gebhart/patrepeval huggingface dataset:
Plasma Ascorbate Protects Coagulation Factors against Photooxidation (1996)

Summary It has been suggested that proteins, unlike lipids, are not protected against oxidative damage by antioxidants in plasma. We have studied the effect of photodynamic virus inactivation treatment of fresh human plasma on coagulation factor activities. Photodynamic treatment generates singlet oxygen which causes inactivation of fibrinogen and factor VIII. Other coagulation factors or anticoagulant proteins are clearly less affected. We found that there is an inverse correlation between the extent of coagulation factor inactivation during the treatment and the plasma ascorbate concentration. The inactivation of coagulation factors was prevented in a dose-dependent manner by adding ascorbate to the plasma before the treatment. Ascorbate was consumed during the treatment at an apparently linear rate. Oxidation of urate and coagulation factors was enhanced when ascorbate had disappeared from plasma. These results indicate that ascorbate is a primary antioxidant against photooxidation in plasma and that it effectively prevents oxidative damage to coagulation factors and other proteins.
Synthesis and chemistry of dynemicin A models (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and chemistry of dynemicin A modelsK. C. Nicolaou, A. L. Smith, S. V. Wendeborn, and C. K. HwangCite this: J. Am. Chem. Soc. 1991, 113, 8, 3106–3114Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ja00008a045https://doi.org/10.1021/ja00008a045research-articleACS PublicationsRequest reuse permissionsArticle Views592Altmetric-Citations86LEARN 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
Resolution and characterization of pro-B and pre-pro-B cell stages in normal mouse bone marrow. (1991)

We have resolved B220+ IgM- B-lineage cells in mouse bone marrow into four fractions based on differential cell surface expression of determinants recognized by S7 (leukosialin, CD43), BP-1, and 30F1 (heat stable antigen). Functional differences among these fractions can be correlated with Ig gene rearrangement status. The largest fraction, lacking S7, consists of pre-B cells whereas the others, expressing S7, include B lineage cells before pre-B. These S7+ fractions, provisionally termed Fr. A, Fr. B, and Fr. C, can differentiate in a stromal layer culture system. Phenotypic alteration during such culture suggests an ordering of these stages from Fr. A to Fr. B to Fr. C and thence to S7- pre-B cells. Using polymerase chain reaction amplification with pairs of oligonucleotide primers for regions 5' of JH1, DFL16.1, and Jk1, we find that the Ig genes of Fr. A are in germline configuration, whereas Fr. B and C are pro-B cell stages with increasing D-J rearrangement, but no V-D-J. Finally, functional analysis demonstrates that the proliferative response to IL-7, an early B lineage growth factor, is restricted to S7+ stages and, furthermore, that an additional, cell contact-mediated signal is essential for survival of Fr. A.
Functional expression and characterisation of membrane transport proteins (2012)

Membrane transporters set the framework organising the complexity of plant metabolism in cells, tissues and organisms. Their substrate specificity and controlled activity in different cells is a crucial part for plant metabolism to run pathways in concert. Transport proteins catalyse the uptake and exchange of ions, substrates, intermediates, products and cofactors across membranes. Given the large number of metabolites, a wide spectrum of transporters is required. The vast majority of in silico annotated membrane transporters in plant genomes, however, has not yet been functionally characterised. Hence, to understand the metabolic network as a whole, it is important to understand how transporters connect and control the metabolic pathways of plant cells. Heterologous expression and in vitro activity studies of recombinant transport proteins have highly improved their functional analysis in the last two decades. This review provides a comprehensive overview of the recent advances in membrane protein expression and functional characterisation using various host systems and transport assays.
Mammalian cell transient expression of tissue factor for the production of antigen (1990)

