gebhart/patrepeval huggingface dataset:
Analysis of proteins encoded by the ptx and ptl genes of Bordetella bronchiseptica and Bordetella parapertussis (1996)

Bordetella pertussis is the only bacteria] species which is known to produce pertussis toxin (PT); however, both Bordetella bronchiseptica and Bordetella parapertussis contain regions homologous to the ptx genes of B. pertussis that encode the toxin subunits. After finding that several children with B. parapertussis infections exhibited modest antibody titers to PT, we examined the ptx genes of both B. parapertussis and B. bronchiseptica to determine whether they would encode stable, functional proteins even though their promoters are thought to be inactive under the conditions that have been examined. We inserted a functional promoter directly upstream of the ptx-ptl region of both species and examined culture supernatants of the resulting strains for PT activity. Biologically active PT was found in the culture supernatants of both engineered species. The toxin encoded by the B. parapertussis ptx genes appeared more labile in culture supernatants than did toxin produced by either B. pertussis or the engineered strain of B. bronchiseptica. This lability might be due to the lack of a full-length S2 subunit. We also investigated the ptl genes of these species, which are necessary for the secretion of this toxin, and found that both B. bronchiseptica and B. parapertussis contain at least certain of these genes, including ptlE and ptlF. Moreover, B. bronchiseptica appeared to contain all essential ptl genes since the introduction of a functional promoter directly upstream of the ptx-ptl region resulted in both production and efficient secretion of toxin. These results indicate that despite a number of amino acid changes in the sequences of the toxins, the toxins encoded by B. bronchiseptica and B. parapertussis are active.
Multiple beam tilt microscopy for super resolved imaging (1997)

In this paper we report a super-resolved reconstruction of a thin crystal of H-Nb2O5 in which the limit of continuous transfer has been extended from about 0.2 nm in the conventional axial image to 0.13 nm. To allow the reconstruction of crystalline fragments containing little stable amorphous material, modifications to the standard procedure for image registration have been developed. Both the modulus and phase of the reconstruction appear to contain directly interpretable information.
Phosphorylation of Osteopontin Is Required for Inhibition of Calcium Oxalate Crystallization (2008)

Under near-physiological pH, temperature, and ionic strength, a kinetics constant composition (CC) method was used to examine the roles of phosphorylation of a 14 amino acid segment (DDVDDTDDSHQSDE) corresponding to potential crystal binding domains within the osteopontin (OPN) sequence. The phosphorylated 14-mer OPN peptide segment significantly inhibits both the nucleation and growth of calcium oxalate monohydrate (COM), inhibiting nucleation by markedly increasing induction times and delaying subsequent growth by at least 50% at concentrations less than 44 nM. Molecular modeling predicts that the doubly phosphorylated peptide binds much more strongly to both (-101) and (010) faces of COM. The estimated binding energies are, in part, consistent with the CC experimental observations. Circular dichroism spectroscopy indicates that phosphorylation does not result in conformational changes in the secondary peptide structure, suggesting that the local binding of negatively charged phosphate side chains to crystal faces controls growth inhibition. These in vitro results reveal that the interactions between phosphorylated peptide and COM crystal faces are predominantly electrostatic, further supporting the importance of macromolecules rich in anionic side chains in the inhibition of kidney stone formation. In addition, the phosphorylation-deficient form of this segment fails to inhibit COM crystal growth up to concentrations of 1450 nM. However, at sufficiently high concentrations, this nonphosphorylated segment promotes COM nucleation. Dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) results confirm that aggregation of the nonphosphorylated peptide segment takes place in solution above 900 nM when the aggregated peptide particles may exceed a well-defined minimum size to be effective crystallization promoters.
Growth factors and oncogenes in prostate cancer. (1990)

Prostatic cancer is an increasing medical problem. Investigations of the biology of the prostate and the development of prostate cancer have shown that the prostate gland contains high levels of polypeptide growth factors, especially members of the fibroblast growth factor (FGF) and transforming growth factor (TGF)-beta family. Activated oncogenes and elevated proto-oncogene activities including ras and myc have been detected in human prostate cancer tissues, but there is no consensus as to the predominant genetic alterations involved in the progression of this disease. In vivo animal models have shown that relevant growth factors and oncogenes can induce both premalignant and malignant changes in prostate tissue. Additional experimental and clinical studies are needed to present a clearer molecular profile of this important malignancy.
Complete Characterization of a Quantum Process: The Two-Bit Quantum Gate (1997)

