gebhart/patrepeval huggingface dataset:
Rational design of a triple helix-specific intercalating ligand (1998)

DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.
Characterization of a recombinant pneumolysin and its use as a protein carrier for pneumococcal type 18C conjugate vaccines (1995)

Pneumolysin from Streptococcus pneumoniae was expressed in Escherichia coli as a glutathione S-transferase fusion protein and purified by affinity and hydroxylapatite chromatography. The purified recombinant pneumolysin (rPL), with a molecular mass of 53 kDa, had a specific activity of 3 x 10(5) hemolytic units per mg of protein on rabbit erythrocytes and reacted identically in immunodiffusion with the antisera against native pneumolysin. The rPL was used as a protein carrier to prepare conjugate vaccine with pneumococcal type 18C polysaccharide (PS18C). The PS18C was directly coupled to rPL by reductive animation or was indirectly coupled to rPL via a spacer molecule, adipic acid dihydrazide. The conjugates were nontoxic for mice and guinea pigs at 100 micrograms per dose. The immunogenicity and protective efficacy of both conjugates were tested in mice. A single dose of either of the vaccines elicited a rise in immunoglobulin G antibody production; after two booster injections of the vaccines, statistically significant booster responses (P &lt; 0.001) to both rPL and PS18C were produced. The sera containing the antibodies to rPL were capable of neutralizing the hemolytic activity of rPL to rabbit erythrocytes and the cytotoxicity of rPL to bovine pulmonary endothelial cells. Immunization with the conjugate vaccines conferred statistically significant protection in mice against lethal challenge with type 18C pneumococci.
Arctangent Demodulation With DC Offset Compensation in Quadrature Doppler Radar Receiver Systems (2007)

Direct-conversion microwave Doppler radar can be used to detect cardiopulmonary activity at a distance. One challenge for such detection in single channel receivers is demodulation sensitivity to target position, which can be overcome by using a quadrature receiver. This paper presents a mathematical analysis and experimental results demonstrating the effectiveness of arctangent demodulation in quadrature receivers. A particular challenge in this technique is the presence of dc offset resulting from receiver imperfections and clutter reflections, in addition to dc information related to target position and associated phase. These dc components can be large compared to the ac motion-related signal, and thus, cannot simply be included in digitization without adversely affecting resolution. Presented here is a method for calibrating the dc offset while preserving the dc information and capturing the motion-related signal with maximum resolution. Experimental results demonstrate that arctangent demodulation with dc offset compensation results in a significant improvement in heart rate measurement accuracy over quadrature channel selection, with a standard deviation of less than 1 beat/min
Activation of an inactive immunophilin by mutagenesis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTActivation of an inactive immunophilin by mutagenesisMichael K. Rosen, Dan Yang, Patrick K. Martin, and Stuart L. SchreiberCite this: J. Am. Chem. Soc. 1993, 115, 2, 821–822Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/ja00055a082https://doi.org/10.1021/ja00055a082research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations39LEARN 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 Get e-Alerts
Synthesis of enantiomerically pure (S)-(+)-3-hydroxytetrahydrofuran, and its (R)-enantiomer, from malic or tartaric acid (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of enantiomerically pure (S)-(+)-3-hydroxytetrahydrofuran, and its (R)-enantiomer, from malic or tartaric acidVishnu K. Tandon, Albert M. Van Leusen, and Hans WynbergCite this: J. Org. Chem. 1983, 48, 16, 2767–2769Publication Date (Print):August 1, 1983Publication History Published online1 May 2002Published inissue 1 August 1983https://doi.org/10.1021/jo00164a027RIGHTS & PERMISSIONSArticle Views1614Altmetric-Citations38LEARN 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 PDF (441 KB) Get e-Alerts Get e-Alerts
Traumatic axonal injury: practical issues for diagnosis in medicolegal cases (2000)

In the 25 years or so after the first clinicopathological descriptions of diffuse axonal injury (DAI), the criterion for diagnosing recent traumatic white matter damage was the identification of swollen axons ('bulbs') on routine or silver stains, in the appropriate clinical setting. In the last decade, however, experimental work has given us greater understanding of the cellular events initiated by trauma to axons, and this in turn has led to the adoption of immunocytochemical methods to detect markers of axonal damage in both routine and experimental work. These methods have shown that traumatic axonal injury (TAI) is much more common than previously realized, and that what was originally described as DAI occupies only the most severe end of a spectrum of diffuse trauma-induced brain injury. They have also revealed a whole field of previously unrecognized white matter pathology, in which axons are diffusely damaged by processes other than head injury; this in turn has led to some terminological confusion in the literature. Neuropathologists are often asked to assess head injuries in a forensic setting: the diagnostic challenge is to sort out whether the axonal damage detected in a brain is indeed traumatic, and if so, to decide what - if anything - can be inferred from it. The lack of correlation between well-documented histories and neuropathological findings means that in the interpretation of assault cases at least, a diagnosis of 'TAI' or 'DAI' is likely to be of limited use for medicolegal purposes.
New pharmacological strategies against metastatic spread (2008)

