gebhart/patrepeval huggingface dataset:
Antibody Selection for the Abbott AxSYM Troponin I Assay (1999)

A recent report by Apple et al. (1) presented the performance characteristics of the AxSYM Troponin I (cTnI) assay, which included method comparison data with the Dade-Behring Stratus, Behring Opus, and Beckman Access cTnI assays. In commenting on the absolute differences in measured cTnI between methods (2- to 100-fold), the authors spoke of the need for unified rationale for antibody selection in assays for cTnI. Indeed, this has been a topic of substantial discussion in the recent literature in view of the large differences observed between cTnI methods [e.g., see Ref. (2)]. Most recently, Shi et al. (3) added to earlier results of Katrukha et al. (4) on cTnI degradation. In both reports, degradation of cTnI and differential epitope specificities between commercial methods were cited as significant contributors to between-method variation. Both studies also indicated that the C-terminal portion of the molecule is labile to proteolytic degradation, whereas the N-terminal half of the molecule is relatively stable. Katrukha …
Lipid recycling between the plasma membrane and intracellular compartments: transport and metabolism of fluorescent sphingomyelin analogues in cultured fibroblasts. (1989)

We examined the metabolism and intracellular transport of the D-erythro and L-threo stereoisomers of a fluorescent analogue of sphingomyelin, N-(N-[6-[(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] caproyl])-sphingosylphosphorylcholine (C6-NBD-SM), in Chinese hamster ovary (CHO-K1) fibroblast monolayers. C6-NBD-SM was integrated into the plasma membrane bilayer by transfer of C6-NBD-SM monomers from liposomes to cells at 7 degrees C. The cells were washed, and within 10-15 min of being warmed to 37 degrees C, C6-NBD-SM was internalized from the plasma membrane to a perinuclear location that colocalized with the centriole and was distinct from the lysosomes and the Golgi apparatus. This perinuclear region was also labeled by internalized rhodamine-conjugated transferrin. C6-NBD-SM endocytosis was not inhibited when the microtubules were disrupted with nocodazole; rather, the fluorescent lipid was distributed in vesicles throughout the cell periphery instead of being internalized to the perinuclear region of the cell. The metabolism of C6-NBD-SM to other fluorescent sphingolipids at 37 degrees C and its effect on C6-NBD-SM transport was also examined. To study plasma membrane lipid recycling, C6-NBD-SM was first inserted into the plasma membrane of CHO-K1 cells and then allowed to be internalized by the cells at 37 degrees C. Any C6-NBD-SM remaining at the plasma membrane was then removed by incubation with nonfluorescent liposomes at 7 degrees C, leaving cells containing only internalized fluorescent lipid. The return of C6-NBD-SM to the plasma membrane from intracellular compartments upon further 37 degrees C incubation was then observed. The half-time for a complete round C6-NBD-SM recycling between the plasma membrane and intracellular compartments was approximately 40 min. Pretreatment of cells with either monensin or nocodazole did not inhibit C6-NBD-SM recycling.
Optogenetic Control of Cardiac Function (2010)

The cardiac pacemaker controls the rhythmicity of heart contractions and can be substituted by a battery-operated device as a last resort. We created a genetically encoded, optically controlled pacemaker by expressing halorhodopsin and channelrhodopsin in zebrafish cardiomyocytes. Using patterned illumination in a selective plane illumination microscope, we located the pacemaker and simulated tachycardia, bradycardia, atrioventricular blocks, and cardiac arrest. The pacemaker converges to the sinoatrial region during development and comprises fewer than a dozen cells by the time the heart loops. Perturbation of the activity of these cells was entirely reversible, demonstrating the resilience of the endogenous pacemaker. Our studies combine optogenetics and light-sheet microscopy to reveal the emergence of organ function during development.
Metallic Mesoporous Nanocomposites for Electrocatalysis (2004)

