gebhart/patrepeval huggingface dataset:
Performance of Eight Methods, Including Two New Rapid Methods, for Detection of Oxacillin Resistance in a Challenge Set of Staphylococcus aureu s Organisms (2001)

Using a set of 55 Staphylococcus aureus challenge organisms, we evaluated six routine methods (broth microdilution, disk diffusion, oxacillin agar screen, MicroScan conventional panels, MicroScan rapid panels, and Vitek cards) currently used in many clinical laboratories and two new rapid methods, Velogene and the MRSA-Screen, that require less than a day to determine the susceptibility of S. aureus to oxacillin. The methods were evaluated by using the presence of the mecA gene, as detected by PCR, as the "gold standard." The strains included 19 mecA-positive heterogeneously resistant strains of expression class 1 or 2 (demonstrating oxacillin MICs of 4 to >16 microg/ml) and 36 mecA-negative strains. The oxacillin MICs of the latter strains were 0.25 to 4 microg/ml when tested by broth microdilution with 2% NaCl-supplemented cation-adjusted Mueller-Hinton broth as specified by the NCCLS. However, when tested by agar dilution with 4% salt (the conditions used in the oxacillin agar screen method), the oxacillin MICs of 16 of the mecA-negative strains increased to 4 to 8 microg/ml. On initial testing, the percentages of correct results (% sensitivity/% specificity) were as follows: broth microdilution, 100/100; Velogene, 100/100; Vitek, 95/97; oxacillin agar screen, 90/92; disk diffusion, 100/89; MicroScan rapid panels, 90/86; MRSA-Screen, 90/100; and MicroScan conventional, 74/97. The MRSA-Screen sensitivity improved to 100% if agglutination reactions were read at 15 min. Repeat testing improved the performance of some but not all of the systems.
Subcortical 18F‐AV‐1451 binding patterns in progressive supranuclear palsy (2016)

The PSP and PD patients showed distinct subcortical <sup>18</sup> F-AV-1451 binding patterns reflecting subcortical tau pathology in PSP and reduced nigral neuromelanin in PD. However, there was no correlation with the severity of motor dysfunction, no cortical regions with increased binding in PSP patients, and variable degrees of subcortical binding even in the controls. Therefore, the <sup>18</sup> F-AV-1451 PET may be less than ideal for assessing tau pathology in PSP. Further studies will be required to validate the clinical correlation and to understand the clinical utility of <sup>18</sup> F-AV-1451 PET for PSP patients. © 2016 International Parkinson and Movement Disorder Society.
A Direct Route toward Assembly of Nanoparticle−Carbon Nanotube Composite Materials (2004)

The preparation of nanocomposite materials from carbon nanotubes (CNTs) and metal or metal oxide nanoparticles has important implications to the development of advanced catalytic and sensory materials. This paper reports findings of an investigation of the preparation of nanoparticle-coated carbon nanotube composite materials. Our approach involves molecularly mediated assembly of monolayer-capped nanoparticles on multiwalled CNTs via a combination of hydrophobic and hydrogen-bonding interactions between the capping/mediating shell and the CNT surface. The advantage of this route is that it does not require tedious surface modification of CNTs. We have demonstrated its simplicity and effectiveness for assembling alkanethiolate-capped gold nanoparticles of 2-5 nm core sizes onto CNTs with controllable coverage and spatially isolated character. The loading and distribution of the nanoparticles on CNTs depend on the relative concentrations of gold nanoparticles, CNTs, and mediating or linking agents. The composite nanomaterials can be dispersed in organic solvent, and the capping/linking shells can be removed by thermal treatment to produce controllable nanocrystals on the CNT surfaces. The nanocomposite materials are characterized using transmission electron microscopy and Fourier transform infrared spectroscopy techniques. The results will be discussed in terms of developing advanced catalytic and sensory nanomaterials.
Heterotrophic Production Potential of Omega-3 Polyunsaturated Fatty Acids by Microalgae and Algae-like Microorganisms (1998)

Article Heterotrophic Production Potential of Omega-3 Polyunsaturated Fatty Acids by Microalgae and Algae-like Microorganisms was published on January 1, 1998 in the journal Botanica Marina (volume 41, issue 1-6).
Microneural anastomosis with fibrin glue: an experimental study. (2002)

