gebhart/patrepeval huggingface dataset:
Elimination of Bacterial DNA from Taq DNA Polymerases by Restriction Endonuclease Digestion (1999)

The incidence of false positives due to the presence of bacterial DNA in Taq DNA polymerase is an obstacle to the use of PCR in the diagnosis of infection. We describe a method that uses a restriction enzyme to destroy the ability of contaminating sequences to act as templates for a nested PCR which uses primers based on the 16S rRNA genes. The method was used prior to a PCR that amplified 10 fg of bacterial DNA. This method can be readily adapted to suit other sensitive PCRs required for clinical applications.
Tyrosine Kinase Inhibitors. 14. Structure−Activity Relationships for Methyl- amino-Substituted Derivatives of 4-[(3-Bromophenyl)amino]-6-(methylamino)- pyrido[3,4-d]pyrimidine (PD 158780), a Potent and Specific Inhibitor of the Tyrosine Kinase Activity of Receptors for the EGF Family of Growth Factors (1998)

The 4-[(3-bromophenyl)amino]pyrido[3,4-d]pyrimidine PD 158780 is a very potent in vitro inhibitor of the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) (IC50 0.08 nM), and other members of the erbB family, by competitive binding at the ATP site of these signal transduction enzymes. A series of analogues of PD 158780 bearing solubilizing functions off the 6-methylamino substituent were prepared by reaction of the 6-fluoro derivatives with appropriate amine nucleophiles. These were evaluated for their ability to inhibit the tyrosine phosphorylating action of EGF-stimulated full-length EGFR enzyme and for inhibition of autophosphorylation of the EGFR in A431 human epidermoid carcinoma cells in culture. The most effective analogues were those bearing weakly basic substituents through a secondary amine linkage, which proved water-soluble (> 10 mM) and potent (IC50S generally < 1 nM). No clear SAR could be discerned for these compounds with respect to amine base strength or the distance of the cationic center from the chromophore, suggesting that 6-substituents are in a favorable area of bulk tolerance in the enzyme binding site. More distinct SAR emerged for the ability of the compounds to inhibit EGFR autophosphorylation in A431 cells, where analogues bearing lipophilic weak bases were preferred. Representative analogues were evaluated for antitumor effectiveness against four in vivo tumor models. Significant in vivo activity was observed in estrogen-dependent MCF-7 breast and A431 epidermoid tumors. Marginal activity was seen in an EGFR-transfected tumor model, suggesting that while this cell line requires EGF for clone formation in soft agar, other growth factors may be able to replace EGF in vivo. Also, no activity was seen against the SK-OV-3 ovarian cancer model, which is known to express other EGF receptor family members (although it is not clear whether these are absolutely required for growth in vivo). While substantial growth delays were seen in A431 and MCF-7 tumor models, the treated tumors remained approximately the same size throughout therapy, suggesting that the compounds are cytostatic rather than cytotoxic under these test conditions. It remains to be determined if more prolonged therapy has cytotoxic effects in vivo, resulting in net tumor cell kill.
Biologic Fate of Autogenous Vein lmplants as Arterial Substitutes (1973)

SZILAGYI, D. EMERICK M.D.; ELLIOTT, JOSEPH P. M.D.; HACEMAN, JOHN H. M.D.; SMITH, ROGER F. M.D.; DALL'OLMO, CARLO A. M.D. Author Information
Buckling of Aligned Carbon Nanotubes as Stretchable Conductors: A New Manufacturing Strategy (2012)

A new manufacturing strategy for buckling of aligned carbon nanotubes is developed, which does not involve prestretching the substrate but relies on the interface interaction between the nanotubes and the substrate. More specifically, upon stretching the substrate the nanotubes slide on the substrate, but upon releasing the nanotubes buckle. Following this manufacturing strategy, stretchable conductors based on aligned carbon nanotubes are demonstrated.
33 Rhizobium lipopolysaccharides; their structures and evidence of their importance in the nitrogen-fixing symbiotic infection of their host legumes (2024)

