gebhart/patrepeval huggingface dataset:
Ferric reductase of Saccharomyces cerevisiae: molecular characterization, role in iron uptake, and transcriptional control by iron. (1992)

The principal iron uptake system of Saccharomyces cerevisiae utilizes a reductase activity that acts on ferric iron chelates external to the cell. The FRE1 gene product is required for this activity. The deduced amino acid sequence of the FRE1 protein exhibits hydrophobic regions compatible with transmembrane domains and has significant similarity to the sequence of the plasma membrane cytochrome b558 (the X-CGD protein), a critical component of a human phagocyte oxidoreductase, suggesting that FRE1 is a structural component of the yeast ferric reductase. FRE1 mRNA levels are repressed by iron. Fusion of 977 base pairs of FRE1 DNA upstream from the translation start site of an Escherichia coli lacZ reporter gene confers iron-dependent regulation on expression of beta-galactosidase in yeast. An 85-base-pair segment of FRE1 5' noncoding sequence contains a RAP1 binding site and a repeated sequence, TTTTTGCTCAYC; this segment is sufficient to confer iron-repressible transcriptional activity on heterologous downstream promoter elements.
Specific PCR Primers for the Identification of Endomycorrhizal Fungi (2003)

The sensitivity of the polymerase chain reaction (PCR) (,), coupled to the specificity afforded by taxon-specific primers allows the analysis of a variety of samples, like minute amounts of cultured organisms (, ), or even endosymbionts like the endomycorrhizal fungi present in the roots of field collected plants (, , , ).
Effects of One Night without Nasal CPAP Treatment on Sleep and Sleepiness in Patients with Obstructive Sleep Apnea (1993)

Nasal continuous positive airway pressure (CPAP) has become the nonsurgical treatment of choice for obstructive sleep apnea syndrome (OSAS). Recent evidence suggests that intermittent use of CPAP by patients is more common than nightly compliance. To determine the consequences of intermittent CPAP use, in terms of a return of sleep-disordered breathing and daytime hypersomnolence, 15 OSAS subjects were evaluated at three times: (1) before CPAP treatment (pretreatment), (2) after 30 to 237 days posttreatment during a night of CPAP use (on CPAP), and (3) during a night without CPAP (off CPAP). Evaluations of sleep-disordered breathing and three domains of hypersomnolence, physiologic sleep tendency, subjective sleepiness, and performance, were accomplished with the respiratory disturbance index (RDI), multiple sleep latency test (MSLT), Stanford sleepiness scale (SSS), and psychomotor vigilance task (PVT), respectively. CPAP use was encouraged and monitored from pretreatment to post-treatment by daily diaries for most subjects and an electronic device for a subset of subjects. As expected, CPAP eliminated apneas and hypopneas, and following the on CPAP night, there were statistically significant improvements in objective measures of sleepiness (MSLT and PVT). Subjective measures of sleepiness and fatigue also showed improvement. Sleeping without CPAP for one night reversed virtually all of the sleep and daytime alertness gains derived from sleeping with CPAP. This occurred despite a statistically significant reduction in the RDI on the night off CPAP (M = 36.8, SD = 28.0 events/h) relative to the pretreatment night (M = 56.6, SD = 24.8 events/h), which may be due to a lessening of the edema of the upper airway following CPAP use.(ABSTRACT TRUNCATED AT 250 WORDS)
Multi-mode phonon controlled field emission from carbon nanotubes: Modeling and experiments (2007)

The main idea proposed in this paper is that in a vertically aligned array of short carbon nanotubes (CNTs) grown on a metal substrate, we consider a frequency dependent electric field, so that the mode-specific propagation of phonons, in correspondence with the strained band structure and the dispersion curves, take place. We perform theoretical calculations to validate this idea with a view of optimizing the field emission behavior of the CNT array. This is the first approach of its kind, and is in contrast to the the conventional approach where a DC bias voltage is applied in order to observe field emission. A first set of experimental results presented in this paper gives a clear indication that phonon-assisted control of field emission current in CNT based thin film diode is possible.
Localization of the CD44 Glycoprotein to Fibrous Astrocytes in Normal White Matter and to Reactive Astrocytes in Active Lesions in Multiple Sclerosis (1991)

