gebhart/patrepeval huggingface dataset:
Characterization of a Strain of Community-AssociatedMethicillin-Resistant Staphylococcus aureus WidelyDisseminated in the UnitedStates (2006)

A highly stable strain of Staphylococcus aureus with a pulsed-field gel electrophoresis type of USA300 and multilocus sequence type 8 has been isolated from patients residing in diverse geographic regions of the United States. This strain, designated USA300-0114, is a major cause of skin and soft tissue infections among persons in community settings, including day care centers and correctional facilities, and among sports teams, Native Americans, men who have sex with men, and military recruits. The organism is typically resistant to penicillin, oxacillin, and erythromycin (the latter mediated by msrA) and carries SCCmec type IVa. This strain is variably resistant to tetracycline [mediated by tet(K)]; several recent isolates have decreased susceptibility to fluoroquinolones. S. aureus USA300-0114 harbors the genes encoding the Panton-Valentine leucocidin toxin. DNA sequence analysis of the direct repeat units within the mec determinant of 30 USA300-0114 isolates revealed differences in only a single isolate. Plasmid analysis identified a common 30-kb plasmid that hybridized with blaZ and msrA probes and a 3.1-kb cryptic plasmid. A 4.3-kb plasmid encoding tet(K) and a 2.6-kb plasmid encoding ermC were observed in a few isolates. DNA microarray analysis was used to determine the genetic loci for a series of virulence factors and genes associated with antimicrobial resistance. Comparative genomics between USA300-0114 and three other S. aureus lineages (USA100, USA400, and USA500) defined a set of USA300-0114-specific genes, which may facilitate the strain's pathogenesis within diverse environments.
Screening of marine cyanobacteria for high palmitoleic acid production (1995)

Screening of fatty acid composition in 150 strains of marine microalgae, cyanobacteria and green algae was carried out, and 20 strains showed relatively high contents of palmitoleic acid. Among them, two cyanobacteria, Phormidium sp. NKBG 041105 and Oscillatoria sp. NKBG 091600, showed an unusually high cis-palmitoleic acid content (54.5% and 54.4% of total fatty acid, respectively). Phormidium sp. NKBG 041105 had the highest cis-palmitoleic acid content per biomass (46.3 mg (g dry cell weight)−1), and cis-palrnitoleic acid composition was found to be constant with varying temperature. These results indicate that this cyanobacterium could be considered as a new source for palmitoleic acid.
Utility of pheasant call counts and brood counts for monitoring population density and predicting harvest (2003)

Call counts and brood counts are frequently used to evaluate Ring-necked Pheasant (Phasianus colchicus) populations and to forecast harvest. Given the variability commonly observed in these counts, I evaluated their utility in performing these functions in the state of Washington. Pheasant harvest, call counts, and brood counts have all declined in Washington State since 1982. Power for detecting trends in call counts was higher than for brood counts, but substantial sampling was required to reliably detect even large changes in the short term (e.g., power = 0.9 for a 40% decline between 2 years with 12 routes). Brood counts predicted harvest with greater precision than did call counts, but predictions were meaningful only at the statewide scale (i.e., not for counties or major river basins). This was true for predicting total harvest and relative harvest (high, medium, or low).
Characterization of cisplatin degradation as affected by pH and light (1991)

The stability of cisplatin in 0.9% sodium chloride solution was studied. Cisplatin was reconstituted with sterile water for injection to achieve a concentration of approximately 1 mg/mL in 0.9% sodium chloride solution. The solutions were placed in flexible polyvinyl chloride containers, clear and amber glass flasks, and plastic syringes and stored at 22-25 degrees C in the dark or exposed to measured amounts of light and assayed periodically for up to 96 days. The initial pH of some of the solutions was adjusted. The stability of cisplatin in the solutions was determined by measuring the concentrations of cisplatin, trichloroammineplatinate(II) (TCAP), and trans-dichlorodiammineplatinum(II) (transplatin) with high-performance liquid chromatography and by measuring solution pH. The effect of adding ethylene oxide and other materials was also determined. TCAP was identified as the predominant degradation product of cisplatin in all the solutions. The rate of degradation was dependent on pH: In the dark, about 0.04% and 0.21% of the cisplatin degraded to TCAP per week at pH 4.3 and 6.3, respectively. The presence of ethylene oxide accelerated cisplatin degradation. Degradation also occurred during exposure to short-wavelength (350-490-nm) visible light. Storage in amber glass flasks offered more protection than storage in clear flasks. Isomerization of cisplatin to transplatin was not observed. The major degradation product of cisplatin was trichloroammineplatinate(II). Solution pH was the predominant factor affecting cisplatin stability.
Planning for stream processing systems (2005)

