gebhart/patrepeval huggingface dataset:
Requirements for synthesis of ribonucleic acid primers during lagging strand synthesis by the DNA polymerase and gene 4 protein of bacteriophage T7. (1979)

DNA polymerase and gene 4 protein of bacteriophage T7 catalyze DNA synthesis on duplex DNA templates. Synthesis is initiated at nicks in the DNA template, and this leading strand synthesis results in displacement of one of the parental strands. In the presence of ribonucleoside 5'-triphosphates the gene 4 protein catalyzes the synthesis of oligoribonucleotide primers on the displaced single strand, and their extension by T7 dna polymerase accounts for lagging strand synthesis. Since all the oligoribonucleotide primers bear adenosine 5'-triphosphate residues at their 5' termini, [gamma 32P]ATP is incorporated specifically into the product molecule, thus providing a rapid and sensitive assay for the synthesis of the RNA primers. Both primer synthesis and DNA synthesis are stimulated 3- to 5-fold by the presence of either Escherichia coli or T7 helix-destabilizing protein (DNA binding protein). ATP and CTP together fully satisfy the requirement for rNTPs and provide maximum synthesis of primers and DNA. Provided that T7 DNA polymerase is present, RNA-primed DNA synthesis occurs on either duplex or single-stranded DNA templates and to equal extents on either strand of T7 DNA. No primer-directed DNA synthesis occurs on poly(dT) or poly(dG) templates, indicating that synthesis of primers is template-directed.
Multicentric evaluation of model for end-stage liver disease-based allocation and survival after liver transplantation in Germany - limitations of the ‘sickest first’-concept (2010)

Since the introduction of model for end-stage liver disease (MELD) in 2006, post-orthotopic liver transplantation (OLT) survival in Germany has declined. The aim of this study was to evaluate risk factors and prognostic scores for outcome. All adult OLT recipients in seven German transplant centers after MELD implementation (December 2006-December 2007) were included. Recipient data were analyzed for their influence on 1-year outcome. A total of 462 patients (mean calculated MELD = 20.5, follow-up: 1 year) were transplanted for alcoholic cirrhosis (33.1%), hepatocellular carcinoma (26.6%), Hepatitis-C (17.1%), Hepatitis-B (9.5%), primary sclerosing cholangitis (5.6%) and late graft-failure after first OLT before December 2006 (8.7%). 1-year patient survival was 75.8% (graft survival 71.2%) correlating with MELD parameters and serum choline esterase. MELD score >30 [odds ratio (OR) = 4.17, confidence interval: 2.57-6.78, 12-month survival = 52.6%, c-statistic = 0.669], hyponatremia (OR = 2.07), and pre-OLT hemodialysis (OR = 2.35) were the main death risk factors. In alcoholic cirrhosis (n = 153, mean MELD = 21.1) and hepatocellular carcinoma (n = 123, mean MELD = 13.5), serum bilirubin and the survival after liver transplantation score were independent outcome parameters, respectively. MELD >30 currently represents a major risk factor for outcome. Risk factors differ in individual patient subgroups. In the current German practice of organ allocation to sicker patients, outcome prediction should be considered to prevent results below acceptable standards.
Bonding and Thermal Reactivity in Thin a-SiC:H Films Grown by Methylsilane CVD (1997)

The bonding and thermal reactivity of thin a-SiC:H films have been studied and compared with that of methyl groups on single-crystalline Si and in thick polymer films. The films were deposited on silicon substrates at 200 K by hot-wire chemical vapor deposition (CVD) using methylsilane (CH3SiH3) as the precursor. The resulting films were probed by in situ multiple internal reflection−Fourier transform infrared (MIR−FTIR) spectroscopy, and the thermal decomposition products were measured by temperature-programmed reaction/desorption (TPR/D). According to MIR−FTIR measurements, hydrogen is present in the films in the form of mixed silicon hydride species (SiH, SiH2, and SiH3) and intact methyl groups. TPR/D and MIR−FTIR annealing studies following growth at 200 K indicate that the film is stable up to 550 K. Above 550 K, a number of thermal etching processes are observed, leading to silane and methylsilane evolution at 600 K, followed by the loss of methane and molecular hydrogen by 780 K. Annealing studies show that the SiH3 species are more reactive at thermal energies than are methyl groups. The stability of methyl groups and the silicon mono- and dihydride groups in the films largely parallels that observed on single-crystalline silicon, but more reaction pathways are available in the thin films. Mechanisms for the film growth and thermal decomposition are proposed.
Advanced biobanking and good management (2013)

