gebhart/patrepeval huggingface dataset:
Doping in Carbon Nanotubes Probed by Raman and Transport Measurements (2007)

In situ Raman experiments together with transport measurements have been carried out on carbon nanotubes as a function of gate voltage. In metallic tubes, a large increase in the Raman frequency of the G(-) band, accompanied by a substantial decrease of its linewidth, is observed with electron or hole doping. In addition, we see an increase in the Raman frequency of the G(+) band in semiconducting tubes. These results are quantitatively explained using ab initio calculations that take into account effects beyond the adiabatic approximation. Our results imply that Raman spectroscopy can be used as an accurate measure of the doping of both metallic and semiconducting nanotubes.
An introduction to super audio cd and dvd-audio (2003)

Highlights the latest developments in consumer audio and specifically in DVD-Audio and SACD. The DVD-Audio specification allows for up to 24-b PCM data and uses the Meridian lossless packing (MLP) algorithm to provide up to six channels of high-quality, multichannel audio at sampling rates of up to 96 kHz for six channels or 192 kHz for two channels. Super-audio CD (SACD), introduced in March 1999, integrates a variety of new technologies, such as the hybrid disc, direct stream digital (DSD), and direct stream transfer coding.
Investigation of MALDI-TOF Mass Spectrometry of Diverse Synthetic Metalloporphyrins, Phthalocyanines and Multiporphyrin Arrays (1999)

We investigated the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for analyzing porphyrinic compounds using a variety of different synthetic porphyrins, azaporphyrins, phthalocyanines and multiporphyrin arrays. Comparisons of spectra obtained from these analytes deposited either as neat samples or codeposited with neutral or acidic matrices have been made with the goal of identifying conditions that yield minimal demetalation, transmetalation, adduct formation and fragmentation. It was found that the molecular masses of many porphyrins can be successfully measured from neat sample preparations and do not require a matrix to facilitate desorption and ionization, although the measurement of large multiporphyrin arrays was facilitated by the use of matrices. Demetalation of magnesium porphyrins occurred in the presence of acidic matrices, but not with neutral matrices such as 1,4-benzoquinone. Positive ion spectra were obtained for each compound and negative ion spectra were also collected for the azaporphyrins and phthalocyanines. Examination of selected samples (prepared neat, with 1,4-benzoquinone, 2,3,5,6-tetrachloro-1,4-benzoquinone or α-cyano-4-hydroxycinnamic acid) showed that the dominant process of ionization involved oxidation yielding the radical cation M +· rather than the protonated molecule [M+H] + . MALDI-TOF-MS is shown to be a powerful analytical tool for the characterization of diverse synthetic porphyrinic compounds.
Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction barrier (2002)

Progress towards understanding the molecular basis of virulence in Clostridium difficile has been hindered by the lack of effective gene transfer systems. We have now, for the first time, developed procedures that may be used to introduce autonomously replicating vectors into this organism through their conjugative, oriT-based mobilization from Escherichia coli donors. Successful transfer was achieved through the use of a plasmid replicon isolated from an indigenous C. difficile plasmid, pCD6, and through the characterization and subsequent circumvention of host restriction/modification (RM) systems. The characterized replicon is the first C. difficile plasmid replicon to be sequenced and encodes a large replication protein (RepA) and a repetitive region composed of a 35 bp iteron sequence repeated seven times. Strain CD6 has two RM systems, CdiCD6I/M.CdiCD6I and CdiCD6II/M. CdiCD6II, with equivalent specificities to Sau96I/M. Sau96I (5'-GGNMCC-3') and MboI/M. MboI (5'-GMATC-3') respectively. A second strain (CD3) possesses a type IIs restriction enzyme, Cdi I, which cleaves the sequence 5'-CATCG-3' between the fourth and fifth nucleotide to give a blunt-ended fragment. This is the first time that an enzyme with this specificity has been reported. The sequential addition of this site to vectors showed that each site caused between a five- and 16-fold reduction in transfer efficiency. The transfer efficiencies achieved with both strains equated to between 1.0 x 10-6 and 5.5 x 10-5 transconjugants per donor.
HETEROCYST FORMATION (1996)