The purpose of this brief chapter is to describe what is known about the structure of Rhizobium lipopolysaccharides (LPSs), and to summarize the evidence showing that these molecules are important in establishing a nitrogen-fixing symbiosis between a Rhizobium and its legume host. Work regarding other Rhizobium surface polysaccharides, e.g. extracellular polysaccharides (EPSs), is discussed when it relates to, or clarifies, the role of LPS in symbiosis. The readers are referred to recent and comprehensive reviews describing Rhizobium polysaccharies, their genetics and possible roles in symbiosis (Gray & Rolfe, 1990; Noel, 1991).
Heterogenity of genes encoding the low molecular weight glutenin subunits of bread wheat (2007)

International audience
Theoretical Studies of the Mechanism of Aerobic Alcohol Oxidation with Palladium Catalyst Systems (2005)

Density functional theory (DFT) was applied to a comprehensive mechanistic study of the Pd(II)-catalyzed oxidation of alcohols by molecular oxygen. Both parts of the catalytic cycle, i.e., the oxidative dehydrogenation of the substrate and the regeneration of the catalyst by the co-oxidant, molecular oxygen, were studied. The catalytic cycle under consideration consists of intramolecular deprotonation, β-hydride elimination, and migratory insertion steps, and it is relevant for a wide class of catalytic systems. In particular, a Pd(II) cyclometalated system was addressed and qualitatively compared with the Uemura system (Pd(OAc)2/pyridine) and with the Pd−carbene system. Geometries of the intermediate complexes and relative Gibbs free energies were identified along the proposed reaction path with the help of computational methods. The transition state for the β-hydride elimination, which is the highest point on the energy profile of the catalytic cycle, was identified.
A general approach to connected-component labeling for arbitrary image representations (1992)

An improved and general approach to connected-component labeling of images is presented. The algorithm presented in this paper processes images in predetermined order , which means that the processing order depends only on the image representation scheme and not on specific properties of the image. The algorithm handles a wide variety of image representation schemes (rasters, run lengths, quadrees, bintrees, etc.). How to adapt the standard UNION-FIND algorithm to permit reuse of temporary labels is shown. This is done using a technique called age balancing , in which, when two labels are merged, the older label becomes the father of the younger label. This technique can be made to coexist with the more conventional rule of weight balancing , in which the label with more descendants becomes the father of the label with fewer descendants. Various image scanning orders are examined and classified. It is also shown that when the algorithm is specialized to a pixel array scanned in raster order, the total processing time is linear in the number of pixels. The linear-time processing time follows from a special property of the UNION-FIND algorithm, which may be of independent interest. This property states that under certain restrictions on the input, UNION-FIND runs in time linear in the number of FIND and UNION operations. Under these restrictions, linear-time performance can be achieved without resorting to the more complicated Gabow-Tarjan algorithm for disjoint set union.
An improved collagen scaffold for skeletal regeneration (2010)

Bone repair and regeneration is one of the most extensively studied areas in the field of tissue engineering. All of the current tissue engineering approaches to create bone focus on intramembranous ossification, ignoring the other mechanism of bone formation, endochondral ossification. We propose to create a transient cartilage template in vitro, which could serve as an intermediate for bone formation by the endochondral mechanism once implanted in vivo. The goals of the study are (1) to prepare and characterize type I collagen sponges as a scaffold for the cartilage template, and (2) to establish a method of culturing chondrocytes in type I collagen sponges and induce cell maturation. Collagen sponges were generated from a 1% solution of type I collagen using a freeze/dry technique followed by UV light crosslinking. Chondrocytes isolated from two locations in chick embryo sterna were cultured in these sponges and treated with retinoic acid to induce chondrocyte maturation and extracellular matrix deposition. Material strength testing as well as microscopic and biochemical analyzes were conducted to evaluate the properties of sponges and cell behavior during the culture period. We found that our collagen sponges presented improved stiffness and supported chondrocyte attachment and proliferation. Cells underwent maturation, depositing an abundant extracellular matrix throughout the scaffold, expressing high levels of type X collagen, type I collagen and alkaline phosphatase. These results demonstrate that we have created a transient cartilage template with potential to direct endochondral bone formation after implantation.
The role of learning in nocebo and placebo effects (2008)