This paper has three main propositions. First, the success of translational research requires changes in practice and culture by universities, hospitals and industry. Second, biobanking networks are one of the most effective ways of enabling those changes – if the networks have standards that can reach across universities, hospitals and industry. Third, a network quality management system based on ISO9001 requirements can be an effective tool to drive the changes required for a biobanking network to function. The goal of academic biomedical research has been to serve a scientific good: to understand the human organism in health and disease. The goal of clinical and industrial research has been to serve a public good: to develop and innovate for the alleviation of human disease and ill-health. Today, in the rapidly changing landscape of biomedical research, academic researchers are capable of and are being encouraged by society to address both goals. To address two goals in place of one goal requires changes in work practices by, and shifts in culture of, academia, clinicians and industry. One important change in practices is due to large research infrastructures whose use is also driving cultural shifts. One basic research infrastructure – the biobanking network – can provide large-scale sample management to support the analysis and meta-analysis of biomarkers required across translational research - from research to development to innovation. The EU and some Member States have made progress in constructing such a network. The problem of ensuring consistency and interoperability across network has not been fully resolved. In the UK, an academic national DNA banking network introduced a system to promote consistency and interoperability - an ISO9001 quality management system - driven by the need for stakeholder engagement. Recently, this system was overhauled to create for the first time a Quality Network Management System (QNMS). This may be one of the most effective ways of achieving the changes in practices and culture that we require for successful translation to improved health of populations.
Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis (2013)

The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity. The putative function of MJ0391 is discussed, based on structural homology.
Clinical improvement by farnesyltransferase inhibition in NK large granular lymphocyte leukemia associated with imbalanced NK receptor signaling (2008)

Large granular lymphocyte (LGL) leukemia is commonly associated with poor hematopoiesis. The first case of pulmonary artery hypertension (PAH) was observed in a 57-year-old woman with natural killer (NK)-LGL leukemia and transfusion-dependent anemia. Using a genetic approach, we demonstrated that killing of pulmonary endothelial cells by patient NK cells was mediated by dysregulated balance in activating and inhibitory NK-receptor signaling. Elevated pulmonary artery pressure and erythroid differentiation improved after disrupting the NK-receptor signaling pathway with 4 courses of a farnesyltransferase inhibitor, tipifarnib. Coincidental association between PAH and LGL leukemia suggest a causal relationship between the expanded lymphocyte population and these clinical manifestations. This trial is registered at www.ClinicalTrials.gov as NCI 6823.
Abstract ED01-03: Metabolomics of disease progression (2010)

Abstract While the total potential of a biological systems response is defined by their genes, and the organism's desired response (to its current status) may be embodied in their transcripts, the metabolome embodies what an organism is actually of doing at a biochemical level. For this reason the metabolomic data may be quite diagnostic of a given disease state, that may or may not be dictated by either the genetic or transcriptomic levels. In this presentation we will discuss an application of metabolomics to define a series of biomarkers. The subsequent explorations of the details of this biomarker have revealed mechanisms that are likely to be significant to the progression of cancer. Citation Information: Cancer Prev Res 2010;3(12 Suppl):ED01-03.
High Performance TiP2O7 Based Intercalation Negative Electrode for Aqueous Lithium-Ion Batteries Via a Facile Synthetic Route (2015)

