gebhart/patrepeval huggingface dataset:
Site of pressure measurement during spontaneous breathing with continuous positive airway pressure (1992)

The results indicate that pressure should be measured as close to the patient's airway as possible, i.e., at the tracheal end of the endotracheal tube, rather than using the traditional approach of measuring pressure and assessing work at the inspiratory or expiratory limbs, or "Y" piece of the breathing tubing.
The eleven-year switch of peptide aptamers (2008)

Peptide aptamers are combinatorial recognition proteins that were introduced more than ten years ago. They have since found many applications in fundamental and therapeutic research, including their recent use in microarrays to detect individual proteins from complex mixtures.
An Automated Observing System for Passive Evaluation of Cloud Cover and Visibility (1992)

The Automated Observing System is a passive system for determination of cloud cover and sector visibility. This system was developed from related systems, the Whole Sky Imager for cloud field assessment, and the Horizon Scanning Imager for determination of the sector visibility. During the past funding interval, much of the effort on this system was directed toward development of night visibility capability. This report discusses the theoretical development of the equations and analytic approaches to night visibility. A variety of hardware and software adaptations are discussed, which allow the sensor to utilize multiple integration periods for increased system sensitivity. Sample results are included. Secondary developments discussed in this report include an in-depth sensitivity analysis of the daytime visibility system, as well as achievement of more accurate cloud algorithms and night cloud capability funded separately. This is followed by recommendations for improvements to tile current system, and for development of tactical systems based on the existing capability.... Visibility, Contrast transmittance, Atmosphere, Sector visibility, Weather sensors, Aviation weather observations, Weather, Atmospheric visibility, Cloud, Cloud cover, Cloud free line of sight.
Comparative genome mapping of Pseudomonas aeruginosa PAO with P. aeruginosa C, which belongs to a major clone in cystic fibrosis patients and aquatic habitats (1996)

A physical and genetic map was constructed for Pseudomonas aeruginosa C. Mainly, two-dimensional methods were used to place 47 SpeI, 8 PacI, 5 SwaI, and 4 I-CeuI sites onto the 6.5-Mb circular chromosome. A total of 21 genes, including the rrn operons and the origin of replication, were located on the physical map. Comparison of the physical and genetic map of strain C with that of the almost 600-kb-smaller genome of P. aeruginosa reference strain PAO revealed conservation of gene order between the two strains. A large-scale mosaic structure which was due to insertions of blocks of new genetic elements which had sizes of 23 to 155 kb and contained new SpeI sites was detected in the strain C chromosome. Most of these insertions were concentrated in three locations: two are congruent with the ends of the region rich in biosynthetic genes, and the third is located in the proposed region of the replication terminus. In addition, three insertions were scattered in the region rich in biosynthetic genes. The arrangement of the rrn operons around the origin of replication was conserved in C, PAO, and nine other examined independent strains.
Factor I-Dependent Inactivation of Human Complement C4b of the Classical Pathway by C3b/C4b Receptor (CR1, CD35) and Membrane Cofactor Protein (MCP, CD46)1 (1992)

Proteolytic inactivation of C4b is a crucial step for regulation of the classical complement pathway. A plasma protease factor I and membrane cofactors, C3b/C4b receptor (CR1) and membrane cofactor protein (MCP), participate in the regulation of cell-bound C4b although the physiological potency of these cofactors remains unknown. We have examined the optimal conditions of the factor I-mediated C4b regulatory system using purified cofactors. CR1 being a cofactor at a cofactor/C4b ratio less than 0.1 (w/w), fluid phase C4b, and methylamine-treated C4 (C4ma) were degraded by factor I into C4bi: minimal Cd4 was generated in the fluid phase. Liposome-bound C4b (LAC4b), on the other hand, was degraded into C4c and C4d. CR1 showed two optimal pHs (6.0 and 7.5) for fluid phase C4b, but one (6.0) for LAC4b, and in both cases low conductivity conditions enhanced the C4bi generation. CR1 cofactor activity was barely influenced by the NP-40 concentration. On the other hand, MCP degraded C4b and C4ma, as a factor I-cofactor, more efficiently into C4c and C4d. Though MCP cofactor activity, like that of CR1, was enhanced under low conductivity conditions, it has only one optimal pH, 6.0, in both fluid and solid phases. Furthermore, as in the case of C3b cleavage, a sufficient NP-40 concentration to solubilize membrane was needed for MCP to express full cofactor activity for C4b, in contrast to CR1. MCP was less potent for C4b inactivation than for C3b inactivation, while CR1 acted as a slightly more effective cofactor for C4b cleavage than for C3b cleavage.(ABSTRACT TRUNCATED AT 250 WORDS)
Human cytomegalovirus in a SCID-hu mouse: thymic epithelial cells are prominent targets of viral replication. (1993)