We describe a mammalian cell expression system used to rapidly produce microgram quantities of a membrane protein used as an immunogen. A fusion protein expression vector was constructed which contained the signal sequence and 27 amino acids of the Herpes simplex virus glycoprotein D (gD), followed by a factor VIII (fVIII) thrombin cleavage site and the mature tissue factor (TF) sequence. This fusion protein was transiently expressed and then purified using an antibody to gD. The purified fusion protein, gDTF, was incubated with thrombin to remove the gD-fVIII moiety and the resulting rTF served as antigen for the generation of TF-specific antibodies. The antibodies produced were then used for a comparison of the turnover rates of the constitutively and transiently produced fusion protein. In addition, sensitivity to glycosidases indicated that the transiently and constitutively produced recombinant proteins do not contain identical carbohydrate structures.
Determinants for Membrane Fusion Induced by Cholesterol-Modified DNA Zippers (2008)

Intracellular membrane fusion is coordinated by membrane-anchored fusion proteins. The cytosolic domains of these proteins form a specific complex that pulls the membranes into close proximity. Although some results indicate that membrane merger can be accomplished solely on the basis of proximity, others emphasize the importance of bilayer stress exerted by transmembrane peptides. In a reductionist approach, we recently introduced a fusion machinery built from cholesterol-modified DNA zippers to mimic fusion protein function. Aiming to further optimize DNA-mediated fusion, we varied in this work length and number of DNA strands and used either one or two cholesterol groups for membrane anchoring of DNA. The results reveal that the use of two cholesterol anchors is essential to prevent cDNA strands from shuttling to the same membrane, which leads to vesicle release instead of membrane merger. A surface coverage of 6-13 DNA strands was a precondition for efficient fusion, whereas fusion was insensitive to DNA length within the tested range. Besides lipid mixing, we also demonstrate DNA-induced content mixing of large unilamellar vesicles composed of the most abundant cellular lipids phosphatidylcholine, phosphatidylethanolamine, cholesterol, and sphingomyelin. Taken together, DNA-mediated fusion emerges as a promising tool for the functionalization of artificial and biological membranes and may help to dissect the functional role of fusion proteins.
Learning to Optimize (2016)

Algorithm design is a laborious process and often requires many iterations of ideation and validation. In this paper, we explore automating algorithm design and present a method to learn an optimization algorithm, which we believe to be the first method that can automatically discover a better algorithm. We approach this problem from a reinforcement learning perspective and represent any particular optimization algorithm as a policy. We learn an optimization algorithm using guided policy search and demonstrate that the resulting algorithm outperforms existing hand-engineered algorithms in terms of convergence speed and/or the final objective value.
A National Tissue Bank to Track HIV Eradication and Immune Reconstitution (1998)

Understanding of HIV reservoirs that can complicate and confound current approaches to antiretroviral therapy will require better resources than are currently available. Cavert and Haase propose the creation of tissue banks from HIV-positive individuals who have died from other causes such as accidents or trauma. They estimate that it might be possible to collect tissues from 10 to 30 individuals over a 2-year period at a cost of $1 million per year.
Nonsteroidal anti-inflammatory drugs in Alzheimer's disease (1995)

We reviewed the records of 210 patients in the Johns Hopkins Alzheimer's Disease Research Center to evaluate the role of nonsteroidal anti-inflammatory drugs (NSAIDs) on clinical features and progression of the disease. We compared patients taking NSAIDs or aspirin on a daily basis (N = 32) to non-NSAID patients (N = 177) on clinical, cognitive, and psychiatric measures. The NSAID group had a significantly shorter duration of illness at study entry. Even after controlling for this difference, the NSAID group performed better on the Mini-Mental State Examination, Boston Naming Test, and the delayed condition of the Benton Visual Retention Test. Furthermore, analysis of longitudinal changes over 1 year revealed less decline among NSAID patients than among non-NSAID patients on measures of verbal fluency, spatial recognition, and orientation. These findings support other recent studies suggesting that NSAIDs may serve a protective role in Alzheimer's disease.
A dynamic reaction cell for inductively coupled plasma mass spectrometry (ICP-DRC-MS) (2000)