We describe the fabrication, characterization, and applications of ultrathin, free-standing mesoporous metal membranes uniformly decorated with catalytically active nanoparticles. Platinum-plated nanoporous gold leaf (Pt-NPG) made by confining a plating reaction to occur within the pores of dealloyed silver/gold leaf is 100 nm thick and contains an extremely high, uniform dispersion of 3 nm diameter catalytic particles. This nanostructured composite holds promise as a prototypical member of a new class of fuel cell electrodes, showing good electrocatalytic performance at low platinum loading (less than 0.05 mg cm-2), while also maintaining long-term stability against coarsening and aggregation of catalytic nanoparticles.
Gonadotropin-releasing hormone (GnRH) and GnRH receptor gene expression in human myometrium and leiomyomata and the direct action of GnRH analogs on myometrial smooth muscle cells and interaction with ovarian steroids in vitro. (1996)

The objective of the present study was to determine whether GnRH and GnRH receptor are expressed in myometrium and leiomyomata, and if GnRH analogs alone or in the presence of ovarian steroids can modulate the rate of DNA synthesis, proliferation, and transforming growth factor-beta 1 (TGF beta 1) production in myometrial smooth muscle cells in vitro. Reverse transcription-PCR revealed that leiomyomata, unaffected myometrium, and isolated myometrial smooth muscle cells express GnRH and GnRH receptor messenger ribonucleic acid. Furthermore, in a dose-dependent manner, GnRH agonist (leuprolide acetate) inhibited, but GnRH antagonist [D-pGlu1,D-Phe2,D-Trp3.6] (GnRH-Ant1) stimulated, the rate of [3H]thymidine incorporation into myometrial smooth muscle cells (P < 0.05), whereas GnRH-Ant2 (Ac-D-P-Cl-Phe1.2,D-Trp3,D-Arg6,D-Ala10) had no effect. 17 beta-Estradiol (E2) medroxyprogesterone acetate (MPA), and E2 plus MPA (1 micromol/L) stimulated the rate of DNA synthesis by smooth muscle cells (P < 0.05), which was inhibited by GnRH analogs used at 5 micromol/L (P < 0.05). GnRH analogs had no significant effect on myometrial smooth muscle cell proliferation, with the exception of GnRH-Ant1; however, they inhibited the stimulatory action of E2, MPA, and E2 plus MPA in a time-dependent manner (P < 0.05). These cells also synthesized and released approximately 1.32 +/- 0.02 ng/mL total (active plus latent) TGF beta 1, of which 0.73 +/- 0.02 ng/mL was in an active form. E2, MPA, E2 plus MPA, and GnRH analog treatments resulted in an increase in total TGF beta 1 production, whereas GnRH agonist and GnRH-Ant2, but not GnRH-An1, inhibited active TGF beta 1 (P < 0.05). GnRH analogs also inhibited the action of E2 plus MPA on total and active TGF beta 1 production, whereas GnRH-Ant1 further stimulated E2, MPA, or E2 plus MPA action on active TGF beta 1 production (P < 0.05). The data demonstrate for the first time that GnRH and GnRH receptor messenger ribonucleic acid are expressed in myometrium, leiomyomata, and myometrial smooth muscle cells. The local expression of GnRH and receptor along with the direct action of GnRH analogs on the smooth muscle cell DNA synthesis and TGF beta 1 production suggest an autocrine/paracrine role for GnRH in these tissues, a mechanism that may be involved in leiomyomata regression in women receiving GnRH agonist therapy.
Subpopulations of long-lived and short-lived T cells in advanced HIV-1 infection (2003)

Antigenic stimulation of T cells gives rise to short-lived effector cells and long-lived memory cells. We used two stable isotope-labeling techniques to identify kinetically distinct subpopulations of T cells and to determine the effect of advanced infection with HIV-1. Long-term deuterated water ((2)H(2)O) incorporation into DNA demonstrated biphasic accrual of total and of memory/effector (m/e)–phenotype but not naive-phenotype T cells, consistent with the presence of short-lived and longer-lived subpopulations within the m/e-phenotype T cell pool. These results were mirrored by biphasic die-away kinetics in m/e- but not naive-phenotype T cells after short-term (2)H-glucose labeling. Persistent label retention was observed in a subset of m/e-phenotype T cells (presumably memory T cells), confirming the presence of T cells with very different life spans in humans. In advanced HIV-1 infection, much higher proportions of T cells were short-lived, compared to healthy controls. Effective long-term anti-retroviral therapy restored values to normal. These results provide the first quantitative evidence that long-lived and quiescent T cells do indeed predominate in the T cell pool in humans and determine T cell pool size, as in rodents. The greatest impact of advanced HIV-1 infection is to reduce the generation of long-lived, potential progenitor T cells.
High prevalence of low HDL cholesterol concentrations and mixed hyperlipidemia in a Mexican nationwide survey (2001)