Animal models of human cytomegalovirus (CMV) infections have not been available to study pathogenesis or to evaluate antiviral drugs. Severe combined immunodeficient mice implanted with human fetal tissues (SCID-hu) were found to support CMV replication and may provide a model for this species-specific virus. When conjoint implants of human fetal thymus and liver were inoculated with a low-passage-number isolate of CMV, strain Toledo, consistent high-level viral replication was detected 5, 12, 15, 28, and 35 days after inoculation and virus replication continued for up to 9 months. Other human tissue implants, including lung and colon, were also found to support viral growth but with greater variability in levels and for a shorter duration. As expected, the species specificity of human CMV was preserved in this model such that virus was detected in the human conjoint thymus/liver implant but not in surrounding mouse tissues. The majority of virus-infected cells were localized in the thymic medulla rather than cortical region of the implant and immunofluorescence analysis identified epithelial cells rather than any hematopoietic cell population as the principal hosts for viral replication. Finally, treatment of infected animals with ganciclovir reduced viral replication, thereby demonstrating the value of this system for evaluating antiviral therapies. This animal model opens the way for a range of investigations not previously possible with human CMV.
Stimulation of Hepatitis C Virus (HCV) Nonstructural Protein 3 (NS3) Helicase Activity by the NS3 Protease Domain and by HCV RNA-Dependent RNA Polymerase (2005)

Hepatitis C virus (HCV) nonstructural protein 3 (NS3) possesses multiple enzyme activities. The N-terminal one-third of NS3 primarily functions as a serine protease, while the remaining two-thirds of NS3 serve as a helicase and nucleoside triphosphatase. Whether the multiple enzyme activities of NS3 are functionally interdependent and/or modulated by other viral NS proteins remains unclear. We performed biochemical studies to examine the functional interdependence of the NS3 protease and helicase domains and the modulation of NS3 helicase by NS5B, an RNA-dependent RNA polymerase (RdRp). We found that the NS3 protease domain of the full-length NS3 (NS3FL) enhances the NS3 helicase activity. Additionally, HCV RdRp stimulates the NS3FL helicase activity by more than sevenfold. However, the helicase activity of the NS3 helicase domain was unaffected by HCV RdRp. Glutathione S-transferase pull-down as well as fluorescence anisotropy results revealed that the NS3 protease domain is required for specific NS3 and NS5B interaction. These findings suggest that HCV RdRp regulates the functions of NS3 during HCV replication. In contrast, NS3FL does not increase NS5B RdRp activity in vitro, which is contrary to a previously published report that the HCV NS3 enhances NS5B RdRp activity.
Receptors : structure and function : a practical approach (2001)

1. Probing G protein-coupled receptors by fluorescence spectroscopy 2. From receptor to endogenous ligand 3. Point mutations and chimeric receptors in studies of ligand binding domains 4. Determination of the subunit composition of native and cloned NMDA receptors 5. Evaluating receptor stoichiometry by fluorescence resonance energy transfer (FRET) 6. Monitoring intracellular trafficking of receptors 7. Monitoring the turnover kinetics of G protein-coupled receptors 8. Real time receptor function in vitro: microphysiometry and fluorometric imaging plate reader (FLIPR) 9. Regulation of receptors and receptor-coupled ion channels by protein phosphorylation 10. Using confocal imaging to measure changes in intracellular ions 11. Monitoring nuclear receptor function 12. In vivo gene transfer of antisense to receptors
Cancer Cells Ablation with Irreversible Electroporation (2005)

