gebhart/patrepeval huggingface dataset:
Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. (1975)

Escherichia coli RNA polymerase (EC 2.7.7.6), bound in a tight complex at an early T7 promoter, protects 41 to 43 base pairs of DNA from digestion by DNase. I. The protected DNA fragment contains both the binding site for RNA polymerase and the mRNA initiation point for the promoter. The sequence of the DNA fragment and the sequence of the mRNA that it codes for are presented here. A seven-base-pair sequence, apparently common to all promoters, is implicated in the formation of a tight binary complex with RNA polymerase.
Electronic Structure of Pd(111) using Angle-Resolved Phothemission Spectroscopy (1996)

We have investigated atomic and electronic structures of a clean Pd(111) surface using low energy electron diffraction (LEED) and angle-resolved photoemission spectroscopy (ARPES). A typical clean LEED pattern with a 3-fold symmetry has been observed, corresponding to that for an fcc (111) surface. ARPES measurements have been performed along the TEX> symmetry lines, from which the experimental band structure of Pd(111) has been determined. The experimental band structure and work function of Pd(111) surface are found to agree well with the calculated band structure of bulk Pd and the calculated work function of Pd(111), respectively. However, the peak positions in the experimental band structure are located closer to the Fermi level than in the theoretical band structure by 0.1~0.8 eV, depending on the -points in the Brillouin zone. In additin, the experimental band widths are narrower than the theoretical band widths by about 0.5eV. The effects of the localized surface Pd 4d states and the Coulomb interaction between Pd 4d bulk electrons have been discussed as possible origins of such discrepancies between experiment and theory.
Stability of Intramolecular DNA Quadruplexes:  Comparison with DNA Duplexes (2003)

We have determined the stability of intramolecular quadruplexes that are formed by a variety of G-rich sequences, using oligonucleotides containing appropriately placed fluorophores and quenchers. The stability of these quadruplexes is compared with that of the DNA duplexes that are formed on addition of complementary C-rich oligonucleotides. We find that the linkers joining the G-tracts are not essential for folding and can be replaced with nonnucleosidic moieties, though their sequence composition profoundly affects quadruplex stability. Although the human telomere repeat sequence d[G(3)(TTAG(3))(3)] folds into a quadruplex structure, this forms a duplex in the presence of the complementary C-rich strand at physiological conditions. The Tetrahymena sequence d[G(4)(T(2)G(4))(3)], the sequence d[G(3)(T(2)G(3))(3)], and sequences related to regions of the c-myc promoter d(G(4)AG(4)T)(2) and d(G(4)AG(3)T)(2) preferentially adopt the quadruplex form in potassium-containing buffers, even in the presence of a 50-fold excess of their complementary C-rich strands, though the duplex predominates in the presence of sodium. The HIV integrase inhibitor d[G(3)(TG(3))(3)] forms an extremely stable quadruplex which is not affected by addition of a 50-fold excess of the complementary C-rich strand in both potassium- and sodium-containing buffers. Replacing the TTA loops of the human telomeric repeat with AAA causes a large decrease in quadruplex stability, though a sequence with AAA in the first loop and TTT in the second and third loops is slightly more stable.
Zinc-finger protein 545 is a novel tumour suppressor that acts by inhibiting ribosomal RNA transcription in gastric cancer (2012)

ZNF545 acts as a functional tumour suppressor in gastric cancer by inhibiting rRNA transcription. Its methylation at early stages of gastric carcinogenesis is an independent prognostic factor.
Restoration of the velocity field of the heart from two-dimensional echocardiograms (1989)

A method to quantify the motion of the heart from digitized sequences of two-dimensional echocardiograms (2-D) echos was recently proposed. This method computes on every point of the 2-D echoes, the 2-D apparent velocity vector (or optical flow) which characterizes its interframe motion. However, further analysis is required to determine what part of this motion is due to translation, rotation, contraction, and deformation of the myocardium. A method to locally obtain this information is presented. The proposed method assumes that the interframe velocity field U(xy), V(x,y) can be locally described by linear equations in the form U(x,y)=a+Ax+By; V(x,y)=b+Cx+Dy. The additional constraint was introduced in the computation of the local velocity field by the method of projections onto convex sets. Since this constraint is only valid locally, the myocardium must be first divided into sectors and the velocity fields computed independently for each sector.
Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20 (1994)

