gebhart/patrepeval huggingface dataset:
Acyclic Stereocontrol Induced by Allylic Alkoxy Groups. Synthetic Applications of Stereoselective Dihydroxylation in Natural Product Synthesis (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcyclic Stereocontrol Induced by Allylic Alkoxy Groups. Synthetic Applications of Stereoselective Dihydroxylation in Natural Product SynthesisJin Kun Cha and No-Soo KimCite this: Chem. Rev. 1995, 95, 6, 1761–1795Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/cr00038a003https://doi.org/10.1021/cr00038a003research-articleACS PublicationsRequest reuse permissionsArticle Views2441Altmetric-Citations177LEARN 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
Removal of Metal Ions from Aqueous Solutions by Extraction with Ionic Liquids (2009)

This work analyzed the extraction of Zn2+, Cd2+, and Fe3+ from aqueous hydrochloride solutions using ionic liquids in the absence of chelating agents. For this purpose, ionic liquids based on 1-(n-alkyl)-3-methylimidazolium and tetraalkylammonium cations and several anions (hexafluorophosphate, bis[(trifluoromethyl)sulfonyl]imide, tetrafluoroborate, and chloride) were tested. It was found that the ionic liquid methyltrioctylammonium chloride, [MTOA+][Cl−], allowed almost complete removal (extraction percentage > 94) of Zn2+, Cd2+, and Fe3+ from the aqueous solutions. Furthermore, efficient selective separation of Zn2+/Fe3+and Cd2+/Fe3+ was achieved using 1-methyl-3-octylimidazolium tetrafluoroborate, [omim+][BF4−], since high extraction percentages were reached for Zn2+ and Cd2+ (extraction percentage > 90) while this parameter was very low for Fe3+. These results indicate that the use of ionic liquids as an alternative to traditional extraction agents in liquid/liquid extraction of heavy metal ions is very promising.
PerR vs OhrR: selective peroxide sensing in Bacillus subtilis (2009)

Abstract Bacteria adapt to elevated levels of reactive oxygen species (ROS) by increasing the expression of detoxification enzymes and repair proteins. These defences are regulated by transcription factors that activate specific genes in response to ROS. In Bacillus subtilis, the adaptive response to peroxide stress is mainly under control of three proteins: σB, PerR and OhrR. σB is a general stress response transcription factor. PerR is a dimeric zinc protein with a regulatory site that coordinates either a Fe2+ or a Mn2+ metal ion. In the presence of iron, PerR mediates strong induction of the perRregulon in response to hydrogen peroxide (H2O2). In contrast to PerR, the OhrR protein is weakly activated by H2O2 but it shows a much higher reactivity for organic hydroperoxides. OhrR controls the expression of a thiol-dependent peroxidase that reduces organic hydroperoxides into their corresponding alcohols. In this review we emphasis peroxide sensing mechanisms for both proteins, focusing on recent biochemical and structural data.
Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity (2008)

Lens epithelium-derived growth factor (LEDGF)/p75 functions as a bimodal tether during lentiviral DNA integration: its C-terminal integrase-binding domain interacts with the viral preintegration complex, whereas the N-terminal PWWP domain can bind to cellular chromatin. The molecular basis for the integrase-LEDGF/p75 interaction is understood, while the mechanism of chromatin binding is unknown. The PWWP domain is homologous to other protein interaction modules that together comprise the Tudor clan. Based on primary amino acid sequence and three-dimensional structural similarities, 24 residues of the LEDGF/p75 PWWP domain were mutagenized to garner essential details of its function during human immunodeficiency virus type 1 (HIV-1) infection. Mutating either Trp-21 or Ala-51, which line the inner wall of a hydrophobic cavity that is common to Tudor clan members, disrupts chromatin binding and virus infectivity. Consistent with a role for chromatin-associated LEDGF/p75 in stimulating integrase activity during infection, recombinant W21A protein is preferentially defective for enhancing integration into chromatinized target DNA in vitro. The A51P mutation corresponds to the S270P change in DNA methyltransferase 3B that causes human immunodeficiency, centromeric instability, and facial anomaly syndrome, revealing a critical role for this amino acid position in the chromatin binding functions of varied PWWP domains. Our results furthermore highlight the requirement for a conserved Glu in the hydrophobic core that mediates interactions between other Tudor clan members and their substrates. This initial systematic mutagenesis of a PWWP domain identifies amino acid residues critical for chromatin binding function and the consequences of their changes on HIV-1 integration and infection.
The Mitogen-Activated Protein Kinase Signal-Integrating Kinase Mnk2 Is a Eukaryotic Initiation Factor 4E Kinase with High Levels of Basal Activity in Mammalian Cells (2001)