With the advent of compositional programming models in computer science, applying planning technologies to automatically build workflows for solving large and complex problems in such a paradigm becomes not only technically appealing but also feasible approach. The application areas that will benefit from automatic composition include, among others, Web services, Grid computing and stream processing systems. Although the classical planning formalism is expressive enough to describe planning problems that arise in a large variety of different applications, it can pose significant limitations on planner performance in compositional applications, in particular, in stream processing systems. In this paper we extend the classical planning formalism by introducing new language constructs that support the structure of stream processing domains. Exposing this structure to the planner can result in dramatic performance improvements: our experiments show exponential planning time reduction in comparison to most recent metric planners.
Purification and Characterization of Fumarase fromCorynebacterium glutamicum (2006)

Fumarase (EC 4.2.1.2) from Corynebacterium glutamicum (Brevibacterium flavum) ATCC 14067 was purified to homogeneity. Its amino-terminal sequence (residues 1 to 30) corresponded to the sequence (residues 6 to 35) of the deduced product of the fumarase gene of C. glutamicum (GenBank accession no. BAB98403). The molecular mass of the native enzyme was 200 kDa. The protein was a homotetramer, with a 50-kDa subunit molecular mass. The homotetrameric and stable properties indicated that the enzyme belongs to a family of Class II fumarase. Equilibrium constants (K(eq)) for the enzyme reaction were determined at pH 6.0, 7.0, and 8.0, resulting in K(eq)=6.4, 6.1, and 4.6 respectively in phosphate buffer and in 16, 19, and 17 in non-phosphate buffers. Among the amino acids and nucleotides tested, ATP inhibited the enzyme competitively, or in mixed-type, depending on the buffer. Substrate analogs, meso-tartrate, D-tartrate, and pyromellitate, inhibited the enzyme competitively, and D-malate in mixed-type.
The molecular basis for apoptotic defects in patients with CD95 (Fas/Apo-1) mutations (1999)

Heterozygous mutations of the receptor CD95 (Fas/Apo-1) are associated with defective lymphocyte apoptosis and a clinical disease characterized by lymphadenopathy, splenomegaly, and systemic autoimmunity. From our cohort of 11 families, we studied eight patients to define the mechanisms responsible for defective CD95-mediated apoptosis. Mutations in and around the death domain of CD95 had a dominant-negative effect that was explained by interference with the recruitment of the signal adapter protein, FADD, to the death domain. The intracellular domain (ICD) mutations were associated with a highly penetrant Canale-Smith syndrome (CSS) phenotype and an autosomal dominant inheritance pattern. In contrast, mutations affecting the CD95 extracellular domain (ECD) resulted in failure of extracellular expression of the mutant protein or impaired binding to CD95 ligand. They did not have a dominant-negative effect. In each of the families with an ECD mutation, only a single individual was affected. These observations were consistent with differing mechanisms of action and modes of inheritance of ICD and ECD mutations, suggesting that individuals with an ECD mutation may require additional defect(s) for expression of CSS.
Clinical Laboratory Improvement Amendment (1997)

Principal and Home Care Consultant for Home Health Systems, Inc., Marietta, Georgia. She is also an adjunct professor at Mercer University, Graduate School of Business and Economics, Atlanta, Georgia, and a Joint Commission on Accreditation of Healthcare Organizations (JCAHO) home care surveyor and faculty member for the JCAHO department of education programs
Electrospun PVA/HAp nanocomposite nanofibers: biomimetics of mineralized hard tissues at a lower level of complexity (2008)