Murine monoclonal antibody 2B8 specifically recognizes the CD20 phosphoprotein expressed on the surface of normal B lymphocytes and B- cell lymphomas. The light- and heavy-chain variable regions of 2B8 were cloned, after amplification by the polymerase chain reaction, into a cDNA expression vector that contained human IgG1 heavy chain and human kappa-light chain constant regions. High-level expression of chimeric- 2B8 antibody (C2B8) was obtained in Chinese hamster ovary cells. Purified C2B8 exhibited antigen binding affinity and human-tissue reactivity similar to the native murine antibody. In vitro studies showed the ability of C2B8 to bind human C1q, mediate complement- dependent cell lysis of human B-lymphoid cell lines, and lyse human target cells through antibody-dependent cellular cytotoxicity. Infusion of macaque cynomolgus monkeys with doses ranging from 1.6 mg/kg to 6.4 mg/kg resulted in greater than 98% depletion of peripheral blood (PB) B cells and 40% to 70% depletion of lymph node B cells. Recovery of PB B cells usually started at 2 weeks after treatment and required 60 to greater than 90 days to reach normal levels. As much as 95% depletion of B cells in peripheral lymph nodes and bone marrow was observed following weekly injections of 16.8 mg/kg antibody. No toxicity was observed in any of the animals. These results offer the possibility of using an “immunologically active” chimeric anti-CD20 antibody as an alternative approach in the treatment of B-cell lymphoma.
Vpr-GFP Virion Particle Identifies HIV-Infected Targets and Preserves HIV-1Vpr Function in Macrophages and T-Cells (2000)

Human immunodeficiency virus type 1 (HIV-1) is known for its ability to infect immune cells, including T-cells and macrophages. The 96-amino acid Vpr, a virion-associated protein, is essential for viral replication in monocytes/macrophages and increases viral replication in primary and established T-cell lines. The Vpr protein regulates a number of host cellular events, including proliferation, differentiation, apoptosis, cytokine production, and NF-kappaB-mediated transcription. Most of these functions have been analyzed using either endogenous Vpr protein or cells transfected with a Vpr expression plasmid. We developed a lentiviral vector complemented with a Vpr expression plasmid that results in viral particles packaged with Vpr protein. To facilitate identification of the target cells infected with the particles containing Vpr, we fused green fluorescent protein (GFP) with the Vpr open reading frame and analyzed the biology of this novel particle. Vpr itself is expressed as a 14-kDa protein; however, in vitro translation of the pVpr-GFP plasmid resulted in the expression of 39-kDa fusion protein. The fusion molecule exhibited the same activity in arresting the cell cycle in G2 as does the wildtype Vpr molecule. Subcellular localization of Vpr and Vpr-GFP by immunofluoresence in human and murine cell lines indicated that Vpr by itself or with the reporter GFP showed a perinuclear staining pattern. Replication kinetics showed no significant difference between Vpr-GFP and native complemented pseudovirus replication in a single-round infectivity assay. A flow cytometry analysis of peripheral blood lymphocytes and macrophages infected with Vpr-GFP-packaged virions and selected by GFP showed 56.7% infectivity for lymphocytes and 84.6% infectivity for macrophages. Additional analysis of CD24 (HSA)-positive cells showed infection of CD4+ cells, macrophages, and, importantly, dendritic cells. This system will allow us to identify specific cell populations including antigen-presenting cells, and allow quantitative analysis of the precise effect of Vpr on both target and bystander cells in vitro as well as in vivo.
Multi-link active catheter snake-like motion (1996)

SUMMARY A prototype of a catheter which can move like a snake, incorporating distributed shape memory alloy actuators, is described. Since this active catheter has an instrumental navigation ability, minimally invasive diagnosis and interventional therapy will be possible. The outer diameter of the active catheter is 2.8 mm and it has many links fabricated by 3-dimensional silicon micromachining. The silicon batch process was used for the fabrication of the link to minimize assembly work. A new heating method (indirect heating) is suggested which is necessary when the JC chip is mounted on the link.
Dependence of Electrochemical Behavior on Concentration and Annealing Temperature of Li[sub x]CoPO[sub 4] Phase-Grown LiNi[sub 0.8]Co[sub 0.16]Al[sub 0.04]O[sub 2] Cathode Materials (2008)