The nocebo effect consists in delivering verbal suggestions of negative outcomes so that the subject expects clinical worsening. Here we show that nocebo suggestions, in which expectation of pain increase is induced, are capable of producing both hyperalgesic and allodynic responses. By extending previous findings on the placebo effect, we investigated the role of learning in the nocebo effect by means of a conditioning procedure. To do this, verbal suggestions of pain increase were given to healthy volunteers before administration of either tactile or low-intensity painful electrical stimuli. This nocebo procedure was also carried out after a pre-conditioning session in which two different conditioned visual stimuli were associated to either pain or no-pain. Pain perception was assessed by means of a Numerical Rating Scale raging from 0=tactile to 10=maximum imaginable pain. We found that verbal suggestions alone, without prior conditioning, turned tactile stimuli into pain as well as low-intensity painful stimuli into high-intensity pain. A conditioning procedure produced similar effects, without significant differences. Therefore, in contrast to placebo analgesia, whereby a conditioning procedure elicits larger effects compared to verbal suggestions alone, learning seems to be less important in nocebo hyperalgesia. Overall, these findings indicate that, by defining hyperalgesia as an increase in pain sensitivity and allodynia as the perception of pain in response to innocuous stimulation, nocebos can indeed produce both hyperalgesic and allodynic effects. These results also suggest that learning is not important in nocebo hyperalgesia compared to placebo analgesia.
The Distribution of Macrophages with a M1 or M2 Phenotype in Relation to Prognosis and the Molecular Characteristics of Colorectal Cancer (2012)

High macrophage infiltration has been correlated to improved survival in colorectal cancer (CRC). Tumor associated macrophages (TAMs) play complex roles in tumorigenesis since they are believed to hold both tumor preventing (M1 macrophages) and tumor promoting (M2 macrophages) activities. Here we have applied an immunohistochemical approach to determine the degree of infiltrating macrophages with a M1 or M2 phenotype in clinical specimens of CRC in relation to prognosis, both in CRC in general but also in subgroups of CRC defined by microsatellite instability (MSI) screening status and the CpG island methylator phenotype (CIMP). A total of 485 consecutive CRC specimens were stained for nitric oxide synthase 2 (NOS2) (also denoted iNOS) as a marker for the M1 macrophage phenotype and the scavenger receptor CD163 as a marker for the M2 macrophage phenotype. The average infiltration of NOS2 and CD163 expressing macrophages along the invasive tumor front was semi-quantitatively evaluated using a four-graded scale. Two subtypes of macrophages, displaying M1 (NOS2(+)) or M2 (CD163(+)) phenotypes, were recognized. We observed a significant correlation between the amount of NOS2(+) and CD163(+) cells (P<0.0001). A strong inverse correlation to tumor stage was found for both NOS2 (P<0.0001) and CD163 (P<0.0001) infiltration. Furthermore, patients harbouring tumors highly infiltrated by NOS2(+) cells had a significantly better prognosis than those infiltrated by few NOS2(+) cells, and this was found to be independent of MSI screening status and CIMP status. No significant difference was found on cancer-specific survival in groups of CRC with different NOS2/CD163 ratios. In conclusion, an increased infiltration of macrophages with a M1 phenotype at the tumor front is accompanied by a concomitant increase in macrophages with a M2 phenotype, and in a stage dependent manner correlated to a better prognosis in patients with CRC.
MR of carcinoma-specific monoclonal antibody conjugated to monocrystalline iron oxide nanoparticles: the potential for noninvasive diagnosis. (1996)

