gebhart/patrepeval huggingface dataset:
The binding site for the beta gamma subunits of heterotrimeric G proteins on the beta-adrenergic receptor kinase. (1993)

The beta gamma subunits of heterotrimeric G proteins play important roles in regulating receptor-stimulated signal transduction processes. Recently appreciated among these is their role in the signaling events that lead to the phosphorylation and subsequent desensitization of muscarinic cholinergic (Haga, K., and Haga, T. (1992) J. Biol. Chem. 267, 2222-2227) and beta-adrenergic (Pitcher, J. A., Inglese, J., Higgins, J. B., Arriza, J. L., Casey, P. J., Kim, C., Benovic, J. L., Kwatra, M. M., Caron, M. G., and Lefkowitz, R. J. (1992) Science 257, 1264-1267) receptors. Beta gamma mediates the membrane targeting of the beta-adrenergic receptor kinase (beta ARK), in response to receptor activation, through a specific beta ARK-beta gamma interaction. This process utilizes the membrane-anchoring properties of the isoprenylated gamma subunit of beta gamma. In the present study, we have employed three distinct approaches to identify the region within the carboxyl terminus of beta ARK which binds beta gamma and thereby results in membrane translocation. We studied the ability of beta gamma to enhance the enzymatic activity of a series of truncated mutants of bovine beta ARK1, the ability of glutathione S-transferase fusion proteins containing various lengths of the carboxyl terminus of beta ARK to bind beta gamma subunits, and the ability of synthetic peptides comprised of beta ARK sequences to inhibit beta gamma activation of beta ARK1. We find that the minimal beta gamma binding domain of beta ARK is localized to a 125-amino acid residue stretch, the distal end of which is located 19 residues from the carboxyl terminus. A single 28-mer peptide (Trp643 to Ser670) derived from this sequence effectively inhibited beta gamma activation of beta ARK1, with an IC50 of 76 microM. The identification of this "beta gamma binding domain" on beta ARK and the development of peptide inhibitors provide important tools for the study of G protein-coupled receptor desensitization, as well as for the investigation of beta gamma activation of other G protein-effector systems.
Interleukin 6 production in experimental cerebral malaria: modulation by anticytokine antibodies and possible role in hypergammaglobulinemia. (1990)

The production of Interleukin 6 (IL-6) was studied during experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA (PbA) infection. IL-6 is present in the serum of mice with ECM, the highest concentrations being observed in mice with full-blown neurological syndrome. High IL-6 levels were also observed, however, in the absence of pathology in nonlethal malaria infection. These data suggest that IL-6 is produced in large amounts during malaria infection, but does not play a major role in the pathogenesis of ECM. A modulation of IL-6 production in ECM was achieved by in vivo treatment with other anticytokine antibodies: antibodies to interferon (IFN-gamma) or to tumor necrosis factor (TNF) abolished the rise of IL-6, while anti-IL-3 and anti-granulocyte/macrophage colony-stimulating factor antibodies only partially prevented this rise, suggesting that the two cytokines IFN-gamma and TNF are important intermediates in IL-6 production. Passive immunization against IL-6 did not prevent ECM, but significantly reduced serum IgG levels in malaria-infected mice. Thus, by its effects on B cells, IL-6 may be involved in hypergammaglobulinemia and immune-complex diseases, e.g., glomerulonephritis observed during malaria infection.
Arabidopsis thaliana expresses a second functional phytochelatin synthase (2001)

Phytochelatins represent a major detoxifying pathway for heavy metals in plants and many other organisms. The Arabidopsis thaliana CAD1 (=AtPCS1) gene encodes a phytochelatin synthase and cad1 mutants are phytochelatin deficient and cadmium hypersensitive. The Arabidopsis genome contains a highly homologous gene, AtPCS2, of which expression and function were studied in order to understand the apparent non-redundancy of the two genes. Low constitutive AtPCS2 expression is detected in all plant organs analyzed. The AtPCS2 gene encodes a functional phytochelatin synthase as shown by expression in Saccharomyces cerevisiae and the complementation of a Schizosaccharomyces pombe phytochelatin synthase knockout strain.
Uniform, Axial‐Orientation Alignment of One‐Dimensional Single‐Crystal Silicon Nanostructure Arrays (2005)

