gebhart/patrepeval huggingface dataset:
Nearly-linear time algorithms for graph partitioning, graph sparsification, and solving linear systems (2004)

We present algorithms for solving symmetric, diagonally-dominant linear systems to accuracy ε in time linear in their number of non-zeros and log (κf (A) ε), where κf (A) is the condition number of the matrix defining the linear system. Our algorithm applies the preconditioned Chebyshev iteration with preconditioners designed using nearly-linear time algorithms for graph sparsification and graph partitioning.
[Recognition of early risky factors in patients suffering from critical influenza A H1N1]. (2011)

Emergency physician can predict the development of critical condition in patients with influenza A H1N1 by using clinical characteristics including comorbidity, myalgia/arthralgia, dyspnea, and oxygen saturation at admission, and it is helpful in making clinical decision.
External validation of multivariable prediction models: a systematic review of methodological conduct and reporting (2014)

The vast majority of studies describing some form of external validation of a multivariable prediction model were poorly reported with key details frequently not presented. The validation studies were characterised by poor design, inappropriate handling and acknowledgement of missing data and one of the most key performance measures of prediction models i.e. calibration often omitted from the publication. It may therefore not be surprising that an overwhelming majority of developed prediction models are not used in practice, when there is a dearth of well-conducted and clearly reported (external validation) studies describing their performance on independent participant data.
Numerical Analysis on the Impact Behavior of Molten Metal Droplets Using a Modified Splat-Quench Solidification Model (2004)

A simple model is formulated for the analysis of the spreading and solidification processes of a molten metal droplet impinging on a solid substrate. At the first stage, the model evaluates the diameter and the radial velocity of the spreading molten metal layer at the instant t0=D/W from the start of impact using analytical relations. Here D and W are, respectively, the diameter and the velocity of the impinging droplet. Numerical predictions on the evolution of the spreading metal layer are obtained by using a modified splat-quench solidification model with initial conditions described at the instant t0=D/W. The model predictions are compared with the experimental data available from the literature. A systematic parametric study is carried out to illustrate the model predictions at different impinging conditions.
Efficacy of disodium-clodronate in the management of joint pain in rheumatoid arthritis. Six months open study. (2003)

Disodium-clodronate may be considered an adjunctive therapy in the pain management of RA patients.
Role of MicroRNAs in Plant and Animal Development (2003)

Small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are key components of an evolutionarily conserved system of RNA-based gene regulation in eukaryotes. They are involved in many molecular interactions, including defense against viruses and regulation of gene expression during development. miRNAs interfere with expression of messenger RNAs encoding factors that control developmental timing, stem cell maintenance, and other developmental and physiological processes in plants and animals. miRNAs are negative regulators that function as specificity determinants, or guides, within complexes that inhibit protein synthesis (animals) or promote degradation (plants) of mRNA targets.
Expression of an Antimicrobial Peptide via the Chloroplast Genome to Control Phytopathogenic Bacteria and Fungi (2001)

The antimicrobial peptide MSI-99, an analog of magainin 2, was expressed via the chloroplast genome to obtain high levels of expression in transgenic tobacco (Nicotiana tabacum var. Petit Havana) plants. Polymerase chain reaction products and Southern blots confirmed integration of MSI-99 into the chloroplast genome and achievement of homoplasmy, whereas northern blots confirmed transcription. Contrary to previous predictions, accumulation of MSI-99 in transgenic chloroplasts did not affect normal growth and development of the transgenic plants. This may be due to differences in the lipid composition of plastid membranes compared with the membranes of susceptible target microbes. In vitro assays with protein extracts from T(1) and T(2) plants confirmed that MSI-99 was expressed at high levels to provide 88% (T(1)) and 96% (T(2)) inhibition of growth against Pseudomonas syringae pv tabaci, a major plant pathogen. When germinated in the absence of spectinomycin selection, leaf extracts from T(2) generation plants showed 96% inhibition of growth against P. syringae pv tabaci. In addition, leaf extracts from transgenic plants (T(1)) inhibited the growth of pregerminated spores of three fungal species, Aspergillus flavus, Fusarium moniliforme, and Verticillium dahliae, by more than 95% compared with non-transformed control plant extracts. In planta assays with the bacterial pathogen P. syringae pv tabaci resulted in areas of necrosis around the point of inoculation in control leaves, whereas transformed leaves showed no signs of necrosis, demonstrating high-dose release of the peptide at the site of infection by chloroplast lysis. In planta assays with the fungal pathogen, Colletotrichum destructivum, showed necrotic anthracnose lesions in non-transformed control leaves, whereas transformed leaves showed no lesions. Genetically engineering crop plants for disease resistance via the chloroplast genome instead of the nuclear genome is desirable to achieve high levels of expression and to prevent pollen-mediated escape of transgenes.
Effects of an Oral Ghrelin Mimetic on Body Composition and Clinical Outcomes in Healthy Older Adults (2008)

Over 12 months, the ghrelin mimetic MK-677 enhanced pulsatile growth hormone secretion, significantly increased fat-free mass, and was generally well tolerated. Long-term functional and, ultimately, pharmacoeconomic, studies in elderly persons are indicated.
An efficient model-based multirate method for reconstruction of audio signals across long gaps (2006)