Monoclonal antibodies conjugated with monocrystalline iron oxide particles may provide a method to obtain specific diagnoses with the use of MR imaging.
Preliminary structure analysis of the DH/PH domains of leukemia-associated RhoGEF (2003)

Leukemia-associated RhoGEF (LARG) is a multidomain protein that relays signals from Galpha(12/13)-coupled heptahelical receptors to GTPases that regulate the cytoskeleton. To understand the molecular basis of LARG-mediated signal transduction, structural analysis of its DH/PH domains has been initiated. The LARG DH/PH domains have been overexpressed in Escherichia coli as a TEV protease-cleavable fusion protein containing maltose-binding protein and a hexahistidine tag at the N- and C-termini, respectively. Crystals of the DH/PH domains were obtained (space group C2; unit-cell parameters a = 195.5, b = 46.0, c = 75.1 A, beta = 105.0 degrees ) and xenon and NaBr derivatives were generated which should allow the structure to be determined by MIRAS.
CXCR4 and CD4 mediate a rapid CD95-independent cell death in CD4+T cells (1998)

AIDS is characterized by a progressive decrease of CD4(+) helper T lymphocytes. Destruction of these cells may involve programmed cell death, apoptosis. It has previously been reported that apoptosis can be induced even in noninfected cells by HIV-1 gp120 and anti-gp120 antibodies. HIV-1 gp120 binds to T cells via CD4 and the chemokine coreceptor CXCR4 (fusin/LESTR). Therefore, we investigated whether CD4 and CXCR4 mediate gp120-induced apoptosis. We used human peripheral blood lymphocytes, malignant T cells, and CD4/CXCR4 transfectants, and found cell death induced by both cell surface receptors, CD4 and CXCR4. The induced cell death was rapid, independent of known caspases, and lacking oligonucleosomal DNA fragmentation. In addition, the death signals were not propagated via p56(lck) and Gialpha. However, the cells showed chromatin condensation, morphological shrinkage, membrane inversion, and reduced mitochondrial transmembrane potential indicative of apoptosis. Significantly, apoptosis was exclusively observed in CD4(+) but not in CD8(+) T cells, and apoptosis triggered via CXCR4 was inhibited by stromal cell-derived factor-1, the natural CXCR4 ligand. Thus, this mechanism of apoptosis might contribute to T cell depletion in AIDS and might have major implications for therapeutic intervention.
Multi-carrier spread spectrum and its relationship to single-carrier transmission (2002)

The combination of orthogonal frequency division multiplexing (OFDM) and code division multiplexing (CDM) has found great interest. In contrast to a conventional OFDM system the information is spread over several subcarriers using orthogonal codes which leads to a diversity gain in frequency-selective channels. In this paper it is shown that such a system is technically equivalent to a single-carrier system with a guard interval if the columns of a Fourier matrix are used as spreading codes. The pros and cons of such a system compared to an OFDM-CDM system with arbitrary spreading matrix are described and discussed.
Professional Views of Children's Participation (2008)

This chapter compares the views of the professionals involved in family law disputes: the mediators, counsellors, lawyers, and judges. These professionals play an important role as advisers, gatekeepers, and adjudicators. The advice of counsellors and lawyers may play an important role in how parents see the views of children and the participation of children. Counsellors in the courts who write family reports and lawyers who represent children in the most highly contested disputes also provide two of the more influential means of presenting children's views to the court, or not, depending on the role they play.
Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes (2003)

Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters. For the crenarchaeon Sulfolobus solfataricus P2, the repeats in the genome fall mainly into two closely related sequence families that are arranged in seven clusters containing a total of 441 repeats which constitute ca. 1% of the genome. The Sulfolobus conjugative plasmid pNOB8 contains a small cluster of six repeats that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure at the center of each DNA repeat and thereby produces a binding site for another protein, possibly a more conserved one, in a process that may be essential for higher-order stucturing of the SRSR clusters.
The Use of Intravitreal Ranibizumab for Choroidal Neovascularization Associated with Vogt-Koyanagi-Harada Syndrome (2011)

