gebhart/patrepeval huggingface dataset:
Use of Mutated FLP Recognition Target (FRT) Sites for the Exchange of Expression Cassettes at Defined Chromosomal Loci (1994)

Using the FLP/FRT system for site-specific recombination and the wild-type recognition site (FRT) in conjunction with certain mutant FRT sites, it becomes possible to provoke, with high yield, a double-reciprocal crossover event in cultured mammalian cells. It is demonstrated that this technology enables a targeting of expression cassettes to appropriate chromosomal reference sites in the recipient cell to improve the concepts of reverse genetics. The design of mutant FRT sites promoting such a process will be delineated. Our results show that the five spacer mutations tested are functional as the wild type but differ in the extent of their cross-recombination, which has to be minimized for their simultaneous usage.
Sequence-specific interactions between cellular DNA-binding proteins and the adenovirus origin of DNA replication. (1987)

The adenovirus origin of DNA replication contains three functionally distinct sequence domains (A, B, and C) that are essential for initiation of DNA synthesis. Previous studies have shown that domain B contains the recognition site for nuclear factor I (NF-I), a cellular protein that is required for optimal initiation. In the studies reported here, we used highly purified NF-I, prepared by DNA recognition site affinity chromatography (P. J. Rosenfeld and T. J. Kelly, Jr., J. Biol. Chem. 261:1398-1408, 1986), to investigate the cellular protein requirements for initiation of viral DNA replication. Our data demonstrate that while NF-I is essential for efficient initiation in vitro, other cellular factors are required as well. A fraction derived from HeLa cell nuclear extract (BR-FT fraction) was shown to contain all the additional cellular proteins required for the complete reconstitution of the initiation reaction. Analysis of this complementing fraction by a gel electrophoresis DNA-binding assay revealed the presence of two site-specific DNA-binding proteins, ORP-A and ORP-C, that recognized sequences in domains A and C, respectively, of the viral origin. Both proteins were purified by DNA recognition site affinity chromatography, and the boundaries of their binding sites were defined by DNase I footprint analysis. Additional characterization of the recognition sequences of ORP-A, NF-I, and ORP-C was accomplished by determining the affinity of the proteins for viral origins containing deletion and base substitution mutations. ORP-C recognized a sequence between nucleotides 41 and 51 of the adenovirus genome, and analysis of mutant origins indicated that efficient initiation of replication is dependent on the presence of a high-affinity ORP-C-binding site. The ORP-A recognition site was localized to the first 12 base pairs of the viral genome within the minimal origin of replication. These data provide evidence that the initiation of adenovirus DNA replication involves multiple protein-DNA interactions at the origin.
Glycolipids as Immune Modulatory Tools (2006)

NKT cells are a subset of regulatory lymphocytes characterized by co-expression of the NK cell receptor-CD161 and an invariant TCR-alpha chain (Valpha14-Jalpha28). They are most abundant in the liver, spleen, and bone marrow. NKT lymphocytes have been implicated in the regulation of autoimmune processes in both mice and humans. Activation of NKT lymphocytes leads to rapid amplification of either IFNgamma or IL4, endowing these cells with the capability to mediate both pro-inflammatory and anti-inflammatory immune responses. Activation of this subset of cells is associated with significant liver damage in the Concanavalin A immune mediated hepatitis model. Administration of CD1d ligand has a protective role in collagen-induced arthritis in mice. Disease amelioration was associated with a shift in the immune balance from a pathological Th1 type response towards a protective Th2 type response. In humans, patients with SLE, scleroderma, diabetes, multiple sclerosis, and rheumatoid arthritis have lower numbers of peripheral NKT cells. NKT lymphocytes promote tumor rejection in experimental models of tumor immunotherapy. In contrast, NKT lymphocyte-related anti-tumor activity is associated with pro-inflammatory Th1-type immune responses. NKT cells were shown to have a role in suppression of hepatocellular carcinoma (HCC) via immune regulation towards tumor derived antigens, and adoptive transfer of dendritic cells pulsed ex vivo with the same antigens. NKT lymphocytes are activated by interaction of their TCR with glycolipids presented by CD1d, a nonpolymorphic, MHC class I-like molecule expressed by antigen presenting cells, and also by hepatocytes. Several possible ligands for NKT cells have recently been suggested including CD1d bound Glucocerebroside. Glucocerebroside (GC, beta-glucosylceramide), a naturally occurring glycolipid, is a metabolic intermediate in the anabolic and catabolic pathways of complex glycosphingolipids. Its synthesis from ceramide is catalyzed by the enzyme glucosylceramide synthase. Inherited deficiency of glucocerebrosidase, a lysosomal hydrolase, results in Gaucher's disease. Patients with Gaucher's disease have altered humoral and cellular immune profiles and increased peripheral blood NKT lymphocytes. CD1d-bound glucocerebroside does not activate NKT cells directly, and may inhibit activation of NKT cells by alpha-GalCer. On the other hand, glucosylceramide-synthase deficiency was shown to lead to defective ligand presentation by CD1d, with secondary inhibition of NKT cell activation. Recent studies have suggested that a number of glycolipids, including GC, have an immune modulatory effect in several immune mediated disorders. The ability to alter NKT lymphocyte function in various settings and the potential application of natural glycolipids for treatment are discussed.
Robust raspberry-like metallo-dielectric nanoclusters of critical sizes as SERS substrates (2017)