The prevalence of lipid abnormalities revealed in a survey done in 417 Mexican cities is described. Information was obtained on 15,607 subjects, aged 20 to 69 years. In this report, only samples obtained after a 9- to 12-h fast were included (2,256 cases: 953 men and 1,303 women). The population is representative of Mexican urban adults. Mean lipid concentrations were: cholesterol, 4.80 mmol/l; triglycerides, 2.39 mmol/l; HDL cholesterol, 1.00 mmol/l; and LDL cholesterol, 3.06 mmol/l. The most prevalent abnormality was HDL cholesterol below 0.9 mmol/l (46.2% for men and 28.7% for women). Hypertriglyceridemia (>2.26 mmol/l) was the second most prevalent abnormality (24.3%). Severe hypertriglyceridemia (>11.2 mmol/l) was observed in 0.42% of the population. Increased LDL cholesterol (> or =4.21 mmol/l) was observed in 11.2% of the sample. Half of the hypertriglyceridemic subjects had a mixed dyslipidemia or low HDL cholesterol. More than 50% of the low HDL cholesterol cases were not related to hypertriglyceridemia. Insulin resistance was found in 59% of them. In conclusion, the prevalence of hypoalphalipoproteinemia and other forms of dyslipidemia in Mexican adults is very high and it is among the highest previously reported worldwide.
From in vitro to in vivo Models of Bacterial Biofilm-Related Infections (2013)

The influence of microorganisms growing as sessile communities in a large number of human infections has been extensively studied and recognized for 30-40 years, therefore warranting intense scientific and medical research. Nonetheless, mimicking the biofilm-life style of bacteria and biofilm-related infections has been an arduous task. Models used to study biofilms range from simple in vitro to complex in vivo models of tissues or device-related infections. These different models have progressively contributed to the current knowledge of biofilm physiology within the host context. While far from a complete understanding of the multiple elements controlling the dynamic interactions between the host and biofilms, we are nowadays witnessing the emergence of promising preventive or curative strategies to fight biofilm-related infections. This review undertakes a comprehensive analysis of the literature from a historic perspective commenting on the contribution of the different models and discussing future venues and new approaches that can be merged with more traditional techniques in order to model biofilm-infections and efficiently fight them.
Dynamics and sound attenuation in viscoelastic polymer containing hollow glass microspheres (2007)

The practical design of composite material suggests that there is a need for an improved quantitative understanding of the interaction between acoustic waves and microspheres. The multiple scattering method is used to investigate the sound attenuation of the viscoelastic polymer containing hollow glass microspheres. Then the dynamics of the hollow glass microspheres is investigated by reference to the elements of the scattering matrices. It shows that the dilatational vibration of the microsphere plays a key role in the sound attenuation within the viscoelastic polymer composite at the quasistatic region. The thinner glass shell undergoes more severe dilatational vibration and induces more attenuation in the polymer composite.
Online Certificate Status Protocol-OCSP (1999)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements. Please refer to the current edition of the &amp;quot;Internet Official Protocol Standards &amp;quot; (STD 1) for the standardization state and status of this protocol. Distribution of this memo is unlimited. Copyright Notice Copyright (C) The Internet Society (1999). All Rights Reserved. This document specifies a protocol useful in determining the current status of a digital certificate without requiring CRLs. Additional mechanisms addressing PKIX operational requirements are specified in separate documents. An overview of the protocol is provided in section 2. Functional requirements are specified in section 4. Details of the protocol are in section 5. We cover security issues with the protocol in section 6. Appendix A defines OCSP over HTTP, appendix B accumulates ASN.1 syntactic elements and appendix C specifies the mime types for the messages.
Magnetodielectric Substrates in Antenna Miniaturization: Potential and Limitations (2006)