The dynamic reaction cell (DRC) is a rf/dc quadrupole which may be pressurized with a reactive gas in order to promote ion–molecule reactions intended to suppress plasma-based isobaric interferences for trace elemental analysis. The bandpass of the DRC is adjusted in order to suppress the appearance of new interferences produced through sequential reactions within the reaction cell. The DRC may alternatively be operated at low pressure (vented, under collision-free conditions) to emulate conventional ICP-MS. A practical optimization procedure for both the vented and pressurized modes is described, with examples showing the suppression of both plasma-based and cell-based isobaric interferences. The analytical performance characteristics of the instrument, including efficiency of isobar rejection, detection limits in clean water and in neat hydrogen peroxide, short- and long-term stability, determination of arsenic in chloride solution and Se isotope determination, are provided.
NMR studies of the antimicrobial salivary peptides histatin 3 and histatin 5 in aqueous and nonaqueous solutions (1998)

Conformational studies of the salivary peptides histatin 3 (H3) and histatin 5 (H5) were performed by NMR and circular dichroism (CD) in aqueous and nonaqueous solutions. Histatin 5 has no defined structure in H 2 O but adopts a more helical conformation in dimethyl sulfoxide and aqueous trifluoroethanol. This is in agreement with the CD analysis, which shows no secondary structure in H 2 O but increasing helical content in the presence of trifluoroethanol. CD analysis shows that H3 has less propensity to form a helical structure than H5 in similar conditions. The NMR analysis of H3 in H 2 O at pH 7.4 reveals that its conformational mobility is less than that of H5 as indicated by the observation of backbone cross peaks alphaN (i, i + 1) and NN (i, i + 1) and the slow exchanging amide protons in the C-terminus. However, H3 remains essentially unordered as suggested by the lack of longer range nuclear Overhauser effects (NOEs) in the NOESY spectrum. H3 becomes much more ordered in a mixture of 50:50 H 2 O - dimethyl sulfoxide as indicated by the numerous NOEs, including several side chain to side chain and side chain to backbone conectivities. Our data suggest that in these conditions H3 contains a turn in the region of K 13 to K 17 and possibly a 3 10 helix at the C-terminus. This study demonstrates that H3 and H5 are both conformationally mobile and that each adopt different types of conformations in aqueous and nonaqueous solutions.Key words: histatins, NMR, antimicrobial.
RETmutation p.S891A in a Chinese family with familial medullary thyroid carcinoma and associated cutaneous amyloidosis bindingOSMRvariant p.G513D (2015)

There are no reports on the relationship between familial medullary thyroid carcinoma (FMTC) associated with cutaneous amyloidosis (CA) and RET or OSMR/IL31RA gene mutations. In this study, we investigated a Chinese family with FMTC/CA and found a recurrent RET c.2671T>G (p.S891A) mutation in six of 17 family members. Three of the six p.S891A mutation carriers presented with medullary thyroid carcinoma (MTC). Of them, three (two with and one without MTC) were diagnosed as having combined lichen/macular biphasic CA. We also identified a novel RET variant, c.1573C>T (p.R525W) in five members. Of them, three carriers had no evidence of thyroid/skin or basal serum/stimulated calcitonin abnormalities. In vitro cell proliferation assay indicated that oncogenic activity of RET p.S891A was slightly enhanced by p.R525W, whereas p.R525W alone had no effect on cell proliferation. Meanwhile, we identified a novel OSMR variant, c.1538G>A (p.G513D) in seven members. We noticed that three OSMR p.G513D carriers presenting with CA also had the RET p.S891A mutation. Our investigation indicated that the RET p.S891A mutation combined with OSMR p.G513D may underlie a novel phenotype manifesting as FMTC and CA.
Polymorphism within the herpes simplex virus (HSV) ribonucleotide reductase large subunit (ICP6) confers type specificity for recognition by HSV type 1-specific cytotoxic T lymphocytes (1995)