We show how to fully characterize a quantum process in an open quantum system. We particularize the procedure to the case of a universal two-qubit gate in a quantum computer. We illustrate the method with a numerical simulation of a quantum gate in the ion trap quantum computer.
Cytokines activate the nuclear factor κB (NF‐κB) and induce nitric oxide production in human pancreatic islets (1996)

We studied the ability of cytokines to activate the nuclear transcription factor NF-kappaB in human pancreatic islets and the putative role of NF-kappaB for cytokine-induced NO production. Brief exposure (20 min) of human islets of Langerhans to a combination of interleukin-1beta + interferon-gamma + tumor necrosis factor-alpha induced a 2.6-fold increase in nuclear NF-kappaB activity in gel shift analysis. This increase was prevented by the NF-kappaB inhibitor, pyrrolidine dithiocarbamate (PDTC), which also counteracted NO production by human islets exposed for 14 h to the cytokine combination. High concentrations of interleukin-1beta alone (150 and 250 U/ml) increased NF-kappaB nuclear binding but failed to induce NO formation in human islets. The present data are the first to demonstrate that cytokines activate NF-kappaB in primary adult human pancreatic islets and suggest that activation of NF-kappaB may be a necessary but not sufficient signal for cytokine-induced iNOS expression in human islets of Langerhans.
Cotransfection of Nucleic Acid Segments by Sendai Virus Envelopes (1989)

It is reported here that Sendai virus envelopes (SVE) can be used to transfect multiple copies of DNA segments of different varieties and size. This capability further increases the usefulness of SVE. In addition, the ability to simultaneously transfect multiple copies of different genome segments promises to be a powerful tool in the field of molecular biology. The simultaneous transfection of NEO gene and cytomegalovirus immediate early antigen gene was successfully done. Sendai virus envelopes (SVE)1 have been used successfully to study carcinogenesis of Epstein-Barr virus (1, 2). SVE have been shown to have a large carrying capacity (3) for the microinjection of macromolecules into target cells. SVE are hollow vesicles constructed from the viral proteins hemagglutinin HN and fusion factor F.
Vinyl-type polymerization of norbornene by a nickel-based catalyst with phosphoraneiminato ligands (1999)

High molecular weight vinyl-type polynorbornene was obtained in high yields with a highly active nickel-based phosphoraneiminato complex in the presence of methylaluminoxane. This polynorbornene is soluble at room temperature in chlorobenzene and shows no indication of crystallinity in the solid state. Catalyst activity, polymer yield, and polymer molecular weight can be controlled over a wide range by variation of reaction parameters.
Clinical experience with gemcitabine in pancreatic carcinoma. (1997)

The treatment of advanced pancreatic carcinoma has been viewed with pessimism. Because of the lack of activity of commonly used agents, there is no consensus regarding a standard chemotherapy regimen. Assessment of response is neither uniform nor reproducible. Debilitating tumor-related symptoms, including pain, anorexia, weight loss, and impaired performance status, are common. Many studies have failed to evaluate the palliative benefit of treatments, although many patients consider such benefit to be of the utmost importance. Tools have been developed to uniformly assess tumor-related symptoms, and the concept of clinical benefit response has been developed as an end point to quantify symptomatic improvement utilizing these tools. Clinical benefit response incorporates palliative measures, such as pain control, analgesic consumption, performance status, and weight gain. In early phase I and II trials, gemcitabine (Gemzar) has shown activity in patients with chemotherapynaive advanced pancreatic carcinoma. In addition to producing some responses and symptomatic benefit, gemcitabine has a favorable toxicity profile. Two recent trials using clinical benefit response as the primary end point have demonstrated that gemcitabine significantly improves disease-related symptoms in approximately one-quarter of patients. These trials also showed improved survival with gemcitabine, as compared with fluorouracil. Additional studies are required to fully assess the role of gemcitabine in both adjuvant and advanced disease settings.
Improved folding of apo-retinol-binding protein in the periplasm of Escherichia coli: positive influences of dsbC coexpression and of an amino acid exchange in the vitamin A binding site (1998)