The cap-binding translation initiation factor eukaryotic initiation factor 4E (eIF4E) is phosphorylated in vivo at Ser209 in response to a variety of stimuli. In this paper, we show that the mitogen-activated protein kinase (MAPK) signal-integrating kinase Mnk2 phosphorylates eIF4E at this residue. Mnk2 binds to the scaffolding protein eIF4G, and overexpression of Mnk2 results in increased phosphorylation of endogenous eIF4E, showing that it can act as an eIF4E kinase in vivo. We have identified eight phosphorylation sites in Mnk2, of which at least three potential MAPK sites are likely to be essential for Mnk2 activity. In contrast to that of Mnk1, the activity of overexpressed Mnk2 is high under control conditions and could only be reduced substantially by a combination of PD98059 and SB203580, while the activity of endogenous Mnk2 in Swiss 3T3 cells was hardly affected upon treatment with these inhibitors. These compounds did not abolish phosphorylation of eIF4E, implying that Mnk2 may mediate phosphorylation of eIF4E in Swiss 3T3 cells. In vitro phosphorylation studies show that Mnk2 is a significantly better substrate than Mnk1 for extracellular signal-regulated kinase 2 (ERK2), p38MAPKalpha, and p38MAPKbeta. Therefore, the high levels of activity of Mnk2 under several conditions may be explained by efficient activation of Mnk2 by low levels of activity of the upstream kinases. Interestingly, we found that the association of both Mnk1 and Mnk2 with eIF4G increased upon inhibition of the MAPK pathways while activation of ERK resulted in decreased binding to eIF4G. This might reflect a mechanism to ensure rapid, but transient, phosphorylation of eIF4E upon stimulation of the MAPK pathways.
Elevated Matrix Metalloproteinase-9 Associated With Stroke or Cardiovascular Death in Patients With Carotid Stenosis (2006)

Elevated levels of matrix metalloproteinase-9 in patients with > or = 50% carotid stenosis were associated with a 2-fold risk of ipsilateral stroke or cardiovascular death. Combining elevated matrix metalloproteinase-9 and plaque echolucency was associated with a 4-fold risk for ipsilateral stroke or cardiovascular death and a 3-fold risk for ipsilateral stroke.
Sequence and analysis of the gene for bacteriophage T3 RNA polymerase (1985)

The RNA polymerases encoded by bacteriophages T3 and T7 have similar structures, but exhibit nearly exclusive template specificities. We have determined the nucleotide sequence of the region of T3 DNA that encodes the T3 RNA polymerase (the gene 1.0 region), and have compared this sequence with the corresponding region of T7 DNA. The predicted amino acid sequence of the T3 RNA polymerase exhibits very few changes when compared to the T7 enzyme (82% of the residues are identical). Significant differences appear to cluster in three distinct regions in the amino-terminal half of the protein. Analysis of the data from both enzymes suggests features that may be important for polymerase function. In particular, a region that differs between the T3 and T7 enzymes exhibits significant homology to the bi-helical domain that is common to many sequence-specific DNA binding proteins. The region that flanks the structural gene contains a number of regulatory elements including: a promoter for the E. coli RNA polymerase, a potential processing site for RNase III and a promoter for the T3 polymerase. The promoter for the T3 RNA polymerase is located only 12 base pairs distal to the stop codon for the structural gene.
Autoantigen recognition by human CD8 T cell clones: enhanced agonist response induced by altered peptide ligands (1997)

