gebhart/patrepeval huggingface dataset:
Circuits and programmable self-assembling DNA structures (2002)

Self-assembly is beginning to be seen as a practical vehicle for computation. We investigate how basic ideas on tiling can be applied to the assembly and evaluation of circuits. We suggest that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as the program or circuit that leads to the computation of a particular Boolean expression. This layer templates the assembly of tiles, and their associations then lead to the actual evaluation involving the input data. We describe DNA motifs that can be used for this purpose; we show how the template layer can be programmed, in much the way that a general-purpose computer can run programs for a variety of applications. The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers.
An Enantiomeric Synthesis ofallo-Threonines and β-Hydroxyvalines (1996)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTAn Enantiomeric Synthesis of allo-Threonines and β-HydroxyvalinesHui Shao and Murray GoodmanView Author Information Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0343 Cite this: J. Org. Chem. 1996, 61, 8, 2582–2583Publication Date (Web):April 19, 1996Publication History Received22 January 1996Revised28 February 1996Published online19 April 1996Published inissue 1 January 1996https://doi.org/10.1021/jo960141cCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1294Altmetric-Citations32LEARN 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 InReddit Read OnlinePDF (130 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Antimicrobial agents,Monomers,Peptides and proteins,Purification Get e-Alerts
Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis (1997)

Little is known about how cell shape is controlled. We are using the morphogenesis of trichomes (plant hairs) on the plant Arabidopsis thaliana as a model to study how cell shape is controlled. Wild-type Arabidopsis trichomes are large, single epidermal cells with a stalk and three or four branches, whereas in zwichel (zwi) mutants the trichomes have a shortened stalk and only two branches. To further understand the role of the ZWI gene in trichome morphogenesis we have cloned the wild-type ZWICHEL (ZWI) gene by T-DNA tagging, and report here that it encodes a member of the kinesin superfamily of microtubule motor proteins. Kinesin proteins transport diverse cellular materials in a directional manner along microtubules. Kinesin-like proteins are characterized by a highly conserved "head" region that comprises the motor domain, and a nonconserved "tail" region that is thought to participate in recognition and binding of the appropriate cargo.
Effect of 2'-O-methyl antisense ORNs on expression of thymidylate synthase in human colon cancer RKO cells (2001)

Translation of thymidylate synthase (TS) mRNA is controlled by its own protein end-product TS in a negative autoregulatory manner. Disruption of this regulation results in increased synthesis of TS and may lead to the development of cellular drug resistance to TS-directed anticancer agents. As a strategy to inhibit TS expression, antisense 2'-O-methyl RNA oligoribonucleotides (ORNs) were designed to directly target the 5' upstream cis-acting regulatory element (nucleotides 80-109) of TS mRNA. A 30 nt ORN, HYB0432, inhibited TS expression in human colon cancer RKO cells in a dose-dependent manner but had no effect on the expression of beta-actin, alpha-tubulin or topoisomerase I. TS expression was unaffected by treatment with control sense or mismatched ORNs. HYB0504, an 18 nt ORN targeting the same core sequence, also repressed expression of TS protein. However, further reduction in oligo size resulted in loss of antisense activity. Following HYB0432 treatment, TS protein levels were reduced by 60% within 6 h and were maximally reduced by 24 h. Expression of p53 protein was inversely related to that of TS, suggesting that p53 expression may be directly linked to intracellular levels of TS. Northern blot analysis demonstrated that TS mRNA was unaffected by HYB0432 treatment. The half-life of TS protein was unchanged after antisense treatment suggesting that the mechanism of action of antisense ORNs is mediated through a process of translational arrest. These findings demonstrate that an antisense ORN targeted at a critical cis-acting element on TS mRNA can specifically inhibit expression of TS protein in RKO cells.
The stabilization of β‐lactoglobulin by glycine and NaCl (1989)