The in vivo folding of the serum retinol-binding protein (RBP), a representative of the lipocalin structural family, is known to be complex. In order to gain insight into the essential steps along its folding pathway the heterologous production of the functional protein in Escherichia coli was investigated. Simultaneous overexpression of the bacterial dsbC gene, which codes for a periplasmic thiol-disulphide oxidoreductase, prevented the formation of soluble RBP variants with non-native disulphide bonds that were otherwise observed. Although the coexpression of dsbC had furthermore a stabilizing effect on the cell viability, the relative yield of the solubly produced RBP was not much better. In an attempt to enhance its folding efficiency, a favourable point mutation in the inner part of the retinol-binding pocket was predicted. Replacement of the polar Gln117 with an lie side chain seemed not only to relieve the unfavourable energetics of the carboxamide group in the environment of predominantly non-polar residues but also to fill an adjacent cavity in the hydrophobic core. Indeed, this single substitution reproducibly resulted in a more than threefold increase in the amount of functional recombinant RBP. Ligand binding experiments showed that the affinity of this mutant for retinol was slightly enhanced. Kinetic measurements revealed that this was due to a higher association rate whereas the dissociation of the complex with retinol was essentially unaffected. Although the question remained why nature did not select this obviously beneficial mutation, our results demonstrate that the folding pathway of a lipocalin can be optimized by protein engineering.
Multiuser subcarrier allocation for OFDM transmission using adaptive modulation (2003)

A multiuser OFDM (orthogonal frequency division multiplexing) downlink transmission with adaptive modulation is considered. Assuming that the base station knows the instantaneous channel gains for all users, we propose an algorithm which minimizes the total transmit power by assigning, to each user, a set of subcarriers within an OFDM symbol and by determining, for each sub-carrier, the number of bits to be transmitted and the power level used. We obtained the performance of our proposed algorithm in a multiuser frequency selective fading environment with various root-mean-square (RMS) delay spread. The results show that our proposed algorithm outperforms conventional OFDM systems with or without optimal bit allocation using TDMA or FDMA as multiaccess techniques. We have also quantified the improvement in terms of the required transmit power, for fixed bit error rate.
Low index contrast imaging fibers (2017)

We present high-resolution imaging fibers made from low-cost commercially available fiber preforms manufactured for the telecommunications industry. Our fabrication method involves multi-stacking arrays of different sized cores in order to suppress core-to-core crosstalk whilst building up a large array of cores. One of the fibers, based on a square array of cores, has comparable imaging performance to commercial imaging fibers but without the need for exceptionally high refractive index contrasts, and will enable the development of economically viable single-use disposable imaging fibers.
Gamma-ray burst studies using the H.E.S.S. Cherenkov array (2009)

Gamma-ray bursts (GRBs) are the most intense and unpredictable gamma-ray events from the Universe. Without prior signal, an enormous amount of energy is released for seconds, energizing particles and generating the observed 10e5-10e6 eV gamma-ray photons. The emitting regions can produce Very-High-Energy (VHE) gamma-ray photons of energy about 10e11 eV during and after the burst. These VHE gamma-rays may be attenuated in the source or by the extragalactic background light (EBL). The H.E.S.S. array of four imaging atmospheric Cherenkov telescopes (IACT) is sensitive to VHE gamma-rays. H.E.S.S. observations of 34 GRBs were carried out during 2003-2008, with the shortest response time being six minutes. No evidence of VHE gamma-rays was found. Flux upper limits derived for GRB030329 and GRB060505 are compared and are found consistent with the synchrotron self-Compton flux calculated in the context of relativistic blast-wave model. Absorption by EBL was taken into consideration. Accidentally, GRB060602B was observed with H.E.S.S. throughout the GRB duration, during which no signal of VHE gamma-rays was found. The distance scale and origin of GRB060602B remain unclear and different possibilities and implications are presented. Future prospects of VHE gamma-ray observations of GRBs are discussed.
Biochemical Analysis of Histone Deacetylase-independent Transcriptional Repression by MeCP2 (2013)