An experimental study was designed to compare the histological analysis of nerve anastomosis with 10-0 microsurgical sutures and fibrin adhesive. Wistar albino rats' sciatic nerves were transected and repaired either with fibrin adhesive-Beriplast P (M/s Centeon-Cadila Health Care) or with 10-0 monofilament microsutures. Histological assessment was performed at 10, 20, 30, 60 and 90 days after surgery. Functional recovery of the sciatic nerves started at two months and was near normal by three months. Separation of the stumps did not occur in any of the glued nerves. Histological evaluation showed no appreciable difference in the outcome of nerve regeneration after microsurgical repair using sutures or fibrin tissue adhesive. However, inflammation and granuloma formation were appreciated at the suture site, which presented a focal hindrance to myelin and axonal regeneration. Fibrin glueing is attractive for clinical purposes, since it is simpler and less time consuming than suturing.
Bivalirudin in Combination with Heparin to Control Mesenchymal Cell Procoagulant Activity (2012)

Islet and hepatocyte transplantation are associated with tissue factor-dependent activation of coagulation which elicits instant blood mediated inflammatory reaction, thereby contributing to a low rate of engraftment. The aim of this study was i) to evaluate the procoagulant activity of human adult liver-derived mesenchymal progenitor cells (hALPCs), ii) to compare it to other mesenchymal cells of extra-hepatic (bone marrow mesenchymal stem cells and skin fibroblasts) or liver origin (liver myofibroblasts), and iii) to determine the ways this activity could be modulated. Using a whole blood coagulation test (thromboelastometry), we demonstrated that all analyzed cell types exhibit procoagulant activity. The hALPCs pronounced procoagulant activity was associated with an increased tissue factor and a decreased tissue factor pathway inhibitor expression as compared with hepatocytes. At therapeutic doses, the procoagulant effect of hALPCs was inhibited by neither antithrombin activators nor direct factor Xa inhibitor or direct thrombin inhibitors individually. However, concomitant administration of an antithrombin activator or direct factor Xa inhibitor and direct thrombin inhibitor proved to be a particularly effective combination for controlling the procoagulant effects of hALPCs both in vitro and in vivo. The results suggest that this dual antithrombotic therapy should also improve the efficacy of cell transplantation in humans.
Targeted Virus Replication Plus Immunotherapy Eradicates Primary and Distant Pancreatic Tumors in Nude Mice (2005)

Pancreatic cancer is an aggressive neoplasm with no current viable, effective treatment options. In the majority of cases, at first diagnosis, pancreatic cancer has already become metastatic so that conventional treatment regimens provide minimal, if any, clinical benefit in prolonging life or ameliorating the negative prognosis of this disease. These harsh realities underscore the need for developing improved treatment paradigms for this cancer, with gene therapy and immunotherapy currently being evaluated as potential therapeutic options. We currently describe an adenovirus-based therapy for successfully managing pancreatic cancer, the cancer terminator virus (CTV), which is founded on targeted induction of viral replication from a cancer-specific progression elevated gene-3 (PEG-3) promoter (PEG-Prom) and immune modulation by IFN-gamma. The PEG-Prom functions selectively in cancer cells of diverse lineages compared with their normal cellular counterparts. In the CTV, the PEG-Prom drives expression of the adenoviral early region 1A (E1A) gene, necessary for virus replication, with IFN-gamma simultaneously being expressed from the E3 region. Infection of normal cells and pancreatic cancer cells with the CTV confirmed cancer cell-selective adenoviral replication, robust IFN-gamma production coupled with virus replication, growth inhibition, and apoptosis induction. Infection of established pancreatic tumors in nude mice with the CTV promoted viral replication, IFN-gamma production, and activation of antitumor immunity resulting in complete eradication of both primary and distant tumors, curing animals of disease. The CTV provides a novel reagent for treating pancreatic and other human cancers with potential for eliminating both primary tumors and metastatic disease.
Dynamic Thiol–Michael Chemistry for Thermoresponsive Rehealable and Malleable Networks (2016)

