gebhart/patrepeval huggingface dataset:
Structure-based programming of lymph-node targeting in molecular vaccines (2014)

In cancer patients, visual identification of sentinel lymph nodes (LNs) is achieved by the injection of dyes that bind avidly to endogenous albumin, targeting these compounds to LNs where they are efficiently filtered by resident phagocytes1,2. Here we translate this “albumin hitchhiking” approach to molecular vaccines, via the synthesis of amphiphiles (amph-vaccines) comprised of an antigen or adjuvant cargo linked to a lipophilic albumin-binding tail by a solubility-promoting polar polymer chain. Structurally-optimized CpG-DNA/peptide amph-vaccines exhibited dramatic increases in LN accumulation and decreased systemic dissemination relative to their parent compounds, leading to 30-fold increases in T-cell priming and enhanced anti-tumor efficacy while greatly reducing systemic toxicity. Amph-vaccines provide a simple, broadly-applicable strategy to simultaneously increase the potency and safety of subunit vaccines. *Correspondence to:
Extending dictionary-based entity extraction to tolerate errors (2010)

Entity extraction (also known as entity recognition) extracts entities (e.g., person names, locations, companies) from text. Approximate (dictionary-based) entity extraction is a recent trend to improve extraction quality, which extracts substrings in text that approximately match predefined entities in a given dictionary. In this paper, we study the problem of approximate entity extraction with edit-distance constraints. A straightforward method first extracts all substrings from the text and then for each substring identifies its similar entities from the dictionary using existing methods for approximate string search. However many substrings of the text have overlaps, and we have an opportunity to utilize the shared computation across the overlaps to avoid unnecessary duplicate computations. To this end, we propose a heap-based framework to efficiently extract entities. We have implemented our techniques, and the experimental results show that our method achieves high performance and outperforms existing studies significantly.
The Isolation and Physiology of Inhibin and Related Proteins (1989)

Inhibin, a glycoprotein that preferentially suppresses follicle-stimulating hormone (FSH) secretion, has been isolated from follicular fluid as a heterodimer of two dissimilar subunits linked by disulphide bonds. The larger subunit is termed alpha and the smaller is designated beta. Two forms of inhibin termed A and B have been isolated, the differences being due to variations in the amino acid sequence of the beta-subunit; Inhibin A consists of alpha-beta and Inhibin B of alpha-beta B. Dimers of the beta-subunit, termed activins, have also been found in follicular fluid; these stimulate pituitary FSH secretion. Inhibin is produced in the female by the granulosa cell and corpus luteum under the control of FSH and luteinizing hormone (LH), respectively. The levels in serum rise to peak at mid-cycle and in the mid-luteal phase of the human menstrual cycle, and decline prior to menstruation. In pregnancy, the late-luteal phase decline in inhibin does not occur and the levels increase slowly. Studies suggest that the levels in pregnancy arise from an embryonic source, particularly the placenta. In the male, inhibin is produced by the Sertoli cells under the control of FSH by mechanisms involving cyclic adenosine 3', 5'-monophosphate. Testosterone exerts a minor inhibitory control at supraphysiological levels (10(-5) M), but human chorionic gonadotropin stimulation results paradoxically in a rise in serum inhibin levels. Disruption of spermatogenesis in the rat by cryptorchidism, heat treatment, or efferent duct ligation results in a decline in inhibin levels and a rise in FSH levels, findings consistent with the negative feedback action of inhibin on FSH secretion. As well as their roles in the reproductive system, inhibin and activin have more widespread actions in the haemopoietic, immune and nervous systems as evidenced by the finding of mRNA for its subunits in a range of tissues. Other studies have shown actions on erythroid differentiation and on mitotic activity in thymocytes. These actions suggest that inhibin and activin may function as growth factors as well as regulators of FSH.
Estrogen's role in endometrial cancer. (1982)

