gebhart/patrepeval huggingface dataset:
Molecular characterization of the 5'-UTR of retinal dystrophin reveals a cryptic intron that regulates translational activity. (2010)

An evolutionarily-acquired cryptic intron was identified in the 5'-UTR of the human R-dystrophin transcript. The two abundant R-dystrophin transcripts in the retina showed different translational activities in vitro owing to their differential splicing of the cryptic intron. This evolutionarily-acquired alternative splicing may act as a molecular switch that regulates translation of the R-dystrophin transcript.
The “Perivascular Pump” Driven by Arterial Pulsation Is a Powerful Mechanism for the Distribution of Therapeutic Molecules within the Brain (2006)

We investigated the movement of interstitially infused macromolecules within the central nervous system (CNS) in rats with high and low blood pressure (BP)/heart rate and in rats euthanized immediately before infusion (no heart action). Adeno-associated virus 2 (AAV2), fluorescent liposomes, or bovine serum albumin was infused into rat striatum (six hemispheres per group) by convection-enhanced delivery (CED). After infusion, distribution volumes were evaluated. The rats with high BP/heart rate displayed a significantly larger distribution of the infused molecules within the injected site and more extensive transport of those molecules to the globus pallidus. This difference was particularly apparent for AAV2, for which a 16.5-fold greater distribution of viral capsids was observed in the rats with high BP/heart rate than in the rats with no heartbeat. Similar results were observed for liposomes, despite their larger diameter. The distribution of all infused molecules in all rats that had low or no blood flow was confined to the space around brain blood vessels. These findings show that fluid circulation within the CNS through the perivascular space is the primary mechanism by which viral particles and other therapeutic agents administered by CED are spread within the brain and that cardiac contractions power this process.
Capacity of channels with uncoded side information (1995)

Abstract Parallel independent channels where no encoding is allowed for one of the channels are studied. The Slepian‐Wolf theorem on source coding of correlated sources is used to show that any information source whose entropy rate is below the sum of the capacity of the coded channel and the input/output mutual information of the uncoded channel is transmissible with arbitrary reliability. The converse is also shown. Thus, coding of the side information channel is unnecessary when its mutual information is maximized by the source distribution. Applications to superposed coded/uncoded transmission on Gaussian channels are studied and an information‐theoretic interpretation of Parallel‐Concatenated channel codes and, in particular. Turbo codes is put forth.
Characterization and cloning of fasciclin I and fasciclin II glycoproteins in the grasshopper. (1988)

Monoclonal antibodies were previously used to identify two glycoproteins, called fasciclin I and II (70 and 95 kDa, respectively), which are expressed on different subsets of axon fascicles in the grasshopper (Schistocerca americana) embryo. Here the monoclonal antibodies were used to purify these two membrane-associated glycoproteins for further characterization. Fasciclin II appears to be an integral membrane protein, whereas fasciclin I is an extrinsic membrane protein. The amino acid sequences of the amino terminus and fragments of both proteins were determined. Using synthetic oligonucleotide probes and antibody screening, we isolated genomic and cDNA clones. Partial DNA sequences of these clones indicate that they encode fasciclins I and II.
Aspirin Induces Platelet Receptor Shedding via ADAM17 (TACE) (2005)

Aspirin is effective in the therapy of cardiovascular diseases, because it causes acetylation of cyclooxygenase 1 (COX-1) leading to irreversible inhibition of platelets. Additional mechanisms can be suspected, because patients treated with other platelet COX inhibitors such as indomethacin do not display an increased bleeding tendency as observed for aspirin-treated patients. Recently, aspirin and other anti-inflammatory drugs were shown to induce shedding of L-selectin in neutrophils in a metalloproteinase-dependent manner. Therefore, we investigated the effects of aspirin on the von Willebrand Factor receptor complex glycoprotein (GP) Ib-V-IX, whose lack or dysfunction causes bleeding in patients. As quantified by fluorescence-activated cell sorting analysis in whole blood, aspirin, but not its metabolite salicylic acid, induced dose-dependent shedding of human and murine GPIbalpha and GPV from the platelet surface, whereas other glycoproteins remained unaffected by this treatment. Biotinylated fragments of GPV were detected by immunoprecipitation in the supernatant of washed mouse platelets, and the expression level of GPIbalpha was decreased in these platelets as measured by Western blot analysis. Although shedding occurred normally in COX-1-deficient murine platelets, shedding was completely blocked by a broad-range metalloproteinase inhibitor and, more importantly, in mouse platelets expressing an inactive form of ADAM17. Shed fragments of GPIbalpha and GPV were elevated in the plasma of aspirin-injected mice compared with animals injected with control buffer. These data demonstrate that aspirin at high concentrations induces shedding of GPIbalpha and GPV by an ADAM17-dependent mechanism and that this process can occur in vivo.
mSlo , a Complex Mouse Gene Encoding "Maxi" Calcium-Activated Potassium Channels (1993)