Heterocysts are microaerobic, N2-fixing cells that form in a patterned array within O2-producing filamentous cyanobacteria. Structural features of heterocysts can be predicted from consideration of their physiology. This review focuses on the spacing mechanism that determines which cells will differentiate, and on the regulation of the progression of the differentiation process. Applicable genetic tools, developed primarily using Anabaena PCC 7120, but employed also with Nostoc spp., are reviewed. These tools include localization of transcription using fusions to lux, lac, and gfp, and mutagenesis with oriV-containing derivatives of transposon Tn5. Mature and developing heterocysts inhibit nearby vegetative cells from differentiating; genes patA, devA, hetC, and the hetMNI locus may hold keys to understanding intercellular interactions that influence heterocyst formation. Regulatory and other genes that are transcriptionally activated at different times after nitrogen stepdown have been identified, and should permit analysis of mechanisms that underlie the progression of heterocyst differentiation.
Site-Directed Mutagenesis Using a Uracil-Containing Phagemid Template (2003)

Site-directed mutagenesis is a powerful technique by which specific changes can be generated in a target DNA molecule for either structure function investigations or for creating and deleting endonuclease restriction sites. There have been several oligonucleotide-directed mutagenesis procedures described in the literature that allow for selection against the wild-type DNA, thereby giving enrichment in those sequences carrying the desired mutation (, , , ). Collectively, these methods suffer from a number of drawbacks, including multi enzymatic steps, the necessity for DNA precipitation, the need for convenient restriction sites, and a requirement for specialized vec tors. An elegant method for achieving site-directed mutagenesis has been described by Kunkel et al. (,) that avoids these problems and at the same time produces a high percentage of DNA molecules with the designed mutation. This process is schematically outlined in Fig. 1. It relies on the observation that an E. coli strain lacking two key enzymes, dUTPase (dut) and uracil iV‐glycosylase (ung), will synthe size DNA with a small number of uracil bases substituted for thym ine. Uracil‐containing single‐stranded DNA (ssDNA) prepared from this dut −, ung − host strain can be used as a template for a mutagenic oligonucleotide to prime in vitro DNA synthesis of a complementary strand
Persistent Inhibition of Neointimal Hyperplasia After Sirolimus-Eluting Stent Implantation (2002)

Sirolimus-eluting stents showed persistent inhibition of neointimal hyperplasia for up to 2 years of follow-up.
Supplementation of Influenza Split Vaccines with Conserved M2 Ectodomains Overcomes Strain Specificity and Provides Long-term Cross Protection (2014)

Current influenza vaccines do not provide good protection against antigenically different influenza A viruses. As an approach to overcome strain specificity of protection, this study demonstrates significantly improved long-term cross protection by supplementing split vaccines with a conserved molecular target, a repeat of the influenza M2 ectodomain (M2e) expressed on virus-like particles (M2e5x VLPs) in a membrane-anchored form. Intramuscular immunization with H1N1 split vaccine (A/California/07/2009) supplemented with M2e5x VLPs induced M2e-specific humoral and cellular immune responses, and shaped the host responses to the vaccine in the direction of T-helper type 1 responses inducing dominant IgG2a isotype antibodies as well as interferon-γ (IFN-γ) producing cells in systemic and mucosal sites. Upon lethal challenge, M2e5x VLP-supplemented vaccination lowered lung viral loads and induced long-term cross protection against H3N2 or H5N1 subtype influenza viruses over 12 months. M2e antibodies, CD4 T cells, and CD8 T cells were found to contribute to improving heterosubtypic cross protection. In addition, improved cross protection by supplemented vaccination with M2e5x VLPs was mediated via Fc receptors. The results support evidence that supplementation with M2e5x VLPs is a promising approach for overcoming the limitation of strain-specific protection by current influenza vaccination.
Structure-immunogenicity relationship of melittin, its transposed analogues, and D-melittin. (1994)