Neatly scratching the surface: A facile etching technique assisted by a silver-nanoparticle network to produce large-area 1D silicon nanostructure arrays with desired orientation and doping characteristics is demonstrated (see picture). A mechanism for the highly selective etching is proposed on the basis of experimental evidence.
Identification of a new family of human epithelial protein kinases containing two leucine/isoleucine‐zipper domains (1993)

Using the polymerase chain reaction to study mRNA expressed in human epithelial tumor cells, a member of a new family of protein kinases was identified. The catalytic domain of this kinase has amino-acid-sequence similarity to both the Tyr-specific and the Ser/Thr-specific kinase classes. Clones representing two members of this new family have been isolated from a human colonic epithelial cDNA library and sequenced. The predicted amino-acid sequences of these clones reveal that, in addition to the unusual nature of their kinase catalytic domains, they contain two Leu/Ile-zipper motifs and a basic sequence, near their C-termini. As they possess domains associated with proteins from two distinct functional groups, these kinases have been named mixed-lineage kinases (MLK) 1 and 2. mRNA from MLK1 has been found to be expressed in epithelial tumor cell lines of colonic, breast and esophageal origin. The MLK1 gene has been mapped to human chromosome 14q24.3-31.
Thermostable endoglucanases in the liquefaction of hydrothermally pretreated wheat straw (2011)

Endoglucanases were shown to have a superior ability to rapidly reduce the viscosity of the 15% (w/w; dry matter) hydrothermally pretreated wheat straw. Based on temperature profiling studies, Thermoascus aurantiacus EGII/Cel5A was the most promising enzyme for biomass liquefaction. Even though they were not optimized for saccharification, many of the thermostable enzyme mixtures had superior hydrolytic properties compared with the commercial reference enzymes at 55°C.
Aberrant expression of high mobility group chromosomal protein 14 affects cellular differentiation (1993)

High mobility group (HMG) 14 is a ubiquitous chromosomal protein that binds specifically to nucleosomal DNA and may be involved in a process that confers distinct properties to the chromatin structure of transcriptionally active genes. To explore the involvement of this protein in regulation of gene expression, we studied the effect of aberrant expression of HMG-14 protein on cellular differentiation. We produced stably transfected C2C12 mouse myoblasts expressing the human HMG-14 protein under the control of the mouse mammary tumor virus promoter. Transformed colonies retained their potential do differentiate into myotubes. Induction of human HMG-14 expression by dexamethasone inhibited the myogenic process. Revertant colonies, which lost the ability to express human HMG-14, regained the ability to differentiate into myotubes. Inhibition of myoblast differentiation by aberrantly expressed HMG-14 correlated with down-regulation of myogenic determination factors. The results suggest that proper cellular differentiation requires regulated expression of HMG-14 protein and are consistent with the possibility that this protein may be involved in gene regulation.
S2‐04–01: Recommendations and outcomes of disease‐modifying drugs (2008)

After symptomatic treatments, the new target for therapeutic approaches in the field of Alzheimer's disease (AD) is the development of Disease Modifying Agents. The concept of disease-modification in AD is subject to debate and these trials raise many questions. Which population(s) should be studied? For how long? With which principal and secondary criteria? Are surrogate markers available? Complex diseases like Alzheimer's Disease have many different, although interdependent, outcomes. Two International task Force (Lancet neurology 2007). We present the point of vue of 2 European Task Force on disease modifying trials methodology and on endpoints to be used in clinical trials in Alzheimer's disease, agreed under the auspices of the European Alzheimer Disease Consortium (EADC). We present here: the concept of disease modification; the study designs to be used; the role for biomarkers; and risk benefit and pharmaco-economic issues. Moreover suitable endpoints are suggested for the following types of trials: primary and secondary preventive trials, very early, mild, moderate, severe, and disease modifying AD trials. A clear and consensual definition of endpoints is a key element for the success of further clinical trials in the field and will allow comparison of data across studies.
Magnetic‐resonance imaging techniques for detection of elasticity variation (1995)