Complementary DNAs (cDNAs) from mSlo, a gene encoding calcium-activated potassium channels, were isolated from mouse brain and skeletal muscle, sequenced, and expressed in Xenopus oocytes. The mSlo-encoded channel resembled "maxi" or BK (high conductance) channel types; single channel conductance was 272 picosiemens with symmetrical potassium concentrations. Whole cell and single channel currents were blocked by charybdotoxin, iberiotoxin, and tetraethylammonium ion. A large number of variant mSlo cDNAs were isolated, indicating that several diverse mammalian BK channel types are produced by a single gene.
Stereoselective Cyclopropanation Reactions (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereoselective Cyclopropanation ReactionsHélène Lebel, Jean-François Marcoux, Carmela Molinaro, and André B. CharetteView Author Information Département de Chimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7 Cite this: Chem. Rev. 2003, 103, 4, 977–1050Publication Date (Web):April 9, 2003Publication History Received30 August 2002Published online9 April 2003Published inissue 1 April 2003https://pubs.acs.org/doi/10.1021/cr010007ehttps://doi.org/10.1021/cr010007eresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views26779Altmetric-Citations1587LEARN 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:Cyclopropanation,Hydrocarbons,Molecular structure,Reagents,Stereoselectivity Get e-Alerts
Lycotoxins, Antimicrobial Peptides from Venom of the Wolf SpiderLycosa carolinensis (1998)

Two peptide toxins with antimicrobial activity, lycotoxins I and II, were identified from venom of the wolf spider Lycosa carolinensis (Araneae: Lycosidae) by virtue of their abilities to reduce ion and voltage gradients across membranes. Both peptides were purified to homogeneity by reversed-phase liquid chromatography and determined to have the following primary structures by Edman microsequencing: IWLTALKFLGKHAAKHLAKQQLSKL-NH2 for lycotoxin I and KIKWFKTMKSIAKFIAKEQMKKHLGGE-OH for lycotoxin II. The predicted secondary structures of the lycotoxins display amphipathic alpha-helix character typical of antimicrobial pore-forming peptides. Antimicrobial assays showed that both lycotoxins potently inhibit the growth of bacteria (Escherichia coli) and yeast (Candida glabrata) at micromolar concentrations. To verify its hypothesized pore-forming activity, lycotoxin I was synthesized and shown to promote efflux of Ca2+ from synaptosomes, to cause hemolysis of erythrocytes, and to dissipate voltage gradients across muscle membrane. The lycotoxins may play a dual role in spider-prey interaction, functioning both in the prey capture strategy as well as to protect the spider from potentially infectious organisms arising from prey ingestion. Spider venoms may represent a potentially new source of novel antimicrobial agents with important medical implications.
Maleimidocysteineamido-DOTA Derivatives:  New Reagents for Radiometal Chelate Conjugation to Antibody Sulfhydryl Groups Undergo pH-Dependent Cleavage Reactions (1998)