The thiol–Michael adduct is used as a thermoresponsive dynamic cross-linker in polymeric materials. Recently, the thiol–Michael reaction between thiols and conjugated alkenes has been used as a ligation reaction for polymer synthesis and functionalization. Here, the thiol–Michael reaction is demonstrated to be thermally responsive and dynamic. Small molecule model experiments demonstrate the potential for the thiol–Michael adducts to be used in dynamic covalent chemistry. Thiol–acrylate adducts are incorporated into a cross-linker to form a soft polymeric material. These thiol–Michael cross-linked materials display healing after being cut and malleability characteristics at 90 °C. Additionally, the data suggest that there is limited creep and stress relaxation at room temperature with complete recovery of creep once the strain is removed. These thiol–Michael cross-linked polymers show dynamic properties upon thermal stimulus, with long-term stability against mechanical deformation in the absence of this stimulus, opening the way for them to be used in various applications.
Droplet-based microfluidic analysis and screening of single plant cells (2018)

Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.
Roots and Fruits: Materials Relating to the Quaker Peace Testimony in the Commonweal Collection (2003)

This article includes a select review of books, pamphlets, journals and archives in the Commonweal Collection relating to the Quaker Peace Testimony. It provides an introduction to and background information about the Collection, an independent library which focuses on non-violence and movements for social change. The materials reviewed relate to the Peace Testimony's beginnings, development and interpretation; to Conscientious Objection in two world wars including the Friends Ambulance Unit; and to the witness of individual Friends. Many books and pamphlets reviewed illustrate the transition to a broader understanding of the peace testimony encompassing nonviolent action, mediation, and postwar peace campaigns.
Reactivation of the Human Cytomegalovirus Major Immediate-Early Regulatory Region and Viral Replication in Embryonal NTera2 Cells: Role of Trichostatin A, Retinoic Acid, and Deletion of the 21-Base-Pair Repeats and Modulator (2001)

Inactivity of the human cytomegalovirus (HCMV) major immediate-early regulatory region (MIERR), which is composed of promoter, enhancer, unique region, and modulator, is linked to lack of HCMV replication in latently infected cells and in other nonpermissive cell types, including human embryonal NTera2 carcinoma (NT2) cells. I refined the embryonal NT2 cell model to enable characterization of the unknown mechanistic basis for silencing of HCMV MIERR-dependent transcription and viral replication in nonpermissive cells. These infected NT2 cells contain nonreplicating viral genomes with electrophoretic mobility equivalent to a supercoiled, bacterial artificial chromosome of comparable molecular weight. MIERR-dependent transcription is minimal to negligible. Increasing the availability of positive-acting transcription factors by retinoic acid (RA) treatment after infection is largely insufficient in reactivating the MIERR. In contrast, trichostatin A (TSA), a histone deacetylase inhibitor, reactivates MIERR-dependent transcription. Contrary to prior findings produced from transfected MIERR segments, deletion of the 21-bp repeats and modulator from the MIERR in the viral genome does not relieve MIERR silencing. To demonstrate that MIERR silencing likely results from enhancer inactivity, I examined an HCMV with a heterologous MIERR promoter that is enhancer dependent but exempt from IE2 p86-mediated negative autoregulation. This heterologous promoter, like its neighboring native MIERR promoter, exhibits immediate-early transcriptional kinetics in fibroblasts. In embryonal NT2 cells, the heterologous MIERR promoter is transcriptionally inactive. This silence is relieved by TSA but not by RA. Remarkably, TSA-induced reactivation of MIERR-dependent transcription from quiescent viral genomes is followed by release of infectious virus. I conclude that a mechanism of active repression imposes a block to MIERR-dependent transcription and viral replication in embryonal NT2 cells. Because TSA overcomes the block, viral gene silencing may involve histone deacetylase-based modification of viral chromatin, which might account for the covalently closed circular conformation of quiescent HCMV genomes.
Acetylcholine enhancement in the nucleus accumbens prevents addictive behaviors of cocaine and morphine (2003)