A panel of herpes simplex virus type 1 (HSV-1)-specific, CD8+, major histocompatibility complex class I (H-2Kb)-restricted cytotoxic T-lymphocyte (CTL) clones was derived from HSV-1-immunized C57BL/6 (H-2b) mice in order to identify the HSV-1 CTL recognition epitope(s) which confers type specificity. HSV-1 x HSV-2 intertypic recombinants were used to narrow the region encoding potential CTL recognition epitopes to within 0.51 to 0.58 map units of the HSV-1 genome. Using an inhibitor of viral DNA synthesis and an ICP6 deletion mutant, the large subunit of ribonucleotide reductase (ICP6, RR1) was identified as a target protein for these type-specific CTL. Potential CTL recognition epitopes within RR1 were located on the basis of the peptide motif predicted to bind to the MHC class I H-2Kb molecule. A peptide corresponding to residues 822 to 829 of RR1 was shown to confer susceptibility on H-2Kb-expressing target cells to lysis by the type 1-specific CTL. On the basis of a comparison of the HSV-1 RR1 epitope (residues 822 to 829) with the homologous sequence of HSV-2 RR1 (residues 828 to 836) and by the use of amino acid substitutions within synthetic peptides, we identified HSV-1 residue 828 as being largely responsible for the type specificity exhibited by HSV-1-specific CTL. This HSV-1 RR1 epitope, when expressed in recombinant simian virus 40 large T antigen in primary C57BL/6 cells, was recognized by the HSV-1 RR1-specific CTL clones. These results indicate that an early HSV protein with enzymatic activity provides a target for HSV-specific CTL and that type specificity is dictated largely by a single amino acid.
Suppression of Bulboreticular Unit Responses to Noxious Stimuli by Analgesic Mesencephalic Stimulation (1983)

The responses of 302 neurons in the medial medullary reticular formation (MRF) to a variety of noxious and innocuous somatic stimuli were studied in anesthetized and awake rats. In addition, the effects of analgesic electrical stimulation in the mesencephalon (MES) on unit responses were examined. Tail shock was the most effective stimulus, exciting more than 80% of all units recorded. This stimulus was considered separately during data analysis, since it could not be classified as noxious or innocuous. Noxious somatic stimuli (including pinch, firm pressure, pin prick, and radiant heating of the tail above 45 degrees C were especially effective in eliciting discharge in a significant fraction of all cells in both awake (123/205) and anesthetized (45/97) animals. Nociceptive neurons could be classified as nociceptive specific (NS) or wide dynamic range (WDR) depending on their responses to all somatic stimuli tested. Nociceptive neurons showed no preferential anatomical distribution. Most neurons, including those responsive to noxious inputs, exhibited large, often bilateral receptive fields which frequently covered the tail, one or more limbs, and extensive areas of the body or head. Electrical stimulation within or adjacent to the mesencephalic periaqueductal gray matter depressed the spontaneous and evoked discharge of MRF neurons in both acute and chronic preparations. This inhibition showed a significant preference (p less than 0.001, chi-square statistic) for units that were excited by somatic and especially noxious stimuli. No units were facilitated by MES stimulation. In the awake rat, unit suppression closely followed the time course and level of MES-induced analgesia. Excitability data from the acute experiments suggest that this response inhibition may be the result of a direct action on MRF neurons. Anesthesia severely depressed the spontaneous discharge of MRF neurons as well as the activity evoked by innocuous somatic stimulation. Our data suggest that analgesia produced by MES stimulation is at least in part due to the depression of MRF unit activity, and support the hypothesis that MRF neurons play a critical role in the mediation of behavioral responses to noxious stimuli.
Regulated expression and subcellular localization of HMGB1, a chromatin protein with a cytokine function (2004)