Data reported since 1975 indicate that the natural hormone estrogen may act as a carcinogen when unopposed by an adequate amount of progesterone. Carcinogenesis may proceed when it is present at a high level for a short time. It is generally accepted that 3 groups of women have been at risk of developing cancer from exogenous estrogen exposure: 1) women who took sequential oral contraceptives; 2) post-menopausal women who received estrogen replacement therapy; 3) girls with ovarian dysgenesis who received unopposed estrogen therapy at puberty. Similarly, 4 groups of women appear to be at risk of developing cancer form endogenous estrogen sources: 1) women with granulosa-cell or theca-cell ovarian tumors; 2) anovulatory women; 3) obese postmenopausal women; 4) women with liver disease. The falling incidence of endometrial cancer associated with diminished estrogen sales is the final proof of an association of estrogen exposure with development of disease.
Coordinating Radiometals of Copper, Gallium, Indium, Yttrium, and Zirconium for PET and SPECT Imaging of Disease (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTCoordinating Radiometals of Copper, Gallium, Indium, Yttrium, and Zirconium for PET and SPECT Imaging of DiseaseThaddeus J. Wadas*†, Edward H. Wong‡§, Gary R. Weisman‡§, and Carolyn J. Anderson*†View Author Information Mallinckrodt Institute of Radiology, Washington University School of Medicine, 510 S. Kingshighway Blvd., Campus Box 8225 St. Louis, Missouri 63110, and Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824-3598* Corresponding authors: Carolyn J. Anderson, phone 314.362.8427, fax 314.362.9940, e-mail [email protected]; Thaddeus J. Wadas, phone 314.362.8441, fax 314.362.9940, e-mail [email protected]†Washington University School of Medicine.‡University of New Hampshire.§Contact information: Edward H. Wong, phone 603-862-1788, fax 603-862-4278, e-mail [email protected]; Gary R. Weisman, phone 603-862-2304, fax 603-862-4278, e-mail [email protected].Cite this: Chem. Rev. 2010, 110, 5, 2858–2902Publication Date (Web):April 23, 2010Publication History Received29 September 2009Published online23 April 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr900325hhttps://doi.org/10.1021/cr900325hreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views12391Altmetric-Citations748LEARN 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 SUBJECTS:Mechanisms of action,Nuclear medicine,Peptides and proteins,Pharmaceuticals,Tumors Get e-Alerts
Regulation of phosducin phosphorylation in retinal rods by Ca2+/calmodulin-dependent adenylyl cyclase. (1996)

The phosphoprotein phosducin (Pd) regulates many guanine nucleotide binding protein (G protein)-linked signaling pathways. In visual signal transduction, unphosphorylated Pd blocks the interaction of light-activated rhodopsin with its G protein (Gt) by binding to the beta gamma subunits of Gt and preventing their association with the Gt alpha subunit. When Pd is phosphorylated by cAMP-dependent protein kinase, it no longer inhibits Gt subunit interactions. Thus, factors that determine the phosphorylation state of Pd in rod outer segments are important in controlling the number of Gts available for activation by rhodopsin. The cyclic nucleotide dependencies of the rate of Pd phosphorylation by endogenous cAMP-dependent protein kinase suggest that cAMP, and not cGMP, controls Pd phosphorylation. The synthesis of cAMP by adenylyl cyclase in rod outer segment preparations was found to be dependent on Ca2+ and calmodulin. The Ca2+ dependence was within the physiological range of Ca2+ concentrations in rods (K1/2 = 230 +/- 9 nM) and was highly cooperative (n app = 3.6 +/- 0.5). Through its effect on adenylyl cyclase and cAMP-dependent protein kinase, physiologically high Ca2+ (1100 nM) was found to increase the rate of Pd phosphorylation 3-fold compared to the rate of phosphorylation at physiologically low Ca2+ (8 nM). No evidence for Pd phosphorylation by other (Ca2+)-dependent kinases was found. These results suggest that Ca2+ can regulate the light response at the level of Gt activation through its effect on the phosphorylation state of Pd.
Synthesis and study of Pt(II)–nitrile complexes. Multinuclear NMR spectra and crystal structures of compounds of the types [Pt(R-CN)Cl3]− and cis and trans-Pt(R-CN)2Cl2 (1996)

