gebhart/patrepeval huggingface dataset:
Phage lambda Cro protein and cI repressor use two different patterns of specific protein-DNA interactions to achieve sequence specificity in vivo. (1989)

By assaying the binding of wild-type Cro to a set of 40 mutant lambda operators in vivo, we have determined that the 14 outermost base pairs of the 17 base pair, consensus lambda operator are critical for Cro binding. Cro protein recognizes 4 base pairs in a lambda operator half-site in different ways than cI repressor. The sequence determinants of Cro binding at these critical positions in vivo are nearly perfectly consistent with the model proposed by W. F. ANDERSON, D. H. OHLENDORF, Y. TAKEDA and B. W. MATTHEWS and modified by Y. TAKEDA, A. SARAI and V. M. RIVERA for the specific interactions between Cro and its operator, and explain the relative order of affinities of the six natural lambda operators for Cro. Our data call into question the idea that lambda repressor and Cro protein recognize the consensus lambda operator by nearly identical patterns of specific interactions.
Application of high-throughput screening to identify a novel αIIb-specific small- molecule inhibitor of αIIbβ3-mediated platelet interaction with fibrinogen (2007)

Small-molecule alphaIIbbeta3 antagonists competitively block ligand binding by spanning between the D224 in alphaIIb and the MIDAS metal ion in beta3. They variably induce conformational changes in the receptor, which may have undesirable consequences. To identify alphaIIbbeta3 antagonists with novel structures, we tested 33 264 small molecules for their ability to inhibit the adhesion of washed platelets to immobilized fibrinogen at 16 muM. A total of 102 compounds demonstrated 50% or more inhibition, and one of these (compound 1, 265 g/mol) inhibited ADP-induced platelet aggregation (IC(50): 13+/- 5 muM), the binding of soluble fibrinogen to platelets induced by mAb AP5, and the binding of soluble fibrinogen and a cyclic RGD peptide to purified alphaIIbbeta3. Compound 1 did not affect the function of GPIb, alpha2beta1, or the other beta3 family receptor alphaVbeta3. Molecular docking simulations suggest that compound 1 interacts with alphaIIb but not beta3. Compound 1 induced partial exposure of an alphaIIb ligand-induced binding site (LIBS), but did not induce exposure of 2 beta3 LIBS. Transient exposure of purified alphaIIbbeta3 to eptifibatide, but not compound 1, enhanced fibrinogen binding ("priming"). Compound 1 provides a prototype for small molecule selective inhibition of alphaIIbbeta3, without receptor priming, via targeting alphaIIb.
Medical Applications of Magnetic Nanoparticles (2006)

In recent years biomedical research indicated, that magnetic nanoparticles can be a promising tool for several applications in vitro and in vivo. In medicine many approaches were investigated for diagnosis and therapy and offered a great variety of applications. Magnetic cell separation, magnetic resonance imaging (MRI), magnetic targeted delivery of therapeutics or magnetically induced hyperthermia are approaches of particular clinical relevance. For medical use, especially for in vivo application it is of great importance that these particles do not have any toxic effects or incompatibility with biological organism. Investigations on applicable particles induced a variability of micro- and nanostructures with different materials, sizes, and specific surface chemistry.
Comparative Efficacy of Enrofloxacin, Oxytetracycline, and Sulfadimethoxine for the Control of Morbidity and Mortality Caused by Escherichia coli in Broiler Chickens (2004)

The purpose of the present study was to compare the ability of enrofloxacin, oxytetracycline, and sulfadimethoxine to reduce morbidity and mortality caused by Escherichia coli (colibacillosis) in broiler chickens. The chickens were raised in 80 pens (20 birds per pen) with 20 pens representing each treatment group under simulated commercial conditions that produced a colibacillosis challenge scenario. Each group of 20 randomized pens (replicates) was given one of four water treatments. Chickens that received enrofloxacin had significantly less mortality (P < 0.01), lower average gross pathology (colibacillosis) scores (P < 0.01), and better feed-conversion ratios (P < 0.05) than did chickens that received either oxytetracycline or no medication. Chickens that received enrofloxacin had significantly less mortality and lower pathology scores than those that received sulfadimethoxine and numerically lower feed conversion than the sulfadimethoxine group. Results from the present study show that enrofloxacin is superior to oxytetracycline and sulfadimethoxine for the control of morbidity and mortality caused by E. coli in broiler chickens. Our findings will help veterinarians choose and prescribe the most efficacious antimicrobial when treating colibacillosis.
In Vivo Tumor Suppression by Adenovirus-Mediated Interferon alpha2b Gene Delivery (1999)