Determination of immunodominant epitopes of MHC class I-restricted self-Ags and elucidation of TCR contact residues is of potential importance in providing a means of manipulating the immune response to self-Ags in human autoimmune diseases. A computer algorithm was used to examine the sequences of the two major encephalitogenic proteins of myelin, MBP and PLP, for HLA-A2 binding motifs. Thirty-eight peptides with HLA-A2.1 binding motifs were synthesized and their binding to HLA-A2.1 was measured. A panel of HLA-A2-restricted T cell clones directed against the PLPp80-88 epitope, which exceeded the binding affinity of the other myelin-peptides tested by at least one order of magnitude, was generated. Using a set of analogue peptides with single amino acid substitutions, we detected a distinct pattern of TCR contact residues for each clone. Surprisingly, modification of different presumed TCR contact residues generated superagonist peptides, which are defined as peptides with equal or lower MHC binding affinity to HLA-A2 that induce half-maximal effector responses at 100-fold lower concentrations than the original peptide. These agonist peptides could drive cytotoxic T cell clones to proliferate, secrete cytokines, and clonally expand at concentrations at which the native peptide induced only cytotoxic responses. The proliferation induced by the superagonist peptides gives additional evidence that the clonal expansion of CD8 T cell clones may in part be regulated on the level of Ag recognition by the TCR.
Inferring tumour purity and stromal and immune cell admixture from expression data (2013)

Infiltrating stromal and immune cells form the major fraction of normal cells in tumour tissue and not only perturb the tumour signal in molecular studies but also have an important role in cancer biology. Here we describe ‘Estimation of STromal and Immune cells in MAlignant Tumours using Expression data’ (ESTIMATE)—a method that uses gene expression signatures to infer the fraction of stromal and immune cells in tumour samples. ESTIMATE scores correlate with DNA copy number-based tumour purity across samples from 11 different tumour types, profiled on Agilent, Affymetrix platforms or based on RNA sequencing and available through The Cancer Genome Atlas. The prediction accuracy is further corroborated using 3,809 transcriptional profiles available elsewhere in the public domain. The ESTIMATE method allows consideration of tumour-associated normal cells in genomic and transcriptomic studies. An R-library is available on https://sourceforge.net/projects/estimateproject/ . Tumour biopsies contain contaminating normal cells and these can influence the analysis of tumour samples. In this study, Yoshihara et al.develop an algorithm based on gene expression profiles from The Cancer Genome Atlas to estimate the number of contaminating normal cells in tumour samples.
Copper-62-labeled pyruvaldehyde bis(N4-methylthiosemicarbazonato)copper(II): synthesis and evaluation as a positron emission tomography tracer for cerebral and myocardial perfusion. (1990)

Generator produced positron-emitting radionuclides could potentially expand the application of positron emission tomography (PET) to centers that do not have access to a local cyclotron. The zinc-62/copper-62 radionuclide generator system could serve as a source of positron-emitting copper-62 (62Cu) (t1/2 = 9.74 min) for physiologic imaging. Accordingly, we have prepared zinc-62/copper-62 generators capable of high output (greater than 300 mCi) and used the no-carrier-added eluate in a rapid high yield synthesis of [62Cu] Cu(PTSM) that provides the radiopharmaceutical in a form suitable for intravenous injection (where Cu(PTSM) = pyruvaldehyde bis(N4-methylthiosemicarbazonato) copper(II]. We then demonstrated in pilot studies that [62Cu]Cu(PTSM) provides high quality brain and heart images with PET, accurately delineating cerebral and myocardial perfusion in both experimental animals and in humans (corroborating results of previous experimental studies utilizing longer-lived copper isotopes). The results of this work demonstrate that 62Cu can be conveniently obtained from high-level generators and, when used to label Cu(PTSM), provides a generator-produced radiopharmaceutical capable of providing estimates of cerebral and myocardial perfusion independent of cyclotron-produced radionuclides.
Evidence for and Pathophysiologic Implications of Hypothalamic‐Pituitary‐Adrenal Axis Dysregulation in Fibromyalgia and Chronic Fatigue Syndrome (1998)