Raspberry-like nano-objects made of large plasmonic satellites (>10 nm) covering a central dielectric particle have many potential applications as photonic materials, superlenses and (bio-) sensors, but their synthesis remains challenging. Herein, we show how to build stable and robust raspberry-like nano-systems with close-packed satellites, by combining monodisperse silica particles (80 or 100 nm diameter) and oppositely charged noble metal nanoparticles (Au or Ag) with well-defined sizes (10-50 nm). The spectral characteristics of their associated plasmonic resonances (wavelength, linewidth, extinction cross-section) and the electromagnetic coupling between satellites were observed using the spatial modulation spectroscopy technique and interpreted through a numerical model. The composite nano-objects exhibit numerous hot spots at satellite junctions, resulting in excellent surface-enhanced Raman scattering (SERS) performance. The SERS efficiency of the raspberry-like clusters is highly dependent on their structure.
Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. (2004)

To detect diseases early in the general population, new diagnostic approaches are needed that have adequate sensitivity and specificity. Recent studies have used mass spectrometry to identify a serum proteomic pattern for breast and ovarian cancer. Serum contains 60-80 mg/mL protein, but 57-71% of this is serum albumin, and 8-26% are gamma-globulins. These large proteins must be depleted before smaller, less-abundant proteins can be detected using mass spectrometry, but because serum albumin is known to act as a carrier for smaller proteins, removal of these molecules using columns or filtration may result in the loss of molecules of interest. The objective of this study was to develop a reproducible method to deplete serum samples of high-abundance proteins in order to analyze the less-abundant proteins present in serum. We used organic solvents to precipitate the large proteins out of solution. We also predicted that this would cause many smaller proteins to dissociate from their carrier molecules, allowing for detection of a larger number of peptides and small proteins. These treated samples were analyzed using capillary liquid chromatography coupled with electrospray ionization mass spectrometry. Analysis demonstrated reproducible results. Acetonitrile treatment clearly released many carrier-bound molecular species and was superior to ultrafiltration alone for serum proteomic analysis.
Analysis of Protease Activity Using Quantum Dots and Resonance Energy Transfer (2012)

This review demonstrates the detection of protease activity based on the energy transfer of quantum dots (QDs). By incorporation of varying protease substrates into designed QD probes both in fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) system, proteolytic activity led to changes in the energy transfer efficiency. Especially due to the superior properties of QDs, it can be served as an excellent probe for a multiplexed and high-throughput protease assay with high sensitivity. It is anticipated that the QD-based FRET/BRET probes will have a great potential for dissecting the fundamental roles of proteases and designing potential protease inhibitors as therapeutic drugs in biology and nanomedicine.
Epitope-Mapping Studies Define Two Major Neutralization Sites on the Vaccinia Virus Extracellular Enveloped Virus Glycoprotein B5R (2005)