A replication-deficient adenovirus encoding human interferon alpha2b, driven by the human cytomegalovirus (CMV) promoter, was constructed and characterized. This construct was used to infect human cells derived from different types of cancer. The production of protein and its secretion into the culture medium were tested by Western blotting and immunoassay. Inhibition of cell proliferation and antiviral activity, two of the most important biological activities of interferon, were observed with this construct. PC-3 cells, derived from human prostatic cancer, or Hep3B cells, derived from human hepatocellular carcinoma, were injected subcutaneously to generate and establish in vivo tumors in athymic nude mice. Intratumoral injection with the recombinant adenovirus expressing interferon alpha2b resulted in complete regression of tumor growth. Our results demonstrate that interferon gene delivery using recombinant adenoviral vectors may be a useful approach to treat a variety of cancers.
Photonic crystal fiber designs for power scaling of single-polarization amplifiers (2007)

Photonic crystal fiber designs for power scaling of single-polarization amplifiers are presented. These fibers incorporate a core with a refractive index slightly lower than that of pure silica and borosilicate stress rods embedded within the photonic crystal lattice. They are realizable as rod-type as well as conventional photonic crystal fibers. The core index change results in a fundamental mode profile that is flattened relative to that of standard photonic crystal fibers. A continuum of mode profiles ranging from approximately Gaussian to approximately top-hat can be achieved in this manner. The optimal parameters of these designs depend on the desired coiling radius, birefringence, and mode area. Preliminary experimental results are presented.
High quality factor subwavelength grating waveguide micro-ring resonator based on trapezoidal silicon pillars (2016)

Subwavelength grating waveguide-based micro-ring resonators (SWGMRs) are a promising platform for research in light-matter interaction. However, it is extremely difficult to achieve small radius SWGMR devices (e.g., 5 μm) with satisfying quality factors (e.g., ∼10,000). One major issue is the large bend loss of small radius SWGMRs. In this work, we report the use of trapezoidal silicon pillars instead of conventional rectangular silicon pillars as building blocks of SWGMRs. We found that an asymmetric effective refractive index profile created by trapezoidal silicon pillars can significantly reduce the bend loss and therefore increase the quality factors of SWGMRs. For the first time to the best of our knowledge, we have experimentally demonstrated a 5 μm radius SWGMR made of trapezoidal silicon pillars (T-SWGMR) with an applicable quality factor as high as 11,500, 4.6 times of that (∼2800) offered by a conventional SWGMR made of rectangular silicon pillars, which indicates an 81.4% reduction of the propagation loss. This approach can also be readily employed to enhance SWGMRs with larger radii. We have also experimentally demonstrated a 10 μm radius T-SWGMR with a quality factor as high as 45,000, which indicates a propagation loss as low as 6.07 dB/cm.
Increased expression of both insulin receptor substrates 1 and 2 confers increased sensitivity to IGF-1 stimulated cell migration (2009)