Chronic fatigue syndrome (CFS) is characterized by profound fatigue and an array of diffuse somatic symptoms. Our group has established that impaired activation of the hypothalamic-pituitary-adrenal (HPA) axis is an essential neuroendocrine feature of this condition. The relevance of this finding to the pathophysiology of CFS is supported by the observation that the onset and course of this illness is excerbated by physical and emotional stressors. It is also notable that this HPA dysregulation differs from that seen in melancholic depression, but shares features with other clinical syndromes (e.g., fibromyalgia). How the HPA axis dysfunction develops is unclear, though recent work suggests disturbances in serotonergic neurotransmission and alterations in the activity of AVP, an important co-secretagogue that, along with CRH, influences HPA axis function. In order to provide a more refined view of the nature of the HPA dusturbance in patients with CFS, we have studied the detailed, pulsatile characteristics of the HPA axis in a group of patients meeting the 1994 CDC case criteria for CFS. Results of that work are consistent with the view that patients with CFS have a reduction of HPA axis activity due, in part, to impaired central nervous system drive. These observations provide an important clue to the development of more effective treatment to this disabling condition.
An RNA G-Quadruplex Is Essential for Cap-Independent Translation Initiation in Human VEGF IRES (2010)

RNA G-quadruplexes located within the 5'-UTR of mRNA are almost always known to be associated with repression of cap-dependent translation. However, in this report we present functional as well as structural evidence that sequence redundancy in a G-rich segment within the 5'-UTR of human VEGF mRNA supports a 'switchable' RNA G-quadruplex structure that is essential for IRES-mediated translation initiation. Additionally, utilization of a specific combination of G-tracts within this segment allows for the conformational switch that implies a tunable regulatory role of the quadruplex structure in translation initiation. A sequence engineered from a functionally handicapped mutant moderately rescued the activity, further indicating the importance of G-quadruplex structure for VEGF IRES-A function. This to our knowledge is the first report of a conformationally flexible RNA G-quadruplex which is essential for IRES-mediated translation initiation.
Reliability and performance of hierarchical RAID with multiple controllers (2001)

Redundant arrays of inexpensive disks (RAID) offer fault tolerance against disk failures. However a storage system having more disks suffers from less reliability and performance. A RAID architecture tolerating multiple disk failures shows severe performance degradation in comparison to the RAID Level 5 due to the complexity of implementation. We present a new RAID architecture that tolerates at least three disk failures and offers similar throughout to the RAID Level 5. We call it the hierarchical RAID, which is hierarchically composed of RAID Levels. Furthermore, we formally introduce the mean-time-to-data-loss (MTTDL) of traditional RAID and the hierarchical RAID using Markov process for detailed comparison.
Droplet formation in a microchannel network (2002)

A method is given for generating droplets in a microchannel network. With oil as the continuous phase and water as the dispersed phase, pico/nanoliter-sized water droplets can be generated in a continuous phase flow at a -junction. The channel for the dispersed phase is 100 microm wide and 100 microm deep, whereas the channel for the continuous phase is 500 microm wide and 100 microm deep. For given experimental parameters, regular-sized droplets are reproducibly formed at a uniform speed. The diameter of these droplets is controllable in the range from 100-380 microm as the flow velocity of the continuous phase is varied from 0.01 m s(-1) to 0.15 m s(-1).
Review article: the incidence and prevalence of colorectal cancer in inflammatory bowel disease (2003)

Although colorectal cancer (CRC), complicating ulcerative colitis and Crohn's disease, only accounts for 1-2% of all cases of CRC in the general population, it is considered a serious complication of the disease and accounts for approximately 15% of all deaths in inflammatory bowel disease (IBD) patients. The magnitude of the risk was found to differ, even in population-based studies. Recent figures suggest that the risk of colon cancer for people with IBD increases by 0.5-1.0% yearly, 8-10 years after diagnosis. The magnitude of CRC risk increases with early age at IBD diagnosis, longer duration of symptoms, and extent of the disease, with pancolitis having a more severe inflammation burden and risk of the dysplasia-carcinoma cascade. Considering the chronic nature of the disease, it is remarkable that there is such a low incidence of CRC in some of the population-based studies, and possible explanations have to be investigated. One possible cancer-protective factor could be treatment with 5-aminosalicylic acid preparations (5-ASAs). Adenocarcinoma of the small bowel is extremely rare, compared with adenocarcinoma of the large bowel. Although only few small bowel cancers have been reported in Crohn's disease, the number was significantly increased in relation to the expected number.
Spatially continuous six degree of freedom position and orientation sensor (1999)