We discuss patch antenna miniaturization using magnetodielectric substrates. Recent results found in the literature reveal that with passive substrates advantages over conventional dielectric substrates can only be achieved if natural magnetic inclusions are embedded into the substrate. This observation is revised and the physical background is clarified. We present a detailed discussion concerning magnetic materials available in the microwave regime and containing natural magnetic constituents. The effects of magnetic dispersion and loss are studied: constraints on the microwave permeability are used to estimate the effect of magnetic substrates on the achievable impedance bandwidth. Microwave composites filled with thin ferromagnetic films are considered as a prospective antenna substrate. We calculate the impedance bandwidth of a lambda/2-patch antenna loaded with the proposed substrate, and challenge the results against those obtained with conventional dielectric substrates. The results are verified using full-wave simulations, and it is shown that the radiation quality factor is strongly minimized with the proposed substrate even in the presence of realistic losses. Estimates for the radiation efficiency are given as a function of the magnetic loss factor
An interactive constraint-based system for drawing graphs (1997)

The GLIDE system is an interactive constraint-based editor for drawing small-and medium-sized graphs (50 nodes or fewer) that organizes the interaction in a more collaborative manner than in previous systems. Its distinguishing features are a vocabulary of specialized constraints for graph drawing, and a simple constraintsatisfaction mechanism that allows the user to manipulate the drawing while the constraints are active. These features result in a graph-drawing editor that is superior in many ways to those based on more general and powerful constraint-satisfaction methods.
Thermo-mechanical characterization of shape memory alloy torque tube actuators (2000)

A parametric study was performed on NiTiCu shape memory alloy torque tubes. Four samples with varying wall thickness values were evaluated for their thermo-mechanical response. The torque against the angular displacement was measured for each sample when purely martensitic and purely austenitic. The recovery torque was measured as a function of the pretwist applied during loading in the martensite phase. The trends observed were compared to three models with relatively good agreement. The recovery torque for biaxial tension/compression-torsion tests were measured with values comparable to pure torsional loadings. During the biaxial loading, a time-dependent phenomenon was observed. To evaluate the time dependence, standard creep tests were performed to elucidate the influence of the load on the temporal response of the material.
Dark-Field Oxidative Addition-Based Chemosensing:  New Bis-cyclometalated Pt(II) Complexes and Phosphorescent Detection of Cyanogen Halides (2006)

Heavy metal complexes that are phosphorescent at room temperature are becoming increasingly important in materials chemistry, principally due to their use in phosphorescent organic light-emitting devices (OLEDs). Their use in optical sensory schemes, however, has not been heavily explored. Homoleptic bis-cyclometalated Pt(II) complexes are known to undergo oxidative addition with appropriate electrophiles (principally alkyl halides) by either thermal or photochemical activation. We have applied this general reaction scheme to the development of a phosphorescence-based sensing system for cyanogen halides. To carry out structure-property relationship studies, a series of previously unreported Pt(II) complexes was prepared. Most of the complexes (excluding those that incorporated substituents on the ligands that forced steric crowding in the square plane) were strongly orange-red phosphorescent (Phi = 0.2-0.3) in a room-temperature oxygen-free solution. These sterically demanding ligands also accelerated the addition of cyanogen bromide to these complexes but slowed the addition of methyl iodide, indicating that the oxidative addition mechanisms for these two electrophiles is different. The lack of solvent-polarity effect on the addition of BrCN suggests a radical mechanism. Oxidative addition of BrCN to the metal complexes in solution or dispersed in poly(methyl methacrylate) gave blue-shifted emissive Pt(IV) complexes. The blue-shifted products give a dark-field sensing scheme that is in sharp contrast to energy transfer-based sensing schemes, which have limited signal-to-noise because of the presence of lower-energy vibronic bands of the energy donor that can overlap with the emission of the acceptor.
Identification of essential nucleotides in an upstream repressing sequence of Saccharomyces cerevisiae by selection for increased expression of TRK2. (1995)