Insulin-like growth factors (IGFs) are thought to promote tumour progression and metastasis in part by stimulating cell migration. Insulin receptor substrate-1 (IRS-1) and IRS-2 are multisite docking proteins positioned immediately downstream from the type I IGF and insulin receptors. IRS-2 but not IRS-1 has been reported to be involved in the migratory response of breast cancer cells to IGFs. The purpose of this investigation was to determine if IRS-1 is involved in, and to assess the contributions of IRS-1 and IRS-2 to, the migratory response of breast cancer cells to IGFs. The expression of IRS-1 and IRS-2 varied considerably between ten breast cancer cell lines. Oestrogen increases expression of the type I IGF receptor, IRS-1 and IRS-2 in MCF-7 and ZR-75 cells. Oestrogens may control the sensitivity of breast cancer cells to IGFs by regulating the expression of components of the IGF signal transduction pathway. The migratory response to a range of IGF-1 concentrations was measured in MCF-7 and MDA-MB-231 breast cancer cells in which IRS-1 and IRS-2 levels were modulated using a doxycycline-inducible expression system. Induction of both IRS-1 and IRS-2 expression increased the sensitivity of the migratory response to IGF-1 but did not increase the magnitude of the response stimulated at higher concentrations of IGF-1. Knockdown of IRS-1, IRS-2 and the type I IGF receptor in MCF-7 and MDA-MB-2231 cells decreased sensitivity to IGF-1. We conclude that both IRS-1 and IRS-2 control the migratory response of breast cancer cells to IGF-1 and may, therefore, be key molecules in determining breast cancer spread.
Passing data and supplying power to neural implants (2006)

This work investigates two important components in neural implants, the information link and the energy source. In this paper, a new concept in which neural implants operate on the biological resources readily available to them is adopted. The volume conduction property of human tissue is employed to pass information, and the electrons released during cellular metabolic process are collected to supply power. The x-antenna has been developed for data communication wherein the volume conduction mechanism has been used. The paper has shown that the body's own energy stores can be converted to electrical current using a biofuel cell. The biofuel cell approach would provide not only uninterrupted power but also an opportunity to explore new methods fostering improved biocompatibility for implantable devices
Expansion of HIV-specific CD4+ and CD8+ T cells by dendritic cells transfected with mRNA encoding cytoplasm- or lysosome-targeted Nef (2005)

Transfection with synthetic mRNA is a safe and efficient method of delivering antigens to dendritic cells for immunotherapy. Targeting antigens to the lysosome can sometimes enhance the CD4+ T-cell response. We transfected antigen-presenting cells (APCs) with mRNA encoding Gag-p24 and cytoplasmic, lysosomal, and secreted forms of Nef. Antigen-specific cytotoxic T cells were able to lyse the majority of transfected targets, indicating that transfection was efficient. Transfection of APCs with a Nef construct bearing lysosomal targeting signals produced rapid and prolonged antigen presentation to CD4+ and CD8+ T cells. Polyclonal CD4+ and CD8+ T-cell lines recognizing multiple distinct epitopes were expanded by coculture of transfected dendritic cells with peripheral blood mononuclear cells from viremic and aviremic HIV-infected subjects. Importantly, lysosome-targeted antigen drove a significantly greater expansion of Nef-specific CD4+ T cells than cytoplasmic antigen. The frequency of recognition of CD8 but not CD4 epitopes by mRNA-expanded T cells was inversely proportional to sequence entropy and was similar to ex vivo responses from a large chronic cohort. Thus human dendritic cells transfected with mRNA encoding lysosome-targeted HIV antigen can expand a broad, polyclonal repertoire of antiviral T cells, offering a promising approach to HIV immunotherapy.
Efficacy and safety of abatacept, a T-cell modulator, in a randomised, double-blind, placebo-controlled, phase III study in psoriatic arthritis (2017)

ClinicalTrials.gov number, NCT01860976 (funded by Bristol-Myers Squibb).
Correlation of overlay performance and reticle substrate non-flatness effects in EUV lithography (2009)

Image placement (IP) and overlay error specifications in the International Technology Roadmap for Semiconductors (ITRS) continue to get tighter with each successive technology node. One of the significant contributors to IP error is the non-flatness of the reticle substrate. In this paper, we will discuss in detail the effect of reticle substrate shape on the overlay performance in extreme ultraviolet (EUV) tools. Substrate shape-induced overlay effects are important when multiple device levels are printed using EUV lithography. We present an analysis of 20 blanks with different flatness specifications for overlay signatures when used for printing multiple device levels. A comprehensive analysis of scanner correctable and non-correctable errors for different substrate shapes will also be presented. Non-flatness specifications for EUV blanks will be reviewed based on these reticle-matching results. We will discuss results from flatness measurements and the effect on overlay budget due to mismatched substrates using several substrates with different flatness specifications.
Mechanism of Ligand-Induced Folding of a Natively Unfolded Helixless Variant of Rabbit I-BABP (2009)