Abstract Although metastatic spread is the most frequent cause of death in cancer patients, there are very few drugs specifically targeting this process. Bases for a new antimetastatic drug discovery strategy are weak because a great number of unknowns characterize the complete understanding of the metastatic cascade mechanisms. Moreover, the current experimental models are too simplistic and do not account for the complexity of the phenomenon. Some targets have been identified but too few are validated. Among them, the metastasis suppressor genes seem to be the most promising. In spite of this, during recent years, a dozen of molecules, which fulfil the definition of a specific metastatic drug that inhibits the metastases without altering the growth of the primary tumour (which can be eradicated by surgery), have been identified and assessed for the proof of the concept. The continuation of this effort would benefit in terms of efficiency, if the objectives were defined more precisely. It is particularly important to distinguish molecules that prevent spread of the metastatic cells of the early‐stage primary tumour from the ones which induce a regression of the established metastases or to inhibit the transition from disseminated occult tumour cells to dormant micrometastasis. This second goal is a priori more relevant in the current clinical setting where the detection of early metastatic spread is very difficult, and therefore would call for greater effort on the part of the scientific community.
Broadly Neutralizing Activity of Zika Virus-Immune Sera Identifies a Single Viral Serotype (2016)

Recent epidemics of Zika virus (ZIKV) have been associated with congenital malformation during pregnancy and Guillain-Barré syndrome. There are two ZIKV lineages (African and Asian) that share >95% amino acid identity. Little is known regarding the ability of neutralizing antibodies elicited against one lineage to protect against the other. We investigated the breadth of the neutralizing antibody response following ZIKV infection by measuring the sensitivity of six ZIKV strains to neutralization by ZIKV-confirmed convalescent human serum or plasma samples. Contemporary Asian and early African ZIKV strains were similarly sensitive to neutralization regardless of the cellular source of virus. Furthermore, mouse immune serum generated after infection with African or Asian ZIKV strains was capable of neutralizing homologous and heterologous ZIKV strains equivalently. Because our study only defines a single ZIKV serotype, vaccine candidates eliciting robust neutralizing antibody responses should inhibit infection of both ZIKV lineages, including strains circulating in the Americas.
House Committee Sets Agenda For Huge Science Policy Study (1984)

RETURN TO ISSUEPREVNewsNEXTHouse Committee Sets Agenda For Huge Science Policy StudyMajor theme of planned two-year study could be politicization of science; hope is to rewrite classic Bush report of 1940sWIL LEPKOWSKI C&EN WASHINGTONCite this: Chem. Eng. News 1984, 62, 43, 16–19Publication Date (Print):October 22, 1984Publication History Published online7 November 2010Published inissue 22 October 1984https://pubs.acs.org/doi/10.1021/cen-v062n043.p016https://doi.org/10.1021/cen-v062n043.p016newsACS PublicationsCopyright © 1984 American Chemical SocietyArticle Views5Altmetric-Citations1LEARN 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 options SUBJECTS:Power Get e-Alerts
Sodium butyrate ameliorates phenotypic expression in a transgenic mouse model of spinal and bulbar muscular atrophy (2004)

Spinal and bulbar muscular atrophy (SBMA) is an inherited motor neuron disease caused by the expansion of a polyglutamine (polyQ) tract within the androgen receptor. Unifying mechanisms have been implicated in the pathogenesis of polyQ-dependent neurodegenerative diseases including SBMA, Huntington disease and spinocerebellar ataxias. It has been suggested that mutant protein containing polyQ inhibits histone acetyltransferase activity, resulting in transcriptional dysfunction and subsequent neuronal dysfunction. Histone deacetylase (HDAC) inhibitors alleviate neurological phenotypes in fly and mouse models of polyQ disease, although the therapeutic effect is limited by the toxicity of these compounds. We studied the therapeutic effects of sodium butyrate (SB), an HDAC inhibitor, in a transgenic mouse model of SBMA. Oral administration of SB ameliorated neurological phenotypes as well as increased acetylation of nuclear histone in neural tissues. These therapeutic effects, however, were seen only within a narrow range of SB dosage. Our results indicate that SB is a possible therapeutic agent for SBMA and other polyQ diseases, although an appropriate dose should be determined for clinical application.
Finding experts and their eetails in e-mail corpora (2006)

