gebhart/patrepeval huggingface dataset:
Anaerobic Conditions Induce Expression of Polysaccharide Intercellular Adhesin in Staphylococcus aureus and Staphylococcus epidermidis (2001)

Products of the intercellular adhesion (ica) operon in Staphylococcus aureus and Staphylococcus epidermidis synthesize a linear beta-1,6-linked glucosaminylglycan. This extracellular polysaccharide mediates bacterial cell-cell adhesion and is required for biofilm formation, which is thought to increase the virulence of both pathogens in association with prosthetic biomedical implants. The environmental signal(s) that triggers ica gene product and polysaccharide expression is unknown. Here we demonstrate that anaerobic in vitro growth conditions lead to increased polysaccharide expression in both S. aureus and S. epidermidis, although the regulation is less stringent in S. epidermidis. Anaerobiosis also dramatically stimulates ica-specific mRNA expression in ica- and polysaccharide-positive strains of both S. aureus and S. epidermidis. These data suggest a mechanism whereby ica gene expression and polysaccharide production may act as a virulence factor in an anaerobic environment in vivo.
EIA/NRSC DAR systems subjective tests. II. Transmission impairments (1997)

For pt.I see ibid., vol.43, no.3, p.261-7 (1997). This paper describes the methods, results and conclusions of a series of subjective tests which were performed at the Communications Research Centre, Ottawa, Canada, to assess the audio quality of digital audio radio (DAR) systems in the presence of transmission errors. Testing has been performed in a laboratory environment on the hardware implementation of nine DAR systems. One of the systems operated in the AM broadcast band, five in the FM broadcast band, two in the L-band and one in the S-band. Testing was done in the presence of transmission errors generated by additive white gaussian noise, co-channel interference and five different multipath mobile channels. In addition, one system was tested with an interfering signal in the lower first adjacent DAR channel. The test results are presented and discussed, for each type of transmission impairments, in terms of (a) the E/sub b//N/sub 0/ ratios (D/U ratios for co-channel and adjacent channel interference) at the threshold of audibility (TOA) of transmission errors and at the point where transmission errors are so important that the audio quality is unacceptable (point of failure or POF) and (b) the failure margin which is a measure of how quickly DAR systems fail when the received signal power is reduced. A new parameter, labeled C/sub SP//N/sub 0/, is proposed to quantify the power efficiency of the overall DAR systems (i.e. source coding plus channel coding and modulation subsystems). The spectral efficiency of DAR systems is also presented and discussed.
96 shRNAs designed for maximal coverage of HIV-1 variants (2009)

In summary, our novel selection process resulted in a large panel of highly active shRNAs spanning the HIV-1 genome, representing excellent candidates for use in multiple shRNA gene therapies. Our core selection method ensuring maximal conservation in the processed product(s) is also widely applicable to other shRNA applications.
Adrenergic effects on the biology of the adult mammalian cardiocyte. (1992)

These results constitute the initial demonstration at the cellular level that adrenergic stimulation leads to cyclic AMP-mediated calcium overload of the cell, with a resultant decrease in synthetic activity and/or viability.
Photoreactivity of Platinum(II) in Cisplatin-Modified DNA Affords Specific Cross-Links to HMG Domain Proteins (1996)