Drug addiction poses serious social, medical, and economic problems, but effective treatments for drug addiction are still limited. Cocaine and morphine elevate dopamine levels in the nucleus accumbens (NAc), and the overwhelming actions of dopamine are implicated in reinforcement and addiction of abusive drugs. In our previous studies, we reported the regulatory role of acetylcholine (ACh) in the NAc function by selectively ablating the NAc cholinergic neurons with use of immunotoxin-mediated cell targeting. These studies indicated that ACh and dopamine acted convergently but oppositely on the NAc circuit and that cholinergic cell ablation enhanced long-lasting behavioral changes of cocaine addiction. In this investigation, we showed that immunotoxin-mediated ablation of the NAc cholinergic neurons enhanced not only the sensitivity to morphine in conditioned place preference but also negative reinforcement of morphine withdrawal in conditioned place aversion. Remarkably, acetylcholinesterase (AChE) inhibitors that act on the brain AChE suppressed both cocaine- and morphine-induced conditioned place preference and blocked the induction and persistence of cocaine-evoked hyperlocomotion. Importantly, this inhibition was abolished by ablation of the NAc cholinergic neurons. These results demonstrate that centrally active AChE inhibitors prevent long-lasting behavioral abnormalities associated with cocaine and morphine addictions by potentiating the actions of ACh released from the NAc cholinergic neurons. Centrally active AChE inhibitors could thus be approached as novel and potential therapeutic agents for drug addiction.
A bifunctional oleate 12‐hydroxylase: desaturase from Lesquerella fendleri (1998)

LFAH12, an oleate 12-hydroxylase gene from Lesquerella fendleri (L.) was isolated on the basis of nucleotide sequence similarity to an oleate hydroxylase gene from Ricinus communis (L.). Transgenic Arabidopsis plants containing the Lesquerella gene under transcriptional control of the cauliflower mosaic virus 35S promoter accumulated ricinoleic, lesquerolic and densipolic acids in seeds, but not in leaves or roots. However, hydroxylase activity was detectable in crude extracts of vegetative tissues. The discrepancy between the presence of activity and the lack of hydroxy fatty acids suggests selective removal and breakdown of hydroxy fatty acids in vegetative organs. High levels of LFAH12 mRNA accumulation did not lead to correspondingly high levels of protein accumulation, suggesting that accumulation of the hydroxylase may be controlled post-transcriptionally. Expression of the L. fendleri gene in transgenic plants of a fad2 mutant of Arabidopsis, which is deficient in cytoplasmic oleate delta 12 desaturase activity, resulted in partial suppression of the mutant phenotype in roots. Thus, unlike the hydroxylase from R. communis, the L. fendleri enzyme has both hydroxylase and desaturase activities. Fusion of the 5' flanking region of the LFAH12 gene to the beta-glucuronidase coding sequence resulted in a high level of early seed-specific expression of beta-glucuronidase activity in transgenic Arabidopsis plants.
Alteration in Obstructive Apnea Pattern Induced by Changes in Oxygen- and Carbon-Dioxide—inspired Concentrations (1988)

In patients with obstructive apnea, it was hypothesized that stimulation of the ventilatory system by hypercapnia during sleep would increase pharyngeal inspiratory muscle activity and thereby increase upper airway caliber. We predicted that this increase in caliber would decrease the number of apneas and sleep time spent apneic. In contrast, suppression of the ventilatory system activity with hyperoxia was predicted to decrease both inspiratory muscle activity and pharyngeal caliber and thereby increase the number of apneas and apnea time. In all 7 patients with symptomatic obstructive sleep apnea studied, 3 with upper airway narrowing obvious during wakefulness, inhalation of 3 to 6% CO2 preferentially stimulated upper airway inspiratory muscle tonic electrical activity relative to the activity of chest wall inspiratory muscles and diminished periodic breathing. Apnea time decreased from 60 +/- 2% (mean +/- SEM) of sleep time during ambient air inhalation to 12 +/- 3% during CO2 inhalation; 50% O2 had the reverse effect on inspiratory muscle tonic electrical activity and increased apnea time to 75 +/- 5% of sleep time. We conclude that manipulation of inspiratory muscle tonic activity and alteration of the pattern of breathing by CO2 and O2 inhalation lead to significant changes in the pattern of upper airway inspiratory collapse during sleep. We speculate that physiologic variables related to the control of upper airway inspiratory muscle function are instrumental in the pathophysiology of obstructive sleep apnea.
Identification of an ADAMTS-4 Cleavage Motif Using Phage Display Leads to the Development of Fluorogenic Peptide Substrates and Reveals Matrilin-3 as a Novel Substrate (2007)