Complexes of the type [Pt(R-CN)Cl 3 ] − were synthesized and studied by 1 H, 13 C, and 195 Pt NMR spectroscopies. The 2 J( 195 Pt- 13 C) coupling constants are about 240 Hz. The signals due to the cyano carbon atoms of the coordinated ligands were observed at higher fields than those of the free ligands. The shielding on the cyano carbon increases as the alkyl chain lengthens and also when the branching increases. The 195 Pt signals of all the complexes were observed around −2000 ppm. The crystal structures of (NMe 4 )[Pt(C 3 H 7 -CN)Cl 3 ] (1) and (NMe 4 )[Pt(p-HO-C 6 H 4 -CN)Cl 3 ] (2) were determined. Compound 1 is monoclinic, P2 1 /c, a = 8.384(5), b = 15.336(19), c = 11.759(9) Å, β = 99.52(6)°, Z = 4, R = 0.054, and wR = 0.051. Crystal 2 is tetragonal with a = 16.222(6), c = 12.052(5) Å, Z = 8, R = 0.059, and wR = 0.044. The Pt—CL bond trans to the nitrile ligand is shorter than normal (2.276(3) Å for 1 and 2.264(7) Å for 2) while the two other bonds are normal (2.293(4), 2.287(3) Å for 1 and 2.320(7), 2.275(8) Å for 2). The Pt—N bonds are 1.97(1) Å (1) and 1.92(2) Å (2) and the segments Pt-N≡C-C are linear. Disubstituted compounds were also synthesized and studied by multinuclear NMR. The 195 Pt signals of the cis isomers were observed at lower fields than those of the trans isomers (Δ ≈ 65 ppm), while the 13 C signals of the cyano carbons of the trans isomers were observed at lower fields than those of the cis compounds (Δ ≈ 0.6 ppm). The cis complexes isomerize to the trans compounds upon heating. The crystal structures of cis-(3) and trans-Pt(C 2 H 5 -CN) 2 Cl 2 (4) and also of cis-Pt(p-HO-C 6 H 4 -CN) 2 Cl 2 (5) were determined. Crystal 3 is monoclinic, P2 1 /c, a = 7.506(5), b = 9.539(5), c = 14.823(7) Å, β = 92.31(4)°, Z = 4, R = 0.050, and wR = 0.042. The trans isomer 4 is monoclinic with the Pt atom on an inversion centre, P2 1 /c, a = 5.149(4), b = 9.394(8), c = 10.944(10) Å, β = 97.84(7)°, Z = 4, R = 0.017 and wR = 0.020. Finally, compound 5 is triclinic, P-1, a = 7.464(3), b = 10.712(6), c = 12.291(5) Å, α = 75.63(4)°, β = 75.63(4)°, γ = 80.32(4)°, Z = 2, R = 0.045, and wR = 0.056. The Pt—Cl bond distances for the cis isomers are 2.269(5), 2.270(4) Å for 3 and 2.274(2), 2.279(3) Å for 5 while they are 2.289(3) Å for the trans isomer (4). The Pt—N bonds are 1.962(14), 1.988(11) Å (3), 1.972(7), 1.976(7) Å (5) and 1.969(5) Å for 4. Key words: platinum, nitrile, NMR, isomerization, crystal structure.
Enhanced Charge-Collection Efficiencies and Light Scattering in Dye-Sensitized Solar Cells Using Oriented TiO2 Nanotubes Arrays (2006)

We report on the microstructure and dynamics of electron transport and recombination in dye-sensitized solar cells (DSSCs) incorporating oriented TiO2 nanotube (NT) arrays. The morphology of the NT arrays, which were prepared from electrochemically anodized Ti foils, were characterized by scanning and transmission electron microscopies. The arrays were found to consist of closely packed NTs, several micrometers in length, with typical wall thicknesses and intertube spacings of 8-10 nm and pore diameters of about 30 nm. The calcined material was fully crystalline with individual NTs consisting of about 30 nm sized crystallites. The transport and recombination properties of the NT and nanoparticle (NP) films used in DSSCs were studied by frequency-resolved modulated photocurrent/photovoltage spectroscopies. While both morphologies display comparable transport times, recombination was much slower in the NT films, indicating that the NT-based DSSCs have significantly higher charge-collection efficiencies than their NP-based counterparts. Dye molecules were shown to cover both the interior and exterior walls of the NTs. Analysis of photocurrent measurements indicates that the light-harvesting efficiencies of NT-based DSSCs were higher than those found for DSSCs incorporating NPs owing to stronger internal light-scattering effects.
Electrospinning as a New Technique To Control the Crystal Morphology and Molecular Orientation of Polyoxymethylene Nanofibers (2008)