The CD44 antigen is a proteoglycan recently implicated in several adhesion events including that of lymphocytes to endothelium. The CD44 antigen, reactive with monoclonal antibody (MAb) 44D10, has been shown previously to be expressed in normal human white matter homogenates and to be found at higher concentrations in brain homogenates of victims of multiple sclerosis (MS). The cellular localization of CD44 in human brain of normal individuals and in those afflicted with MS has now been determined. Monoclonal antibody 44D10 reacted with astrocyte-like cells in 40 microns thick paraformaldehyde-fixed sections but not in thin (6 microns) fixed sections. A double labeling experiment performed on a frozen brain section with MAb 44D10 and rabbit anti-glial fibrillary acidic protein (GFAP), a cytoplasmic marker of astrocytes, confirmed the co-localization of these two antigens. The reactivity with brain tissue sections of a rabbit antiserum produced against lymphocyte-CD44 could be absorbed by a preparation of the CD44 glycoprotein, purified 2,100-fold from a white matter homogenate. The antiserum was shown by Western blot analysis to be specific for p80 glycoprotein in brain extracts derived from a normal and MS patients. This antibody reacted with fibrous astrocytes predominantly in white matter; staining was also noted in subependymal and subpial regions. Inhibition studies using a cellular radioimmunoassay indicated that the highest concentrations of CD44 in three MS victims were found in plaques, followed by periplaques and non-involved areas of white matter which were higher than normal white matter. Reactive astrocytes, identified in active lesions, expressed high levels of CD44 on their surfaces. Thus, CD44 is associated with astrocytes in human brain and the increased expression observed in MS brain may reflect activation and/or proliferation of astrocytes implicated in the pathogenesis of this disease.
Physics and Applications of the Josephson Effect (1982)

Weak Superconductivity - Phenomenological Aspects. Microscopic Theory. Magnitude and Temperature Dependence of the Critical Current. ''Small'' Junctions in a Magnetic Field. Large Junctions - Static Self Field Effects. Current Voltage Characteristics. Other Superconducting Weak Link Structures. Device Fabrication Technology. Resonant Modes in Tunneling Structures. Fluxon Dynamics. High Frequency Properties and Applications of the Josephson Effect. Josephson Junctions in Super-conducting Loops. Squid's Theory and Applications. Computer Elements. Appendix. Systems of Units. Comments of Systems of Units. Conversion Tables. References.
Online Learning of Relaxed CCG Grammars for Parsing to Logical Form (2007)

We consider the problem of learning to parse sentences to lambda-calculus representations of their underlying semantics and present an algorithm that learns a weighted combinatory categorial grammar (CCG). A key idea is to introduce non-standard CCG combinators that relax certain parts of the grammar—for example allowing flexible word order, or insertion of lexical items— with learned costs. We also present a new, online algorithm for inducing a weighted CCG. Results for the approach on ATIS data show 86 % F-measure in recovering fully correct semantic analyses and 95.9% F-measure by a partial-match criterion, a more than 5 % improvement over the 90.3% partial-match figure reported by He and Young (2006).
Electronic portal imaging devices: a review and historical perspective of contemporary technologies and research. (2002)

A review of electronic portal imaging devices (EPIDs) used in external beam, megavoltage radiation therapy is presented. The review consists of a brief introduction to the definition, role and clinical significance of portal imaging, along with a discussion of radiotherapy film systems and the motivations for EPIDs. This is followed by a summary of the challenges and constraints inherent to portal imaging along with a concise, historical review of the technologies that have been explored and developed. The paper then examines, in greater depth, the two first-generation technologies that have found widespread clinical use starting from the late 1980s. This is followed by a broad overview of the physics, operation, properties and advantages of active matrix, flat-panel, megavoltage imagers, presently being commercially introduced to clinical environments or expected to be introduced in the future. Finally, a survey of contemporary research efforts focused on improving portal imaging performance by addressing various weaknesses in existing commercial systems is presented.
Sertraline and Relapse Prevention Training Following Treatment by Very‐Low‐Calorie Diet: A Controlled Clinical Trial (1995)