Lix CoPO4 phase-grown LiNi0.86 Co0.1 Al0.04 O2 cathode materials were prepared by varying the coating concentration of precipitated Co3 (PO4)2 nanoparticles and the annealing temperature. These materials were characterized by analyzing their electrochemical properties, moisture uptake, and thermal stability. Among the various coating concentrations, 3 wt % coating showed no decrease in the first discharge capacity (193 mAhg) and a much improved capacity retention (90%) at a 1 C cycling rate after 40 cycles, compared to the bare cathode (193 mAhg and 44% for first discharge capacity and capacity retention, respectively). Using this concentration, the annealing time was varied from 2 to 7 h at 700, 800, and 900°C. The coated cathode annealed at 700°C for 7 h showed comparable electrochemical properties and moisture uptake to that annealed at 700°C for 5 h. Even after annealing at 700°C for 7 h, P ions remained on the particle surface with a similar coating thickness to that at 700°C for 5 h. However, increasing the annealing temperature led to a further decrease in electrochemical properties and was related to deeper diffusion of P ions into the bulk particle, which likely formed a solid solution consisting of bulk elements and P elements. The amounts of Li2 CO3 and LiOH formation of the coated samples upon exposure to air with a relative humidity of 40% showed a similar result when annealing at 700°C, but increasing the annealing temperature to 800 and 900°C resulted in a significant increase of the amount of Li2 CO3 and LiOH. Thermal stability was also greatly improved by the coating, and the sample annealed at 700°C for 7 h exhibited a decreased total heat capacity (240 Jg) compared to the 5 h annealed samples (380 Jg) even though those values were much smaller than the bare sample (980 Jg).
Localization of Genomic Regions Specific for the Attenuated, Mouse-adapted Poliovirus Type 2 Strain W-2 (1990)

In order to begin to elucidate the genomic basis of the attenuation of mouse-adapted, poliovirus type 2 strain W-2 (PV2/W-2), we have cloned and sequenced the virus and compared it with the virulent, mouse-adapted PV2/Lansing strain. In addition, we have performed computer-generated comparisons of PV2/W-2 to the non-mouse-adapted, attenuated PV2/Sabin strain to determine whether mutational patterns occur that result in attenuation. The PV2/W-2 genome is 7434 nucleotides in length, which is three bases shorter than PV2/Lansing. The 5' non-coding region of PV2/W-2 is 747 nucleotides in length (compared to 744 in PV2/Lansing) and shares 98.8% identity with PV2/Lansing and 82.3% identity with PV2/Sabin. Overall, the PV2/W-2 polyprotein (2205 amino acids) is two amino acids shorter than that of either PV2/Lansing or PV2/Sabin (2207 amino acids). These contiguous deletions fall within the P3-D region (polymerase). Within these 2205 amino acid residues only 26 differences were observed between PV2/W-2 and PV2/Lansing (98.8% identity), whereas 92 occurred between PV2/W-2 and PV2/Sabin (95.8% identity). The 3' non-coding region of PV2/W-2 is 72 nucleotides in length and shares 100% identity with PV2/Lansing and 98.6% identity with PV2/Sabin. Amino acid changes in the capsid protein region occurred in neutralization sites 1 and 3, areas previously shown to be important for pathogenicity. The cleavage site between non-structural proteins P2-C/P3-A consisted of a glutamine-serine pair, in contrast to other sequenced polioviruses which have a glutamine-glycine dipeptide.
Single-crystal structure validation with the programPLATON (2003)

The results of a single-crystal structure determination when in CIF format can now be validated routinely by automatic procedures. In this way, many errors in published papers can be avoided. The validation software generates a set of ALERTS detailing issues to be addressed by the experimenter, author, referee and publication journal. Validation was pioneered by the IUCr journal Acta Crystallographica Section C and is currently standard procedure for structures submitted for publication in all IUCr journals. The implementation of validation procedures by other journals is in progress. This paper describes the concepts of validation and the classes of checks that are carried out by the program PLATON as part of the IUCr checkCIF facility. PLATON validation can be run at any stage of the structure refinement, independent of the structure determination package used, and is recommended for use as a routine tool during or at least at the completion of every structure determination. Two examples are discussed where proper validation procedures could have avoided the publication of incorrect structures that had serious consequences for the chemistry involved.
Fresnel Zone-Plate Diffraction Patterns (1969)