In this study we perform in vitro irreversible electroporation (IRE) experiments with human hepatocarcinoma cells (HepG2) to investigate IRE as a new technique for undesirable tissue ablation. Irreversible electroporation (IRE) is the irreversible permeabilization of the cell membrane through the application of microsecond through millisecond electrical pulses. Until now IRE was studied only as an undesirable condition during the use of reversible electroporation in gene therapy and electrochemotherapy. There was a possibility that the IRE ablation domain is mostly superimposed on the electrical pulses induced Joule heating thermal ablation domain. This study demonstrates that there is a real and substantial domain of electrical parameters for IRE ablation of cancer that is distinct from the thermal domain and which results in complete cancer cell ablation. Experiments show that the application of 1500 V/cm in three sets of ten pulses of 300 microseconds each can produce complete cancer cell ablation. We also find that the use of multiple pulses appears to be more effective for cancer cell ablation than the application of the same energy in one single pulse.
Aberrant MicroRNA-155 Expression Is an Early Event in the Multistep Progression of Pancreatic Adenocarcinoma (2010)

Abnormalities of miRNA expression are observed in the multistep progression of pancreatic cancer, with miR-155 aberrations demonstrable at the stage of PanIN-2, and miR-21 abnormalities at the stage of PanIN-3 lesions. and IAP.
Light Propagation in the Brain Depends on Nerve Fiber Orientation (1994)

In this study, the penetration of red laser light (632.8 nm) in fresh bovine brain was measured parallel, oblique, and perpendicular to the axis of white matter tracts. The measurements were performed in eight samples with an isotropic light source and detector and were obtained by advancing the detector tip toward the light source in the tissue. A statistically significant difference in the effective attenuation coefficient of the light (mueff) was found between the parallel and perpendicular directions, 0.47 +/- 0.06 mm -1 and 0.63 +/- 0.13 mm-1, respectively (P = 0.005). The measurements taken at an angle of 45 degrees in the same sample resulted in an intermediate mueff of 0.58 +/- 0.09 mm-1. These results suggest a preferential guidance of light along the axis of the white matter tracts of the brain.
Identification of two transactlvation domains in the mouse oestrogen receptor (1989)

We have identified two discrete transactivation domains within the mouse oestrogen receptor whose relative activities vary according to the target promoter. One domain lies within the N-terminal region and is active in the absence of oestradiol. The second domain is contained within the C-terminal portion of the protein and depends upon oestrogen binding for its activity. The location and oestrogen dependence of this domain has been confirmed using chimaeric receptors containing the Lex A DNA binding domain. Although transactivation by the C-terminal domain is dependent upon ligand binding the analysis of receptor deletion mutants has demonstrated that these two functions are not entirely coincident.
CD4 antibody treatment in patients with active Crohn's disease: a phase 1 dose finding study. (1997)

This study shows the moderate potential efficacy of treatment of patients with Crohn's disease using a depleting chimeric monoclonal anti-CD4 antibody.
Structure and reactivity of α,β‐unsaturated ethers. XIII. Cationic copolymerization and acid‐catalyzed hydrolysis of 1,2‐dialkoxyethylenes (1971)

Abstract The cationic copolymerizations of geometrical isomers of 1,2‐dimethoxy‐ and 1,2‐diethoxyethylenes with vinyl isobutyl ether as a reference monomer have been carried out in methylene chloride at −70° using boron trifluoride etherate as catalyst. The kinetics of the acid‐catalyzed hydrolysis of these ethers has also been investigated in 80% aqueous dioxane, in order to compare the results with the polymerizabilities. It has been found that the cis ethers are ca. four times as reactive as their trans isomers in both reactions. On the other hand, it has been proved that a β‐alkoxyl substitution reduces the hydrolysis reactivity of vinyl alkyl ethers by a factor of ca. 10 −3 while it even enchances the cationic polymerizability. These contrasting results are interpretable from the nature of the transition states which are different for the two reactions.
Generation of Fractional Harmonics in a Resonant Ultrasonic Wave System (1970)

The problem of a fluid-filled cavity caused to resonate by an ultrasonic wave is described as a parametric phenomenon. Variation of the cavity resonance frequency as a result of the periodic change of length produces the condition for parametric resonance. As a result, fractional harmonics of the driver transducer frequency are generated. The wave equation describing the system is transformed into an ordinary differential equation with periodic coefficients. The solution of this differential equation (Mathieu's equation) predicts frequency doublets which have been observed experimentally. A threshold condition of parametric excitation is derived from the region of unstable solutions of Mathieu's equation. This threshold condition relates the amplitude and frequency of the driver transducer to the cavity length and to the absorption per wavelength of the medium. Reasonable agreement between theory and experiment is obtained.
Bone turnover and mineral metabolism in adult patients with hypophosphatasia treated with asfotase alfa (2021)