Based on the biomimetic approaches the present work describes a straightforward technique to mimic not only the architecture (the morphology) but also the chemistry (the composition) of the lowest level of the hierarchical organization of bone. This technique uses an electrospinning (ES) process with polyvinyl alcohol (PVA) and hydroxyapatite (HAp) nanoparticles. To determine morphology, crystalline structures and thermal properties of the resulting electrospun fibers with the pure PVA and PVA/HAp nanocomposite (NC) before electrospinning various techniques were employed, including transmission electron microscopy (TEM), high-resolution TEM (HR-TEM), scanning electron microscopy (SEM), x-ray diffraction (XRD), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). In addition, FT-IR spectroscopy was carried out to analyze the complex structural changes upon undergoing electrospinning as well as interactions between HAp and PVA. The morphological and crystallographic investigations revealed that the rod-like HAp nanoparticles exhibit a nanoporous morphology and are embedded within the electrospun fibers. A large number of HAp nanorods are preferentially oriented parallel to the longitudinal direction of the electrospun PVA fibers, which closely resemble the naturally mineralized hard tissues of bones. Due to abundant OH groups present in PVA and HAp nanorods, they strongly interact via hydrogen bonding within the electrospun PVA/HAp NC fibers, which results in improved thermal properties. The unique physiochemical features of the electrospun PVA/HAp NC nanofibers prepared by the ES process will open up a wide variety of future applications related to hard tissue replacement and regeneration (bone and dentin), not limited to coating implants.
Resonance frequency of microbubbles in small blood vessels: a numerical study (2005)

Microbubbles are currently used as ultrasound contrast agents. Their potential therapeutic applications are also under investigation. This work is designed to provide some insight into the mechanisms of energy absorption and deposition by a preformed gas bubble in the microvasculature to optimize its efficacy. In the linear regime, the most favourable condition for the transfer of energy from an ultrasonic field to a gas bubble occurs when the centre frequency of the ultrasonic field equals the resonance frequency of the bubble. The resonance frequency of gas microbubbles has been investigated up to now mainly in unbounded liquids; however when bubbles are confined in small regions, their resonance frequency is strongly affected by the surrounding boundaries. A parametric study on how the resonance frequency of microbubbles in blood vessels is affected by the bubble radius, vessel radius and the bubble position in the vessel is presented. The resonance frequency decreases below its free value with decreasing vessel radius for vessels smaller than 200-300 microm depending on the bubble size. This model suggests the possibility of using ultrasound in a range of frequencies that are, in general, lower than the ones used now for therapeutic and diagnostic applications of ultrasound (a few MHz). When microbubbles oscillate at their resonance frequency they absorb and therefore emit more energy. This energy may allow specific blood vessels to be targeted for both diagnostic and therapeutic applications of ultrasound.
Skip lists: a probabilistic alternative to balanced trees (1990)

Skip lists are data structures that use probabilistic balancing rather than strictly enforced balancing. As a result, the algorithms for insertion and deletion in skip lists are much simpler and significantly faster than equivalent algorithms for balanced trees.
A randomized, placebo-controlled, blind anti-AIDS clinical trial: safety and immunogenicity of a specific anti-IFN alpha immunization. (1994)

HIV-induced cytokine dysregulation, including overproduction of the antiproliferative and cytolytic IFN alpha cytokine, represents a major component of the immune disorders characterizing AIDS. To block the overproduction of IFN alpha we designed an AIDS vaccine combination which included both an anti-HIV and/or an anti-IFN alpha immunization. The safety and immunogenicity of this multicomponent vaccine were tested in mice, Cercopithecus, two HIV noninfected individuals, and six HIV-1 seropositive immunocompromised patients enrolled in a 1-year open clinical trial. We now report the result of a 9-month short-term randomized, blind, placebo-controlled clinical trial (Phase I/II) performed in HIV-1 patients (22 individuals) to confirm safety/tolerance of the anti-IFN alpha vaccine and its immunogenicity and to evaluate whether the complex vaccine initially used could be simplified by removal of HIV component(s). Three groups of patients received inactivated IFN alpha (i-IFN alpha) associated with the immunomodulator P40 with HIV-1 antigens (groups B and C) or without (group A), and one group (D) was placebo. The clinical follow-up documented among those receiving i-IFN-alpha showed that none developed AIDS and/or required antiretroviral chemotherapy. Viral load did not increase and CD4 cell count as well as cell-mediated immunity (CMI) stabilized or even significantly increased in group A. Immunogenicity of the preparations was determined by a positive delayed-type hypersensitivity (DTH) reaction to i-IFN alpha and the presence of serum antibodies to i-IFN alpha and to HIV-1 peptides, occurring only in treated patients. As previously planned, based on these safety data, the trial has been extended for an additional year and all patients were switched to protocol A (i-IFN alpha+P40). This second period of the trial, now open and ongoing, should allow us to evaluate further the innocuity of the i-IFN alpha preparation and whether anti-IFN alpha vaccine could provide a long-lasting CD4 cell count as well as CMI stabilization.
Substrate-like inhibition of the transgalactosylation reaction catalyzed by β-galactosidase fromAspergillus oryzae (2013)