The diffraction patterns of the central aperture and the first 10 rings of the classical Fresnel zone plate are calculated in the principal focal plane for off-axis distances as large as the radius of the 10th ring. The zone-plate pattern is found by summation; near the axis it is compared with closed-form approximations. The integrated flux within circles as large as the 10th ring is also calculated.
PEGylation of Proteins and Liposomes: a Powerful and Flexible Strategy to Improve the Drug Delivery (2011)

PEGylation is one of the most successful strategies to improve the delivery of therapeutic molecules such as proteins, macromolecular carriers, small drugs, oligonucleotides, and other biomolecules. PEGylation increase the size and molecular weight of conjugated biomolecules and improves their pharmacokinetics and pharmacodinamics by increasing water solubility, protecting from enzymatic degradation, reducing renal clearance and limiting immunogenic and antigenic reactions. PEGylated molecules show increased half-life, decreased plasma clearance, and different biodistribution, in comparison with non-PEGylated counterparts. These features appear to be very useful for therapeutic proteins, since the high stability and very low immunogenicity of PEGylated proteins result in sustained clinical response with minimal dose and less frequent administration. PEGylation of liposomes improves not only the stability and circulation time, but also the 'passive' targeting ability on tumoral tissues, through a process known as the enhanced permeation retention effect, able to improve the therapeutic effects and reduce the toxicity of encapsulated drug. The molecular weight, shape, reactivity, specificity, and type of bond of PEG moiety are crucial in determining the effect on PEGylated molecules and, at present, researchers have the chance to select among tens of PEG derivatives and PEG conjugation technologies, in order to design the best PEGylation strategy for each particular application. The aim of the present review will be to elucidate the principles of PEGylation chemistry and to describe the already marketed PEGylated proteins and liposomes by focusing our attention to some enlightening examples of how this technology could dramatically influence the clinical application of therapeutic biomolecules.
RF photonic signal processing components: From high order tunable filters to high stability tunable oscillators (2009)

We report on our research and development efforts toward realizing tunable RF photonic filters and tunable local oscillators. In particular, we demonstrate a high order RF photonic filter having 250–1000 MHz bandwidth and more than 70 dBc rejection rate at 2 GHz detuning from the pass-band center. The filter can be tuned across 1–40 GHz frequency range. We also report on our design of a compact tunable RF photonic oscillator with phase noise less than −140 dBc at 100 kHz. The frequency of the oscillator can be tuned from 20 GHz till 35 GHz. We present a theoretical analysis of the capabilities of the devices as well as recent experimental data.
Differentially-private release of check-in data for venue recommendation (2014)

Recommender systems suggesting venues offer very useful services to people on the move and a great business opportunity for advertisers. These systems suggest venues by matching the current context of the user with the venue features, and consider the popularity of venues, based on the number of visits (“check-ins”) that they received. Check-ins may be explicitly communicated by users to geo-social networks, or implicitly derived by analysing location data collected by mobile services. In general, the visibility of explicit check-ins is limited to friends in the social network, while the visibility of implicit check-ins limited to the service provider. Exposing check-ins to unauthorized users is a privacy threat since recurring presence in given locations may reveal political opinions, religious beliefs, or sexual orientation, as well as absence from other locations where the user is supposed to be. Hence, on one side mobile app providers host valuable information that recommender system providers would like to buy and use to improve their systems, and on the other we recognize serious privacy issues in releasing that information. In this paper, we solve this dilemma by providing formal privacy guarantees to users and trusted mobile providers while preserving the utility of check-in information for recommendation purposes. Our technique is based on the use of differential privacy methods integrated with a pre-filtering process, and protects against both an untrusted recommender system and its users, willing to infer the venues and sensitive locations visited by other users. Extensive experiments with a large dataset of real users' check-ins show the effectiveness of our methods.
High-efficiency solar cells from FZ, CZ and MC silicon material (1993)