MeCP2 is an abundant methyl-cytosine-guanine (CG)-binding protein and transcriptional repressor. We developed a biochemical system that exhibits CG methylation-specific transcriptional repression by purified human MeCP2. MeCP2 represses transcription by histone deacetylase (HDAC)-dependent and HDAC-independent mechanisms. Our system appears to recreate the HDAC-independent component of MeCP2-mediated repression and occurs via inhibition of the assembly of transcription preinitiation complexes. At a ratio of approximately one molecule of MeCP2 per two methyl-CG dinucleotides, as found in mammalian neurons, the magnitude of methylation-specific repression was greater than 10-fold. Notably, the HDAC inhibitor trichostatin A had no effect on MeCP2-mediated repression with either naked DNA or chromatin templates. We designed a CG-deficient core promoter that is resistant to MeCP2-mediated repression when placed in a plasmid lacking CG dinucleotides. By using this CG-deficient reporter as a reference, we found that eight CG dinucleotides in the core promoter region are sufficient for strong methylation-specific repression by MeCP2. In contrast, MeCP2 does not repress a construct with 13 CG dinucleotides located ∼1.7 kbp upstream of the promoter. Furthermore, by analysis of C-terminally truncated MeCP2 proteins, we found that binding of MeCP2 to methyl-CG dinucleotides is not sufficient for transcriptional repression. Hence, MeCP2-mediated repression is not due to the simple steric blockage of the transcriptional machinery. These experiments suggest that MeCP2 can function as a global methyl-CG-specific, HDAC-independent repressor. This HDAC-independent mechanism of MeCP2-mediated repression may be important in cells, such as mammalian neurons, that have high levels of CG methylation and MeCP2.
Generalized autocorrelation analysis of spectral regrowth from bandpass nonlinear circuits (2002)

Estimation of spectral regrowth generated by a digitally modulated carrier passed through a nonlinear RF circuit is analyzed using a formulation of the output autocorrelation function. The estimation is based on developing an analytical expression for the output power spectrum when the nonlinearity is modeled as a complex power series model extracted from measured amplitude-to-amplitude (AM-AM) and amplitude-to-phase (AM-PM) characteristics. An analytical expression of the output power spectrum is developed from statistical moments for a complex Gaussian input signal. Comparisons are presented of measured versus predicted ACPR values for a CDMA amplifier.
Use of RNase H and primer extension to analyze RNA splicing (1988)

A new method for the characterization of pre-mRNA splicing products is presented. In this method RNA molecules are hybridized to an oligodeoxynucleotide complementary to exon sequences upstream of a given 5' splice site, and the RNA strands of the resulting RNA:DNA hybrids are cleaved by RNase H. The cleaved RNAs are then subjected to primer extension using a 32P-labelled primer complementary to exon sequences downstream of an appropriate 3' splice site. Since the primer extension products all terminate at the site of RNase H cleavage, their lengths are indicative of the splice sites utilized. The method simplifies the study of the processing of complex pre-mRNAs by allowing the splicing events between any two exons to be analyzed. We have used this approach to characterize the RNAs generated by expression of the rat tropomyosin 1 (Tm 1) gene in various rat tissues and in cultured cells after transient transfection. The results demonstrate that this method is suitable for the analysis of alternative RNA processing in vivo.
Measurement of swine aortic resistivity (1997)

The authors measured impedance of swine aorta from 10 Hz to 500 kHz. The resistivity is 184 /spl Omega//spl middot/cm at low frequencies, it starts to decrease above 10 kHz and becomes 149 /spl Omega//spl middot/cm at 500 kHz.
Highly stretchable electroluminescent skin for optical signaling and tactile sensing (2016)

Cephalopods such as octopuses have a combination of a stretchable skin and color-tuning organs to control both posture and color for visual communication and disguise. We present an electroluminescent material that is capable of large uniaxial stretching and surface area changes while actively emitting light. Layers of transparent hydrogel electrodes sandwich a ZnS phosphor-doped dielectric elastomer layer, creating thin rubber sheets that change illuminance and capacitance under deformation. Arrays of individually controllable pixels in thin rubber sheets were fabricated using replica molding and were subjected to stretching, folding, and rolling to demonstrate their use as stretchable displays. These sheets were then integrated into the skin of a soft robot, providing it with dynamic coloration and sensory feedback from external and internal stimuli.
Characterization ofPseudomonas aeruginosaIsolates: Occurrence Rates, Antimicrobial Susceptibility Patterns, and Molecular Typing in the Global SENTRY Antimicrobial Surveillance Program, 1997–1999 (2001)