Electrospinning is widely accepted as a simple and versatile technique for producing nanofibers. The present work, however, introduces a new concept of the electrospinning method for controlling the crystal morphology and molecular orientation of the nanofibers through an illustration of a case study of polyoxymethylene (POM) nanofibers. Isotropic and anisotropic electrospun POM nanofibers are successfully prepared by using a stationary collector and a rotating disk collector. By controlling the voltage and the take-up velocity of the disk rotator, the morphology changes between an extended chain crystal (ECC) and a folded chain crystal (FCC) as clarified by a detailed analysis of the X-ray diffraction and polarized infrared spectra of the POM nanofibers. Herman's orientation function and dichroic ratio lead us to a schematic conclusion--that (i) molecular orientation is parallel to the fiber axis in both isotropic and anisotropic POM nanofibers, (ii) a single nanofiber consists of a nanofibril assembly with a size of 60-70 A and tilting at a certain degree, and (iii) the higher the take-up velocity, the smaller the nanofibril under the (9/5) helical structure of the POM chains. It should be emphasized here that the electrospinning method is no longer a single nanofiber producer but that it can be applied as a new instrument to control the morphology and chain orientation characteristics of polymer materials, opening a new research field in polymer science where we can understand the relationship between structure at the molecular level and the properties and performance at the macroscopic level.
Contracting CAG/CTG repeats using the CRISPR-Cas9 nickase (2016)

CAG/CTG repeat expansions cause over 13 neurological diseases that remain without a cure. Because longer tracts cause more severe phenotypes, contracting them may provide a therapeutic avenue. No currently known agent can specifically generate contractions. Using a GFP-based chromosomal reporter that monitors expansions and contractions in the same cell population, here we find that inducing double-strand breaks within the repeat tract causes instability in both directions. In contrast, the CRISPR-Cas9 D10A nickase induces mainly contractions independently of single-strand break repair. Nickase-induced contractions depend on the DNA damage response kinase ATM, whereas ATR inhibition increases both expansions and contractions in a MSH2- and XPA-dependent manner. We propose that DNA gaps lead to contractions and that the type of DNA damage present within the repeat tract dictates the levels and the direction of CAG repeat instability. Our study paves the way towards deliberate induction of CAG/CTG repeat contractions in vivo.
Bladder cancer: current optimal intravesical treatment. (2005)

Superficial bladder cancer can be treated surgically, but patients are at high risk for recurrence. Tumors are categorized as low, intermediate, and high-risk based on grade, stage, and pattern of recurrence. Low-risk tumors are best treated with a single instillation of chemotherapy (thiotepa, doxorubicin, or mitomycin) (Lamm, 2002). Though effective, the toxicity of bacillus Calmette-Guerin immunotherapy (BCG) restricts its use to treat higher-grade tumors. Intermediate risk tumors can be treated with chemotherapy as well, but will often require immunotherapy. High-risk tumors are best treated with intravesical BCG using a 3-week maintenance schedule. Side effects of BCG immunotherapy can be decreased by logarithmic reductions in dose. Patients who fail BCG may be rescued with BCG plus interferon alfa or radical cystectomy.
(BDP)CuH:  A “Hot” Stryker's Reagent for Use in Achiral Conjugate Reductions (2007)

A ligand-modified, economical version of Stryker's reagent (SR) has been developed based on a bidentate, achiral bis-phosphine. Generated in situ, "(BDP)CuH" smoothly effects conjugate reductions of a variety of unsaturated substrates, including those that are normally unreactive toward SR. Substrate-to-ligand ratios typically on the order of 1000-10000:1 can be used leading to products in high yields.
A multi-drop in-house ADSL distribution network (2002)

In this paper, we propose an all digital, multi-drop in-house asymmetric digital subscriber line (ADSL) distribution network, utilizing the existing wiring on customer premises. The proposed in-house network is based on a simple quadrature phase-shift keyed (QPSK) signaling format with frequency diversity. The network signal resides between approximately 1.5 MHz to 20 MHz of the frequency band and will not interfere with existing POTS and ADSL signals. The proposed in-house ADSL network will allow multiple users in the same household to share a single, high speed (6+ Mbps) ADSL line with only one ADSL remote transceiver unit plus a number of inexpensive service modules. This flexible, cost-effective solution will, therefore, eliminate the need for expensive internal rewiring or wireless distribution of ADSL signal to service multiple users in the same household.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3) (2002)