Significant changes in bone turnover and mineral metabolism markers after asfotase alfa treatment suggest that treatment-mediated mineralization may enable remodeling and bone turnover on previously unmineralized surfaces. Urine PEA/Cr ratios may be a useful parameter in monitoring treatment during routine care.
Factor substitution in a human HSP70 gene promoter: TATA-dependent and TATA-independent interactions. (1990)

To investigate interactions between transcription factors on mammalian promoters, we constructed a set of 24 variations of the human HSP70 gene promoter in which six upstream sequence motifs are paired in every possible combination with four TATA motifs. These promoters were analyzed for in vivo expression, and selected constructs were examined by in vitro template commitment studies. Activation transcription factor (ATF) and CP1 showed dramatically different interactions with the factor(s) bound to the TATA region. CP1 functioned in vivo regardless of the TATA motif that it was paired with and was not capable of sequestering the core promoter complex in a template commitment assay. ATF activity was dramatically altered by changing the TATA motif, and ATF was able to sequester the core promoter complex. These data suggest that CP1 and ATF function by distinct mechanisms that differ with respect to interaction with the factor(s) at the TATA box. Factor Sp1 also appeared to function by a TATA-independent mechanism. These data imply that the ability of a factor to function is determined not only by the intrinsic properties of the factor but also by promoter context.
Synthesis and Optical Properties of “Branched” Gold Nanocrystals (2004)

We report the synthesis of new “branched” gold nanocrystals in high yield (over 90%) via a wet-chemical route. The branched nanocrystals exhibit a shape-dependent plasmon resonance that is red-shifted by 130−180 nm from the spherical particle wavelength. Discrete dipole approximation (DDA) calculations qualitatively replicate the observed optical extinction spectra of the nanocrystals, indicating that the surface plasmon resonance is mainly determined by in-plane dipole excitation associated with the sharp tips.
Light detection enhanced by surface plasmon resonance in metal film (2010)

Light detection enhanced by surface plasmons was confirmed in Au film/n-type Si Schottky structures. Electrons excited directly with light in Au film overflowed into the n-type silicon, and this excitation was enhanced by surface plasmons induced by Au nanorods attached to the Au film. Excitation was clearly observed in a wavelength range corresponding to the energy of less than the band gap of silicon. The feasibility of Schottky-type photodiodes, in which electrons were never generated by absorption in semiconductors but directly excited in metal, was experimentally demonstrated.
Expression and Functional Analysis of Apaf-1 Isoforms (2000)

Apaf-1 is an important apoptotic signaling molecule that can activate procaspase-9 in a cytochrome c/dATP-dependent fashion. Alternative splicing can create an NH(2)-terminal 11-amino acid insert between the caspase recruitment domain and ATPase domains or an additional COOH-terminal WD-40 repeat. Recently, several Apaf-1 isoforms have been identified in tumor cell lines, but their expression in tissues and ability to activate procaspase-9 remain poorly characterized. We performed analysis of normal tissue mRNAs to examine the relative expression of the Apaf-1 forms and identified Apaf-1XL, containing both the NH(2)-terminal and COOH-terminal inserts, as the major RNA form expressed in all tissues tested. We also identified another expressed isoform, Apaf-1LN, containing the NH(2)-terminal insert, but lacking the additional WD-40 repeat. Functional analysis of all identified Apaf-1 isoforms demonstrated that only those with the additional WD-40 repeat activated procaspase 9 in vitro in response to cytochrome c and dATP, while the NH(2)-terminal insert was not required for this activity. Consistent with this result, in vitro binding assays demonstrated that the additional WD-40 repeat was also required for binding of cytochrome c, subsequent Apaf-1 self-association, binding to procaspase-9, and formation of active Apaf-1 oligomers. These experiments demonstrate the expression of multiple Apaf-1 isoforms and show that only those containing the additional WD-40 repeat bind and activate procaspase-9 in response to cytochrome c and dATP.
Platelet Immunoreceptor Tyrosine-Based Activation Motif (ITAM) Signaling and Vascular Integrity (2014)