Substitution of the helix-turn-helix capping motif (residues 9-35) of rabbit I-BABP with a flexible Gly-Gly-Ser-Gly linker results in the loss of stabilizing hydrophobic contacts and renders the beta-clamshell structure of this steroidal bile acid transport protein unfolded. However, in the presence of a bile acid ligand, we observe strong coupling between binding and folding, resulting in an enthalpy-driven high-affinity interaction (K(A) approximately 4 x 10(5) M(-1)) that "rescues" the native state. We investigate the mechanism of induced folding using fluorescence stopped-flow kinetic measurements to distinguish between conformational selection and induced-fit models. We observe both ligand-dependent and -independent kinetic phases which, together with their relative amplitudes, we attribute to an induced-fit "fly casting" type of model in which transient encounter complexes between the ligand and the extended polypeptide chain may act as nucleation sites for folding. An initial fast ligand-dependent kinetic process appears to be consistent with formation of a hydrophobically collapsed intermediate state which slowly rearranges to a nativelike beta-clamshell structure. We show that the intermediate forms at a rate 1000 times slower than the rate of ligand association with wild-type I-BABP, reflecting the large configurational entropic barrier to the coupled binding and folding steps of Deltaalpha-I-BABP. We have provided mechanistic insights into how natively disordered states, now commonly identified in biology, may fold on binding a target substrate or ligand.
Air Filtration in the Free Molecular Flow Regime: A Review of High‐Efficiency Particulate Air Filters Based on Carbon Nanotubes (2014)

Air filtration in the free molecular flow (FMF) regime is important and challenging because a higher filtration efficiency and lower pressure drop are obtained when the fiber diameter is smaller than the gas mean free path in the FMF regime. In previous studies, FMF conditions have been obtained by increasing the gas mean free path through reducing the pressure and increasing the temperature. In the case of carbon nanotubes (CNTs) with nanoscale diameters, it is possible to filtrate in the FMF regime under normal conditions. This paper reviews recent progress in theoretical and experimental studies of air filtration in the FMF regime. Typical structure models of high-efficiency particulate (HEPA) air filters based on CNTs are introduced. The pressure drop in air filters operated in the FMF regime is less than that predicted by the conventional air filtration theory. The thinnest HEPA filters fabricated from single-walled CNT films have an extremely low pressure drop. CNT air filters with a gradient nanostructure are shown to give a much better filtration performance in dynamic filtration. CNT air filters with a hierarchical structure and an agglomerated CNT fluidized bed air filter are also introduced. Finally, the challenges and opportunities for the application of CNTs in air filtration are discussed.
Relaxed channel polarization for reduced complexity polar coding (2015)

Arıkan's polar codes are proven to be capacity-achieving error correcting codes while having explicit constructions. They are characterized to have encoding and decoding complexities of l log l, for code length l. In this work, we construct another family of capacity-achieving codes that have even lower encoding and decoding complexities, by relaxing the channel polarizations for certain bit-channels. We consider schemes for relaxing the polarization of both sufficiently good and sufficiently bad bit-channels, in the process of channel polarization. We prove that, similar to conventional polar codes, relaxed polar codes also achieve the capacity of binary memoryless symmetric channels. We analyze the complexity reductions achievable by relaxed polarization for asymptotic and finite-length codes, both numerically and analytically. We show that relaxed polar codes can have better bit error probabilities than conventional polar codes, while having reduced encoding and decoding complexities.
Annular Lichenoid Dermatitis of Youth: A Chronic Case Managed Using Pimecrolimus (2016)

Annular lichenoid dermatitis of youth, first described in 2003, is a rare and occasionally chronic skin disease. We report a case of annular lichenoid dermatitis of youth relapsing over the course of 5 years successfully treated and maintained with topical pimecrolimus cream.
A Metal–Organic Framework with the Zeolite MTN Topology Containing Large Cages of Volume 2.5 nm3 (2005)

