gebhart/patrepeval huggingface dataset:
Detection and direct sequence identification of BCR-ABL mRNA in Ph+ chronic myeloid leukemia. (1993)

The reverse transcriptase-polymerase chain reaction (RT-PCR) for BCR-ABL mRNA is increasingly used to diagnose and monitor patients with Ph+ chronic myeloid leukemia (CML). We investigated an alternative approach to detect BCR-ABL mRNA in CML in order to overcome some of the potential drawbacks of RT-PCR. Nucleic acid sequence based amplification (NASBA) is a homogeneous, isothermal, in vitro process that provides the direct amplification of RNA. Peripheral blood from seven patients with Ph+ CML and Ph+ EM-2 cells were investigated by NASBA and RT-PCR. A nested set of four primers flanking the BCR-ABL junction was used in two serial NASBA reactions performed for 2 hours. The two methods were fully concordant for detection of transcripts with bcr3-abl2 and bcr2-abl2 junctions. Ethidium bromide fluorescence with NASBA indicated in repeated experiments that similar quantities of total RNA from patient material contained different amounts of BCR-ABL mRNA. The data suggest that direct amplification of RNA is suitable for identifying and monitoring patients with Ph+ CML and may provide a means to quantify BCR-ABL mRNA levels.
Chemical Fixation of Carbon Dioxide Catalyzed by Binaphthyldiamino Zn, Cu, and Co Salen-Type Complexes (2003)

Binaphthyldiamino salen-type Zn, Cu, and Co complexes can efficiently catalyze reactions of epoxides with carbon dioxide in the presence of various catalytic amounts of organic bases. The simplest binaphthyldiamino salen-type Zn complex gave the five-membered cyclic carbonate 2 in excellent yield in the presence of triethylamine. A Lewis acid and Lewis base cocatalyzed mechanism is proposed.
The AAA ATPase p97/VCP Interacts with Its Alternative Co-factors, Ufd1-Npl4 and p47, through a Common Bipartite Binding Mechanism (2004)

The AAA ATPase p97/VCP forms complexes with different adapters to fulfill distinct cellular functions. We analyzed the structural organization of the Ufd1-Npl4 adapter complex and its interaction with p97 and compared it with another adapter, p47. We found that the binary Ufd1-Npl4 complex forms a heterodimer that cooperatively interacts with p97 via a bipartite binding mechanism. Binding site 1 (BS1) is a short hydrophobic stretch in the C-terminal domain of Ufd1. The second binding site is located at the N terminus of Npl4 and is activated upon binding of Ufd1 to Npl4. It consists of about 80 amino acids that are predicted to form a ubiquitin fold domain (UBD). Despite the lack of overall homology between Ufd1-Npl4 and p47, both adapters use identical binding mechanisms. Like the ubiquitin fold ubiquitin regulatory X (UBX) domain in p47, the Npl4-UBD interacts with p97 via the loop between its strands 3 and 4 and a conserved arginine in strand 1. Furthermore, we identified a region in p47 homologous to Ufd1-BS1. The UBD/UBX and the BS1 of both adapters interact with p97 independently, whereas homologous binding sites in both adapters compete for binding to p97. In contrast to p47, however, Ufd1-Npl4 does not regulate the ATPase activity of p97; nor does a variant of p47 that contains both binding sites but lacks the N-terminal domains. Therefore, the binding sites alone do not regulate p97 directly but rather serve as anchor points to position adapter-specific domains at critical locations to modulate p97-mediated reactions.
A method for linking yeast artificial chromosomes (1996)

A method for linking any standard yeast artificial chromosomes (YAC) is described. YACs are introduced into the same cell and joined by mitotic recombination between the vector arms and the homologous sequence in a linking vector; several YACs can be recombined sequentially. The linking vectors also contain the beta-galactosidase gene as an expression reporter in mammalian cells.
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome (2010)