Melittin, a 26-residue bee venom peptide, is known to induce murine Abs specific for its hydrophilic C-terminus of residues 20-26 and T cell responses specific for its hydrophobic mid-region of residue 11-19. Synthetic melittin analogues with transposed sequences of Ac(21-26) (1-20) and Ac(26-21) (1-20) are found to induce murine Abs specific for the transposed peptide segment and to induce T cell responses that are cross-reactive with melittin. Compared with melittin, the transposed melittin analogues are weaker immunogens and have lower hemolytic activities, lower helical contents, and a lower degree of association in micelles. A melittin analogue with a lactoside group at its C-terminus was found to induce lactoside-specific murine Abs. Present studies show that another analogue with a lactoside group at its N-terminus induces only Abs specific for the C-terminal region of melittin, and no lactoside-specific Abs are detected. These immunochemical observations suggest that the immunogenicity of melittin or its analogues is a consequence of its binding to cell membranes with subsequent oligomer formation in lipid bilayers. Apparently melittin or its analogues bind to cell membrane in an asymmetric manner with the exposed and the buried segments functioning as B and T cell epitopes, respectively. D-melittin is non-immunogenic in mice, although D-melittin has the same hemolytic activity as melittin. This finding may be correlated with the known resistance of D-melittin to proteolysis and hence to processing for Ag presentation to T lymphocytes.
Using Hardware Memory Protection to Build a High-Performance, Strongly-Atomic Hybrid Transactional Memory (2008)

We demonstrate how fine-grained memory protection can be used in support of transactional memory systems: first showing how a software transactional memory system (STM) can be made strongly atomic by using memory protection on transactionally-held state, then showing how such a strongly-atomic STM can be used with a bounded hardware TM system to build a hybrid TM system in which zero-overhead hardware transactions may safely run concurrently with potentially-conflicting software transactions. We experimentally demonstrate how this hybrid TM organization avoids the common-case overheads associated with previous hybrid TM proposals, achieving performance rivaling an unbounded HTM system without the hardware complexity of ensuring completion of arbitrary transactions in hardware. As part of our findings, we identify key policies regarding contention management within and across the hardware and software TM components that are key to achieving robust performance with a hybrid TM.
Accelerated High-Dimensional MR Imaging With Sparse Sampling Using Low-Rank Tensors (2016)

High-dimensional MR imaging often requires long data acquisition time, thereby limiting its practical applications. This paper presents a low-rank tensor based method for accelerated high-dimensional MR imaging using sparse sampling. This method represents high-dimensional images as low-rank tensors (or partially separable functions) and uses this mathematical structure for sparse sampling of the data space and for image reconstruction from highly undersampled data. More specifically, the proposed method acquires two datasets with complementary sampling patterns, one for subspace estimation and the other for image reconstruction; image reconstruction from highly undersampled data is accomplished by fitting the measured data with a sparsity constraint on the core tensor and a group sparsity constraint on the spatial coefficients jointly using the alternating direction method of multipliers. The usefulness of the proposed method is demonstrated in MRI applications; it may also have applications beyond MRI.
Fast Pressure Control in Managed Pressure Drilling (2014)

In drilling operations, it is of great importance to efficiently and safely control the pressure in the well. To avoid possible damage to the reservoir, equipment, personnel and the environment, the pressure in the well bore must be kept within certain limits, determined by the formations around the well. An emerging drilling technique, intended to increase the efficiency and safety of drilling operations, is known as Managed Pressure Drilling (MPD). MPD differs from conventional drilling by closing the mud system with a controlled choke, often in combination with a backpressure pump to ensure circulation through the choke. The controller objective is to automatically adjust the choke to reach the desired downhole pressure. For optimal control of the downhole pressure, a model describing the flows and pressures in the well is necessary. A modal discretization method is considered and implemented in this thesis, resulting in a rational approximation of a two-dimensional distributed parameter model. The discretized model is used to design a LQG controller, for comparison with a PI controller. Both controllers are implemented in MATLAB to perform computer simulations and experiments in lab. Simulations indicated that the transient response of the LQG stabilized at the desired set-point, more efficiently relative to PI controller. This difference was significantly improved when increasing the length of the simulated well. In experiments performed on a tailor made experimental lab located at NTNU, the performance of the two controllers were about equally great. It is discussed whether the lab is inadequate to demonstrate possible improvements due to the introduction of the two-dimensional model.
Microbial Behavior in a Heterogeneous World (2002)