The TRK2 gene in Saccharomyces cerevisiae encodes a membrane protein involved in potassium transport and is expressed at extremely low levels. Dominant cis-acting mutations (TRK2D), selected by their ability to confer TRK2-dependent growth on low-potassium medium, identified an upstream repressor element (URS1-TRK2) in the TRK2 promoter. The URS1-TRK2 sequence (5'-AGCCGCACG-3') shares six nucleotides with the ubiquitous URS1 element (5'-AGCCGCCGA-3'), and the protein species binding URS1-CAR1 (URSF) is capable of binding URS1-TRK2 in vitro. Sequence analysis of 17 independent repression-defective TRK2D mutations identified three adjacent nucleotides essential for URS1-mediated repression in vivo. Our results suggest a role for context effects with regard to URS1-related sequences: several mutant alleles of the URS1 element previously reported to have little or no effect when analyzed within the context of a heterologous promoter (CYC1) [Luche, R.M., Sumrada, R. & Cooper, T.G. (1990) Mol. Cell. Biol. 10, 3884-3895] have major effects on repression in the context of their native promoters (TRK2 and CAR1). TRK2D mutations that abolish repression also reveal upstream activating sequence activity either within or adjacent to URS1. Additivity between TRK2D and sin3 delta mutations suggest that SIN3-mediated repression is independent of that mediated by URS1.
Proteolytic conversion of hepatitis B virus e antigen precursor to end product occurs in a postendoplasmic reticulum compartment (1991)

At least two proteolytic events are involved in the biogenesis of hepatitis B virus e antigen. The first proteolytic event removes the signal peptide and results in the translocation of the precursor protein, P22, into the lumen of the endoplasmic reticulum (ER). The second proteolytic event removes the carboxy-terminal arginine-rich sequence of P22 and converts it to the 16-kDa hepatitis B virus e antigen end product. In contrast to the first proteolytic event, the second proteolytic event is suppressed by brefeldin A, a chemical that inhibits the transport of protein from the ER to the Golgi apparatus. In subcellular fractionation experiments, P22 was detected in both the ER and the Golgi fractions, but P16 was detected only in the Golgi fraction. On the basis of these results, we conclude that the conversion of P22 to P16 occurs ina post-ER compartment, mostly likely the Golgi apparatus.
Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations (2005)

We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.
Results from a phase I safety trial of hAADC gene therapy for Parkinson disease (2008)

Thus far, this gene therapy approach has been well tolerated and shows PET evidence of sustained gene expression. These initial findings demonstrate the safety of the therapy; higher doses of adeno-associated viral vector containing the human aromatic l-amino acid decarboxylase gene in the next cohort of patients may further increase dopamine production in the putamen and provide more profound clinical benefit.
Direct, Solid Phase Assembly of Dihydropyrroloindole Peptides with Conjugated Oligonucleotides (1996)

A new controlled pore glass (CPG) support is described that allows for the direct synthesis of oligonucleotide derivatives carrying a minor groove binding (MGB) agent at the 3'-terminus. The MGB consisted of three repeating 1,2-dihydro-3H-pyrrolo[2,3-e]indole-7-carboxylate (DPI) subunits. The DPI trimer (DPI3) was prepared directly on the CPG support using repeated addition of the DPI subunit. The subunit was protected at the N-3-position with tert-butyloxycarbonyl residue and activated at the 7-carboxy residue by esterification with the 2,3,5,6-tetrafluorophenyl group. A linker, which provided the starting point for oligonucleotide synthesis, was introduced by reaction of the terminal N-3 with p-nitrophenyl 4-[bis(4-methoxyphenyl)phenylmethoxy]butyrate. When used as a support for oligonucleotide synthesis, this modified CPG gave the desired 3'-DPI3-octathymidylate [(dTp)8-DPI3] conjugate in good yield. This conjugate formed hyperstabilized complexes with complementary polyribo- (Tmax = 35 degrees C) and polydeoxyriboadenylic (Tmax = 69 degrees C) acids. In contrast to the N-carbamoyl derivative reported earlier by us, it demonstrated higher cooperativity of melting transitions.
Prostate specific membrane antigen expression in prostatic intraepithelial neoplasia and adenocarcinoma (1998)

PSM was expressed in all cases of prostate adenocarcinoma, with the greatest extent and intensity observed in the highest grades. The expression increased incrementally from benign epithelium to high grade PIN or adenocarcinoma. Conversely, PSA showed the greatest staining in benign epithelium, with decreased expression incrementally from benign epithelium to high grade PIN or adenocarcinoma. Expression of PSM is clinically useful for the identification of prostate epithelium, particularly PIN or adenocarcinoma, and its expression is regulated independent of PSA. The number of PSM immunoreactive cells was not predictive of recurrence, most likely because of the presence of abundant immunoreactivity in most cases, or because of differential expression in primary and metastatic disease.