The mammalian innate immune system uses Toll-like receptors (TLRs) and Nod-LRRs (NLRs) to detect microbial components during infection. Often these molecules work in concert; for example, the TLRs can stimulate the production of the proforms of the cytokines IL-1beta and IL-18, whereas certain NLRs trigger their subsequent proteolytic processing via caspase 1. Gram-negative bacteria use type III secretion systems (T3SS) to deliver virulence factors to the cytosol of host cells, where they modulate cell physiology to favor the pathogen. We show here that NLRC4/Ipaf detects the basal body rod component of the T3SS apparatus (rod protein) from S. typhimurium (PrgJ), Burkholderia pseudomallei (BsaK), Escherichia coli (EprJ and EscI), Shigella flexneri (MxiI), and Pseudomonas aeruginosa (PscI). These rod proteins share a sequence motif that is essential for detection by NLRC4; a similar motif is found in flagellin that is also detected by NLRC4. S. typhimurium has two T3SS: Salmonella pathogenicity island-1 (SPI1), which encodes the rod protein PrgJ, and SPI2, which encodes the rod protein SsaI. Although PrgJ is detected by NLRC4, SsaI is not, and this evasion is required for virulence in mice. The detection of a conserved component of the T3SS apparatus enables innate immune responses to virulent bacteria through a single pathway, a strategy that is divergent from that used by plants in which multiple NB-LRR proteins are used to detect T3SS effectors or their effects on cells. Furthermore, the specific detection of the virulence machinery permits the discrimination between pathogenic and nonpathogenic bacteria.
Spectroscopic Study and Evaluation of Red-Absorbing Fluorescent Dyes (2002)

The spectroscopic characteristics (absorption, emission, and fluorescence lifetime) of 13 commercially available red-absorbing fluorescent dyes were studied under a variety of conditions. The dyes included in this study are Alexa647, ATTO655, ATTO680, Bodipy630/650, Cy5, Cy5.5, DiD, DY-630, DY-635, DY-640, DY-650, DY-655, and EVOblue30. The thorough characterization of this class of dyes will facilitate selection of the appropriate red-absorbing fluorescent labels for applications in fluorescence assays. The influences of polarity, viscosity, and the addition of detergent (Tween20) on the spectroscopic properties were investigated, and fluorescence correlation spectroscopy (FCS) was utilized to assess the photophysical properties of the dyes under high excitation conditions. The dyes can be classified into groups based on the results presented. For example, while the fluorescence quantum yield of ATTO655, ATTO680, and EVOblue30 is primarily controlled by the polarity of the surrounding medium, more hydrophobic and structurally flexible dyes of the DY-family are strongly influenced by the viscosity of the medium and the addition of detergents. Covalent binding of the dyes to biotin and subsequent addition of streptavidin results in reversible fluorescence quenching or changes in the relaxation time of other photophysical processes of some dyes, most likely due to interactions with tryptophan residues in the streptavin binding site.
Effect of Prednisone on the Pharmacokinetics of the Integrase Inhibitor Dolutegravir (2013)

Prednisone, a corticosteroid frequently used to treat common AIDS-related illnesses and comorbidities, has been shown to induce drug metabolism. This study was performed to determine whether prednisone coadministration affected the pharmacokinetics of dolutegravir (DTG). In this open-label, repeat-dose study, 12 healthy subjects were administered DTG at 50 mg daily alone for 5 days and then with concomitant prednisone for 10 days (prednisone at 60 mg daily for 5 days, followed by a 5-day taper). Serial blood sampling and safety assessments were performed during the trial. Pharmacokinetic parameters were determined using noncompartmental methods and geometric least-square mean ratios, and 90% confidence intervals were generated. Coadministration of DTG and 5-day high-dose prednisone with a 5-day taper had a modest effect on DTG exposure. The area under the DTG plasma concentration-time curve, maximum observed DTG concentration, and 24-hour postdose DTG concentration were increased by 11%, 6%, and 17%, respectively, on day 10 of the combination. Similar results were observed after 5 days of DTG and prednisone. Dolutegravir and prednisone coadministration was well tolerated. The changes in plasma exposures of DTG in healthy individuals as a result of prednisone dosing were not clinically significant. No dose adjustment is required for DTG coadministered with prednisone. (This study has been registered at ClinicalTrials.gov under registration no. NCT01425099.).
Protein Coexpression Using FMDV 2A: Effect of “Linker” Residues (2013)