The influence of key parameters in the kinetics of the transglycosylation system catalyzed by Aspergillus oryzae β-galactosidase when applied to the synthesis of galactosyl-ethylene glycol and galactosyl-glycerol has been studied. It was found that both acceptors were inhibitors of the enzyme, causing a decrease of 9 and 68 fold in enzyme catalytic efficiency in the presence of 4.0 M ethylene glycol and glycerol, respectively. The effect was characterized as “substrate-like inhibition”, suggesting the formation of a nonproductive enzyme-acceptor complex. Inhibition constants for both acceptors were determined as 618 mM for ethylene glycol and 244 mM for glycerol.
Muscle Giants: Molecular Scaffolds in Sarcomerogenesis (2009)

Myofibrillogenesis in striated muscles is a highly complex process that depends on the coordinated assembly and integration of a large number of contractile, cytoskeletal, and signaling proteins into regular arrays, the sarcomeres. It is also associated with the stereotypical assembly of the sarcoplasmic reticulum and the transverse tubules around each sarcomere. Three giant, muscle-specific proteins, titin (3-4 MDa), nebulin (600-800 kDa), and obscurin (approximately 720-900 kDa), have been proposed to play important roles in the assembly and stabilization of sarcomeres. There is a large amount of data showing that each of these molecules interacts with several to many different protein ligands, regulating their activity and localizing them to particular sites within or surrounding sarcomeres. Consistent with this, mutations in each of these proteins have been linked to skeletal and cardiac myopathies or to muscular dystrophies. The evidence that any of them plays a role as a "molecular template," "molecular blueprint," or "molecular ruler" is less definitive, however. Here we review the structure and function of titin, nebulin, and obscurin, with the literature supporting a role for them as scaffolding molecules and the contradictory evidence regarding their roles as molecular guides in sarcomerogenesis.
Ca2+ regulation of tight-junction permeability and structure in Necturus gallbladder (1983)

To explore the role of Ca2+ in tight-junction permeability, the Necturus gallbladder was exposed to varying Ca2+ concentrations and to the Ca2+ ionophore A23187 added to the mucosal side (1.9 X 10(-6) to 6.8 X 10(-5) M). Electrophysiological parameters measured in an Ussing-type chamber were correlated with tight-junction morphology revealed by freeze-fracture electron microscopy. In Ca2+-free bathing media, transepithelial resistance decreases and tight-junctional ultrastructure is fragmented. In 1.8 mM Ca2+ media, A23187 induces an initial drop in transepithelial resistance, followed by an increase in transepithelial resistance to a value 20% above base line. At peak response to A23187, NaCl diffusion potentials decrease. Freeze-fracture replicas reveal that the number of junctional strands increase pari passu with junctional depth. Both physiological and morphological changes were partially reversible. The initial decrease in transepithelial resistance coincided with a persistent hyperpolarization of the mucosal cell membrane potential difference and a decrease in the mucosal-to-serosal cell membrane resistance ratio. Thus A23187 alters both the transcellular and paracellular pathway, resulting in opposing effects on transepithelial resistance.
Advantage of yttrium‐90‐labeled over iodine‐131‐labeled monoclonal antibodies in the treatment of a human lung carcinoma xenograft (1997)