We present methods for finding experts (and their contact details) using e-mail messages. We locate messages on a topic, and then find the associated experts. Our approach is unsupervised: both the list of potential experts and their personal details are obtained automatically from e-mail message headers and signatures, respectively. Evaluation is done using the e-mail lists in the W3C corpus.
Single electron transistor using a molecularly linked gold colloidal particle chain (1997)

By applying a dithiol (1,6-hexanedithiol) treatment, it was observed that a submonolayer of gold colloidal particles deposited by using an aminosilane adhesion agent [i.e., 3-(2-aminoethylamino) propyltrimethoxysilane] transform themselves into chains consisting of a few gold colloidal particles. In those chains, gold colloidal particles are believed to be linked by alkane chains derived from the dithiol molecules. The particle chain was formed on a SiO2 substrate with source, drain, and gate metal electrodes defined by electron beam lithography. It was observed that the gold particle chain bridged a gap between the source and drain forming a single electron transistor with a multi-tunnel junction in the particle chain. The electron conduction through the chain exhibited a clear Coulomb staircase and the periodic conductance oscillation as a function of gate voltage. These measurement results corresponded closely to the results of a simulation based on the orthodox theory.
Bacterial Aggregates Establish at the Edges of Acute Epidermal Wounds (2018)

<b>Objective:</b> The bacterial composition and distribution were evaluated in acute standardized epidermal wounds and uninjured skin by a molecular <i>in situ</i> technology benchmarked to conventional culturing. This was done to reveal whether bacterial biofilm is present in acute wounds. <b>Approach:</b> On the buttock of 26 healthy volunteers, 28 suction blisters were made and de-roofed. Four wounds were biopsied immediately after wounding, whereas the remaining 24 wounds were treated daily with sterile deionized water and covered with a moisture-retaining dressing. On day 4 post-wounding, swabs were obtained for culturing from the wounds and adjacent skin, and the wounds including adjacent skin were excised. Tissue sections were stained with peptide nucleic acid (PNA) fluorescence <i>in situ</i> hybridization (FISH) probes, counterstained by 4',6-diamidino-2-phenylindole, and evaluated by confocal laser scanning microscopy (CLSM). <b>Results:</b> No bacterial aggregates were detected at day 0. At day 4, coagulase-negative staphylococci (CoNS) were the sole bacteria identified by CLSM/PNA-FISH and culturing. CoNS was isolated from 78% of the wound swabs and 48% of the skin swabs. Bacterial aggregates (5-150 μm) were detected by PNA-FISH/CLSM in the split stratum corneum and fibrin deposits at the wound edges and in the stratum corneum and the hair follicles of the adjacent skin. The bacterial aggregates were more common (<i>p</i> = 0.0084) and larger (<i>p</i> = 0.0083) at wound edges than in the adjacent skin. <b>Innovation:</b> Bacterial aggregates can establish in all wound types and may have clinical significance in acute wounds. <b>Conclusion:</b> Bacterial aggregates were observed at the edges of acute epidermal wounds, indicating initiated establishment of a biofilm.
Cyanovirin-N, a Potent Human Immunodeficiency Virus-Inactivating Protein, Blocks both CD4-Dependent and CD4-Independent Binding of Soluble gp120 (sgp120) to Target Cells, Inhibits sCD4-Induced Binding of sgp120 to Cell-Associated CXCR4, and Dissociates Bound sgp120 from Target Cells (2001)