Many biomedical applications absolutely require, or are substantially enhanced by, coexpression of multiple proteins from a single vector. Foot-and-mouth disease virus 2A (F2A) and "2A-like" sequences (e.g., Thosea asigna virus 2A; T2A) are used widely for this purpose since multiple proteins can be coexpressed by linking open reading frames (ORFs) to form a single cistron. The activity of F2A "cleavage" may, however, be compromised by both the use of shorter versions of F2A and the sequences (derived from multiple-purpose cloning sites) used to link F2A to the upstream protein. To characterise these effects, different lengths of F2A and T2A were inserted between green and cherry fluorescent proteins. Mutations were introduced in the linker region immediately upstream of both F2A- and T2A-based constructs and activities determined using both cell-free translation systems and transfected cells. In shorter versions of F2A, activity may be affected by both the C-terminal sequence of the protein upstream and, equally strikingly, the residues immediately upstream introduced during cloning. Mutations significantly improved activity for shorter versions of F2A but could decrease activity in the case of T2A. These data will aid the design of cloning strategies for the co-expression of multiple proteins in biomedical/biotechnological applications.
Vacuum-Assisted Closure: A New Method for Wound Control and Treatment (1997)

A series of basic animal studies using a new subatmospheric pressure technique (The V.A.C.) to expedite wound healing are presented. The technique entails placing an open-cell foam into the wound, sealing the site with an adhesive drape, and applying subatmospheric pressure (125 mmHg below ambient) that is transmitted to the wound in a controlled manner. Utilizing a pig model, four studies were undertaken to determine the effect of subatmospheric pressure on laser Doppler-measured blood flow in the wound and adjacent tissue (N = 5), rate of granulation tissue formation (N = 10), clearance of bacteria from infected wounds (N = 5), and measurement of nutrient flow by random-pattern flap survival (N = 5). Blood flow levels increased fourfold when 125 mmHg subatmospheric pressure was applied. Significantly increased rates of granulation tissue formation (p < or = 0.05) occurred with both continuous (63.3 +/- 26.1%) and intermittent (103% +/- 35.3%) application. Tissue bacterial counts significantly decreased (p < or = 0.05) after 4 days of application. Random-pattern flap survival significantly increased (p < or = 0.05) by 21% compared to controls. We determined that the application of controlled subatmospheric pressure creates an environment that promotes would healing.
cDNA clones coding for the heavy chain of human HLA-DR antigen. (1982)

Two cDNA clones, pDRH1 and pDRH2, containing sequences specific for human HLA-DR antigens were isolated from a bank of cDNA clones made from partially purified HLA-DR mRNA from the human lymphoblastoid cell line Maja. The clones were specific for the Mr 34,000 HLA-DR antigen glycoprotein chain. The identity of these clones was established by (i) their ability to hybridize specifically to HLA-DR mRNA in a positive selection assay; (ii) mRNA species hybridizing to the cDNA clones were expressed in B-cell but not in T-cell or fibroblast cell cultures; and (iii) a nucleotide sequence in the longer clone, pDRH2, could be translated into an amino acid sequence that is identical to the limited NH2-terminal amino acid sequence available for the purified HLA-DR antigen Mr 34,000 chain. Analysis of DNA from human, mouse, and human--mouse somatic cell hybrid lines by Southern transfer of restriction endonuclease digests indicated that the HLA-DR heavy chain is encoded in chromosome 6. This finding is compatible with the location of at least one of the HLA-D/DR heavy chain genes within the HLA region. In addition, the sequences coding for HLA-DR heavy chain appear to be present in only one or a few copies in the genome and to be relatively simple in structure.
Crystal Structures of Human SIRT3 Displaying Substrate-induced Conformational Changes (2009)

SIRT3 is a major mitochondrial NAD(+)-dependent protein deacetylase playing important roles in regulating mitochondrial metabolism and energy production and has been linked to the beneficial effects of exercise and caloric restriction. SIRT3 is emerging as a potential therapeutic target to treat metabolic and neurological diseases. We report the first sets of crystal structures of human SIRT3, an apo-structure with no substrate, a structure with a peptide containing acetyl lysine of its natural substrate acetyl-CoA synthetase 2, a reaction intermediate structure trapped by a thioacetyl peptide, and a structure with the dethioacetylated peptide bound. These structures provide insights into the conformational changes induced by the two substrates required for the reaction, the acetylated substrate peptide and NAD(+). In addition, the binding study by isothermal titration calorimetry suggests that the acetylated peptide is the first substrate to bind to SIRT3, before NAD(+). These structures and biophysical studies provide key insight into the structural and functional relationship of the SIRT3 deacetylation activity.
PROPERDIN FACTOR D (1974)