This study examined the combination of sertraline, a selective serotonin reuptake inhibitor, and relapse prevention training in the maintenance of weight loss following treatment by a very-low-calorie diet. A total of 53 women who had lost a mean (+/- SD) of 22.9 +/- 7.1 kg from a pretreatment weight of 103.1 +/- 17.8 kg were randomly assigned to a 54-week weight maintenance program that was combined with either: 1) 200 mg/d of sertraline; or 2) placebo. During the first 6 weeks, sertraline subjects lost significantly more weight and reported significantly greater reductions in hunger and preoccupation with food than did subjects on placebo. After this time, however, women in both conditions regained weight steadily. The 13 sertraline subjects who completed the 54-week study regained 17.7 +/- 10.6 kg of their original 26.3 +/- 7.6 kg loss, equal to a regain of 70.9 +/- 41.7%. The 17 placebo completers regained 11.8 +/- 9.0 kg of their 23.4 +/- 7.8 kg loss, equal to a 46.5 +/- 34.6% regain. End-of-treatment differences between groups in weight change were not statistically significant. Nor were there significant differences between the two conditions at any time in changes in fat-free mass, resting metabolic rate or dysphoria, all of which tended to increase with weight regain. The results are discussed in relation to findings from other long-term studies that combined diet and medication.
A Hardware Implement of Bus Bridge Based on Single CPU and Dual Bus Architecture (2008)

Single CPU dual bus architecture is a new kind of architecture aimed at reducing the security vulnerability of Von Neumann architecture, and it has been proved theoretically reasonable. In this paper, a bus bridge is implemented to bridge CPU and dual bus. The experiment is done and the result has proved that the architecture based on single CPU and dual bus is reasonable and effective.
Cross-Reactive Response to Human Immunodeficiency Virus Type 1 (HIV-l) gp120 and HLA Class I Heavy Chains Induced by Receipt of HIV-1-Derived Envelope Vaccines (1993)

Autoantibodies specific to HLA class I antigens were detected in the sera of persons vaccinated with human immunodeficiency virus type 1-derived recombinant vaccines by using synthetic peptides representing the amino acid sequences recognized by an HLA class I/gp120 cross-reactive monoclonal antibody. Study subjects received recombinant vaccinia gp160 (vacc-env) alone, vacc-env followed by one dose of recombinant gp160 (rgp160, 640 micrograms), or four doses of rgp160 alone (640 or 80 micrograms). All sera from vacc-env/rgp160-vaccinated subjects contained HLA/gp120 cross-reactive antibodies, as did all sera from recipients of the rgp160 alone at 640 micrograms/dose. In contrast, none of the sera from subjects who received either the vacc-env alone or the 80 micrograms/dose rgp160 alone contained detectable HLA cross-reactive antibodies, and these same sera showed little or no envelope reactivity on Western blot. The results showed a striking correlation between immunogenicity and the induction of cross-reactive antibodies by the rgp160 vaccine.
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system (2017)

Designing an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We demonstrate the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner.
Synthesis and muscarinic receptor activity of ester derivatives of 2-substituted 2-azabicyclo[2.2.1]heptan-5-ol and -6-ol (1992)

Radioligand binding affinities of four new muscarinic antagonists and six potential muscarinic agonists which possess the 2-alkyl-2-azabicyclo[2.2.1]heptane ring system have been determined in rat heart, rat brain, and m1- or m3-transfected CHO cell membrane preparations to examine the selectivity for subtypes of muscarinic receptor. The efficacies of the potential muscarinic agonists were determined by the ratio of binding affinities against [3H]QNB and [3H]Oxo-M. Four muscarinic antagonists which have the 2,2-diphenylpropionate side chain at either the C5 (5-endo or 5-exo) or the C6 (6-endo or 6-exo) positions did not discriminate between the subtypes of muscarinic receptors. The 2,2-diphenylpropionate 5-endo substituted compound was the most potent, showing affinities between 4.23 x 10(-10) and 1.18 x 10(-9) M in rat heart, rat brain, and m1- or m3-transfected CHO cell membrane preparations. The rank order of ester potency was 5-endo greater than 5-exo greater than 6-endo greater than 6-exo. A molecular modeling study based on the pharmacophore developed for azaprophen was used to account for the relative potency of these antagonists. Six potential muscarinic agonists which have acetoxy groups in the C5 or C6 position with an N-methyl or N-benzyl substituent did not discriminate subtypes of muscarinic receptors and had affinities between 6.63 x 10(-6) and 4.76 x 10(-5) M in rat heart, rat brain, and m1- or m3-transfected CHO cell membrane preparations. exo-2-Methyl-5-acetoxy-2-azabicyclo[2.2.1]heptane was the most efficacious partial agonist.
On vagal bronchoconstriction in asthmatic patients by nasal irritation. (1983)