Combining high energy mechanical alloying with intimate carbon coating has proven effective in improving electrochemical performance of polyanion-based materials (1, 2). Ball milling with intimate carbon helps to prepare a homogenous mixture of precursors and reduce particle size during following thermal treatment (3, 4). In addition, this combination can decrease the thermal treatment time needed (5). In this study, we demonstrated TiP 2 O 7 /graphite prepared by high energy mechanical alloying combined with intimate carbon coating has superior cycling performance in aqueous lithium-ion electrolyte. The TiP 2 O 7 /graphite composite material was prepared by an intensive mechanical mixing solid state synthesis method at 700 ° C. Physical properties were characterized via powder X-ray diffraction, Rietveld refinement, SEM, BET and TGA. Electrochemical performance was evaluated in both a three electrode test setup and two electrode coin cells via cyclic voltammetry and galvanostatic cycling tests. The TiP 2 O 7 /Graphite composite demonstrates excellent cycling performance in 1M Li 2 SO 4 when matched with LiMn 2 O 4 as a positive electrode: when cycled at C/2 for 150 cycles, the capacity retention is over 91% with coulombic efficiencies exceeding 99%. The initial discharge capacity obtained at a C/10 rate is 91mAh/g which was about 75% of theoretical capacity 121mAh/g. Reference: 1. W. Wu, A. Mohamed and J. F. Whitacre, Journal of The Electrochemical Society , 160 , A497 (2013). 2. W. Wu, J. Yan, A. Wise, A. Rutt and J. F. Whitacre, Journal of The Electrochemical Society , 161 , A561 (2014). 3. J.-K. Kim, G. Cheruvally, J.-W. Choi, J.-U. Kim, J.-H. Ahn, G.-B. Cho, K.-W. Kim and H.-J. Ahn, Journal of Power Sources , 166 , 211 (2007). 4. J.-K. Kim, J.-W. Choi, G. Cheruvally, J.-U. Kim, J.-H. Ahn, G.-B. Cho, K.-W. Kim and H.-J. Ahn, Materials Letters , 61 , 3822 (2007). 5. L.-X. Yuan, Z.-H. Wang, W.-X. Zhang, X.-L. Hu, J.-T. Chen, Y.-H. Huang and J. B. Goodenough, Energy &amp; Environmental Science , 4 , 269 (2011). Figure 1
Type, Density, and Location of Immune Cells within Cholangiocarcinomas Predict Clinical Outcome (2012)

Cholangiocarcinoma (CC) is a rare malignant tumor arising from bile duct cells. The prognosis of affected patients is poor. Several risk factors including cholangiolithiasis, liver fluke infection, and anatomical abnormalities, all associated with inflammation of the biliary tract, have been described. In addition, tumor-infiltrating immune cells (TIC) as well as expression of antigen presenting molecules are known to correlate with patient survival in several tumor entities. Therefore, we aimed to characterize the expression of major histocompatibility complex class I (MHC I) and TIC in a large cohort of CC (n=316) including extrahepatic (ECC) and intrahepatic (ICC) CC. TIC and MHC I-expression of tumor cells were assessed qualitatively and quantitatively by immunohistochemistry (CD4, CD8, CD20, CD68, and MHC I) using tissue microarrays. TIC and MHC I-expression were correlated with each other, clinicopathological variables, and patient survival. CC patients whose tumors displayed CD4+ and CD8+ TIC showed longer patient survival compared to patients without tumor associated inflammation (p=0.004, p=0.013, respectively). This result was also seen in the subgroup of ECC while in the subgroup of ICC CD4+ and CD8+ TIC were not able to predict patient survival. In CC, high MHC I-expression of tumor cells correlated significantly with a longer patient survival compared to CC with a low MHC I-expression of tumor cells (p=0.013). Additionally, high MHC I-expression in tumor cells was associated with increased levels of CD8+ (p=0.003) but not CD4+ or CD20+ TIC. Our findings indicate that tumoral expression of antigen presenting molecules and tumor associated inflammation might be of importance in the progression of CC and ultimately have an influence on the outcome of CC patients. However, our results also indicate that ECC and ICC might be different in this regard.
Studies on the immunosuppressive properties of asparaginase. (1971)