Most microorganisms are motile during at least part of their life cycle, because they need to find optimal conditions in a patchy world. The sheer volume of microorganisms in the biosphere means that their motile sensory behavior also contributes to the global transformation and cycling of matter. How microorganisms move and how they orient themselves using environmental cues are integral to understanding the complex structure and function of microbial communities, but although motility in response to external stimuli was first described more than 120 years ago, understanding of the cellular and molecular mechanisms involved has only been achieved more recently.
Monogenean parasites of Caspian frisian roach (Rutilus frisii kutum ) in Sefid-Rood River and Caspian Sea (2001)

The Caspian frisian roach (Rutilus frisii kutum), economically a very important fish species in Iran, is propagated in fishponds, reared into the rivers in fingerling size and then harvested from the Caspian Sea in adult stage. We found six monogenean parasites on the Caspian frisian roach including five Dactylogyrus spp. on fingerlings cultured in fishponds and rivers and two Dactylogyrus spp. on wild adult specimens living in Caspian Sea. With the exception of D. frisii that proved to be the most common monogenean and found a good milieu for its development both in flowing rivers and in Caspian Sea, the other parasites occurred either in Caspian Sea (D. nybelini) or in freshwater (D. haplogonus, D. rarissimus, D. suecicus, D. turaliensis). The objectives of present research work are to clear the sources of infection of Caspian frisian roach fingerlings to monogenean parasites and to recommend approaches for the improvement of pond technology in order to diminish the intensity of parasites without having to use high amounts of organophosphate insecticide in ponds.
Activation of Human Matrix Metalloproteinases by Various Bacterial Proteinases (1997)

Matrix metalloproteinases (MMPs) are zinc-containing proteinases that participate in tissue remodeling under physiological and pathological conditions. To test the involvement of bacterial proteinases in tissue injury during bacterial infections, we investigated the activation potential of various bacterial proteinases against precursors of MMPs (proMMPs) purified from human neutrophils (proMMP-8 and -9) and from human fibrosarcoma cells (proMMP-1). Each proMMP was subjected to treatment with a series of bacterial proteinases at molar ratios of 0.01-0.1 (bacterial proteinase to proMMP), and activities of MMPs generated were determined. Among six different bacterial proteinases, thermolysin family enzymes (family M4) such as Pseudomonas aeruginosa elastase, Vibrio cholerae proteinase, and thermolysin strongly activated all three proMMPs via limited proteolysis to generate active forms of the MMPs. N-terminal sequence analysis of the active MMPs revealed that cleavage occurred at the Val82-Leu83 and Thr90-Phe91 bonds of proMMP-1 and proMMP-9, respectively, which are located near the N terminus of the catalytic domain of MMPs. In contrast, Serratia 56-kDa proteinase and Pseudomonas alkaline proteinase, both of which are classified as members of the serralysin subfamily of zinc metalloproteinases (family M10), and Serratia 73-kDa thiol proteinase did not evidence proteolytic processing or activation of proMMP-1, -8, and -9 under these experimental conditions. These results indicate that bacterial proteinases may play an important role in tissue destruction and disintegration of extracellular matrix at the site of infections.
Bacterial Chemotaxis And The Molecular Logic Of Intracellular Signal Transduction Networks (1991)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Electrophilic derivatives of purines as irreversible inhibitors of A1 adenosine receptors (1989)

Functionalized congeners derived from 1,3-dipropyl-8-phenylxanthine and from N6-phenyladenosine were derivatized to contain electrophilic groups (isothiocyanate, N-hydroxysuccinimide ester, maleimide, sulfonyl chloride, or alpha-haloacyl group) capable of reaction with nucleophiles on biopolymers. The goal was to inhibit chemically the A1 adenosine receptor by using reactive agonist and antagonist ligands. Some of the electrophilic derivatives were synthesized through acylation of amine-functionalized congeners using hetero- or homobifunctional reagents available for protein cross-linking. The affinity for A1 adenosine receptors was evaluated in competitive binding assays by using rat and bovine brain membranes. Several xanthine and adenosine thiourea derivatives prepared from 1,3- and 1,4-phenylene diisothiocyanate (DITC) were potent irreversible inhibitors of adenosine receptors. Derivatives of m-DITC, at concentrations between 10 and 500 nM, irreversibly eliminated binding at 90% of the A1-receptor sites. Receptor affinity of both xanthine and adenosine derivatives containing distal phenylthiourea substituents was diminished by electron-donating groups on the ring.
Micronucleus assay in vivo provides significant prognostic information in human cervical carcinoma; the updated analysis (2001)

