gebhart/patrepeval huggingface dataset:
Exploration of Dimensions of Estrogen Potency (2011)

The estrogen receptors, ERα and ERβ, are ligand-regulated transcription factors that control gene expression programs in target tissues. The molecular events underlying estrogen action involve minimally two steps, hormone binding to the ER ligand-binding domain followed by coactivator recruitment to the ER·ligand complex; this ligand·receptor·coactivator triple complex then alters gene expression. Conceptually, the potency of an estrogen in activating a cellular response should reflect the affinities that characterize both steps involved in the assembly of the active ligand·receptor·coactivator complex. Thus, to better understand the molecular basis of estrogen potency, we developed a completely in vitro system (using radiometric and time-resolved FRET assays) to quantify independently three parameters: (a) the affinity of ligand binding to ER, (b) the affinity of coactivator binding to the ER·ligand complex, and (c) the potency of ligand recruitment of coactivator. We used this system to characterize the binding and potency of 12 estrogens with both ERα and ERβ. Some ligands showed good correlations between ligand binding affinity, coactivator binding affinity, and coactivator recruitment potency with both ERs, whereas others showed correlations with only one ER subtype or displayed discordant coactivator recruitment potencies. When ligands with low receptor binding affinity but high coactivator recruitment potencies to ERβ were evaluated in cell-based assays, elevation of cellular coactivator levels significantly and selectively improved their potency. Collectively, our results indicate that some low affinity estrogens may elicit greater cellular responses in those target cells that express higher levels of specific coactivators capable of binding to their ER complexes with high affinity.
Role of Bone Marrow-Derived Cells in Presenting MHC Class I-Restricted Tumor Antigens (1994)

Many tumors express tumor-specific antigens capable of being presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules. Antigen presentation models predict that the tumor cell itself should present these antigens to T cells. However, when conditions for the priming of tumor-specific responses were examined in mice, no detectable presentation of MHC class I-restricted tumor antigens by the tumor itself was found. Rather, tumor antigens were exclusively presented by host bone marrow-derived cells. Thus, MHC class I-restricted antigens are efficiently transferred in vivo to bone marrow-derived antigen-presenting cells, which suggests that human leukocyte antigen matching may be less critical in the application of tumor vaccines than previously thought.
Specific expression of soluble adenylyl cyclase in male germ cells (2000)

The cAMP signaling pathway is an important mediator of extracellular signals in organisms from prokaryotes to higher eukaryotes. In mammals two types of adenylyl cyclase synthesize cAMP; a ubiquitous family of transmembrane isoforms regulated by G proteins in response to extracellular signals, and a recently isolated soluble enzyme insensitive to heterotrimeric G protein modulation. Using the very sensitive reverse transcription-polymerase chain reaction (RT-PCR), soluble adenylyl cyclase (sAC) expression is detectable in almost all tissues examined; however, Northern analysis and in situ hybridization indicate that high levels of sAC message are unique to male germ cells. Elevated levels of sAC mRNA are first observed in pachytene spermatocytes and expression increases through spermiogenesis. The accumulation of high levels of message in round spermatids suggests sAC protein plays an important role in the generation of cAMP in spermatozoa, implying possible roles in sperm maturation through the epididymis, capacitation, hypermotility, and/or the acrosome reaction. Mol. Reprod. Dev. 56:6–11, 2000. © 2000 Wiley-Liss, Inc.
Structural and functional characterization of the USP11 deubiquitinating enzyme, which interacts with the RanGTP-associated protein RanBPM (2002)