At ISE, a research project has been carried out which aims at the development of single crystalline solar cells of high efficiency. For this task a clean room laboratory for solar cell processing has been established, various measuring stations for the characterization of processes and cells have been set up, and a processing sequence for the manufacturing of such cells has been established. All systems and all processes are working well. The highest efficiencies (AM1.5) obtained to date are 21.1% for FZ-, 19.3% for CZ-, and 16.2% for MC (multicrystalline)-silicon.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Device-size atomistic models of amorphous silicon (2001)

The atomic structure of amorphous materials is believed to be well described by the continuous-random-network model. We present an algorithm for the generation of large, high-quality continuous random networks. The algorithm is a variation of the sillium approach introduced by Wooten, Winer, and Weaire [Phys. Rev. Lett. 54, 1392 (1985)]. By employing local relaxation techniques, local atomic rearrangements can be tried that scale almost independently of system size. This scaling property of the algorithm paves the way for the generation of realistic device-size atomic networks.
Combined targeted inhibition of bcl-2, bcl-XL, epidermal growth factor receptor, and protein kinase A type I causes potent antitumor, apoptotic, and antiangiogenic activity. (2003)

The combination of 4625, AS-PKAI, and ZD1839 resulted in a strong antiproliferative, proapoptotic, and antiangiogenic response, suggestive of a functional interaction between EGFR, PKAI, and bcl-2/bcl-xL and providing a rationale for the selection of specific molecular treatments for the development of therapeutic strategies. Iressa is a trademark of the AstraZeneca group of companies.
Widely-linear selected mapping for peak-to-average power ratio reduction in OFDM (2007)

Peak-to-average power ratio reduction in OFDM using selected mapping (SLM) is considered. A new low-complexity version of SLM is introduced, which employs the principle of widely-linear signal processing, i.e. real and imaginary parts of the candidate OFDM frames are treated separately. Thereby, investing the numerical complexity of conventional SLM with U candidates, a performance almost equal to U2 candidates can be obtained with widely-linear SLM. Numerical simulations cover this performance.
Shape and Aggregation Control of Nanoparticles: Not Shaken, Not Stirred (2005)

The aggregation of nanoparticles during synthesis, particularly the effect of mechanical agitation, is investigated from a viewpoint of nucleation using a conjugated polymer, polyaniline, as an example. Homogeneous nucleation of polyaniline results in nanofibers, while heterogeneous nucleation leads to granular particulates. Mechanical agitation, which is a common method for disrupting aggregates, instead dramatically triggers aggregation during the synthetic process and favors the formation of granular particulates. Correlating the shape and aggregation of polyaniline nanoparticles with the mode of nucleation, a new aggregation mechanism is proposed in which aggregation is triggered by heterogeneous nucleation. The mechanism may be quite general as indicated by experiments with other materials such as silica nanoparticles. Highly dispersible polyaniline nanofibers can now be reproducibly prepared from a conventional reaction simply by not mechanically agitating the reaction and carrying it out at an elevated temperature. This work may prove to be of great value in reproducibly synthesizing nanoparticles with well-controlled sizes and shapes and in effectively preventing aggregation in chemical, pharmaceutical, and materials production processes.
A General Method for the Spatially Defined Immobilization of Biomolecules on Glass Surfaces Using “Caged” Biotin (1996)

A method has been developed to spatially define the immobilization of proteins on surfaces using the classic avidin-biotin link, for which a wide variety of biochemical reagents are commercially available. A derivative of biotin bearing a photoremovable nitrobenzyl group (MeNPOC-biotin) has been prepared in a form suitable for simple linkage to biomolecules and surfaces. It has been used to functionalize bovine serum albumin (BSA) to form MeNPOC-biotin-BSA, which can then be coated onto glass. On photolithographic patterning of the surface, biotins are freed in the irradiated areas, permitting avidin to be localized at the irradiated sites. Subsequent addition of a biotinylated molecule permits its site-specific localization. Patterning of a biotinylated antibody and dye-labeled avidins or streptavidin using this reagent has been demonstrated by fluorescence microscopy.