High mobility group box protein 1 (HMGB1) has been considered as a ubiquitous nuclear protein with an architectural function, but even early reports have described its presence outside of the nucleus. Today, we have only started to understand the extranuclear and extracellular functions of HMGB1: we know that it participates in developmental and differentiation processes, triggers and modulates many of the inflammatory cascades in the body, and may even be involved in the metastatic invasion programme of cancer cells. Given such diverse roles, it is important to know which cells express HMGB1, where, and how much. The present review deals with the expression pattern of HMGB1 and provides evidence that, far from being housekeeping, the HMGB1 gene is tightly regulated. This can have implications for therapeutic intervention on inflammatory diseases as well as cancer.
Inhibition of alternative pathway factor D by factor B ‐related synthetic hexapeptides (1982)

Hexapeptides mimicking the partial amino acid sequence of factor B surrounding the bond that is cleaved by factor D have been synthesized. These peptides have been assessed for their ability to inhibit factor D enzymatic activity and for their susceptibility to serine proteases. The synthetic peptides were cleaved by bovine trypsin and C1s but not by alpha-thrombin and factor D. The peptides inhibited factor B cleavage and fluid-phase or cell-bound alternative pathway C3 convertase activation by factor D. Altogether, these results suggest that peptides analogous to factor B specifically inhibit factor D enzymatic activity. Thus, they constitute an interesting tool for study of alternative pathway activation and can be of use when attempting to manipulate this pathway, since factor D is an essential component for alternative pathway initiation and amplification.
Differentiation of Bacillus anthracis and other 'Bacillus cereus group' bacteria using IS231-derived sequences (1995)

Sequences based on the conserved 20 bp inverted repeat of IS231 variants were used as polymerase chain reaction-based fingerprinting primers of the member species of the Bacillus cereus group (B. anthracis, B. cereus, B. thuringiensis and B. mycoides), because of their close association with transposons, principally Tn4430 in B. thuringiensis. Fingerprints of B. anthracis were simple, and specifically allowed its identification and sub-differentiation from other members of the group. Fingerprints for B. cereus were strain-specific; those for B. thuringensis gave a 1650 bp product, characteristic of 1S231 variants A-F. The same reaction conditions gave one or two bands for both B. anthracis and B. cereus that differed by restriction endonuclease mapping from the B. thuringiensis PCR product and established IS231 restriction maps; this does not preclude some kind of relationship between these products and IS231.
Size-Selective Hydrogenation of Olefins by Dendrimer-Encapsulated Palladium Nanoparticles (2001)

Nearly monodisperse (1.7 ± 0.2 nm) palladium nanoparticles were prepared within the interiors of three different generations of hydroxyl-terminated poly(amidoamine) (PAMAM) dendrimers. These dendrimer-encapsulated catalysts (DECs) were used to hydrogenate allyl alcohol and four α-substituted derivatives in a 4:1 methanol/water mixture. The results indicate that steric crowding on the dendrimer periphery, which increases with dendrimer generation, can act as an adjustable-mesh nanofilter. That is, by controlling the packing density on the dendrimer periphery, it is possible to control access of substrates to the encapsulated catalytic nanoparticle. In general, higher-generation DECs or larger substrates resulted in lower turnover frequencies (although some interesting exceptions were noted). Although the main products of the olefin hydrogenation reactions were the corresponding alkanes, ketones were also obtained when monosubstituted α-olefins were used as substrates. NMR spectroscopy was used to measure the size selectivity of DECs for the competitive hydrogenation of allyl alcohol and 3-methyl-1-penten-3-ol. The effect on catalytic rate as a function of nanoparticle size is also briefly discussed.
Autonomous Modular Optical Underwater Robot (AMOUR) Design, Prototype and Feasibility Study (2006)

We propose a novel modular underwater robot which can self-reconfigure by stacking and unstacking its component modules. Applications for this robot include underwater monitoring, exploration, and surveillance. Our current prototype is a single module which contains several subsystems that later will be segregated into different modules. This robot functions as a testbed for the subsystems which are needed in the modular implementation. We describe the module design and discuss the propulsion, docking, and optical ranging subsystems in detail. Experimental results demonstrate depth control, linear motion, target module detection, and docking capabilities.