Cisplatin-modified DNA forms specific complexes with proteins that contain the DNA binding motif known as the high-mobility group (HMG) domain. As a tool for investigating the role of these proteins in mediating the cytotoxic effects of cisplatin, a set of cisplatin analogs was prepared in which one of the ammine ligands was replaced with a photoreactive tethered aryl azide ligand. The ability of DNA modified by these platinum complexes to photo-cross-link to HMG1 was investigated. During this study, it was discovered that DNA modified with cisplatin itself can undergo photoinduced cross-linking to HMG1 when irradiated with 300 nm light. The covalent complexes resulting from this latter cross-linking reaction are completely reversed by the addition of sodium cyanide and can be degraded by proteinase K. These results confirm the presence of a protein-DNA cross-link and demonstrate that the platinum atom itself forms the point of attachment. By contrast, DNA modified with transdiamminedichloroplatinum(II), [Pt(dien)Cl]Cl, or [Pt(NH3)3Cl]Cl does not cross-link to HMG1 upon irradiation. The photochemistry was exploited to cross-link a 15-base pair oligonucleotide containing a single, site-specific cis-[Pt(NH3)2{d(GpG)-N7(1),-N7(2)}] intrastrand adduct to domain B of HMG1. Following proteolytic digestion of the resulting covalent complex, the site of attachment to the protein was determined by Edman degradation of the resulting peptide-DNA complex to be a single residue on HMG domain B, Lys-6. The data further suggest that this amino acid binds to platinum at a site made available by photolabilization of a purine ligand. These results afford the first structural information about the interaction of HMG domain proteins with cisplatin-modified DNA.
Methods for Quality-Of-Life Studies (1994)

Methodologies involving the use of quality-of-life patient outcomes in observational and interventional studies of health are drawn from a large and diverse field of research methods. The multidimensional way in which quality of life is conceptualized will affect the way it is measured and the complexity of the measurement. At the earliest stages of research, one must rely on methods common to the fields of tests and measurement, survey research, psychometrics and sociometrics to measure constructs that are not directly observable. Indices measuring performance can either focus on the scale's ability to perform in noninterventional, cross-sectional studies or interventional, longitudinal studies. Indices of stability, internal consistency, responsiveness with respect to true changes in quality of life, and sensitivity to treatment effects can be used to assess the scale's adequacy as a dependent variable of interest. Respondent variability can occur due to factors such as different reporters (patient, spouse, physician), the manner and form of administration (long form vs short form; self-administration vs interview) and the assessment environment (clinic, home). Finally, since quality-of-life research often involves inferential statistics and hypothesis testing, the statistical and epidemiologic principles of good study design should be followed. In addition, one should account for the reliability, responsiveness, and the sensitivity of the scale when designing the scientific hypotheses, and should specifically address the meaning of quality-of-life effect sizes by interventional-based validation. Design considerations must address the statistical issues of power, the determination of effect sizes through validation by external criteria, longitudinal data, effects of withdrawal and early termination, ceiling and floor effects, and heterogeneity of responsiveness and sensitivity among individuals. The problem of estimating quality-of-life summary parameters for use in pharmacoeconomic models is receiving increasing attention in this era of health-care reform and fiscal restraint. While medical decision theory has used cost-effectiveness models and quality-adjusted life years since the early 1970s, estimation of population parameters to differentiate among different medical interventions is relatively new. The assessment of the patient outcomes associated with medical interventions in terms of the risks, benefits and costs will clearly be a major focus of health-care reform. Development of new methodologies in quality-of-life research should build upon the strong foundation already established in the areas of clinical research, epidemiology, biostatistics, economics and behavioral science.(ABSTRACT TRUNCATED AT 400 WORDS)
Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency (1996)

Intron lariat formation between the 5' end of an intron and a branchpoint adenosine is a fundamental aspect of the first step in animal and yeast nuclear pre-mRNA splicing. Despite similarities in intron sequence requirements and the components of splicing, differences exist between the splicing of plant and vertebrate introns. The identification of AU-rich sequences as major functional elements in plant introns and the demonstration that a branchpoint consensus sequence was not required for splicing have led to the suggestion that the transition from AU-rich intron to GC-rich exon is a major potential signal by which plant pre-mRNA splice sites are recognized. The role of putative branchpoint sequences as an internal signal in plant intron recognition/definition has been re-examined. Single nucleotide mutations in putative branchpoint adenosines contained within CUNAN sequences in four different plant introns all significantly reduced splicing efficiency. These results provide the most direct evidence to date for preferred branchpoint sequences being required for the efficient splicing of at least some plant introns in addition to the important role played by AU sequences in dicot intron recognition. The observed patterns of 3' splice site selection in the introns studied are consistent with the scanning model described for animal intron 3' splice site selection. It is suggested that, despite the clear importance of AU sequences for plant intron splicing, the fundamental processes of splice site selection and splicing in plants are similar to those in animals.
Novel Glycopolymer Eradicates Antibiotic- and CCCP-Induced Persister Cells in Pseudomonas aeruginosa (2018)