Vaccinia extracellular enveloped virus (EEV) is critical for cell-to-cell and long-range virus spread both in vitro and in vivo. The B5R gene encodes an EEV-specific type I membrane protein that is essential for efficient EEV formation. The majority of the B5R ectodomain consists of four domains with homology to short consensus repeat domains followed by a stalk. Previous studies have shown that polyclonal antibodies raised against the B5R ectodomain inhibit EEV infection. In this study, our goal was to elucidate the antigenic structure of B5R and relate this to its function. To do this, we produced multimilligram quantities of vaccinia virus B5R as a soluble protein [B5R(275t)] using a baculovirus expression system. We then selected and characterized a panel of 26 monoclonal antibodies (MAbs) that recognize B5R(275t). Five of these MAbs neutralized EEV and inhibited comet formation. Two other MAbs were able only to neutralize EEV, while five others were able only to inhibit comet formation. This suggests that the EEV neutralization and comet inhibition assays measure different viral functions and that at least two different antigenic sites on B5R are important for these activities. We further characterized the MAbs and the antigenic structure of B5R(275t) by peptide mapping and by reciprocal MAb blocking studies using biosensor analysis. The epitopes recognized by neutralizing MAbs were localized to SCR1-SCR2 and/or the stalk of B5R(275t). Furthermore, the peptide and blocking data support the concept that SCR1 and the stalk may be in juxtaposition and may be part of the same functional domain.
Effect of retinoids on the proliferation, morphology and expression of glial fibrillary acidic protein of an anaplastic astrocytoma cell line (1988)

We studied the effect of retinoids on the growth and differentiation of a cell line (U 343 MG-A) derived from a human malignant astrocytoma. Cultures treated with all-trans or 13-cis retinoic acid showed a dose-dependent inhibition of proliferation and a marked reduction in the mean cell number at the plateau phase of growth (3.5 x 10(6) vs. 1 x 10(7) cells/25 cm2) compared with untreated cultures. At confluence, cells treated with all-trans or 13-cis retinoic acid were contact-inhibited, whereas control cultures showed crowding, piling, and overgrowth. All-trans retinol or retinyl acetate did not inhibit growth. Astrocytoma cultures treated with all-trans retinoic acid (10(-6) M) for 5 days were modestly growth-inhibited but by day 16 had the same numbers of cells as controls; cultures that received all-trans retinoic acid for 9 days were markedly growth-inhibited for 7 days after the drug was removed. All-trans and 13-cis retinoic acid (10(-6) M) prevented the EDTA-induced cell detachment seen in control cultures. Strongly adherent all-trans retinoic-acid-treated astrocytoma cells grew at a slower rate than did readily detached all-trans retinoic-acid-treated or control cells. Cell spreading, an increased cytoplasmic:nuclear ratio, and greater numbers of broadly bipolar cells, some bearing thin cytoplasmic processes, were seen in cultures treated with 10(-6) M all-trans or 13-cis retinoic acid. Small tightly packed cuboidal cells and large broadly bipolar cells were seen in astrocytoma cultures from which all-trans retinoic acid was removed on days 5 and 9. Indirect immunofluorescence revealed more intense staining with antiserum to glial fibrillary acidic protein in cultures treated with 10(-6) M all-trans retinoic acid than in control cultures; electron-microscope examination of similarly treated cultures revealed more abundant 8-10 nm intermediate filaments than in control cultures. An enzyme-linked immunosorbent assay showed that all-trans or 13-cis retinoic acid caused a dose-dependent increase in the quantity of glial fibrillary acidic protein in the astrocytoma cells.
Nanowire-based sublithographic programmable logic arrays (2004)

How can Programmable Logic Arrays (PLAs) be built without relying on lithography to pattern their smallest features? In this paper, we detail designs which exploit emerging, bottom-up material synthesis techniques to build PLAs using molecular-scale nanowires. Our new designs accommodate technologies where the only post-fabrication programmable element is a non-restoring diode. We introduce stochastic techniques which allow us to restore the diode logic at the nanoscale so that it can be cascaded and interconnected for general logic evaluation. Under conservative assumptions using 10nm nanowires and 90nm lithographic support, we project yielded logic density around 500,000nm2/or term for a 60 or-term array; a complete 60-term, two-level PLA is roughly the same size as a single 4-LUT logic block in 22nm lithography. Each or term is comparable in area to a 4-transistor hardwired gate at 22nm. Mapping sample datapaths and conventional programmable logic benchmarks, we estimate that each 60-or-term PLA plane will provide equivalent logic to 5--10 4-input LUTs.
Tumor‐infiltrating CD14‐positive myeloid cells and CD8‐positive T‐cells prolong survival in patients with cervical carcinoma (2013)