Effect of glycine and NaCl on the thermal denaturation of beta-lactoglobulin was examined. The results showed that the transition temperature of beta-lactoglobulin is increased by the addition of glycine and NaCl at 0.5 and 1M. This observed stabilization by glycine and NaCl was interpreted in terms of their favorable interactions with the native state of beta-lactoglobulin and unfavorable interactions with the denatured state.
Isolation, sequencing, synthesis, and pharmacological characterization of two brain neuropeptides that modulate the action of morphine. (1985)

Two peptides that crossreact with an antiserum raised against Phe-Met-Arg-Phe-NH2 were purified from bovine brain extract. Their structures were determined to be Ala-Gly-Glu-Gly-Leu-Ser-Ser-Pro-Phe-Trp-Ser-Leu-Ala-Ala-Pro-Gln-Arg-Phe- NH2 and Phe-Leu-Phe-Gln-Pro-Gln-Arg-Phe-NH2. The sequences were determined by gas-phase sequencing, except for the COOH-terminal phenylalaninamides. These were assigned on the basis of the reactivity of the peptides with the anti-Phe-Met-Arg-Phe-NH2 antiserum, which appears to recognize the determinant -Arg-Phe-NH2. Both peptides were synthesized, and the synthetic peptides were found to have the same HPLC retention times as the endogenous Phe-Met-Arg-Phe-NH2-immunoreactive peptides, thus confirming the assignment of phenylalaninamide to the COOH-terminal positions. Both of the synthetic peptides were found to decrease tail-flick latency in rats, and the octapeptide was more active than the octadecapeptide. The octapeptide was found also to attenuate the prolongation of the tail-flick latency induced by morphine.
Enhanced formation and survival of CD4+CD25hiFoxp3+T-cells in chronic lymphocytic leukemia (2009)

Recently, it has been described that patients with chronic lymphocytic leukemia (CLL) have increased numbers of regulatory T (T(reg)) cells. In the present study, we analysed the mechanism behind T(reg) cells expansion in CLL. Neither analysis of the T-cell receptor repertoire nor CD45 isoform expression of T(reg) cells from patients with CLL provided evidence for chronic (tumor) antigenic stimulation as a possible cause for T(reg) cells expansion in CLL. We found evidence however for increased formation of T(reg) cells via CD70 costimulation, because we observed that CD40 ligand activated CLL cells (which might be considered a model of lymph node CLL cells) strongly induced CD70-dependent formation of T(reg) cells. Reverse transcription-multiplex ligation-dependent probe amplification assay expression analysis of 34 apoptosis-regulating genes showed that in comparison with other CD4(+) T-cells, T(reg) cells from both healthy individuals (HD) and patients with CLL had a high expression of pro-apoptotic Noxa and a low expression of anti-apoptotic Bcl-2. Strikingly, Bcl-2 levels of T(reg) cells in patients with CLL were significantly higher than in HD. Finally, the different apoptotic profile resulted in differences at the functional level, because T(reg) cells from patients with CLL were more resistant to drug-induced apoptosis than T(reg) cells from HD. In conclusion, T(reg) cells in CLL may accumulate both by increased formation, facilitated by CD27-CD70 interaction in the lymph node proliferation centres, and decreased sensitivity to apoptosis because of a shifted Noxa-Bcl-2 balance.
ChemInform Abstract: SYNTHESIS OF O,N‐DIACETYL‐3BETA‐HYDROXY‐5ALPHA,12ALPHA‐JERVAN‐11‐ONE WITH 17‐EPI‐CONFIGURATION BY HYPOIODITE REACTION (1974)

Abstract Die Hydrierung von (I) über einem Rhodium‐Platin‐Katalysator liefert als Hauptprodukt das Jervan (II) und als Nebenprodukte die Verbindungen (III) und (IV).
The human cytotoxic T-lymphocyte (CTL) response to cytomegalovirus is dominated by structural protein pp65: frequency, specificity, and T-cell receptor usage of pp65-specific CTL (1996)