The relative success of manual palpation in the detection of breast cancer would suggest that a method for remote palpation resulting in a measurement of tissue elasticity could provide a diagnostic tool for detecting cancerous lesions deeper within the breast. This presumption is based in part on the excellent contrast between neoplastic and normal tissue due to the large (orders of magnitude) relative variation in the shear elastic modulus. By comparison, the bulk deformational modulus maintains the same value to within 20% for most soft tissues. A specific method of magnetic-resonance imaging (MRI) which measures tissue displacements has been used in experiments with a phantom containing regions of increased Young's modulus as a demonstration. The spatial modulation of magnetization technique uses the displacement of a spatial grid pattern caused by spin saturation to track regional motion. Mathematical reconstruction of the distribution of elastic moduli is shown for select examples. Any modality, e.g., MRI, ultrasound, etc., which can detect local tissue motion with sufficient spatial resolution can be used and therefore the results presented here should give an indication of the utility of such motion tracking techniques to future measurement of tissue elasticity.
Compartmentalized ATP pools produced from adenosine are nuclear pools (1980)

Incubation of African green monkey kidney (BS-C-1) cells and mouse fibroblasts (3T6) in the presence of adenosine for 4 hours resulted in increases in the nuclear compartment pools of adenosine 5'-triphosphate (ATP) and nuclear ATP/adenosine 5'-diphosphate (ADP) ratios. Adenine and inosine, which yield increases in total cellular ATP pools and ATP/ADP ratios similar to those promoted by adenosine, do not produce similar increases in the nuclear compartment. Adenosine-promoted increases in nuclear ATP pools were higher in the untransformed, serially propagated, BS-C-1 cells than in the spontaneously transformed 3T6 cells. Adenosine-promoted compartmentalized ATP pools in primary chick embryo fibroblasts were reduced upon transformation of these cells with Rous sarcoma virus, resulting in free mixing of all of the ATP pools synthesized from various salvage precursors. The growth regulatory properties of the nuclear compartment pools of adenine nucleotides is suggested by the big increases in nuclear ATPase and adenosine 5'-monophosphate (AMP) deaminase activities upon the entry of 3T6 cells into the S phase of their cycle. These enzymatic activities would tend to lower the nuclear ATP/ADP ratios and reduce the total adenine nucleotide pools in these nuclei respectively--conditions which were shown by earlier in vitro studies to be favorable to DNA replication.
Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme (2012)

Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes, codon bias is stronger at evolutionarily conserved residues, favoring codons recognized by abundant tRNAs. Although this observation suggests an overall pattern of selection for translation speed and/or accuracy, other work indicates that transcript structure or binding motifs drive codon usage. However, our understanding of codon bias evolution is constrained by limited experimental data on the fitness effects of altering codons in functional genes. To bridge this gap, we generated synonymous variants of a key enzyme-coding gene in Methylobacterium extorquens. We found that mutant gene expression, enzyme production, enzyme activity, and fitness were all significantly lower than wild-type. Surprisingly, encoding the gene using only rare codons decreased fitness by 40%, whereas an allele coded entirely by frequent codons decreased fitness by more than 90%. Increasing gene expression restored mutant fitness to varying degrees, demonstrating that the fitness disadvantage of synonymous mutants arose from a lack of beneficial protein rather than costs of protein production. Protein production was negatively correlated with the frequency of motifs with high affinity for the anti-Shine-Dalgarno sequence, suggesting ribosome pausing as the dominant cause of low mutant fitness. Together, our data support the idea that, although a particular set of codons are favored on average across a genome, in an individual gene selection can either act for or against codons depending on their local context.
Discovery of 3,3‘-(2,4-Diaminopteridine-6,7-diyl)diphenol as an Isozyme-Selective Inhibitor of PI3K for the Treatment of Ischemia Reperfusion Injury Associated with Myocardial Infarction (2007)

In studies aimed toward identifying effective and safe inhibitors of kinase signaling cascades that underlie ischemia/reperfusion (I/R) injury, we synthesized a series of pteridines and pyridopyrazines. The design strategy was inspired by the examination of naturally occurring PI3K inhibitors such as wortmannin and quercetin, and building a pharmacophore-based model used for optimization. Structural modifications led to hybrid molecules which incorporated aminopyrimidine and aminopyridine moieties with ATP mimetic characteristics into the pharmacophore motifs to modulate kinase affinity and selectivity. Elaborations involving substitutions of the 2 and 4 positions of the pyrimidine or pyridine ring and the 6 and 7 positions of the central pyrazine ring resulted in in vivo activity profiles which identified potent inhibitors of vascular endothelial growth factor (VEGF) induced vascular leakage. Pathway analysis identified a diaminopteridine-diphenol as a potent and selective phosphatidylinositol-3-kinase (PI3K) inhibitor. The structure-activity relationship studies of various analogues of diaminopteridine-diphenol-based on biochemical assays resulted in potent inhibitors of PI3K.
Interferon Stimulated Gene 15 Conjugates to Endometrial Cytosolic Proteins and Is Expressed at the Uterine-Placental Interface throughout Pregnancy in Sheep (2004)