One of the hallmarks of cancer is the influx of myeloid cells. In our study, we investigated the constitution of tumor-infiltrating myeloid cells and their relationship to other tumor-infiltrating immune cells, tumor characteristics and the disease-specific survival of patients with cervical cancer (CxCa). Triple-color immunofluorescence confocal microscopy was used to locate, identify and quantify macrophages (CD14), their maturation status (CD33) and their polarization (CD163) in a cohort of 86 patients with cervical carcinoma. Quantification of the numbers of myeloid cells revealed that a strong intraepithelial infiltration of CD14+ cells, and more specifically the population of CD14+CD33-CD163- matured M1 macrophages, is associated with a large influx of intraepithelial T lymphocytes (p = 0.008), improved disease-specific survival (p = 0.007) and forms an independent prognostic factor for survival (p = 0.033). The intraepithelial CD8+ T-cell and regulatory T-cell (Treg) ratio also forms an independent prognostic factor (p = 0.010) and combination of these two factors reveals a further increased benefit in survival for patients whose tumor displays a dense infiltration with intraepithelial matured M1 macrophages and a high CD8 T-cell/Treg ratio, indicating that both populations of immune cells simultaneously improve survival. Subsequently, we made a heatmap including all known immune parameters for these patients, whereby we were able to identify different immune signatures in CxCa. These results indicate that reinforcement and activation of the intratumoral M1 macrophages may form an attractive immunotherapeutic option in CxCa.
Antitumour activity of ANG1005, a conjugate between paclitaxel and the new brain delivery vector Angiopep‐2 (2008)

These results demonstrate the antitumour potential of a new drug, ANG1005, and establish that conjugation of anticancer agents with the Angiopep-2 peptide vector could increase their efficacy in the treatment of brain cancer.
Structural and functional characterization of insulin receptor substrate proteins and the molecular mechanisms of their interaction with insulin superfamily tyrosine kinase receptors and effector proteins. (2000)

The literature data on the role of IRS1/IRS2 proteins, endogenous substrates for insulin receptor tyrosine kinase, in transduction of signals generated by insulin superfamily peptides (insulin, insulin-like growth factor) were analyzed. The molecular mechanisms of the functional coupling of IRS proteins with peptide receptors possessing a tyrosine kinase activity and SH2 domain-containing proteins (phosphatidylinositol 3-kinase, Grb2 adaptor protein, protein phosphotyrosine phosphatase) were discussed. The structural and functional properties of IRS proteins (distribution of functional domains and sites for tyrosine phosphorylation; conservatism of amino acid sequences) were characterized. The data on the alternative pathways of transduction of signals which are generated by insulin and related peptides and do not involve IRS proteins were analyzed. These pathways are realized through Shc proteins or via direct interaction between receptors and SH2 proteins. Amino acid sequences of IRS proteins and insulin superfamily tyrosine kinase receptors were compared. The homologous regions in IRS proteins and receptors, which can be responsible for their coupling with phosphatidylinositol 3-kinase and protein phosphotyrosine phosphatases, were identified.
Nitrosyliron(III) hemoglobin: autoreduction and spectroscopy (1986)