In 27 asthmatic patients a single cold stimulus into the nose resulted in a sudden increase of airway resistance, measured continuously by a forced-oscillation technique. The effect could be blocked by previous intrabronchial application of an anticholinergic drug. In laryngectomised patients, who no longer have a connection between the upper and the lower airways, a cold stimulus into the nose also caused bronchoconstriction. So the cold effect must be based on a reflex mechanism.
The science of adjuvants (2007)

Adjuvants are substances that boost the immunogenicity of vaccines. However, most successful vaccines have been derived empirically and are capable of inducing robust T- and B-cell immunity without any adjuvant additives. Emerging evidence suggests that such live vaccines induce innate immune activation via a range of stimuli, including ligands specific for Toll-like receptors, which, in effect, serve as their own adjuvants. In contrast to these live vaccines, subunit vaccines need to be supplemented with adjuvants to boost their immunogenicity. However, there is a paucity of licensed adjuvants for clinical use and, thus, there is a critical need to develop safe and effective adjuvants. In this context, recent advances in innate immunity are beginning to offer new insights into how empiric vaccines and adjuvants mediate their efficacy. In this article, we review the latest progress and emerging concepts in adjuvant development, which includes novel findings in innate immune biology and their impact on vaccinology.
Conserved Structural Features in the Interaction Between Retroviral Surface and Transmembrane Glycoproteins? (1992)

Among the retroviruses, the surface (SU) and transmembrane (TM) glycoproteins of lentiviruses are linked exclusively by noncovalent bonds. For some C-type retroviruses, however, a small proportion of the SU proteins has been shown to be linked to their TM proteins by a disulfide bond, with the remainder being noncovalently associated. A region near the carboxyl terminus of the HIV-1 SU glycoprotein has been implicated in contacting the TM glycoprotein. Computer modelling indicates that this region of divergent lentivirus and oncovirus SU glycoproteins forms a structurally conserved "pocket" which could accommodate a "knob"-like protrusion formed by an immunodominant region in the TM protein containing the CxxxxxC (lentiviruses) or CxxxxxxCC (C- and D-type viruses) motif. An anti-idiotypic monoclonal antibody, raised against a monoclonal antibody reacting with a sequence in the "pocket" of HIV-1 gp120, was found to bind to synthetic peptides close to the CxxxxxC motif. It is suggested that part of the SU-TM linkage mechanism for the lentiviruses and oncoviruses is a 'knob and socket' structure and that the interaction between SU and TM proteins is similar in one region for lentiviruses and C-type as well as D-type viruses. The conserved knob and socket linkage may be relevant to a mechanism for viral-cell membrane fusion that is broadly common to all of these retroviruses.
Receptor-mediated antigen delivery into macrophages. Complexing antigen to alpha 2-macroglobulin enhances presentation to T cells (1993)

Macrophages secrete alpha 2-macroglobulin (alpha 2M), a protein that may facilitate early Ag handling. alpha 2M is able to entrap and form covalent linkages with diverse proteins during a transient proteinase-activated state. The resulting complexes are rapidly endocytosed after binding to high affinity receptors. Such a system could be capable of efficiently delivering a multitude of proteins to macrophages. We have used T hybridoma clones that respond only to hen egg lysozyme, in a MHC-restricted manner, to probe the effect of complex formation on Ag uptake and processing by murine macrophages. Radiolabeled lysozyme was internalized more rapidly and to a greater extent when bound to alpha 2M than when unbound. Macrophages pulsed with lysozyme-alpha 2M-elastase complexes required 200 to 250 times less Ag than those pulsed with free lysozyme to achieve effective presentation to T cells. Adding equimolar amounts of alpha 2M-elastase complexes, or of alpha 2M-methylamine, to free lysozyme had no effect on basal lysozyme presentation. Receptor-recognized forms of alpha 2M, but not lysozyme or BSA, competed effectively for both uptake and presentation of lysozyme-alpha 2M-elastase complexes. These results indicate that proteinase-activated alpha 2M can enhance Ag processing by carrying Ag into macrophages through a receptor-mediated process.
Shared receptors in axon guidance: SAX-3/Robo signals via UNC-34/Enabled and a Netrin-independent UNC-40/DCC function (2002)