We have synthesized two bifunctional derivatives of the macrocyclic chelating agent 1,4,7,10-tetraazacyclododecane-N,N',N",N"-tetraacetic acid (DOTA) equipped with maleimide groups for conjugation to reduced disulfide bonds of monoclonal antibodies. Using water-soluble carbodiimide chemistry, DOTA was coupled to L-cysteine to incorporate both a "pendant-type" carboxyl group for metal coordination and an orthogonal thiol group for protein attachment. The homobifunctional reagent 1,6-bis(maleimido)hexane was then used to introduce the maleimide functionality via a sulfide linkage to the macrocycle, and alternatively, the sulfide group was converted to a sulfone side chain. Both maleimide derivatives were conjugated to the anticarcinoembryonic antigen chimeric monoclonal antibody cT84.66 after light reduction of the mAb with dithiothreitol. In this manner, antibody conjugates were prepared which afforded near-quantitative labeling with the radiometals 111In(III) and 90Y(III) as well as quantitative immunoreactivity. Radioimmunoconjugates prepared with the sulfide and sulfone compounds exhibited relatively rapid linker-dependent radiometal loss when incubated in human serum and aqueous solutions at physiological temperature and pH. The unconjugated maleimidocysteineamido-DOTA derivatives and their Y(III) complexes were incubated in aqueous solution at 37 degrees C, and the resulting decomposition products were analyzed by HPLC and mass spectrometry. These studies revealed that the two bifunctional chelating agents underwent linker-specific cleavage reactions which were considerably faster at pH 7.4 than at pH 5.4. The chemically labile linker systems are expected to release chelated radiometal from mAb conjugates in a pH-dependent manner. This property may impart favorable tumor uptake and normal tissue clearance on radioimmunoconjugates prepared with these reagents, on the basis of the observation that many solid tumors are significantly more acidic than normal tissues.
Gonadotropin and steroid hormones stimulate proliferation of the rat ovarian surface epithelium (2003)

The ovarian surface epithelium (OSE) is a single layer of flattened or cuboidal cells covering the ovary. Ninety percent of all human ovarian malignancies arise from this layer of cells. Incessant ovulation, hyperovulation induced by infertility treatment, and hormone replacement therapy have been suggested as risk factors for ovarian cancer. In this study, two groups of rats, with and without surgically induced injury to the ovary, were treated with 17beta-estradiol, pregnant mare's serum gonadotropin (PMSG), human chorionic gonadotropin (hCG), or the combination PMSG/hCG, and the proliferative response of the OSE cells was measured using bromodeoxyuridne (BrdU) and (3)H-thymidine. All hormones, alone or in combination with ovarian surgery, were found to increase significantly the rate of proliferation of the rat OSE. These data demonstrate that hormones associated with infertility treatments and hormone replacement therapy, as well as injury- or ovulation-induced rupture of the ovarian surface, stimulate the rat OSE, and hence could have a role in the development of ovarian cancer via proliferation-associated mutagenesis, or alternatively, by promoting the rapid selection of OSE cells with accumulated mutations.
ApoA-I Mimetic Peptides with Differing Ability to Inhibit Atherosclerosis Also Exhibit Differences in Their Interactions with Membrane Bilayers (2006)

Two homologous apoA-I mimetic peptides, 3F-2 and 3F(14), differ in their in vitro antiatherogenic properties (Epand, R. M., Epand, R. F., Sayer, B. G., Datta, G., Chaddha, M., and Anantharamaiah, G. M. (2004) J. Biol. Chem. 279, 51404-51414). In the present work, we demonstrate that the peptide 3F-2, which has more potent anti-inflammatory activity in vitro when administered intraperitoneally to female apoE null mice (20 microg/mouse/day) for 6 weeks, inhibits atherosclerosis (lesion area 15,800 +/- 1000 microm(2), n = 29), whereas 3F(14) does not (lesion area 20,400 +/- 1000 microm(2), n = 26) compared with control saline administered (19,900 +/- 1400 microm(2), n = 22). Plasma distribution of the peptides differs in that 3F-2 preferentially associates with high density lipoprotein, whereas 3F(14) preferentially associates with apoB-containing particles. After intraperitoneal injection of (14)C-labeled peptides, 3F(14) reaches a higher maximal concentration and has a longer half-time of elimination than 3F-2. A study of the effect of these peptides on the motional and organizational properties of phospholipid bilayers, using several NMR methods, demonstrates that the two peptides insert to different extents into membranes. 3F-2 with aromatic residues at the center of the nonpolar face partitions closer to the phospholipid head group compared with 3F(14). In contrast, only 3F(14) affects the terminal methyl group of the acyl chain, decreasing the (2)H order parameter and at the same time also decreasing the molecular motion of this methyl group. This dual effect of 3F(14) can be explained in terms of the cross-sectional shape of the amphipathic helix. These results support the proposal that the molecular basis for the difference in the biological activities of the two peptides lies with their different interactions with membranes.
A Prospective Study of Alzheimer Disease in Down Syndrome (1989)