Cytotoxic T lymphocytes (CTL) appear to play an important role in the control of human cytomegalovirus (HCMV) in the normal virus carrier: previous studies have identified peripheral blood CD8+ CTL specific for the HCMV major immediate-early gene product (IE1) and more recently, by bulk culture and cloning techniques, have identified CTL specific for a structural gene product, the lower matrix protein pp65. In order to determine the relative contributions of CTL which recognize the HCMV proteins IE1, pp65, and glycoprotein B (gB) to the total HCMV-specific CTL response, we have used a limiting-dilution analysis system to quantify HCMV-specific CTL precursors with different specificities, allowing the antigenic specificity of multiple short-term CTL clones to be assessed, in a group of six healthy seropositive donors. All donors showed high frequencies of HCMV-specific major histocompatibility complex-restricted CTL precursors. There was a very high frequency of CTL specific for pp65 (lower matrix protein); IE1-specific CTL were also detectable at lower frequencies in three of five donors, while CTL directed to gB were undetectable. A pp65 gene deletion mutant of HCMV was then used to estimate the contribution of pp65-specific CTL to the total HCMV-specific CTL response; this showed that between 70 and 90% of all CTL recognizing HCMV-infected cells were pp65 specific. Analysis of the peptide specificity of pp65-specific CTL showed that some donors have a highly focused response recognizing a single peptide; the T-cell receptor Vbeta gene usage in these two donors was shown to be remarkably restricted, with over half of the responding CD8+ T cells utilizing a single Vbeta gene rearrangement. Other subjects recognized multiple pp65 peptides: nine new pp65 CTL peptide epitopes were defined, and for five of these the HLA-presenting allele has been identified. All four of the HLA A2 donors tested in this study recognized the same peptide. This apparent domination of the CTL response to HCMV during persistent infection by a single structural protein, irrespective of major histocompatibility complex haplotype, is not clearly described for other persistent virus infections, and the mechanism requires further investigation.
Enzymatic function of hemoglobin as a nitrite reductase that produces NO under allosteric control (2005)

Hypoxic vasodilation is a fundamental, highly conserved physiological response that requires oxygen and/or pH sensing coupled to vasodilation. While this process was first characterized more than 80 years ago, the precise identity and mechanism of the oxygen sensor and mediators of vasodilation remain uncertain. In support of a possible role for hemoglobin (Hb) as a sensor and effector of hypoxic vasodilation, here we show biochemical evidence that Hb exhibits enzymatic behavior as a nitrite reductase, with maximal NO generation rates occurring near the oxy-to-deoxy (R-to-T) allosteric structural transition of the protein. The observed rate of nitrite reduction by Hb deviates from second-order kinetics, and sigmoidal reaction progress is determined by a balance between 2 opposing chemistries of the heme in the R (oxygenated conformation) and T (deoxygenated conformation) allosteric quaternary structures of the Hb tetramer--the greater reductive potential of deoxyheme in the R state tetramer and the number of unligated deoxyheme sites necessary for nitrite binding, which are more plentiful in the T state tetramer. These opposing chemistries result in a maximal nitrite reduction rate when Hb is 40-60% saturated with oxygen (near the Hb P50), an apparent ideal set point for hypoxia-responsive NO generation. These data suggest that the oxygen sensor for hypoxic vasodilation is determined by Hb oxygen saturation and quaternary structure and that the nitrite reductase activity of Hb generates NO gas under allosteric and pH control.
Molecular recognition sites on factor Xa which participate in the prothrombinase complex. (1992)