Antibiotic treatments often fail to completely eradicate a bacterial infection, leaving behind an antibiotic-tolerant subpopulation of intact bacterial cells called persisters. Persisters are considered a major cause for treatment failure and are thought to greatly contribute to the recalcitrance of chronic infections. <i>Pseudomonas aeruginosa</i> infections are commonly associated with elevated levels of drug-tolerant persister cells, posing a serious threat to human health. This study represents the first time a novel large molecule polycationic glycopolymer, poly (acetyl, arginyl) glucosamine (PAAG), has been evaluated against antibiotic and carbonyl cyanide <i>m</i>-chlorophenylhydrazone induced <i>P. aeruginosa</i> persisters. PAAG eliminated eliminated persisters at concentrations that show no significant cytotoxicity on human lung epithelial cells. PAAG demonstrated rapid bactericidal activity against both forms of induced <i>P. aeruginosa</i> persister cells resulting in complete eradication of the <i>in vitro</i> persister cells within 24 h of treatment. PAAG demonstrated greater efficacy against persisters <i>in vitro</i> than antibiotics currently being used to treat persistent chronic infections such as tobramycin, colistin, azithromycin, aztreonam, and clarithromycin. PAAG caused rapid permeabilization of the cell membrane and caused significant membrane depolarization in persister cells. PAAG efficacy against these bacterial subpopulations suggests it may have substantial therapeutic potential for eliminating recurrent <i>P. aeruginosa</i> infections.
Primary Structure and Organization of the Gene for a Procaryotic, Cell Envelope-located Serine Proteinase (1989)

We have determined the complete nucleotide sequence of the gene for the cell envelope-located proteinase of Lactococcus lactis SK11. The gene contains a very AT-rich promoter region followed by the coding sequence of a protein of 1962 amino acids. Comparison of the NH2-terminal amino acid sequence of the mature proteinase and the expected primary translation product of the proteinase gene indicates that the enzyme is probably synthesized as a pre-pro-protein. This is confirmed by expression studies of the proteinase gene in Escherichia coli. The amino acid sequence of the proteinase shows significant homology to a number of serine proteinases of the subtilisin family. Compared with the related proteinase of L. lactis Wg2, the proteinase of L. lactis SK11 contains a 60-amino acids duplication and a total of 44-amino acid substitutions, some of which may account for the different cleavage specificity of both enzymes. Furthermore, a region was identified in the Lactococcus proteinase, which shows homology to the membrane-anchoring domains of a number of proteins from other Gram-positive bacteria.
Stromal-epithelial interactions in aging and cancer: Senescent fibroblasts alter epithelial cell differentiation - eScholarship (2004)

Parrinello et al. Stromal-epithelial interactions in aging and cancer: Senescent fibroblasts alter epithelial cell differentiation Simona Parrinello 1 , Jean-Philippe Coppe 1 , Ana Krtolica 1,† and Judith Campisi 1,2,† Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA Buck Institute for Age Research, Novato CA 94945 USA These senior authors contributed equally to this work Key words: Epithelial to mesenchyme transition (EMT), beta-casein, mammary epithelial cells, matrix metalloproteinase-3 (MMP-3), morphogenesis, tissue structure and function. Running title: Senescent fibroblasts alter differentiation Correspondence: Judith Campisi 510 486-4416 (telephone) 510 486-4545 (fax) jcampisi@lbl.gov
Epidemiology and Natural History of Human Papillomavirus Infections in the Female Genital Tract (2006)