A high frequency of micronuclei before radiotherapy and a slight increase of micronucleus frequency during radiotherapy measured after 10 fractions of 2 Gy were independent on stage, statistically significant adverse predictors of clinical outcome in cervical carcinoma patients treated with radiotherapy.
C1‐Symmetric Heterocyclic Zirconocenes as Catalysts for Propylene Polymerization, 2 (2005)

Abstract Summary: Sixteen C 1 ‐symmetric zirconocene and one hafnocene complexes bearing the 2,5‐R 2 ‐7H‐cyclopenta[1,2‐ b :4,3‐ b ′]dithiophene ligand (R = H, Me, Et, Ph) linked to a substituted indenyl ligand have been synthesized and tested in propylene polymerization. Most of the C 1 ‐symmetric zirconocenes of this type are highly active in propylene polymerization at low MAO/Zr ratios and produce poly(propylene)s (PP) in a broad range of isotacticity and melting points. The molecular weight and crystallinity of the PPs are strongly dependent upon the type of substituents on the indenyl moiety: PPs with T m between 75 and 156 °C and viscosity average molecular weights between 100 000 and 400 000 have been obtained at 50–70 °C in liquid propylene. General formula of the indenyl‐based zirconocenes. magnified image General formula of the indenyl‐based zirconocenes.
A new multiplex-access scheme based on the diversity of autocorrelation (2004)

Based on a new diversity, the diversity of autocorrelation, a new multiple-access scheme, called A-CDMA, is presented here. Like WCDMA, it packs high-density information into transmitted signals. Unlike WCDMA, it can block all the ISI and MAI completely under all noise level. The simulation supports the theory and shows that the total interference due to ISI and MAI is reduced to 1% when SNR varies from 1 to 11. By comparison, it outperforms WCDMA by a factor of 9 in the reduction of ISI and MAI. Its overall performance, as measured by BER is better than WCDMA in general, and by 10-20 dB when SNR ranges from 9 dB to 11 dB.
Myeloid Antigen, CD13, CD14, and/or CD33 Expression Is Restricted to Certain Lymphoid Neoplasms (1996)

The authors examined the expression of myeloid antigens (MyAg): CD11b, CD13, CD14, CD15, and CD33 in 249 adults with lymphoid neoplasms using flow cytometric analysis. In this study, acute leukemia that was myeloperoxidase negative by light microscopy and had at least one lymphoid antigen was defined as acute lymphoblastic leukemia (ALL). The patients were classified as follows: 6 with unclassified ALL, 35 early B precursor ALL, 32 T-ALL, 25 B-cell chronic lymphocytic leukemia (B-CLL) and its variants, 24 B-cell non-Hodgkin's lymphoma (B-NHL), 7 plasma cell disorders, 8 T-CLL, 2 adult T-cell leukemia, and 10 T-NHL. CD11b and CD15 were present in a wide range of lymphoid disorders irrespective of B/T lineage and maturity. Unclassified ALL and phenotypically immature ALL frequently expressed CD13 and CD33, and occasionally expressed CD14. Among early B precursor ALL, CD13, and/or CD33 were significantly associated with the presence of stem cell marker CD34 and the chromosomal abnormality t(9;22). In addition, ALL with deletion of chromosome 7 commonly expressed CD13 and CD33. Taken together, CD13 and/or CD33 positive ALL may originate from a multipotential stem cell. Among mature neoplasms, CD14 was frequently, and CD13 and CD33 were occasionally expressed in B-cell, but not T-cell tumors. These results suggest that CD13, CD14, and CD33 are preferentially expressed in two types of lymphoid neoplasms, namely undifferentiated ALL and mature B-cell lymphoproliferative disorders.