Coagulation factor X, when activated to factor Xa by proteolytic cleavage, itself becomes an active serine protease which participates as a component of the macromolecular prothrombinase complex along with factor Va, phospholipid, and calcium ions. To identify specific structural regions on factor Xa responsible for mediating its function in activating prothrombin, we used 21 synthetic peptides corresponding to 65% of the primary structure of factor X as potential inhibitors of prothrombin activation. Using purified components, thrombin formation was inhibited by seven peptides in a dose-dependent noncompetitive manner. Antibodies to selected inhibitory peptides affinity purified on a factor Xa-agarose column inhibited thrombin formation in a dose-dependent manner, indicating that the corresponding regions on factor Xa are surface-exposed. Kinetic analyses varying the order of reagent addition suggested that peptides 211-222, 254-269, and 263-274 were highly effective in preventing the factor Xa-factor Va interaction. Peptides 275-287 and 415-425 were considered to derive from a distal region involved in substrate binding, based upon mixed inhibition kinetic analyses and assuming that inhibitory peptides not inhibitory in factor Va binding are related to a specific region of substrate interaction. Cross-linking studies confirmed that peptides 263-274 and 263-276 could bind specifically to the light chain of factor V/Va. These findings provide the basis for further pursuing the precise definition of interactive sites on factor Xa using site-directed mutagenesis and molecular modeling.
Layer-by-layer assembly of graphene and gold nanoparticles by vacuum filtration and spontaneous reduction of gold ions (2009)

Layer-by-layer films comprised of alternating graphene and gold nanoparticle layers are readily produced by the two-step procedure involving the use of vacuum filtration of a reduced graphene oxide solution to fabricate the graphene thin film on the quartz substrate, followed by gold nanoparticle formation by spontaneous reduction of gold ions in a gold salt solution on the graphene films.
Evaluation of a new UVB source for irradiation of platelet concentrates (1990)

The application of ultraviolet B (UVB) radiation has been proposed as a new technology to decrease immunogenicity of leucocytes in platelet transfusions. UV radiation also induces platelet aggregation, which occurs most effectively at wavelengths between 240 and 280 nm and falls off sharply above 300 nm. In order to minimize the effects of UV energy on the platelets we evaluated in this study the expected benefit of a new narrow-band UVB source, emitting a narrow peak around 312 nm. Exposure of platelet or lymphocyte suspensions to this source induced in the platelets both aggregation and functional defects at a dose of 12 J/cm2 and in the lymphocytes inhibition of in vitro function at a dose of 2 J/cm2. A conventional UVB source, emitting a broad spectrum between 280 and 340 nm, was more deleterious for the cells and induced similar defects in the platelets at a dose of 6 J/cm2 and inhibition of lymphocyte function at a dose of 1 J/cm2. These data indicate no benefit for the new UVB source, since the ratio of the doses to induce platelet defects and inhibition of lymphocyte function is identical for each of the two sources. Absorption of UV energy by plasma and the plastic material of platelet containers is another criterium for selection of UV sources. In view of the better transmission characteristics of long wavelength UV energy we propose that there is a preference for the new narrow-band UVB source.
AMID Mediates Adenosine-Induced Caspase-Independent HuH-7 Cell Apoptosis (2011)

The results of the present study provide evidence for AMID as a critical factor for adenosine-induced caspase-independent HuH-7 cell apoptosis.
Arginine‐rich cell penetrating peptides: Design, structure–activity, and applications to alter pre‐mRNA splicing by steric‐block oligonucleotides (2008)

Rerouting the splicing machinery with steric-block oligonucleotides (ON) might lead to new therapeutic strategies in the treatment of diseases such as beta-thalassemia, Duchenne muscular dystrophy, or cancers. Interfering with splicing requires the sequence-specific and stable hybridization of RNase H-incompetent ON as peptide nucleic acids (PNA) or phosphorodiamidate morpholino oligomers (PMO). Unfortunately, these uncharged DNA mimics are poorly taken up by most cell types and conventional delivery strategies that rely on electrostatic interaction do not apply. Likewise, conjugation to cell penetrating peptides (CPPs) as Tat, Arg9, Lys8, or Pen leads to poor splicing correction efficiency at low concentration essentially because PNA- and PMO-CPP conjugates remain entrapped within endocytotic vesicles. Recently, we have designed an arginine-rich peptide (R-Ahx-R)4 (with Ahx for aminohexanoic acid) and an arginine-tailed Penetratin derivative which allow sequence-specific and efficient splicing correction at low concentration in the absence of endosomolytic agents. Both CPPs are undergoing structure-activity relationship studies for further optimization as steric-block ON delivery vectors.
Two-Year Follow-up of Infants Enrolled in a Randomized Trial of Surfactant Replacement Therapy for Prevention of Neonatal Respiratory Distress Syndrome (1988)