The protein in the properdin pathway responsible for conversion of precursor factor D to D has been isolated and found to be identical with properdin. Sequential ion exchange and gel filtration chromatography demonstrated identity between properdin protein, measured by radial immunodiffusion, and the capacity to activate D to D, assessed by formation of the intermediate, EAC43B(D). Properdin, purified in this manner, was homogeneous on acid polyacrylamide disc gel electrophoretic analysis, with the band of protein corresponding to the position of eluates in the replicate gel capable of activating highly purified D. Demonstration of the homogeneity of purified D by alkaline disc gel electrophoresis, coupled with the linear stoichiometric hemolytic titrations of each factor, indicates that direct interaction between properdin and D generates D. Thus, activation of D by properdin represents a mechanism in the properdin pathway by which D becomes available for formation of the C3b-dependent C3 convertase.
The nature of hypnotic analgesia: neurophysiological foundation and evidence (1998)

Abstract This paper reviews neurophysiological research (EEG, event‐related potential, regional cerebral blood flow, neurochemical) that supports the proposal that hypnotic analgesia is an active inhibitory process involving several brain systems mediating attentional and nociceptive processes. Even though the processes of hypnotic analgesia may be dissociated from conscious awareness and appear to be out of volitional control, it is proposed that hypnotic analgesia depends on the activation of a supervisory, attention control system – involving the anterior frontal cortex – which then participates with other cortical and subcortical systems in the allocation of thalamocortical activities. Hypnotic analgesia affects the active allocation of attention and disattention associated with the anterior frontal region, as well as spatio‐temporal aspects of pain perception associated with the posterior cortical systems. Copyright © 1998 British Society of Experimental and Clinical Hypnosis
Regioselective acylation of bile acid derivatives with Candida cylindracea lipase in anhydrous benzene (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegioselective acylation of bile acid derivatives with Candida cylindracea lipase in anhydrous benzeneSergio Riva, Roberto Bovara, Gianluca Ottolina, Francesco Secundo, and Giacomo CarreaCite this: J. Org. Chem. 1989, 54, 13, 3161–3164Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/jo00274a036https://doi.org/10.1021/jo00274a036research-articleACS PublicationsRequest reuse permissionsArticle Views239Altmetric-Citations51LEARN 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
Transplantation-related lymphoproliferative disorder: a model for human immunodeficiency virus-related lymphomas. (2000)

Post-transplant lymphoproliferative disorders (PTLD) share many of the features of human immunodeficiency virus (HIV)-related lymphomas, although important differences exist. PTLD ranges from hyperplastic lesions to aggressive lymphoma or multiple myeloma histology. The coexistence of multiple clones, and the strong association with the Epstein-Barr virus (EBV), represent a uniquely different mechanism for lymphomagenesis when compared with de novo lymphoma. The risk of PTLD increases as the duration of immunodeficiency lengthens, with unusual, newly described entities arising after prolonged immunosuppression. The risk is also strongly influenced by the specific anti-T-cell therapies used to prevent graft rejection, providing insight into the nature of immune surveillance. The presence or absence of bcl-6 mutations may be predictive of the reversibility of the PTLD with reduction in immunosuppressive therapy. The use of cytotoxic agents has been complicated by problems similar to those encountered with HIV-related lymphomas, but can nonetheless be very effective. Long-term remission has been achieved with anti-CD21 and anti-CD24 antibodies, although these have not been equally effective for all categories of PTLD. In vitro-expanded EBV-specific T cells have been effective both as treatment and as prophylaxis in the setting of PTLD occurring after marrow transplantation. EBV viral load measurement correlates with the emergence of PTLD, and may make clinical trials of screening, prophylaxis, or early intervention possible.
Inhibition of mitogen-activated protein kinase cascade by baicalein, a flavonoid of natural origin (1999)