This paper describes SHAPE TAPE™, a thin array of fiber optic curvature sensors laminated on a ribbon substrate, arranged to sense bend and twist. The resulting signals are used to build a three dimensional computer model containing six degree of freedom position and orientation information for any location along the ribbon. The tape can be used to derive dynamic or static shape information from objects to which it is attached or scanned over. This is particularly useful where attachment is only partial, since shape tape “knows where it is” relative to a starting location. Measurements can be performed where cameras cannot see, without the use of magnetic fields. Applications include simulation, film animation, computer aided design, robotics, biomechanics, and crash testing.
Low-resistance ohmic contacts to p-type GaN achieved by the oxidation of Ni/Au films (1999)

A contact has been developed to achieve a low specific contact resistance to p-type GaN. The contact consisted of a bi-layer Ni/Au film deposited on p-type GaN followed by heat treatment in air to transform the metallic Ni into NiO along with an amorphous Ni–Ga–O phase and large Au grains. A specific contact resistance as low as 4.0×10−6 Ω cm2 was obtained at 500 °C. This low value was obtained by the optimization of Ni/Au film thickness and heat treatment temperatures. Below about 400 °C, Ni was not completely oxidized. On the other hand, at temperatures higher than about 600 °C, the specific contact resistance increased because the NiO detached from p-GaN and the amount of amorphous Ni–Ga–O phase formed was more than that of the sample annealed at 500 °C. The mechanism of obtaining low-resistance ohmic contacts for the oxidized Ni/Au films was explained with a model using energy band diagrams of the Au/p-NiO/p-GaN structure.
Freeze-Preserved Baboon Red Blood Cells: Effects of Biochemical Modification and Perfusion in Vitro (1981)

Nonrejuvenated and rejuvenated baboon RBC were freeze-preserved with 40% (w/v) glycerol at -80 C. To prepare rejuvenated RBC, a 50-ml solution containing pyruvate, inosine, glucose, phosphate, and adenine was used and RBC were incubated with this solution before glycerolization and freezing. Appropriate steps were taken to minimize osmotic damage to the RBC during glycerolization and deglycerolization. Nonrejuvenated and rejuvenated cryopreserved RBC had freeze-thaw recovery values of 98%, freeze-thaw-wash recovery values of 92%, and 24-hour post-transfusion survival values of 85%. Some units of cryopreserved RBC were autotransfused after thawing, washing, and storage at 4 C for 24 hours. Other units were perfused in vitro before autotransfusion. After 24 hours of postwash storage, the RBC were concentrated by centrifugation and suspended in a plasma protein fraction and/or an electrolyte solution, and then were exposed to extracorporeal perfusion. Serious adverse effects were not observed on posttransfusion survival, function, or hemolysis in nonrejuvenated or rejuvenated baboon RBC as a result of perfusion in vitro.
Structure of hepatitis B surface antigen. Correlation of subtype with amino acid sequence and location of the carbohydrate moiety. (1982)

Hepatitis B surface antigens (HBsAg) of both the adw and ayw subtypes have been purified from four different sources. These antigens have been compared by comparison of the products of tryptic hydrolysis performed under conditions which do not disrupt the overall particle morphology of HBsAg. The resultant peptides were compared by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and high performance liquid chromatography followed by amino acid analysis and Edman degradation of the isolated peptides. The same techniques were also applied to HBsAg which had been labeled with tritium in the carbohydrate moiety of the glycoprotein gp-30. These studies demonstrate that residues 122-150 of the protein p-25 and glycoprotein gp-30 occupy an exposed region of the HBsAg lipoprotein particle and contain the major attachment site for carbohydrate in the case of gp-30. The two subtypes were found to differ at two specific positions in this region, suggesting that this is an antigenically important area of the protein.
Advanced MS-DOS: the Microsoft guide for assembly language and C programmers (1986)

This bestselling guide shows programmers how to fully access the hidden power of MS-DOS. It covers screen, keyboard, file, and record access; the internal structure of MS-DOS disks; how to create installable device drivers and filters to extend MS-DOS and much more.