Ninety-six individuals with Down syndrome over age 35 years were evaluated and followed up for evidence of nontreatable dementia. Dementia was judged to be present when a functional decline occurred in areas such as orientation, memory, verbal and motor skills, and self-care abilities. Forty-nine patients with Down syndrome fit this criterion, with an average onset of dementia at 54.2 +/- 6.1 years. The prevalence of dementia in the institutionalized Down syndrome population of our study (n = 53) was 8% (2/25 patients) between 35 and 49 years, 55% (11/20 patients) between 50 and 59 years, and 75% (6/8 patients) of those over 60 years old. Of note, 41 (84%) demented individuals with Down syndrome developed seizures. Ten (20%) had parkinsonian features. Adequately treated hypothyroidism was present in 27 (59%) of 46 demented patients with Down syndrome tested. The average duration of dementia in the 23 patients who died was 4.6 +/- 3.2 years. Computed tomographic scans in 43 patients all showed brain tissue loss, most pronounced in the temporal lobes. Brains from 12 autopsied cases showed large numbers of plaques and tangles in the same locations as in persons with Alzheimer disease.
HDL-Mediated Efflux of Intracellular Cholesterol Is Impaired in Fibroblasts From Tangier Disease Patients (1995)

To further elucidate the cellular mechanisms leading to HDL deficiency in Tangier disease, HDL-mediated cholesterol efflux was studied in cultured skin fibroblasts from Tangier patients. Both Tangier and control fibroblasts show specific saturable binding of HDL3 to the cell membrane (Bmax = 70 and 52 ng/mg protein, respectively; Kd = 8.8 and 10.6 micrograms/mL, respectively). There was no appreciable uptake of HDL3 by Tangier and control fibroblasts, indicating that cholesterol efflux from fibroblasts occurs at the cell membrane. When cellular cholesterol was labeled to equilibrium by [14C]cholesterol incubation for 48 hours at 37 degrees C, HDL3-mediated cholesterol efflux from Tangier fibroblasts was only 50% of control fibroblasts. To define this abnormality in HDL3-mediated cholesterol efflux more precisely, several additional experiments were performed. First, membrane desorption of cholesterol was determined after cell membranes were labeled with [14C]cholesterol for 3 hours at 15 degrees C. With this labeling protocol, there was no difference in HDL3-mediated cholesterol efflux between control and Tangier fibroblasts. Second, efflux of newly synthesized sterols was determined after incorporation of the precursor [14C]mevalonolactone. Under these conditions, specific HDL3-mediated efflux of sterols was almost absent in Tangier fibroblasts. Third, cells were labeled by incubation with reconstituted [3H]cholesteryl-linoleate-LDL. Efflux of LDL-derived cholesterol was only slightly reduced for the first 4 hours of incubation. After 12 hours, there was no difference between control and Tangier cells. The combined data indicate that the reduced efflux of cholesterol from Tangier fibroblasts observed after homogeneous labeling is due to severely reduced efflux of newly synthesized sterol.(ABSTRACT TRUNCATED AT 250 WORDS)
Predictive user click models based on click-through history (2007)

Web search engines consistently collect information about users interaction with the system: they record the query they issued, the URL of presented and selected documents along with their ranking. This information is very valuable: It is a poll over millions of users on the most various topics and it has been used in many ways to mine users interests and preferences. Query logs have the potential to partially alleviate the search engines from thousand of searches by providing a way to predict answers for a subset of queries and users without knowing the content of a document. Even if the predicted result is at rank one, this analysis might be of interest: If there is enough confidence on a user's click, we might redirect the user directly to the page whose link would be clicked. In this paper, we present three different models for predicting user clicks, ranging from most specific ones (using only past user history for the query) to very general ones (aggregating data over all users for a given query). The former model has a very high precision at low recall values, while the latter can achieve high recalls. We show that it is possible to combine the different models to predict with high accuracy (over 90%) a high subset of query sessions (24% of all the sessions).
Betaine and homocysteine concentrations in infant formulae and breast milk (2001)