-stimulated gene 15 (ISG15) is a ubiquitin homolog expressed in uteri of ruminants in response to interferon (IFN)-and is also induced during pregnancy in the uteri of mice, pigs, humans, and baboons. This study examined expression of ISG15 and its conjugation to target proteins in the ovine uterus beyond the period of IFN secretion by the conceptus. Although steady-state levels of ISG15 mRNA decreased after d 25 of pregnancy, ISG15 persisted in endometrium through d 120. In situ hybridization and immunocytochemistry localized ISG15 across the entire uterine wall through d 25, after which expression was restricted to endometrial stroma along the maternal-placental interface. Western blots revealed ISG15 and ISG15-conjugated proteins in endometrium. Treatment of ovariectomized sheep with progesterone and IFN increased both free and conjugated ISG15. These results are the first to show in vivo regulation of ISG15 function (i.e. conjugation to target proteins) by a type I IFN in the uterus of any species and that ISG15 is expressed at contacts between the placenta and uterus when trophectoderm no longer produces IFN. Interestingly, mRNA for the type II IFN was present in the endometrial stromal compartment on d 15-50, which may stimulate the synthesis of ISG15 through later pregnancy. We hypothesize that ISG15 is not merely a consequence of an antiviral state induced by trophoblast IFN but represents a critical component of the microenvironment at the uterine-placental interface during the progressive events of conceptus development, implantation, and placentation in sheep and perhaps other mammalian species.
Inhibition of Protein Kinase Akt1 by Apoptosis Signal-regulating Kinase-1 (ASK1) Is Involved in Apoptotic Inhibition of Regulatory Volume Increase (2010)

Most animal cell types regulate their cell volume after an osmotic volume change. The regulatory volume increase (RVI) occurs through uptake of NaCl and osmotically obliged water after osmotic shrinkage. However, apoptotic cells undergo persistent cell shrinkage without showing signs of RVI. Persistence of the apoptotic volume decrease is a prerequisite to apoptosis induction. We previously demonstrated that volume regulation is inhibited in human epithelial HeLa cells stimulated with the apoptosis inducer. Here, we studied signaling mechanisms underlying the apoptotic inhibition of RVI in HeLa cells. Hypertonic stimulation was found to induce phosphorylation of a Ser/Thr protein kinase Akt (protein kinase B). Shrinkage-induced Akt activation was essential for RVI induction because RVI was suppressed by an Akt inhibitor, expression of a dominant negative form of Akt, or small interfering RNA-mediated knockdown of Akt1 (but not Akt2). Staurosporine, tumor necrosis factor-alpha, or a Fas ligand inhibited both RVI and hypertonicity-induced Akt activation in a manner sensitive to a scavenger for reactive oxygen species (ROS). Any of apoptosis inducers also induced phosphorylation of apoptosis signal-regulating kinase 1 (ASK1) in a ROS-dependent manner. Suppression of (ASK1) expression blocked the effects of apoptosis, in hypertonic conditions, on both RVI induction and Akt activation. Thus, it is concluded that in human epithelial cells, shrinkage-induced activation of Akt1 is involved in the RVI process and that apoptotic inhibition of RVI is caused by inhibition of Akt activation, which results from ROS-mediated activation of ASK1.
π-Conjugated Polymers for Organic Electronics and Photovoltaic Cell Applications (2010)

The optoelectronic properties of polymeric semiconductor materials can be utilized for the fabrication of organic electronic and photonic devices. When key structural requirements are met, these materials exhibit unique properties such as solution processability, large charge transporting capabilities, and/or broad optical absorption. In this review recent developments in the area of π-conjugated polymeric semiconductors for organic thin-film (or field-effect) transistors (OTFTs or OFETs) and bulk-heterojunction photovoltaic (or solar) cell (BHJ-OPV or OSC) applications are summarized and analyzed.
CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice (2016)