FGFR1, a transmembrane receptor tyrosine kinase for fibroblast growth factors, is constitutively activated by chromosomal translocations in an atypical stem-cell myeloproliferative disorder. The FGFR1 tyrosine domain is fused to dimerization domains encoded by 4 alternative genes: FOP at 6q27, CEP110 at 9q33, FIM/ZNF198 at 13q12, and BCR at 22q11. In this study, we report the molecular cloning of the t(8;19)(p12;q13.3), the fifth translocation associated with this syndrome. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis and fluorescence in situ hybridization (FISH) demonstrated that the translocation resulted in a long terminal repeat of human endogenous retrovirus gene (HERV-K)/fibroblast growth factor receptor 1 (FGFR1) fusion transcript that incorporated 5' sequences from HERV-K fused in frame to 3' FGFR1 sequences encoding the kinase domain. RT-PCR detected only 1 of the 2 possible fusion transcripts, HERV-K/FGFR1.
Amyloid β and Amylin Fibrils Induce Increases in Proinflammatory Cytokine and Chemokine Production by THP‐1 Cells and Murine Microglia (2000)

Activated microglia surrounding amyloid beta-containing senile plaques synthesize interleukin-1, an inflammatory cytokine that has been postulated to contribute to Alzheimer's disease pathology. Studies have demonstrated that amyloid beta treatment causes increased cytokine release in microglia and related cell cultures. The present work evaluates the specificity of this cellular response by comparing the effects of amyloid beta to that of amylin, another amyloidotic peptide. Both lipopolysaccharide-treated THP-1 monocytes and mouse microglia showed significant increases in mature interleukin-1beta release 48 h following amyloid beta or human amylin treatment, whereas nonfibrillar rat amylin had no effect on interleukin-1beta production by THP-1 cells. Lipopolysaccharide-stimulated THP-1 cells treated with amyloid beta or amylin also showed increased release of the proinflammatory cytokines tumor necrosis factor-alpha and interleukin-6, as well as the chemokines interleukin-8 and macrophage inflammatory protein-1alpha and -1beta. THP-1 cells incubated with fibrillar amyloid beta or amylin in the absence of lipopolysaccharide also showed significant increases of both interleukin-1beta and tumor necrosis factor-alpha mRNA. Furthermore, treatment of THP-1 cells with amyloid fibrils resulted in an elevated expression of the immediate-early genes c-fos and junB. These studies provide further evidence that fibrillar amyloid peptides can induce signal transduction pathways that initiate an inflammatory response that is likely to contribute to Alzheimer's disease pathology.
TRANSPARENT TESTA 19 is involved in the accumulation of both anthocyanins and proanthocyanidins in Arabidopsis (2003)

Flavonoid compounds such as anthocyanins and proanthocyanidins (PAs; so-called condensed tannins) have a multitude of functions in plants. They must be transported from the site of synthesis in the cytosol to their final destination, the vacuoles. Three models have been proposed for sequestering anthocyanins in vacuoles, but the transport machinery for PAs is poorly understood. Novel Arabidopsis mutants, transparent testa 19 (tt19), which were induced by ion beam irradiation, showed a great reduction of anthocyanin pigments in the vegetative parts as well as brown pigments in the seed coat. The TT19 gene was isolated by chromosome walking and a candidate gene approach, and was shown to be a member of the Arabidopsis glutathione S-transferase (GST) gene family. Heterologous expression of a putative ortholog, petunia anthocyanin 9 (AN9), in tt19 complemented the anthocyanin accumulation but not the brown pigmentation in the seed coat. This suggests that the TT19 gene is required for vacuolar uptake of anthocyanins into vacuoles, but that it has also a function different from that of AN9. The depositional pattern of PA precursors in the mutant was different from that in the wild type. These results indicate that TT19 participates in the PA pathway as well as the anthocyanin pathway of Arabidopsis. As involvement of GST in the PA pathway was previously considered unlikely, the function of TT19 in the PA pathway is also discussed in the context of the putative transporter for PA precursors.