Purpose. To describe the use of intravitreal ranibizumab for choroidal neovascular membrane (CNVM) secondary to Vogt-Koyanagi-Harada (VKH) syndrome. Methods. Interventional case report. Results. A 50-year-old woman presented with conjunctival injection and bilateral eye pain. Vision was 20/400 and 20/80 in the right and left eyes, respectively. Bilateral iritis, vitritis, and choroidal thickening were evident. Exudative retinal detachment was present in the left eye. Corticosteroid treatment improved vision to 20/40 bilaterally. Methotrexate (MTX) was initiated and vision remained stable for 3 months. After a 5-month loss to follow-up, vision in the left eye decreased to finger counting (CF) and a parafoveal CNVM was identified. After 3 intravitreal ranibizumab injections, vision improved to 20/40. Twelve months later, despite inflammation control, vision decrease to CF due to recurrent CNVM. A fourth ranibizumab injection was given. Twenty months later, best-corrected vision was 20/400, and an inactive CNVM was present in the left eye. Conclusion. After initial CNVM regression and visual acuity improvement due to ranibizumab, the CNVM recurred and became refractory to treatment. Despite control of inflammation and neovascularization, VKH chronicity lead to permanent vision loss in our patient. A combinational treatment approach may be required in such patients.
Levetiracetam: The Profile of a Novel Anticonvulsant Drug—Part I: Preclinical Data (2007)

The objective of this article was to review and summarize the available reports on the preclinical profile of the novel anticonvulsant drug levetiracetam (LEV). Therefore, a careful search was conducted in the MEDLINE database and combined with guidelines from regulatory agencies, proceedings of professional scientific meetings, and information provided by the manufacturers. This article provides detailed information on the anticonvulsant effects of LEV in various animal models of epilepsy and on its pharmacology in laboratory animals. The mechanism of action of LEV is reviewed, with special regard to its recently discovered binding site, the synaptic vesicle protein 2A. In general, LEV is shown to be a safe, broad-spectrum anticonvulsant drug with highly beneficial pharmacokinetic properties and a distinct mechanism of action. The clinical studies with LEV will be discussed in the second part of this review article to be published subsequently.
A Rational Choice Model of Educational Inequality (2001)

Recent empirical research in the sociology of education has consistently reported three major findings. First, differentials in educational attainment between young people coming from different social classes have changed rather little, if at all, over the greater part of the twentieth century. Secondly, social class or other social origin effects seem to diminish in strength as students move to higher levels within the educational system. Thirdly, gender differences in educational attainment have declined dramatically over the past 25 years. In this paper I draw on the Breen and Goldthorpe (1997) model of educational decision making to provide explanations for the first two of these findings. I also show how the Breen and Goldthorpe model, as reformulated here, and drawing on Breen (1999), provides a sound behavioural model for the widely used Mare (1980; 1981) model of educational transitions.
Propane Oxidation over Pt/SrTiO3 Nanocuboids (2011)

Pt/SrTiO3 shows promise as a low temperature hydrocarbon combustion catalyst for automotive applications. In this study, SrTiO3 nanocuboid supports were synthesized using sol-precipitation coupled with hydrothermal synthesis, and platinum was deposited on the nanocuboids with 1, 3, and 5 cycles of atomic layer deposition (ALD). The platinum particles have a highly uniform distribution both before and after reaction testing, and range from 1 to 5 nm in size, depending upon the number of ALD cycles. These materials have a >50 °C lower light-off temperature for propane oxidation than a conventional Pt/Al2O3 catalyst, turn over frequencies up to 3 orders of magnitude higher, and show improved resistance to deactivation. The increased activity is attributed to the stabilization of a Pt/PtO core/shell structure during operating conditions by the strong epitaxy between the Pt and the SrTiO3 support.