Our study suggests that methionine-free formulae should have Hcy eliminated and be fortified with Bet to the concentration of 150 mg/dL for the treatment of homocystinuria.
Optically switchable photonic metasurfaces (2015)

We experimentally demonstrate an optically switchable gallium-based metasurface, in which a reversible light-induced transition between solid and liquid phases occurring in a confined nanoscale surface layer of the metal drives significant changes in reflectivity and absorption. The metasurface architecture resonantly enhances the metal's “active plasmonic” phase-change nonlinearity by an order of magnitude, offering high contrast all-optical switching in the near-infrared range at low, μW μm−2, excitation intensities.
Characterization of an IL-2 mimetic with therapeutic potential. (2001)

Human interleukin-2 (IL-2) interacts with two types of functional receptors (IL-2R alpha betagamma and IL-2R betagamma) and acts on a broad range of target cells involved in inflammatory reactions and immune responses. IL-2 is also used in different clinical trials aimed at improving the treatment of some cancers and the recovery of CD4 lymphocytes by HIV patients. The therapeutic index of IL-2 is limited by various side effects dominated by the vascular leak syndrome. We have shown that a chemically synthesised fragment of the IL-2 sequence can fold into a helical tetramer likely mimicking the quatemary structure of an hemopoietin. Indeed, peptide p1-30 (containing amino acids 1 to 30, including the sequence corresponding to the entire alpha helix A of IL-2) spontaneously folds into an alpha-helical homotetramer and stimulates the growth of T-cell lines expressing human IL-2R beta, whereas shorter versions of the peptide lack helical structure and are inactive. At the cellular level, p1-30 induces lymphokine-activated killer (LAK) cells and preferentially activates CD8 low lymphocytes and natural killer cells, which constitutively express IL-2R beta. A significant IFN-gamma production is also detected following p1-30 stimulation. A mutant form of p1-30 (Asp20-->Lys) which is likely unable to induce vascular leak syndrome remains capable to generate LAK cells like the original p1-30 peptide. Altogether our data suggest that p1-30 has therapeutic potential.
Magnetoresistance in excess of200%in Ballistic Ni Nanocontacts at Room Temperature and 100 Oe (1999)

We present magnetoresistance experiments in magnetic Ni nanocontacts in the ballistic transport regime at room temperature. It is shown that the magnetoresistance for a few-atom contact reaches values of $280%$ at room temperature and for applied magnetic fields of 100 Oe. Results are presented for over 50 samples showing the trend that the smaller the contact the larger the magnetoresistance response. This indicates that the effect arises just at the nanocontact.
Nucleosomes Are Exposed at the Cell Surface in Apoptosis (2004)

Apoptotic cells are considered the source of DNA, histones, and nucleoprotein complexes that drive the production of autoantibodies in systemic lupus erythematosus. However, the role of apoptotic cells in the activation of the immune system is not clear. To explore interactions that may initiate or sustain the production of anti-nuclear autoantibodies, we characterized the binding of a large panel of monoclonal autoantibodies to apoptotic cells. Autoantibodies to DNA, individual core histones, histone-DNA complexes, or the native nucleosome core particle revealed a consistent and specific binding pattern in confocal microscopy. Immunoreactive epitopes were detected in the cytoplasm and accumulated along the surface of the fragmenting nucleus in a caspase-dependent manner. Ag-Ab complexes on nuclear fragments that had emerged from the plasma membrane were accessible to anti-isotype-reactive microparticles. Moreover, autoantibodies specific for the nucleosome core or its molecular components selectively precipitated a complex of core histones and DNA from the cytosol at 4 h after induction of apoptosis. These observations identify distinct steps in the release of nucleosomes from the nucleus and their exposure at the cell surface. Furthermore, the results indicate a direct role for nucleosomes in the execution of apoptosis, clearance of apoptotic cells, and regulation of anti-nuclear autoantibody production.