Nitrosyl complexes of the iron(III) forms of myoglobin, human hemoglobin, Glycera dibranchiata hemoglobins (Hbm and Hbh), and model iron(II) and iron(III) synthetic porphyrins including octaethylporphyrin (OEP) have been prepared. The iron(III) heme proteins are electron spin (paramagnetic) resonance (ESR) silent, while hexacoordinate solution structures are indicated for [Fe(OEP)(NO)2]ClO4 and for Hbm(II)NO, which has an ESR spectrum similar to that of Mb(II)NO and the hexacoordinate iron(II) model complex Fe(OEP)NO(BzIm). The splitting of the alpha- and beta-bands in the optical spectrum of Mb(III)NO and Hbh(III)NO contrasts markedly with the sharp, single bands observed in that of Hbm-(III)NO. The nondegeneracy of the dxz and dyz orbitals in Mb(III)NO and Hbh(III)NO is attributed to the influence of the distal histidine. Circular dichroism spectra were obtained for Hbm(III)NO, Hbm(II)NO, Hbh(III)NO, Hbh(II)NO, Mb(II)NO, and Mb(III)NO. The vicinal chiral center contribution that governs the heme protein CD leads to low Kuhn anisotropies, which have been used to assign certain electronic transitions. The Hb(III)NO spectrum is not stable but transforms into that of Hb(II)NO. This autoredox process follows kinetics that are first order in FeIIINO. The relative rates of autoreduction (25 degrees C, 1 atm NO) are Mb(III)NO less than Hbm(III)NO less than Hb alpha(III)NO less than HbA(III)NO. At high NO partial pressure or after "recycling" of HbA, the rates of reduction decrease. The first step in the reaction of NO with the ferric heme is the reversible formation of the formally iron(III) adduct. This reacts with another molecule of NO, generating the final heme(II)-NO via nitrosylation of NO itself or of an endogenous nucleophile. Kinetic and spectroscopic evidence shows involvement of trans-heme-(NO)2 in the reaction. The activation parameters delta H and delta S were determined. The overall reaction is photoenhanced.
Focusing subwavelength grating coupler for mid-infrared suspended membrane waveguide (2012)

A mid-infrared (mid-IR)-focusing subwavelength grating (SWG) coupler and suspended membrane waveguide (SMW) on a silicon-on-insulator wafer are studied. For a transverse-electric mode uniform SWG, finite-difference time-domain simulation predicts 44.2% coupling efficiency with 1 dB bandwidth of about 220 nm and backreflection of 0.78% at 2.75 μm. Then the uniform SWG is curved to a focusing SWG using a phase-matching formula. The SMWs are analyzed by the finite element method and fabricated. An Er3+-Pr3+ co-doped mid-IR fiber laser is used for device characterization. The fabricated mid-IR SWG coupler has 24.7% coupling efficiency.
Quality Evaluation and Nonuniform Compression of Geometrically Distorted Images Using the Quadtree Distortion Map (2004)

The paper presents an analysis of the effects of lossy compression algorithms applied to images affected by geometrical distortion. It will be shown that the encoding-decoding process results in a nonhomogeneous image degradation in the geometrically corrected image, due to the different amount of information associated to each pixel. A distortion measure named quadtree distortion map (QDM) able to quantify this aspect is proposed. Furthermore, QDM is exploited to achieve adaptive compression of geometrically distorted pictures, in order to ensure a uniform quality on the final image. Tests are performed using JPEG and JPEG2000 coding standards in order to quantitatively and qualitatively assess the performance of the proposed method.
Short PCPs Verifiable in Polylogarithmic Time (2005)

We show that every language in NP has a probabilistically checkable proof of proximity (i.e., proofs asserting that an instance is "close" to a member of the language), where the verifier's running time is polylogarithmic in the input size and the length of the probabilistically checkable proof is only polylogarithmically larger that the length of the classical proof. (Such a verifier can only query polylogarithmically many bits of the input instance and the proof. Thus it needs oracle access to the input as well as the proof, and cannot guarantee that the input is in the language - only that it is close to some string in the language.) If the verifier is restricted further in its query complexity and only allowed q queries, then the proof size blows up by a factor of 2/sup (log n)c/q/ where the constant c depends only on the language (and is independent of q). Our results thus give efficient (in the sense of running time) versions of the shortest known PCPs, due to Ben-Sasson et al. (STOC '04) and Ben-Sasson and Sudan (STOC '05), respectively. The time complexity of the verifier and the size of the proof were the original emphases in the definition of holographic proofs, due to Babai et al. (STOC '91), and our work is the first to return to these emphases since their work. Of technical interest in our proof is a new complete problem for NEXP based on constraint satisfaction problems with very low complexity constraints, and techniques to arithmetize such constraints over fields of small characteristic.