Cyanovirin-N (CV-N), an 11-kDa protein originally isolated from the cyanobacterium Nostoc ellipsosporum, potently inactivates diverse strains of human immunodeficiency virus type 1 (HIV-1), HIV-2, simian immunodeficiency virus, and feline immunodeficiency virus. It has been well established that the HIV surface envelope glycoprotein gp120 is a molecular target of CV-N. We recently reported that CV-N impaired the binding of virion-associated gp120 to cell-associated CD4 and that CV-N preferentially inhibited binding of the glycosylation-dependent neutralizing monoclonal antibody 2G12 to gp120. However, CV-N did not interfere with the interactions of soluble CD4 (sCD4) with either soluble gp120 (sgp120) or virion-associated gp120. In the present study, we have evaluated the effects of CV-N on the binding of sgp120 to cell-associated CD4 to clarify the experimental basis of the previous binding results, and we further address the detailed mechanism of action of CV-N. Here we present evidence that (i) CV-N impairs both CD4-dependent and CD4-independent binding of sgp120 to the target cells, (ii) CV-N blocks the sCD4-induced binding of sgp120 with cell-associated coreceptor CXCR4, and (iii) CV-N dissociates bound sgp120 from target cells. The results illustrate that the measured effects of CV-N on gp120-CD4 binding interactions depend upon the type of CD4 (soluble or cell associated), but not upon the type of gp120 (soluble or virion associated), employed in the experimental protocol. In addition, this study reinforces that CV-N acts uniquely to prevent essential interactions between the envelope glycoprotein and target cell receptors and further supports the potential broad utility of CV-N as a microbicide to prevent the transmission of HIV and AIDS.
Genomic profiling of tumor initiating prostatospheres (2010)

We have developed a model for the culture of PSs, and provide a genomic profile that support CSCs identity. This signature identifies novel markers and pathways that are predicted to correlate with prostate cancer evolution.
Transformation of Lactobacillus casei by electroporation (1987)

Electroporation has been used to introduce DNA into both eucaryotic and procaryotic cells.Since current methods for the transfection and transformation of lactobacilli using protoplasts are slow, inefficient, and inconsistent, we evaluated electroporation as a simple alternative.In initial experiments, PL-1 phage DNA (40 kb) was transfected into untreated cells of Lactobacillus casei by electroporation.Approximately 50% of the CFU survived pulses of 5000 V/cm at 25 /~F; conditions found to be optimal for the transfection process.The fl-galactosidase-encoding plasmid, pLZ15 (28 kb), and the vectors pSA3 (Emr), pLP825 (Cm r) and pNZ12 (Cm r) transformed L. casei at efficiencies of 1.1-8.5 x 104 transformants/~tg DNA.Plasmid DNA isolated from pNZ12 containing transformants was used to retransform L. casei and was indistinguishable from authentic preparations of pNZ12 by gel electrophoretic analysis.2.
A Noc Complex Specifically Involved in the Formation and Nuclear Export of Ribosomal 40 S Subunits (2003)

Formation and nuclear export of 60 S pre-ribosomes requires many factors including the heterodimeric Noc1-Noc2 and Noc2-Noc3 complexes. Here, we report another Noc complex with a specific role in 40 S subunit biogenesis. This complex consists of Noc4p, which exhibits the conserved Noc domain and is homologous to Noc1p, and Nop14p, a nucleolar protein with a role in 40 S subunit formation. Moreover, noc4 thermosensitive mutants are defective in 40 S biogenesis, and rRNA processing is inhibited at early cleavage sites A(0), A(1), and A(2). Using a fluorescence-based visual assay for 40 S subunit export, we observe a strong nucleolar accumulation of the Rps2p-green fluorescent protein reporter in noc4 ts mutants, but 60 S subunit export was normal. Thus, Noc4p and Nop14p form a novel Noc complex with a specific role in nucleolar 40 S subunit formation and subsequent export to the cytoplasm.
Purification and characterization of virus-like particles and pentamers produced by the expression of SV40 capsid proteins in insect cells. (1996)

Three capsid proteins of SV40 (VP1, VP2, and VP3) were expressed in insect cells using recombinant baculoviruses. When the VP1 capsid protein was expressed alone or co-expressed with VP2 and VP3, virus-like particles (VLP) were produced. In the latter case, the minor capsid proteins, VP2 and VP3, were incorporated into the VLP. VLPs with and without VP2 and VP3, and the wild type SV40 virions were indistinguishable under electron microscope. The sedimentation coefficient, S20,w' obtained for the VLP consisting of VP1 alone (VP1-VLP) was 170 S, and that for the VLP consisting of all of the capsid proteins (VP1/2/3-VLP) was 174 S. Treatment of the VP1-VLP with a calcium ion chelating agent and a reducing agent caused dissociation of the VP1-VLP. The dissociated and purified VP1 proteins were identified as pentamers of VP1 based on the molecular weight determination by sedimentation equilibrium. The pentamers were shown to possess the ability to re-assemble into VLP which had the S20,w of 141S. The results are discussed in relation to the morphogenesis of SV40.