If you look for holes, you will find them in a novel 3D metal–organic framework complex with zeolite MTN topology. The framework of [{Cd(H2O)3}34(N4C6H12)17]Cl68⋅46 H2O⋅68 DMF greatly expands the original structure of MTN and contains large cages with a volume of about 2522 Å3 (see structure). MTN=zeolite socony mobil – thirty-nine, DMF=N,N-dimethylformamide. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z462260_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Evaluation of in vitro secondary caries using confocal laser scanning microscope and X-ray analytical microscope. (2003)

Inhibition zones and outer lesions were clearly detected under CLSM around the glass-ionomer and resin-modified glass-ionomer restorations. As expected, an inhibition zone was not detected adjacent to the resin-based composite restoration. Additionally, using the transmission x-ray images of XAM, the inhibition zones were observed as high density areas, and the outer lesions as low density areas. The width of the inhibition zones and the depth of the outer lesions measured under the CLSM were similar to those obtained from the XAM.
Definition of a human T cell epitope from influenza A non-structural protein 1 using HLA-A2.1 transgenic mice (1995)

Previous results from this laboratory demonstrated that the dominant influenza A epitope recognized by HLA-A2.1-restricted cytotoxic T lymphocytes (CTL) from HLA-A2.1 transgenic mice was the matrix protein 1 (M1) peptide epitope that is immunodominant in human CTL responses. However, analysis of a large number of CTL lines revealed a subset of influenza A/PR/8/34-specific murine CTL that recognized an HLA-A2.1-restricted epitope distinct from M1. Using recombinant vaccinia viruses encoding different influenza gene segments, the epitope recognized by these CTL was shown to be derived from A/PR/8 non-structural protein 1 (NS1). Because these CTL did not recognize targets infected with the A/Alaska/6/77 strain of influenza, candidate peptide epitopes were synthesized based on sequences that included an HLA-A2.1-specific binding motif, and that differed between A/PR/8 and A/Alaska. All of these CTL recognized a nonamer and a decamer peptide which contained a common eight amino acid sequence and two distinct sets of binding motif residues. However, the nonamer peptide was able to sensitize CTL for half-maximal lysis at 80- to 2500-fold lower doses than either the octamer or decamer. The homologous peptide derived from A/Alaska NS1 contained conservative amino acid changes at positions 4 and 8, and was not recognized at any tested concentration, although it bound with higher affinity to HLA-A2.1 than the peptide from A/PR/8. The A/PR/8 NS1 nonamer epitope was also recognized by human influenza A-specific CTL derived from two individuals. These results substantiate the general utility of HLA class I transgenic mice for the identification of human CTL epitopes for other pathogens.
Copper-Mediated CRP of Methyl Acrylate in the Presence of Metallic Copper: Effect of Ligand Structure on Reaction Kinetics (2011)

The kinetics of copper-mediated controlled/living radical polymerization (CRP) of methyl acrylate (MA) in the presence of Cu0 and two different ligands that form active catalyst complexes with copper—TPMA (tris(2-pyridylmethyl)amine) and Me6TREN (tris(2-(dimethylamino)ethyl)amine)—are compared. The critical difference between the ligands is that TPMA forms a CuI complex that undergoes essentially no disproportionation in a mixture of MA and dimethyl sulfoxide (DMSO), DMSO/MA (v/v = 1/2), while the complex with Me6TREN undergoes disproportionation to a limited extent. Parameters such as the surface area of Cu0 wire, the concentration of added CuIIX2/L, and ligand concentration were examined. Both the Me6TREN- and TPMA-based catalysts efficiently controlled the polymerization of MA. The TPMA-based system showed a power law order of 0.47 for the apparent propagation rate constant with the Cu0 surface area, very similar to the reported value for the Me6TREN-based system, which showed a power law of 0.44. These results demonstrate that the polymerization of MA in DMSO in the presence of metallic copper can be explained by a core atom-transfer radical polymerization (ATRP) process in which the Cu0 acts as a supplemental activator and reducing agent, rather than through the proposed single-electron-transfer living radical polymerization (SET-LRP) mechanism, which requires additional assumptions, such as complete and instantaneous disproportionation of CuI/L species.