneous Chemical Synthesis of Different DNA Fragments on Solid Support (1986)

A mechanical apparatus for the simultaneous synthesis of different DNA fragments on solid support is described. This new system allows the use of different kinds of supports and is amenable to automation. Utilizing this apparatus the synthesis of DNA fragments can be speeded up considerably. The effectiveness of the system is demonstrated by the simultaneous synthesis of DNA fragments up to 36 nucleotides long using phosphoamidites as building blocks and controlled pore glass as solid support.
ChemInform Abstract: Ionic Liquid as Catalyst and Reaction Medium: A Simple and Efficient Procedure for Paal—Knorr Furan Synthesis. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pool Boiling Heat Transfer of Alumina-Water, Zinc Oxide-Water and Alumina-Water+Ethylene Glycol Nanofluids (2005)

This investigation conducts pool boiling experiments under saturated conditions (Tsat = 60 °C) using nanofluids as the coolants. Three different nanofluids were tested including zinc oxide (ZnO)-water, aluminum oxide (Al2O3)-water and aluminum oxide (Al2O3)-water+ethylene glycol (ethylene glycol solution). At saturation (Tsat = 60°C), the pool boiling performance of the two pure water based nanofluids were similar. The maximum CHF enhancement as compared to the predicted Zuber’s [1] CHF evaluated at an equivalent saturation temperature is ∼180% for Al2O3-water nanofluids and ∼240% for ZnO-water nanofluids. In both cases, no degradation in the boiling heat transfer rate was observed for lower nanoparticle concentrations. However, higher nanoparticle concentrations demonstrate nucleate boiling heat transfer degradation at high heat fluxes. The dispersion of Al2O3 nanoparticles in various ethylene glycol solutions is also found to enhance CHF by as much as ∼130%. A significant difference in the diameter of individual grains/particles (27 ± 16.3 nm) and the volume weighted average diameter of particles in solution (155 ± 80 nm) indicates that the Al2O3-water nanofluids consist primarily of nanoparticle agglomerates. Gravimetric fractionation of the nanofluid produced nanofluids with particle/particle aggregate average diameters that ranged from 69–346 nm. Over the size range tested, there was no significant CHF dependence on the average particle diameter.
Gold Nanoparticles of Diameter 1.4 nm Trigger Necrosis by Oxidative Stress and Mitochondrial Damage (2009)

Gold nanoparticles (AuNPs) are generally considered nontoxic, similar to bulk gold, which is inert and biocompatible. AuNPs of diameter 1.4 nm capped with triphenylphosphine monosulfonate (TPPMS), Au1.4MS, are much more cytotoxic than 15-nm nanoparticles (Au15MS) of similar chemical composition. Here, major cell-death pathways are studied and it is determined that the cytotoxicity is caused by oxidative stress. Indicators of oxidative stress, reactive oxygen species (ROS), mitochondrial potential and integrity, and mitochondrial substrate reduction are all compromised. Genome-wide expression profiling using DNA gene arrays indicates robust upregulation of stress-related genes after 6 and 12 h of incubation with a 2 x IC50 concentration of Au1.4MS but not with Au15MS nanoparticles. The caspase inhibitor Z-VAD-fmk does not rescue the cells, which suggests that necrosis, not apoptosis, is the predominant pathway at this concentration. Pretreatment of the nanoparticles with reducing agents/antioxidants N-acetylcysteine, glutathione, and TPPMS reduces the toxicity of Au1.4MS. AuNPs of similar size but capped with glutathione (Au1.1GSH) likewise do not induce oxidative stress. Besides the size dependency of AuNP toxicity, ligand chemistry is a critical parameter determining the degree of cytotoxicity. AuNP exposure most likely causes oxidative stress that is amplified by mitochondrial damage. Au1.4MS nanoparticle cytotoxicity is associated with oxidative stress, endogenous ROS production, and depletion of the intracellular antioxidant pool.
Detection ofNeospora Caninumin Tissue Sections Using a Murine Monoclonal Antibody (1993)

A murine monoclonal antibody (MAb 6G7), isotype IgG2a, produced against tachyzoites of Neospora caninum (isolate NC-l) reacted specifically with tachyzoites of N. caninum in an indirect immunofluorescent antibody test. MAb 6G7 did not react with tachyzoites of Toxoplasma gondii, sporozoites of Isospora suis, Eimeria bovis, or E. tenella, or merozoites of E. bovis in the indirect immunofluorescent antibody test. MAb 6G7 reacted positively with both tachyzoites and bradyzoites of N. caninum in an avidin-biotin peroxidase complex immunohistochemical test on formalin-fixed paraffin-embedded tissues. No reaction was observed with the following: tachyzoites and bradyzoites of T. gondii, T. gondii-like parasites, or Hammondia hammondi; bradyzoites of Frenkelia microti; schizonts and merozoites of Sarcocystis-like organisms; schizonts, sarcocysts, and oocysts/sporocysts of S. cruzi; schizonts and merozoites of S. canis; schizonts of S. hirsuta, S. tenella, and S. capracanis; merozoites of S. neurona and S. neurona-like organisms, E. bovis, or Haemoproteus sp.; bradyzoites and merozoites of S. montanaensis; bradyzoites of S. odocoileocanis, S. cruzi, and S. tenella; meronts, sexual stages, and caryocysts of Caryospora sp. and C. bigenetica; micromerozoites, macromerozoites, and schizonts of Hepatozoon canis; sporozoites, sexual stages, and oocysts of Cryptosporidium parvum and C. baileyi; trophozoites of Monocystis Zumbrici, Tritrichomonas foetus, and Balantidium coli; tissue cysts and bradyzoites of Besnoitia sp. and B. jellisoni; amastigotes of Leishmania sp.; and trophic theronts of Ichthyopthirius multifilis. MAb 6G7 reacted with tachyzoites and bradyzoites of N. caninum in natural and experimental infections in dogs, cattle, mice, rats, sheep, and goats, indicating that host origin of the tissues did not affect the performance of the test.
Characterization of germline copy number variation in high‐risk African American families with prostate cancer (2012)

The duplication at 14q32.33 encompasses IGHG3 gene which has been shown to have both significant gains in copy number as well as overexpression in prostate tumors in African Americans. These CNVs may represent a component of genetic predisposition which contributes to the high prevalence and mortality of prostate cancer in African American men.
Auto-update (2007)

Internet content is increasingly available for mobile users. Mobile devices are capable of delivering not only full Web pages but also other Web content such as podcasts and RSS feeds. Today, cost, speed of data transfer, and network coverage are among the biggest remaining concerns for mobile Web users. It would be useful to have the interesting content readily available on the device when the user wants to access it. Battery and memory limitations together with the cost of data transfer require delicate content prefetching, as loading content carelessly could result in overloading of device resources and a huge phone bill. This article introduces an Auto-update concept that lets the users control the costs and the mobile device resources by means of high level profiles that hide underlying complexity from the users. We tested the usefulness of the Auto-update prototype in a smallscale field study, and the results indicate that Auto-update is especially useful for prefetching feeds.