Human papillomavirus (HPV) is the most common newly diagnosed sexually transmitted infection in the United States. Although the majority of sexually active adults will be infected with HPV at least once in their lives, it is sexually active women less than 25 years of age who consistently have the highest rates of infection. Besides youth and gender, common risk factors for HPV infection and clinical sequelae of infection include high number of sexual partners and coinfection with Chlamydia trachomatis or herpes simplex virus. Most HPV infections are cleared by the immune system and do not result in clinical complications. Clinical sequelae in cases of low-risk HPV infection consist of genital warts, and clinical manifestations of high-risk HPV infection include abnormal Pap test results, low-grade squamous intraepithelial lesions (LSIL), high-grade squamous intraepithelial lesions (HSIL), and cervical cancer. LSIL, HSIL, and cervical cancer carry significant morbidity and/or mortality; genital warts and abnormal Pap test results are often significant sources of psychosocial distress. Currently, there are neither effective means of preventing HPV transmission nor cures for clinical manifestations: infection can only be prevented via complete sexual abstinence, while treatment for clinical sequelae such as genital warts and cytologic abnormalities consists of removing the problematic cells and watching for recurrence; this method consumes significant health care resources and is costly. New prophylactic HPV vaccines promise to dramatically reduce the incidence of HPV infection, genital warts, and cytologic abnormalities.
Monocytes and Macrophages Form Branched Cell Columns in Matrigel: Implications for a Role in Neovascularization (2004)

Linear arrays of cells, or cell columns, have been observed in the extracellular matrix prior to neovascularization, but their nature and significance remains elusive. Based on the emerging evidence implicating a role for monocytes and macrophages (MC/MPH) in vasculogenesis, we hypothesized that MC/MPH also can form linear or branched columns, facilitating the co-migration and the spatial arrangement of other cell types. To test this hypothesis, we studied the distribution of MC/MPH effected by chemotactic migration in novel in vitro and in vivo models of development. We induced transversal and lateral migration of THP-1 monocytoid cells in Matrigel in vitro. The effect of this process on co-localization of other micro-objects was assessed using erythrocytes and micron-sized plastic beads. In vivo, we analyzed MC/MPH infiltration in subcutaneously implanted Matrigel plugs containing angiogenic factors and across a microporous filter comprising the wall of a chamber filled with Matrigel, also placed subcutaneously in mice. In vitro, we found that migrating THP-1 cells induced the lasting degradation of Matrigel and produced cell columns, a process amplified by monocyte chemoattractant protein-1 (MCP-1). We also report the co-localization of erythrocytes with THP-1 cells in cell columns. Endothelium-free tunnels containing MC/MPH, neutrophils, or erythrocytes were also observed in the Matrigel-filled chambers. In free subcutaneous Matrigel plugs, we found MC/MPH-based columns harboring isolated Tie-2+ cells (a marker of endothelial progenitor phenotype), as well as fibroblasts, dendritic cells, and adypocytes. Many of these cell columns displayed conspicuous branching. Our data demonstrate formation of branched MC/MPH cell columns in vitro and in vivo, a previously unrecognized pattern of penetration of extracellular matrices by inflammatory cells. Thus, monocytes and macrophages influence the distribution of neovessels as well as their branching points. These cells are the "architects of development," assisting organogenesis, tumorigenesis, and wound healing by patterning the tissular space.
Traumatic brain injury (1994)

This review covers reports on the effects of traumatic brain injury, including emotional change and the post-concussive syndrome. Special emphasis is placed on psychosocial aspects such as the response of the family to the injury and their relevance to patient management. Treatment-outcome studies are reported with consideration of specific programme components.
Kinetics of Peroxynitrite Reaction with Amino Acids and Human Serum Albumin (1999)