Targeted gene disrupted mice can be efficiently generated by expressing a single guide RNA (sgRNA)/CAS9 complex in the zygote. However, the limited success of complicated genome editing, such as large deletions, point mutations, and knockins, remains to be improved. Further, the mosaicism in founder generations complicates the genotypic and phenotypic analyses in these animals. Here we show that large deletions with two sgRNAs as well as dsDNA-mediated point mutations are efficient in mouse embryonic stem cells (ESCs). The dsDNA-mediated gene knockins are also feasible in ESCs. Finally, we generated chimeric mice with biallelic mutant ESCs for a lethal gene, Dnajb13, and analyzed their phenotypes. Not only was the lethal phenotype of hydrocephalus suppressed, but we also found that Dnajb13 is required for sperm cilia formation. The combination of biallelic genome editing in ESCs and subsequent chimeric analysis provides a useful tool for rapid gene function analysis in the whole organism.
Strong Internal and External Luminescence as Solar Cells Approach the Shockley–Queisser Limit (2012)

Absorbed sunlight in a solar cell produces electrons and holes. However, at the open-circuit condition, the carriers have no place to go. They build up in density, and ideally, they emit external luminescence that exactly balances the incoming sunlight. Any additional nonradiative recombination impairs the carrier density buildup, limiting the open-circuit voltage. At open circuit, efficient external luminescence is an indicator of low internal optical losses. Thus, efficient external luminescence is, counterintuitively, a necessity for approaching the Shockley–Queisser (SQ) efficiency limit. A great solar cell also needs to be a great light-emitting diode. Owing to the narrow escape cone for light, efficient external emission requires repeated attempts and demands an internal luminescence efficiency 90%.
The isolation of strand-specific nicking endonucleases from a randomized SapI expression library (2004)

The Type IIS restriction endonuclease SapI recognizes the DNA sequence 5'-GCTCTTC-3' (top strand by convention) and cleaves downstream (N1/N4) indicating top- and bottom-strand spacing, respectively. The asymmetric nature of DNA recognition presented the possibility that one, if not two, nicking variants might be created from SapI. To explore this possibility, two parallel selection procedures were designed to isolate either top-strand nicking or bottom-strand nicking variants from a randomly mutated SapI expression library. These procedures take advantage of a SapI substrate site designed into the expression plasmid, which allows for in vitro selection of plasmid clones possessing a site-specific and strand-specific nick. A procedure designed to isolate bottom-strand nicking enzymes yielded Nb.SapI-1 containing a critical R420I substitution near the end of the protein. The top-strand procedure yielded several SapI variants with a distinct preference for top-strand cleavage. Mutations present within the selected clones were segregated to confirm a top-strand nicking phenotype for single variants Q240R, E250K, G271R or K273R. The nature of the amino acid substitutions found in the selected variants provides evidence that SapI may possess two active sites per monomer. This work presents a framework for establishing the mechanism of SapI DNA cleavage.
Dihydropyridopyrazinones and Dihydropteridinones as Corticotropin-Releasing Factor-1 Receptor Antagonists:  Structure−Activity Relationships and Computational Modeling (2007)

The CRF antagonist pharmacophore is a heterocyclic ring bearing a critical hydrogen-bond acceptor nitrogen and an orthogonal aromatic ring. CRFR1 antagonists have shown a 40-fold and 200-fold loss in potency against the CRFR1 H199V and M276I mutant receptors, suggesting key interactions with these residues. We have derived a two component computational model that correlates CRFR1 binding affinity within the reported series to antagoinst/H199 complexation energy and M276 hydrophobic contacts.
Low-cost radar surveillance of inland waterways for homeland security applications (2004)

Low-cost radar systems have been developed for homeland security missions. These detect and track small maneuvering craft in the water. The systems consist of a conventional marine radar, a capture card that digitizes the radar signals, and a computer that processes them. We have an experimental system that can monitor western Lake Ontario. It runs in real time, with operator controls, and can store captured radar video. The achieved detection and tracking is demonstrated with recorded datasets. The combination of lower thresholds plus a sophisticated multi-target tracker gives excellent performance.