The purpose of this investigation was to compare the therapeutic effectiveness of yttrium-90 (90Y)-labeled monoclonal antibodies (MoAbs) with iodine-131 (131I)-labeled MoAbs delivered to human tumor xenografts at their maximum tolerated doses (MTD).Nude mice bearing size-matched human lung adenocarcinoma xenografts (Calu-3) with mean tumor dimensions of approximately 0.8 cm received intravenous injections of the MTD of either 90Y- or 131I-labeled MoAbs. The mice received 125 microCi of 90Y-RS11 or 90Y-RS7, or 300 microCi of 131I-RS11 or 131I-RS7. Tumor size was measured weekly. Body weight and blood counts were monitored to measure toxicity.The calculated average radiation doses delivered to tumors in mice treated with 90Y-RS11 and 90Y-RS7 were 3578 and 3787 centigray (cGy), respectively, versus 1264 and 1368 cGy for 131I-RS11 and 131I-RS7, respectively. These values were calculated taking into consideration the tumor size-dependent absorbed fractions for the beta particles of both radioisotopes. The calculated radiation doses absorbed in the tumor correlated with the tumor responses observed. Mean tumor volume decreases at nadir were 66% and 87% after 90Y-RS11 and 90Y-RS7 therapy, respectively, with 15 of 30 mice treated with either MoAb having complete regression of their tumors. In contrast, only mean stable disease was observed with the 131I MoAb treatments.The results demonstrate the superiority of 90Y-labeled MoAbs over conventionally labeled 131I-labeled MoAbs for therapy in this model. The fact that a substantial percentage of complete remissions was achieved with 90Y-labeled MoAbs suggests a considerable radiosensitivity of the tumor studied, and supports the suitability of choosing this tumor type as an attractive target for future clinical radioimmunotherapy.
Regulation of norrin receptor frizzled-4 by Wnt2 in colon-derived cells (2007)

The data suggests that colonic mucosa and colon tumors may possess two autoregulatory positive Wnt feedback loops, one through canonical signals induced by Wnt:Fz interactions and one through signals resulting from norrin:Fz4 interactions. The latter interactions may be modulated via regulation of Fz4 expression by Wnt2. Retention of Fz4 by cancers, in contrast to the loss of Fz4 by normal mucosal cells, could provide a selective advantage to the tumor cells. Fz4 expression may play a critical role in responses to Wnt signaling in the tumor microenvironment.
Electrospray: Principles and Practice (1997)

The basic principles underlying the electrospray process are reviewed without recourse to detailed discussion of mechanisms. The essential features of the practical implementation of electrospray (at various solution flow rates) are described and the nature of the resultant gas-phase ion population is discussed. The generation by electrospray of multiply charged ions creates complications in that spectral complexity is increased and the determination of charge number must precede the measurement of mass. Multiple charging is beneficial, however, in extending the mass range and improving fragmentation yield in tandem mass spectrometry. The current breadth of application of the technique (including the analysis of non-covalently bound species) and future developments are discussed. © 1997 by John Wiley & Sons, Ltd.
Minimum Lyophilized Plasma Requirement for ISI Calibration (1998)

The minimum requirement of lyophilized plasma samples for a reliable International Sensitivity Index (ISI) was assessed by calibrations based on reducing numbers from a maximum of 60 depleted and 20 plasma samples from patients receiving coumarin using a manual technique and low ISI thromboplastin. The probability of achieving an international normalized ratio (INR) result within a clinically important range of 20% deviation has been assessed at European Concerted Action on Anticoagulation (ECAA) national laboratories in calibrations of ECAA reference thromboplastin against the certified prothrombin time (PT) with a reference thromboplastin. With conventional orthogonal regression using a certified PT and linear regression using certified INR, deviations and the coefficient of variation of the calibration slope increased with reduced numbers. The INR deviations became marked when the number of abnormal plasma samples was reduced to fewer than 20. Calibrations of 3 abnormal plasma samples and 1 lyophilized normal plasma sample gave a high incidence of deviations greater than 10% with an INR of 3.0. The study demonstrates that with both methods of analysis, an optimum minimum number of lyophilized plasma samples is needed for a reliable local ISI.