An initial rate approach was used to study the reaction of peroxynitrite with human serum albumin (HSA) through stopped-flow spectrophotometry. At pH 7.4 and 37 degreesC, the second order rate constant for peroxynitrite reaction with HSA was 9.7 +/- 1.1 x 10(3) M-1 s-1. The rate constants for sulfhydryl-blocked HSA and for the single sulfhydryl were 5.9 +/- 0.3 and 3.8 +/- 0.8 x 10(3) M-1 s-1, respectively. The corresponding values for bovine serum albumin were also determined. The reactivity of sulfhydryl-blocked HSA increased at acidic pH, whereas plots of the rate constant with the sulfhydryl versus pH were bell-shaped. The kinetics of peroxynitrite reaction with all free L-amino acids were determined under pseudo-first order conditions. The most reactive amino acids were cysteine, methionine, and tryptophan. Histidine, leucine, and phenylalanine (and by extension tyrosine) did not affect peroxynitrite decay rate, whereas for the remaining amino acids plots of kobs versus concentration were hyperbolic. The sum of the contributions of the constituent amino acids of the protein to HSA reactivity was comparable to the experimentally determined rate constant, where cysteine and methionine (seven residues in 585) accounted for an estimated 65% of the reactivity. Nitration of aromatic amino acids occurred in HSA following peroxynitrite reaction, with nitration of sulfhydryl-blocked HSA 2-fold higher than native HSA. Carbon dioxide accelerated peroxynitrite decomposition, enhanced aromatic amino acid nitration, and partially inhibited sulfhydryl oxidation of HSA. Nitration in the presence of carbon dioxide increased when the sulfhydryl was blocked. Thus, cysteine 34 was a preferential target of peroxynitrite both in the presence and in the absence of carbon dioxide.
A compact optical flow cell for use in aqueous halide determination (1999)

A compact optical flow cell for use in aqueous halide determination has been developed. The performance of the cell and optical set-up has been tested by studying the halide quenching of fluorescence from thin polymeric films containing a halide-sensitive fluorophore. Aqueous halide is injected into the flow cell and the quenched fluorescence emission observed orthogonal to the plane of excitation after it has undergone total internal reflection within the glass support - an efficient method for observing weak fluorescence intensities. The experimental set-up is both a low-cost and an accurate method for use in the determination of aqueous halide ions. The method can very easily be adopted to determine other aqueous anions which quench the fluorescence of dyes incorporated into thin hydrophilic polymer films. The suitability of this method for the continuous measurement of halide `on-line' rather than a single `static' measurement is discussed.
Thermoviscous Attenuation of Plane, Periodic, Finite-Amplitude Sound Waves (1964)

The propagation of a plane progressive wave of finite amplitude in a thermoviscous fluid is considered. The wave is taken to be purely sinusoidal in shape at its source. The approach is through Burgers equation, which is a very good approximation of the exact equations of fluid motion when effects of nonlinearity and dissipation are relatively small but definitely not negligible. A complicated but exact solution of Burgers' equation is analyzed. The nature of the solution is found to depend strongly on a parameter Γ, which represents the importance of nonlinearity relative to dissipation. Nonlinear effects prove to be significant when Γ&amp;gt;1, a finding in agreement with the criterion proposed by Gol'dberg (Akust. Zh. 2, 325 (1956) [English transl.: Soviet Phys.—Acoust. 2, 346(1956)]) concerning the appearance of shock waves. When Γ&amp;gt;&amp;gt;1, simple asymptotic representations of the exact solution in terms of Fourier series may be obtained. One of these corresponds to Fay's solution [J. Acoust. Soc. Am. 3, 222 (1931)]. An equivalent “time-domain” representation shows clearly the sawtooth behavior of the wave. The sawtooth region is found to extend approximately to the point x=O.6/α, where α is the dimensional small-signal attenuation coefficient. Curves of the extra attenuation suffered by the fundamental as a result of nonlinear effects are given for values of Γ in the range 1–100 000. If Γ is large, the extra attenuation in decibels approaches the asymptotic value −12+20 log10Γ as the distance from the source becomes large. A value 1 dB below the asymptote is attained at a distance x=1/α. Application to waves in argon and air is discussed. It is found that nonlinear effects may be employed to increase the efficiency of long-range sound transmission. A possible application to low-frequency sound in the ocean is also discussed.