The effect of asparaginase on lymphocyte kinetics and on immunological competence of normal and adrenalectomized mice has been studied. Treatment of mice with this enzyme results in lymphocytopenia and atrophy of lymph nodes, thymus and spleen. The lymph node lymphocytes from asparaginase-treated mice do not migrate normally to lymphoid organs when injected intravenously into syngeneic recipients. Splenic lymphocytes from asparaginase-treated mice induce significantly less graft-versus-host reaction when injected into F(1) hybrids and incorporate significantly less thymidine into DNA when cultured in vitro with phytohaemagglutinin than do cells from normal mice. Skin graft rejection and the formation of antibody to sheep erythrocytes is significantly inhibited by administration of asparaginase. The immunosuppressive actions of asparaginase are manifested in adrenalectomized mice. Studies on the inhibition of phytohaemagglutinin-induced lymphocyte transformation by asparaginase suggest that asparagine depletion underlies the effect of asparaginase on lymphocytes.
Efectos sobre la fertilidad del cerdo de dos candidatos vacunales recombinantes basados en la GnRH (2018)

This paper describes for the first time the generation of the K88ab-GnRH hybrid fimbriae, the fusion of N. meningitidis P64k protein (P64k-GnRH), and its evaluation as vaccine candidates to control fertility in mammals. Twenty hybrid male pigs were randomly distributed in four groups: placebos and immunized with K88ab-GnRH, P64k-GnRH and a GnRH analogue (GnRHm1), linked to a tetanus toxoid (TT) T-helper epitope (positive control), respectively. The pigs were immunized at 9-10 weeks of age, using a two-dose scheme, and were sacrificed sixteen weeks later. K88ab-GnRH, P64k-GnRH, and GnRHm1-TT induced higher, similar, and lower testosterone levels in the serum, compared to the placebo, respectively. In the K88ab-GnRH group, the pigs underwent a reduction in testicle size and weight (P < 0.01), and the weight of epididymes compared to the placebo; none of them was able to ejaculate. In the P64k-GnRH group, the pigs had a reduction in testicle weight (P < 0.05), and only one of them was able to ejaculate. The testicles of the pigs immunized with K88ab-GnRH and P64k-GnRH showed structural and functional damage; spermatogenesis was also affected. The accessory sexual glands of the P64k-GnRH group were normal, in contrast to K88ab-GnRH, where interstitial fibrosis was observed. The damage caused by K88ab-GnRH and P64k-GnRH in the target organs evaluated were in all cases lower than the affectations caused by the GnRHm1-TT peptide.
Robust quantum-network memory using decoherence-protected subspaces of nuclear spins (2016)

The realization of a network of quantum registers is an outstanding challenge in quantum science and technology. We experimentally investigate a network node that consists of a single nitrogen-vacancy (NV) center electronic spin hyperfine-coupled to nearby nuclear spins. We demonstrate individual control and readout of five nuclear spin qubits within one node. We then characterize the storage of quantum superpositions in individual nuclear spins under repeated application of a probabilistic optical inter-node entangling protocol. We find that the storage fidelity is limited by dephasing during the electronic spin reset after failed attempts. By encoding quantum states into a decoherence-protected subspace of two nuclear spins we show that quantum coherence can be maintained for over 1000 repetitions of the remote entangling protocol. These results and insights pave the way towards remote entanglement purification and the realisation of a quantum repeater using NV center quantum network nodes.
Type-II Dirac Photons at Metasurfaces (2018)

Topological characteristics of energy bands, such as Dirac and Weyl nodes, have attracted substantial interest in condensed matter systems as well as in classical wave systems. Among these energy bands, the type-II Dirac point is a nodal degeneracy with tilted conical dispersion, leading to a peculiar crossing dispersion in the constant-energy plane. Such nodal points have recently been found in electronic materials. The analogous topological feature in photonic systems remains a theoretical curiosity, with experimental realization expected to be challenging. Here, we experimentally realize the type-II Dirac point using a planar metasurface architecture, where the band degeneracy point is protected by the underlying mirror symmetry of the metasurface. Gapless edge modes are found and measured at the boundary between the different domains of the symmetry-broken metasurface. Our Letter shows that metasurfaces are simple and practical platforms for realizing electromagnetic type-II Dirac points, and their planar structure is a distinct advantage that facilitates applications in two-dimensional topological photonics.
7,8-Dihydroxyflavone exhibits anti-inflammatory properties by downregulating the NF-κB and MAPK signaling pathways in lipopolysaccharide-treated RAW264.7 cells (2012)