Mitogen-activated protein kinase (MAPK) is a family of serine/threonine kinase that appears to be a component common to signalling pathway initiated by a wide range of factors including hormones, differentiation factors and mitogens. Baicalein is a flavonoid derived from the root of Scutellaria baicaleins. From searching the inhibitors of prostaglandin synthesis in C6 rat glioma cells, we found that baicalein had a potent inhibitory activity of prostaglandin synthesis induced by either histamine or A23187, a Ca2+ ionophore. Baicalein inhibited histamine- and A23187-induced phosphorylation of MAPK in the cells, which was known to cause the phosphorylation of cytosolic phospholipase A2. Baicalein also inhibited the phosphorylation of MAPK kinase (MEK) induced by histamine or A23187 in the cells. In vitro kinase assay, baicalein inhibited the activities of raf but not MEK. These results imply that baicalein is a specific inhibitor of MAPK cascade, acting on phosphorylation of MEK by raf.
Regulation of 4‐1BB expression by cell‐cell interactions and the cytokines, interleukin‐2 and interleukin‐4 (1995)

4-1BB expression increased gradually following T cell activation, and by day 3 post-stimulation with immobilized anti-CD3 (anti-CD3i) or concanavalin A (Con A), splenic T cells were routinely 35-45% 4-1BB+ by flow cytometric analysis. 4-1BB was expressed on activated CD8+, CD4+, CD28+ and CD45RB+ T cells. Optimal 4-1BB expression was seen by day 6 post-stimulation and was cell density dependent. When T cells were cultured for 6 days at 1 x 10(6)/well in a 24-well plate with anti-CD3i, 82% of the cells were 4-1BB+. In contrast, at lower cell densities (4 x 10(5), 2 x 10(5) and 1 x 10(5)), optimal 4-1BB expression was observed only if the cultures were supplemented with recombinant interleukin-2 (IL-2) or recombinant IL-4 (IL-4). In agreement, with these results, modes of inducing endogenous IL-2 production such as cross-linking the costimulatory molecule, CD28, or the addition of syngeneic accessory cells to T cells activated with anti-CD3i, resulted in high levels of 4-1BB expression. The addition of interleukin-1 alpha (IL-1 alpha) or interferon-gamma (IFN-gamma) did not increase 4-1BB expression on anti-CD3i-activated T cells. In addition, if T cells were incubated with IL-2, IL-4, IL-1 alpha, IFN-gamma or anti-CD28 alone, no 4-1BB expression was induced. T cells activated with soluble anti-CD3 (anti-CD3s) in the presence of IL-2, IL-4, or accessory cells, did not express higher levels of 4-1BB on their cell surface. These data suggest that initial events crucial for efficient T cell activation, such as signals delivered through the T cell receptor/CD3 complex and the CD28 molecule, are instrumental in regulating subsequent 4-1BB expression.
Bypassing Medicine to Treat Diabetes (2008)

By altering the gut's production of hormones, gastric bypass surgery may be able to eliminate type 2 diabetes. But scientists worry that this radical operation can also cause dangerously low blood sugar
Crystal Structure of the Polymer Electrolyte Poly(ethylene oxide) 3 :LiCF 3 SO 3 (1993)

Ionically conducting polymers (polymer electrolytes) are under intensive investigation because they form the basis of all solid-state lithium batteries, fuel cells, and electrochromic display devices, as well as being highly novel electrolytes. Little is known about the structures of the many crystalline complexes that form between poly(ethylene oxide) and a wide range of salts. The crystal structure is reported of the archetypal polymer electrolyte poly(ethylene oxide)(3):LiCF(3)SO(3), which has been determined from powder x-ray diffraction data. The poly(ethylene oxide) (PEO) chain adopts a helical conformation parallel to the crystallographic b axis. The Li(+) cation is coordinated by five oxygen atoms-three ether oxygens and one from each of two adjacent CF(3)SO(3)(-) groups. Each CF(3)SO(3)(-) in turn bridges two Li(+) ions to form chains running parallel to and intertwined with the PEO chain. There are no interchain links between PEO chains, and the electrolyte can be regarded as an infinite columnar coordination complex.