Platelets are well-known for their critical role in hemostasis, that is, the prevention of blood loss at sites of mechanical vessel injury. Inappropriate platelet activation and adhesion, however, can lead to thrombotic complications, such as myocardial infarction and stroke. To fulfill its role in hemostasis, the platelet is equipped with various G protein-coupled receptors that mediate the response to soluble agonists such as thrombin, ADP, and thromboxane A2. In addition to G protein-coupled receptors, platelets express 3 glycoproteins that belong to the family of immunoreceptor tyrosine-based activation motif receptors: Fc receptor γ chain, which is noncovalently associated with the glycoprotein VI collagen receptor, C-type lectin 2, the receptor for podoplanin, and Fc receptor γII A, a low-affinity receptor for immune complexes. Although both genetic and chemical approaches have documented a critical role for platelet G protein-coupled receptors in hemostasis, the contribution of immunoreceptor tyrosine-based activation motif receptors to this process is less defined. Studies performed during the past decade, however, have identified new roles for platelet immunoreceptor tyrosine-based activation motif signaling in vascular integrity in utero and at sites of inflammation. The purpose of this review is to summarize recent findings on how platelet immunoreceptor tyrosine-based activation motif signaling controls vascular integrity, both in the presence and absence of mechanical injury.
Hematopoietic-Specific Genes Are Not Induced During In Vitro Differentiation of scl-Null Embryonic Stem Cells (1997)

The helix-loop-helix transcription factor, scl, plays an essential role in hematopoietic development. Embryos in which the gene has been disrupted fail to develop yolk sac erythropoiesis, and scl-null embryonic stem cells do not contribute to hematopoiesis in chimeric mice. To analyze the molecular consequences of scl deficiency, we compared the gene expression profiles of control (wild-type and scl-heterozygous) and scl-null embryonic stem cells differentiated in vitro for up to 12 days. In control and scl-null embryoid bodies the temporal expression pattern of genes associated with the formation of ventral mesoderm, such as Brachyury, bone morphogenetic protein-4, and flk-1, was identical. Similarly, GATA-2, CD34, and c-kit, which are coexpressed in endothelial and hematopoietic lineages, were expressed normally in scl-null embryonic stem cell lines. However, hematopoietic-restricted genes, including the transcription factors GATA-1, EKLF, and PU.1 as well as globin genes and myeloperoxidase, were only expressed in wild-type and scl-heterozygous embryonic stem cells. Indirect immunofluorescence was used to confirm the observations that GATA-1 and globins were only present in control embryoid bodies but that CD34 was found on both control and scl-null embryoid bodies. These data extend the previous gene ablation studies and support a model whereby scl is absolutely required for commitment of a putative hemangioblast to the hematopoietic lineage but that it is dispensable for endothelial differentiation.
Amino Acids, XII: (±)Pipecolic Acid Derivatives ‐ Part 2: An Expedient Synthetic Entry to Substituted Pipecolic Acids (1992)

Abstract The Diels‐Alder product 1 is transformed by Noyori reaction and catalytic hydrogenation to 4 . Hydrolysis with concomitant decarboxylation of 4 furnishes the trans configuration amino acid 5 . Functional group transformation (reduction, lactonization) of 5 provides 7 , ring opening affords the pipecolic acid derivative 9 . On the other hand 1 is hydrolyzed to 10 and 4‐oxo‐pipecolic acid 11 . Reduction of 10 and subsequent hydrolysis with decarboxylation of 12 affords the amino acid 13a /13b in a cis/trans ratio of 1:1. Contrary to this result, reduction of 11 provides 13a/13b in a ratio of ≧ 95/5.
Osteoprotegerin Is a Receptor for the Cytotoxic Ligand TRAIL (1998)

TRAIL is a tumor necrosis factor-related ligand that induces apoptosis upon binding to its death domain-containing receptors, DR4 and DR5. Two additional TRAIL receptors, TRID/DcR1 and DcR2, lack functional death domains and function as decoy receptors for TRAIL. We have identified a fifth TRAIL receptor, namely osteoprotegerin (OPG), a secreted tumor necrosis factor receptor homologue that inhibits osteoclastogenesis and increases bone density in vivo. OPG-Fc binds TRAIL with an affinity of 3.0 nM, which is slightly weaker than the interaction of TRID-Fc or DR5-Fc with TRAIL. OPG inhibits TRAIL-induced apoptosis of Jurkat cells. Conversely, TRAIL blocks the anti-osteoclastogenic activity of OPG. These data suggest potential cross-regulatory mechanisms by OPG and TRAIL.