A randomized clinical trial of the use of bovine surfactant for the prevention of neonatal respiratory distress syndrome was completed at our Institution in 1984 (Pediatrics 1985;76:145-153). All infants entering the trial were enrolled in our follow-up clinic and seen at regular intervals for assessment of growth and development, neurologic and sensory status, and incidence of respiratory disease and allergic conditions. Infants have now been followed-up for at least 2 years. Of those infants for whom follow-up is complete, two of 32 (6.3%) surfactant-treated infants died, five (15.6%) had major neuro-developmental handicaps, and five had minor neurodevelopmental handicaps. In the control group, eight of 33 (24%) infants died, whereas only two (6.1%) survived with major neurodevelopmental handicaps, and four (12.1%) were left with minor handicaps. Except for an increased neonatal death rate in the control group, other differences were not statistically significant. The groups were also comparable in terms of the incidence of late respiratory or allergic disease as assessed by history. Treatment with bovine surfactant at birth of premature infants at high risk for respiratory distress syndrome appears to be safe and of short-term benefit, although no decrease in neurodevelopmental handicap at 2 years' follow-up can be demonstrated.
Duocarmycin SA Shortened, Simplified, and Extended Agents:  A Systematic Examination of the Role of the DNA Binding Subunit (1997)

The examination of shortened, simplified, and extended analogs of duocarmycin SA is described and constitutes a detailed study of the role of linked DNA binding subunit. In addition to enhancing the DNA binding affinity and selectivity through minor groove noncovalent contacts, the studies in conjunction with those of the accompanying article illustrate that an extended rigid N2 amide substituent is required for catalysis of the DNA alkylation reaction. This activation for DNA alkylation is independent of pH, and we propose it results from a binding-induced conformational change in the agents which increases their inherent reactivity. The ground state destabilization of the substrate results from a twist in the linking amide that disrupts the vinylogous amide stabilization of the alkylation subunit and activates the agent for nucleophilic addition. This leads to preferential activation of the agents for DNA alkylation within the narrower, deeper AT-rich minor groove sites where the inherent twist in the linking amide and helical rise of the bound conformation is greatest. Thus, shape-selective recognition (preferential AT-rich noncovalent binding) and shape-dependent catalysis (induced twist in linking N2 amide) combine to restrict SN2 alkylation to accessible adenine N3 nucleophilic sites within the preferred binding sites. Additional ramifications of this DNA binding-induced conformational change on the reversibility of the DNA alkylation reaction are discussed. The results of the study illustrate the importance of the C5‘ methoxy group and the C6 methyl ester of duocarmycin SA, and a previously unrecognized role for these substituents is proposed.
Enriched Links: A Framework For Improving Web Navigation Using Pop-Up Views (2000)

We describe a conceptual framework for enriching Web links by displaying small, information-rich visualizations---pop-up views---that provide the user with information about linked pages that can be used to evaluate the appropriateness of the pages before making a commitment to select the link and wait for the page to load. Examples of how the enriched links framework could be applied in contexts, such as e-commerce catalog pages, search results for a video repository, and desktop icons, are also presented. KEYWORDS Visualization, navigation, overviews, previews, World Wide Web, enriched links INTRODUCTION The World Wide Web provides us with a vast number of resources, easily accessible with a click of the mouse. Knowing what we will get when we select a hyperlink, however, is often not so obvious, as the hyperlink itself provides no information about the type of quality of the resource it represents. As any regular user of the Web knows, navigating Web pages can often be a very fr...