RanBPM is a RanGTP-binding protein required for correct nucleation of microtubules. To characterize the mechanism, we searched for RanBPM-binding proteins by using a yeast two-hybrid method and isolated a cDNA encoding the ubiquitin-specific protease USP11. The full-length cDNA of USP11 was cloned from a Jurkat cell library. Sequencing revealed that USP11 possesses Cys box, His box, Asp and KRF domains, which are highly conserved in many ubiquitin-specific proteases. By immunoblotting using HeLa cells, we concluded that 921-residue version of USP11 was the predominant form, and USP11 may be a ubiquitous protein in various human tissues. By immunofluorescence assay, USP11 primarily was localized in the nucleus of non-dividing cells, suggesting an association between USP11 and RanBPM in the nucleus. Furthermore, the association between USP11 and RanBPM in vivo was confirmed not only by yeast two-hybrid assay but also by co-immunoprecipitation assays using exogenously expressed USP11 and RanBPM. We next revealed proteasome-dependent degradation of RanBPM by pulse-chase analysis using proteasome inhibitors. In fact, ubiquitinated RanBPM was detected by both in vivo and in vitro ubiquitination assays. Finally, ubiquitin conjugation to RanBPM was inhibited in a dose-dependent manner by the addition of recombinant USP11. We conclude that RanBPM was the enzymic substrate for USP11 and was deubiquitinated specifically.
Effective Resistance and Capacitance in Simplicial Complexes and a Quantum Algorithm (1995)

This paper clarifies a recurrent structural confusion in advanced computation: the tendency to equate Quantum Mechanical (QM) computation and Cognitional Mechanics (CM) solely because both employ non-commutative structures. While the mathematical resemblance is real, the two frameworks operate at fundamentally different ontological layers and therefore govern distinct domains. Quantum computation represents extreme peak performance. Its advantage appears only after a problem has been fully formalized within a closed mathematical system, such as a fixed Hilbert space with well-defined operators and observables. Algorithms like Shor’s and Grover’s demonstrate that, under these conditions, QM can invalidate classical hardness assumptions or achieve dramatic speedups. However, QM neither generates nor reinterprets problems; it presupposes that all semantic uncertainty has already been resolved. Cognitional Mechanics governs the peripheral domain in which problems are formed, redefined, and semantically stabilized. CM models intelligence as a system of non-commutative semantic operations acting on meaning states within an open and evolving semantic manifold. Its non-commutativity is semantic rather than physical: the order of interpretive operations determines which meaning stabilizes, and this process is intrinsically irreversible. Through the example of RSA cryptanalysis, this paper shows that QM and CM are not competing frameworks. QM dominates isolated computational peaks, while CM governs the surrounding periphery that makes such peaks identifiable as problems at all. Recognizing this structural division is necessary to avoid category errors that conflate physical computational power with intelligence itself.
The LMP2A ITAM Is Essential for Providing B Cells with Development and Survival Signals In Vivo (2000)

In Epstein-Barr virus-transformed B cells, known as lymphoblastoid cell lines (LCLs), LMP2A binds the tyrosine kinases Syk and Lyn, blocking B-cell receptor (BCR) signaling and viral lytic replication. SH2 domains in Syk mediate binding to a phosphorylated immunoreceptor tyrosine-based activation motif (ITAM) in LMP2A. Mutation of the LMP2A ITAM in LCLs eliminates Syk binding and allows for full BCR signaling, thereby delineating the significance of the LMP2A-Syk interaction. In transgenic mice, LMP2A causes a developmental alteration characterized by a block in surface immunoglobulin rearrangement resulting in BCR-negative B cells. Normally B cells lacking cognate BCR are rapidly apoptosed; however, LMP2A transgenic B cells develop and survive without a BCR. When bred into the recombinase activating gene 1 null (RAG(-/-)) background, all LMP2A transgenic lines produce BCR-negative B cells that develop and survive in the periphery. These data indicate that LMP2A imparts developmental and survival signals to B cells in vivo. In this study, LMP2A ITAM mutant transgenic mice were generated to investigate whether the LMP2A ITAM is essential for the survival phenotype in vivo. LMP2A ITAM mutant B cells develop normally, although transgene expression is comparable to that in previously described nonmutated LMP2A transgenic B cells. Additionally, LMP2A ITAM mutant mice are unable to promote B-cell development or survival when bred into the RAG(-/-) background or when grown in methylcellulose containing interleukin-7. These data demonstrate that the LMP2A ITAM is required for LMP2A-mediated developmental and survival signals in vivo.
Nuclear factor kappaB nuclear translocation upregulates c-Myc and p53 expression during NMDA receptor-mediated apoptosis in rat striatum. (1999)