The C. elegans SAX-3/Robo receptor acts in anterior-posterior, dorsal-ventral and midline guidance decisions. Here we show that SAX-3 signaling involves the C. elegans Enabled protein UNC-34 and an unexpected Netrin-independent function of the Netrin receptor UNC-40/DCC. Genetic interactions with gain- and loss-of-function mutations suggest that unc-34 and unc-40 act together with sax-3 in several guidance decisions, but the C. elegans Netrin gene unc-6 does not act in the same genetic pathways. Within the migrating axon, sax-3, unc-34 and unc-40 all act cell-autonomously. Our results support a role for UNC-34/Enabled proteins in SAX-3-mediated repulsion, and show that UNC-40/DCC can potentiate SAX-3/Robo signaling via a mechanism that may involve direct binding of the two guidance receptors. A combinatorial logic dictates alternative functions for UNC-40/DCC, which can act in attraction to UNC-6/Netrin, repulsion from Netrin (with UNC-5), or repulsion from Slit (with SAX-3).
Animal Models ofStreptococcus pneumoniaeDisease (2008)

Streptococcus pneumoniae is a colonizer of human nasopharynx, but it is also an important pathogen responsible for high morbidity, high mortality, numerous disabilities, and high health costs throughout the world. Major diseases caused by S. pneumoniae are otitis media, pneumonia, sepsis, and meningitis. Despite the availability of antibiotics and vaccines, pneumococcal infections still have high mortality rates, especially in risk groups. For this reason, there is an exceptionally extensive research effort worldwide to better understand the diseases caused by the pneumococcus, with the aim of developing improved therapeutics and vaccines. Animal experimentation is an essential tool to study the pathogenesis of infectious diseases and test novel drugs and vaccines. This article reviews both historical and innovative laboratory pneumococcal animal models that have vastly added to knowledge of (i) mechanisms of infection, pathogenesis, and immunity; (ii) efficacies of antimicrobials; and (iii) screening of vaccine candidates. A comprehensive description of the techniques applied to induce disease is provided, the advantages and limitations of mouse, rat, and rabbit models used to mimic pneumonia, sepsis, and meningitis are discussed, and a section on otitis media models is also included. The choice of appropriate animal models for in vivo studies is a key element for improved understanding of pneumococcal disease.
Human Double-Negative T Cells in Systemic Lupus Erythematosus Provide Help for IgG and Are Restricted by CD1c (2000)

To understand the mechanism of T cell help for IgG production in systemic lupus erythematosus (SLE) we investigated the response of CD4- and CD8-negative (double-negative (DN)) T cells because 1) DN T cells are present at unusually high frequency in patients with SLE and can induce pathogenic autoantibodies; 2) the DN T cell repertoire includes cells restricted by CD1 Ag-presenting molecules; and 3) CD1c is expressed on a population of circulating B cells. We derived DN T cell lines from SLE patients and healthy individuals. In the presence of CD1(+) APCs, DN T cell lines from SLE patients produced both IL-4 and IFN-gamma, whereas DN T cells from healthy donors produced IFN-gamma, but no IL-4. In general, cells from patients with highly active disease produced high levels of IFN-gamma; cells from those with little activity produced high IL-4. Coculture of CD1c-directly reactive T cells from healthy donors with CD1c(+) B cells elicited IgM Abs, but little or no IgG. In contrast, CD1c-directly reactive T cells from SLE patients induced isotype switching, with a striking increase in IgG production. Neutralizing Abs to CD1c inhibited the ability of DN T cells to induce IgG production from CD1c(+) B cells, further indicating that CD1c mediated the T and B cell interaction. IgG production was also inhibited by neutralizing Abs to IL-4, correlating with the cytokine pattern of DN T cells derived from these patients. The data suggest that CD1c-restricted T cells from SLE patients can provide help to CD1c(+) B cells for IgG production and could therefore promote pathogenic autoantibody responses in SLE.