During 1997-1999, a total of 70,067 isolates (6631 Pseudomonas aeruginosa isolates) were analyzed in the SENTRY program by geographic region and body site of infection. The respiratory tract was the most common source of P. aeruginosa. P. aeruginosa isolation rates increased during the study interval. Europe was the only region to show a significant decline in beta-lactam and aminoglycoside susceptibility rates. There was a reduction in the rates of susceptibility of Canadian isolates to imipenem and of Latin American isolates to meropenem. A total of 218 multidrug-resistant P. aeruginosa isolates (MDR-PSA; resistant to piperacillin, ceftazidime, imipenem, and gentamicin) were observed; MDR-PSA occurrence rates (percentages of all isolates) ranged from 8.2% (Latin America) to 0.9% (Canada). No antimicrobial inhibited >50% of MDR-PSA strains. Molecular characterization of selected, generally resistant strains was performed. Isolates showing unique ribogroups were found in Europe, Latin America, and the United States, but clonal spread was documented in several medical centers.
Cyclic Sulfites and Cyclic Sulfates: Epoxide like Synthons (1992)

This article reviews the recent developing synthetic utilities of cyclic sulfites and cyclic sulfates in organic chemistry, which rival in reactivity and selectivity with their very well studied friend, the epoxides and in many cases, are found to be superior to them. 1. Introduction 2. Structure 3. Synthesis of Cyclic Sulfites 4. Synthesis of Cyclic Sulfates 5. Reactivity 5.1. Thermal Rearrangement 5.2. Photochemical Rearrangement 5.3. Reaction with Electrophiles 5.3.1.Reaction with Acids 5.3.2.Electrophilic Addition to Double Bonds 5.4. Reaction with Nucleophiles 5.4.1.O-Nucleophiles 5.4.2.S-Nucleophiles 5.4.3. Halide Nucleophiles 5.4.4.C-Nucleophiles 5.4.5. N-Nucleophiles 5.4.6. H-Nucleophiles 5.5. Reaction with Radicals 5.6. Electrochemical Reduction of Cyclic Sulfates 6. Application in Research and Industry 7. Biological Activities 8. Conclusion
Abnormal patterns of D-type cyclin expression and G1 regulation in human head and neck cancer. (1995)

D-type cyclins are proto-oncogenic cell cycle regulators implicated in the pathogenesis of several types of cancer. Amplification of the cyclin D1 gene has been described in 30-50% of human head and neck squamous cell carcinoma (HNSCC). Using immunohistochemistry on archival specimens of human HNSCC and a mAb DCS-6, which is specific for cyclin D1, strong positivity was found in nuclei of 9 (17%) of 52, a moderately elevated signal in 16 (31%) of 52, and weak staining comparable with normal tissues in 27 (52%) of 52 patients. Immunoblotting analysis of five HNSCC-derived cell lines showed three distinct spectra of D-type cyclin proteins: cyclin D1 only (in UMSCC-2 and UMSCC-22b cell lines with 11q13 amplification), cyclins D1 and D3 (in HN5 and HN6), or cyclins D1, D2, and D3 (in UMSCC-1). Electroporation of neutralizing antibodies demonstrated requirement for cyclin D1 in cell cycle progression of all five HNSCC cell lines. Cyclin D2 was essential and showed a cooperative effect with cyclin D1 in positive regulation of G1 in UMSCC-1 cells. These data are consistent with the proposed oncogenic role of cyclin D1 in HNSCC and open up the way for immunohistochemical assessment of cyclin D1 aberrations in archival clinical specimens. It is also suggested that excessive levels of cyclin D1 alone or cooperative effects of several D-type cyclin proteins may lead to deregulation of G1 control in distinct subsets of human HNSCC. These results are discussed in the context of possible functional redundancy of D-type cyclins and the role of the D-type cyclin/p16-CDKN2/pRB pathway in tumorigenesis.