Nuclear factor kappaB (NF-kappaB) appears to participate in the excitotoxin-induced apoptosis of striatal medium spiny neurons. To elucidate molecular mechanisms by which this transcription factor contributes to NMDA receptor-triggered apoptotic cascades in vivo, rats were given the NMDA receptor agonist quinolinic acid (QA) by intrastriatal infusion, and the role of NF-kappaB in the induction of apoptosis-related genes and gene products was evaluated. QA administration induced time-dependent NF-kappaB nuclear translocation. The nuclear NF-kappaB protein after QA treatment was comprised mainly of p65 and c-Rel subunits as detected by gel supershift assay. Levels of c-Myc and p53 mRNA and protein were markedly increased at the time of QA-induced NF-kappaB nuclear translocation. Immunohistochemical analysis showed that c-Myc and p53 induction occurred in the excitotoxin-sensitive medium-sized striatal neurons. NF-kappaB nuclear translocation was blocked in a dose-dependent manner by the cell-permeable recombinant peptide NF-kappaB SN50, but not by the NF-kappaB SN50 control peptide. NF-kappaB SN50 significantly inhibited the QA-induced elevation in levels of c-Myc and p53 mRNA and protein. Pretreatment or posttreatment with NF-kappaB SN50, but not the control peptide, also substantially reduced the intensity of QA-induced internucleosomal DNA fragmentation. The results suggest that NF-kappaB may promote an apoptotic response in striatal medium-sized neurons to excitotoxic insult through upregulation of c-Myc and p53. This study also provides evidence indicating an unique signaling pathway from the cytoplasm to the nucleus, which regulates p53 and c-Myc levels in these neurons during apoptosis.
An energy-efficient, multi-agent sensor network for detecting diffuse events (2007)

Monitoring a diffuse event with a wireless sensor network differs from well studied applications such as target tracking and habitat monitoring and therefore we suggest that new approaches are needed. In this paper we propose a novel low power technique based on a multiple agent framework. We show how a set of simple rules can produce complex behavior that encompasses event characterization and data routing. We demonstrate the approach and examine its accuracy and scalability using a simulated gaseous plume monitoring scenario.
Phytoalexins from the Vitaceae: Biosynthesis, Phytoalexin Gene Expression in Transgenic Plants, Antifungal Activity, and Metabolism (2002)

Resistance of plants to infection by phytopathogenic microorganisms is the result of multiple defense reactions comprising both constitutive and inducible barriers. In grapevine, the most frequently observed and best characterized defense mechanisms are the accumulation of phytoalexins and the synthesis of PR-proteins. Particular attention has been given here to stilbene phytoalexins produced by Vitaceae, specifically, their pathway of biosynthesis (including stilbene phytoalexin gene transfer experiments to other plants) and their biological activity together with fungal metabolism.
Fluid-Solid Coupling Analysis of Deep Foundation Pit’s Seepage Under Non-Saturated Conditions (2010)

The phenomenon which micro-artesian seepage effects on foundation Pit with rainfall is a typical non-saturated seepage process. However, underground water seepage and rainfall infiltration during the deep foundation pit’s excavation and support exert a significant impact upon the stability of engineering itself. The authors have given some countermeasures after modeling and calculating of this phenomenon and make an explanation of problems which confronted during deep foundation pit’s excavation and support by relevant theories. Conclude the flow path and velocity around foundation pit through calculation under non-saturated conditions. Then it combined the predictions and practical applications, proposed correspondingly protective measures.
Analysis of myosin heavy chain mRNA expression by RT-PCR (1997)

An assay was developed for rapid and sensitive analysis of myosin heavy chain (MHC) mRNA expression in rodent skeletal muscle. Only 2 microg of total RNA were necessary for the simultaneous analysis of relative mRNA expression of six different MHC genes. We designed synthetic DNA fragments as internal standards, which contained the relevant primer sequences for the adult MHC mRNAs type I, IIa, IIx, IIb as well as the embryonic and neonatal MHC mRNAs. A known amount of the synthetic fragment was added to each polymerase chain reaction (PCR) and yielded a product of different size than the amplified MHC mRNA fragment. The ratio of amplified MHC fragment to synthetic fragment allowed us to calculate percentages of the gene expression of the different MHC genes in a given muscle sample. Comparison with the traditional Northern blot analysis demonstrated that our reverse transcriptase-PCR-based assay was reliable, fast, and quantitative over a wide range of relative MHC mRNA expression in a spectrum of adult and neonatal rat skeletal muscles. Furthermore, the high sensitivity of the assay made it very useful when only small quantities of tissue were available. Statistical analysis of the signals for each MHC isoform across the analyzed samples showed a highly significant correlation between the PCR and the Northern signals as Pearson correlation coefficients ranged between 0.77 and 0.96 (P < 0.005). This assay has potential use in analyzing small muscle samples such as biopsies and samples from pre- and/or neonatal stages of development.
A Study of Smoothing Methods for Language Models Applied to Ad Hoc Information Retrieval (2017)