ADAMTS-4 and ADAMTS-5 are aggrecanases responsible for the breakdown of cartilage aggrecan in osteoarthritis. Multiple ADAMTS-4 cleavage sites have been described in several matrix proteins including aggrecan, versican, and brevican, but no concise predictive cleavage motif has been identified for this protease. By screening a 13-mer peptide library with a diversity of 10(8), we have identified the ADAMTS-4 cleavage motif E-(AFVLMY)-X(0,1)-(RK)-X(2,3)-(ST)-(VYIFWMLA), with Glu representing P1. Several 13-mer peptides containing this motif, including DVQEFRGVTAVIR and HNEFRQRETYMVF, were shown to be substrates for ADAMTS-4. These peptides were found to be specific substrates for ADAMTS-4 as they were not cleaved by ADAMTS-5. Modification of these peptides with donor (6-FAM) and acceptor (QSY-9) molecules resulted in the development of fluorescence-based substrates with a Km of approximately 35 microM. Furthermore, the role of Glu at P1 and Phe at P1' in binding and catalysis was studied by exploring substitution of these amino acids with the D-isomeric forms. Substitution of P1 with dGlu was tolerable for binding, but not catalysis, whereas substitution of P1' with dPhe precluded both binding and catalysis. Similarly, replacement of Glu with Asp at P1 abolished recognition and cleavage of the peptide. Finally, BLAST results of the ADAMTS-4 cleavage motif identified matrilin-3 as a new substrate for ADAMTS-4. When tested, recombinant ADAMTS-4 effectively cleaved intact matrilin-3 at the predicted motif at Glu435/Ala436 generating two species of 45 and 5 kDa.
Antiseptics and Disinfectants: Activity, Action, and Resistance (1999)

Antiseptics and disinfectants are extensively used in hospitals and other health care settings for a variety of topical and hard-surface applications. A wide variety of active chemical agents (biocides) are found in these products, many of which have been used for hundreds of years, including alcohols, phenols, iodine, and chlorine. Most of these active agents demonstrate broad-spectrum antimicrobial activity; however, little is known about the mode of action of these agents in comparison to antibiotics. This review considers what is known about the mode of action and spectrum of activity of antiseptics and disinfectants. The widespread use of these products has prompted some speculation on the development of microbial resistance, in particular whether antibiotic resistance is induced by antiseptics or disinfectants. Known mechanisms of microbial resistance (both intrinsic and acquired) to biocides are reviewed, with emphasis on the clinical implications of these reports.
A room‐based diagnostic imaging system for measurement of patient setup (1998)

A room-based diagnostic x-ray imaging system for routine measurement of radiotherapy patient orientation has been developed. The system consists of a pair of room-mounted x-ray tubes and a portable imager consisting of an orthogonal pair of phosphor screens, a mirror/lens system, a CCD camera, and computer software for comparing images of the patient to reference images. Orthogonal pairs of images can be acquired quickly and with relatively little exposure, allowing correction of patient setup on a daily basis. This could limit patient setup error to the uncertainty in the measurement and repositioning processes, a potentially significant improvement over the present standard.
Distribution of radioactive octacosanol in response to exercise in rats (1994)

To study the mechanism of action of octacosanol in rats the biodistribution of radioactivity of octacosanol was investigated in response to exercise. The amount of voluntary exercise was significantly higher in octacosanol fed rats than in the control. After ingestion of 14C-octacosanol, the accumulation of radioactivity of octacosanol in the muscle of exercised group given octacosanol was significantly higher in comparison with that of the exercised control group given no octacosanol and also the non-exercised groups irrespective of whether they were given octacosanol or not. The muscle thus seemed to be able to store a considerable amount of octacosanol in response to exercise. Although the exact mechanism of increase in physical exercise caused by octacosanol is not known, it is possible that octacosanol increases the mobilization of free fatty acids from fat cells within muscle. The results indicate that octacosanol possesses an adipokinetic activity, which might affect the lipolysis process of muscle.