7,8-Dihydroxyflavone (7,8-DHF), a member of the flavonoid family, has received considerable attention as a selective tyrosine kinase receptor B agonist. Several studies have indicated that 7,8-DHF has neurotrophic and antioxidant activities. However, little is known about the cellular and molecular mechanisms underlying the anti-inflammatory activity of 7,8-DHF. Therefore, we investigated whether 7,8-DHF affects the expression of inflammatory mediators in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Our results indicated that 7,8-DHF significantly attenuated secretion of LPS-induced inflammatory mediators nitric oxide (NO), prostaglandin E₂ (PGE₂) and interleukin-1β (IL-1β) in RAW264.7 cells. Additionally, LPS-induced expression of inducible NO synthase (iNOS), cyclooxygenase (COX)-2 and IL-1β was decreased by pre-treatment with 7,8-DHF. Our results also showed that 7,8-DHF reduces LPS-induced nuclear factor-κB (NF-κB) activity via the suppression of the nuclear translocation of NF-κB p65 and the degradation of inhibitor κB (lκB). In addition, 7,8-DHF inhibited the phosphorylation of mitogen-activated protein kinases (MAPKs) such as extracellular-signal-related kinase (ERK), p38, and c-Jun N-terminal kinase (JNK). These results suggest that the anti-inflammatory property of 7,8-DHF is related to the downregulation of iNOS, COX-2 and IL-1β, due to NF-κB inhibition as well as to the negative regulation of MAPK activation in RAW264.7 cells. Thus, 7,8-DHF may be a novel therapeutic agent for the prevention of various inflammatory diseases.
A Catalysis-Based Selection for Peroxidase Antibodies with Increased Activity (2004)

A biotin-tyramine conjugate (1) was found to covalently cross-link with peroxidase antibody 7G12 upon the catalytic oxidation of the tyramine moiety in the presence of hydrogen peroxide (H2O2). On the basis of this observation, a novel strategy was developed to select mutants of 7G12 Fab with enhanced peroxidase activity from a library of phage displayed antibodies. In such a selection, tyramine is oxidized by hydrogen peroxide in a process catalyzed by peroxidase antibodies displayed on phage. Antibodies with higher peroxidase activity are preferentially labeled with biotin through irreversible adduct formation between oxidized biotin-linked tyramine molecules and phenolic side chains of the antibody. The corresponding phage particles can then be selected via biotin-streptavidin interactions. Using this strategy, phage displayed libraries of antibody 7G12 were selected for higher peroxidase activity. As a result, mutations of antibody 7G12 that led to 10 to 20-fold increases in the peroxidase activity (kcat/Km) were identified, suggesting the validity of this method for the evolution of peroxidase antibodies based directly on catalytic turnover.
Transient nucleation and manipulation of nucleation sites in solid-state crystallization of a-Si films (1994)

Solid-state nucleation of Si crystals in a-Si films is controlled by Si ion implantation prior to the isothermal annealing. The process of the nucleation includes a long transient period that causes the diminishing shape of the grain size distribution (GSD). The parameters appearing in the kinetic theory of transient nucleation are estimated from the GSD in a-Si. It is found that the ion implantation reduces the steady-state nucleation rate and elongates the time lag, while the growth rate is almost constant. The dependence of the above parameters is simulated based on the model of heterogeneous nucleation. It is qualitatively suggested that the suppression of the nucleation can be attributed to the modification of the interface to the SiO2 underlayer such as the changes in the self-diffusion or in the interfacial energy. When the nucleation rate is spatially controlled in the plane of the film, a small portion provides the artificial nucleation site. If the sites are periodically placed, the GSD shrinks to have a shape like log-normal. A model for the manipulated nucleation site explains the shape of the GSD, and how a single nucleus is selected to grow in the site.