Language modeling approaches to information retrieval are attractive and promising because they connect the problem of retrieval with that of language model estimation, which has been studied extensively in other application areas such as speech recognition. The basic idea of these approaches is to estimate a language model for each document, and then rank documents by the likelihood of the query according to the estimated language model. A core problem in language model estimation is smoothing, which adjusts the maximum likelihood estimator so as to correct the inaccuracy due to data sparseness. In this paper, we study the problem of language model smoothing and its influence on retrieval performance. We examine the sensitivity of retrieval performance to the smoothing parameters and compare several popular smoothing methods on different test collection.
Binding of Propylene Oxide to Porphyrin− and Salen−M(III) Cations, Where M = Al, Ga, Cr, and Co (2005)

The binding of propylene oxide (PO) to a series of metal cations LM(III)(+), where for L = tetraphenylporphyrin (TPP) M = Al, Ga, Cr, and Co, and for L = (R,R)-N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexenediamine (salen) M = Al and Cr, was studied in the gas phase by electrospray tandem mass spectroscopy, and the relative stabilities of LM(PO)(2)(+) and LM(PO)(+) cations were determined. The chromium(III) and aluminum(III) cations most tenaciously bind PO, and for M = Al, coordination to the TPP ligated metal center was favored relative to salen. For (TPP)M(PO)(2)(+), the dissociation of PO followed the order M = Al > Cr, but for (TPP)M(PO)(+) the dissociation was M = Cr > Al. The single-crystal structural determinations on (R,R-salen)AlOCHMe(S)CH(2)Cl.0.5PO and (R,R-salen)AlO(2)CMe.1.5py grown in neat PO and pyridine, respectively, reveal five-coordinate aluminum(III) centers with the alkoxide/acetate ligands in the axial position of a square-based pyramid. These results are discussed in terms of the reactivity of these metal complexes in ring-opening polymerizations and copolymerizations with PO and CO(2), respectively.
The Epithelial Mucin MUC1 Contains at Least Two Discrete Signals Specifying Membrane Localization in Cells (1996)

The MUC1 gene product (PEM, polymorphic epithelial mucin) is a cell-associated glycoprotein expressed on the apical surface of most simple secretory epithelia. The transmembrane and cytoplasmic domains of MUC1 have been shown to be highly conserved between mammalian species, and it has been shown that this molecule interacts with the actin cytoskeleton. Apical targeting signals in polarized cells have yet to be defined. The mechanism by which MUC1 is targeted and maintained on the apical surface is not known; correct localization, however, would be predicted to be crucial for function. In order to determine which domains of MUC1 were important for this localization, mutational analysis of the protein was undertaken. Using cytoplasmic tail deletion mutants, fusion proteins of MUC1 and CD2, and site-directed mutagenesis, it could be shown that MUC1 appeared to contain at least two motifs involved in apical localization. The first was located in the extracellular domain and was sufficient to confer apical localization on the fusion protein. The second was the Cys-GlnCys (CQC) motif at the junction of the cytoplasmic and transmembrane domains. This sequence was necessary for surface expression. These results suggest that MUC1 contains two discrete motifs important in its apical localization.
Über polyarylenalkenylene und polyheteroarylenalkenylene, 13. Synthesen und charakterisierung von poly (dithieno[3,2‐b: 2′, 2′,3′‐d]thiophen‐2, 6‐diylvinylenarylenvinylen)en und einigen modellverbindungen (1982)

Abstract From Witting‐reactions of dithieno[3,2‐ b : 2′, 3′‐ d ]thiophene‐2, 6‐dicarboxaldephyde ( 1 ) with “mono‐and bis‐Wittig‐salts” of the benzene and thiophene series poly(dithieno[3,2‐ b : 2′,3′‐ d ]‐thiophene‐2,6‐diylvinylenearylenevinylene)s 3a—c and some model compounds 5a—c were obtained. Wittig‐reactions of dithieno[3,2‐ b : 2′,3‐ d ]thiophene‐2‐carboxaldehyde ( 6 ) with “mono‐and bis‐Wittig‐salts” gave model compounds 7a—c and 8a, c . The structures of all compounds were confirmed by elements analyses, IR‐and electronic spectra, those of the model compounds additionally by mass spectra, and in case of sufficient solubility by 1 H NMR spectra. The electrical conductivities of all compounds and the thermooxidactive degradation of the polymers 3a, c were investigated.
Tn5 as a model for understanding DNA transposition (2003)

Tn5 is an excellent model system for understanding the molecular basis of DNA-mediated transposition. Mechanistic information has come from genetic and biochemical investigations of the transposase and its interactions with the recognition DNA sequences at the ends of the transposon. More recently, molecular structure analyses of catalytically active transposase; transposon DNA complexes have provided us with unprecedented insights into this transposition system. Transposase initiates transposition by forming a dimeric transposase, transposon DNA complex. In the context of this complex, the transposase then catalyses four phosphoryl transfer reactions (DNA nicking, DNA hairpin formation, hairpin resolution and strand transfer into target DNA) resulting in the integration of the transposon into its new DNA site. The studies that elucidated these steps also provided important insights into the integration of retroviral genomes into host DNA and the immune system V(D)J joining process. This review will describe the structures and steps involved in Tn5 transposition and point out a biologically important although surprising characteristic of the wild-type Tn5 transposase. Transposase is a very inactive protein. An inactive transposase protein ensures the survival of the host and thus the survival of Tn5.
Adding New Chemistries to the Genetic Code (2010)

The development of new orthogonal aminoacyl-tRNA synthetase/tRNA pairs has led to the addition of approximately 70 unnatural amino acids (UAAs) to the genetic codes of Escherichia coli, yeast, and mammalian cells. These UAAs represent a wide range of structures and functions not found in the canonical 20 amino acids and thus provide new opportunities to generate proteins with enhanced or novel properties and probes of protein structure and function.
An anticancer C-Kit kinase inhibitor is reengineered to make it more active and less cardiotoxic (2007)

Targeting kinases is central to drug-based cancer therapy but remains challenging because the drugs often lack specificity, which may cause toxic side effects. Modulating side effects is difficult because kinases are evolutionarily and hence structurally related. The lack of specificity of the anticancer drug imatinib enables it to be used to treat chronic myeloid leukemia, where its target is the Bcr-Abl kinase, as well as a proportion of gastrointestinal stromal tumors (GISTs), where its target is the C-Kit kinase. However, imatinib also has cardiotoxic effects traceable to its impact on the C-Abl kinase. Motivated by this finding, we made a modification to imatinib that hampers Bcr-Abl inhibition; refocuses the impact on the C-Kit kinase; and promotes inhibition of an additional target, JNK, a change that is required to reinforce prevention of cardiotoxicity. We established the molecular blueprint for target discrimination in vitro using spectrophotometric and colorimetric assays and through a phage-displayed kinase screening library. We demonstrated controlled inhibitory impact on C-Kit kinase in human cell lines and established the therapeutic impact of the engineered compound in a novel GIST mouse model, revealing a marked reduction of cardiotoxicity. These findings identify the reengineered imatinib as an agent to treat GISTs with curbed side effects and reveal a bottom-up approach to control drug specificity.
Controlled-Release, Pegylation, Liposomal Formulations: New Mechanisms in the Delivery of Injectable Drugs (2000)

Pegylation of therapeutic proteins is an established process with new applications. However, not all pegylated proteins are alike, and each requires optimization on a protein-by-protein basis to derive maximum clinical benefit. The language required to describe each pegylated therapeutic protein must be more precise to accurately distinguish each protein's differential pharmacologic properties.