This paper presents an efficient model-based interpolator for reconstructing long portions of missing samples in audio signals. A simple modification to an existing interpolation method is proposed, optimizing the balance between computational requirements and qualitative performance. Moreover, a post-processing multirate interpolation scheme is introduced to further enhance the quality of the restored signals. Subjective quality assessments of the reconstructed signals via listening tests substantiate the improved performance of the proposed algorithm
Reactive Applications of Cyclic Alkylene Carbonates (2003)

The synthesis and use of cyclic alkylene carbonates as reactive intermediates first appeared in the literature more than 50 years ago. However, the range of their usefulness in industrial applications has only been fully realized in the past decade. In this article, numerous reactive applications of the cyclic alkylene carbonates, specifically the five-membered cyclics, are discussed. In addition, utilization of the chemistry presented in this review for the preparation of industrially useful monomers, polymers, surfactants, plasticizers, cross-linking agents, curing agents, and solvents, to name a few, is also discussed.
Aggressive treatment of acute limb ischemia due to thrombosed popliteal aneurysms (1998)

The pre-operative use of thrombolytic therapy is a safe and effective method to achieve limb salvage in this patient population. Patients must be capable of withstanding an additional period of ischemia allowing for reconstitution of distal runoff. Isolated limb perfusion is of use when a delay to reperfusion cannot be tolerated.
Ketamine-Induced Deficits in Auditory and Visual Context-Dependent Processing in Healthy Volunteers (2000)

The NMDARs are critically involved in human MMN generation. Deficient MMN in schizophrenia thus suggests deficits in NMDAR-related neurotransmission. N-methyl-D-aspartate receptor dysfunction may also contribute to the impairment of patients with schizophrenia in forming and using transient memory traces in more complex tasks, such as the AX-CPT. Thus, NMDAR-related dysfunction may underlie deficits in transient memory at different levels of information processing in schizophrenia. Arch Gen Psychiatry. 2000;57:1139-1147.
Body composition by 2H dilution in Gambian infants: comparison with UK infants and evaluation of simple prediction methods (2009)

Gambian infants show growth faltering, but the underlying body composition is unknown. The present study aimed to compare body composition in Gambian and UK infants using 2H dilution; and to evaluate accuracy of bioelectrical impedance analysis (BIA) and creatinine excretion for estimating lean mass (LM), using 2H as the reference. Body composition was measured in thirty Gambian infants, aged 3-18 months, using (1) anthropometry, (2) 2H, (3) BIA (equation of Fjeld et al. Pediatr Res (1990), 27, 98-102) and (4) 5 h urinary creatinine excretion. Compared with UK reference data, Gambian infants were light, short and had reduced BMI and skinfolds. The subscapular skinfold standard deviation score (SDS) was greater than the triceps SDS (P < 0.01), indicating central fat preservation. Both LM and fat mass were reduced in Gambian infants, with or without adjustment for length. However, whereas the Gambia-UK difference in LM increased with age, that in fat mass decreased. Average creatinine excretion was similar to that expected (95.5 (sd 23.2) % recovery), but LM estimates showed unacceptable error in individuals. BIA using Fjeld's equation overestimated total body water and LM (P < 0.001), hence a new equation was developed, with standard error of 0.47 kg LM. In conclusion, Gambian infants characterised by growth faltering had LM deficits that increased with age. However, adiposity increased with age, and showed indications of a more central distribution than in the reference infants. A new BIA equation for LM prediction is presented; however, creatinine excretion is not recommended for LM estimation in this population.
Effect of CaRuO3 interlayer on the dielectric properties of Ba(Zr,Ti)O3 thin films prepared by pulsed laser deposition (2006)

Ba ( Zr 0.2 Ti 0.8 ) O 3 (BZT) thin films on Pt(111)∕Ti∕SiO2∕Si(100) substrates without and with CaRuO3 (CRO) buffer layer were fabricated at 650°C in situ by pulsed laser deposition. The BZT thin films showed a dense morphology, many clusters are found on the surface images of BZT/Pt films, which are composed by nanosized grains of 25–35nm; the average grain size of BZT/CRO films is about 80nm, which lager than that of BZT/Pt thin film. The dielectric constants and dissipation factors of BZT/Pt and BZT/CRO thin films were 392 and 0.019 and 479 and 0.021 at 1MHz, respectively. The dielectric constant of BZT/Pt and BZT/CRO thin films changes significantly with applied dc bias field and has high tunabilities and figures of merit of ∼70% and 37 and 75% and 36, respectively, under an applied field of 400kV∕cm. The possible microstructural background responsible for the high dielectric constant and tunability was discussed.
Investigations on cell disruption of oleaginous microorganisms: Hydrochloric acid digestion is an effective method for lipid extraction (2014)

Cell disruption is an important step used to substantially increase lipid recovery prior to extraction. This is the first study exploring the effects of cell disruption methods on lipid recovery from different oleaginous microorganisms. Specifically, we examined the effects of cell disruption methods, including autoclaving, bead‐beating, microwaving, sonication, acid digestion, and Soxhlet extraction on the yeast Cryptococcus curvatus , the fungus Mortierella isabellina and the microalga Chlorella sorokiniana . Although lipid recovery by cell disruption methods varied with microbial species, autoclaving and microwaving resulted in the lowest lipid contents for all tested strains. The Soxhlet method achieved the highest lipid content of 63.4% for M. isabellina and 12.8% for C. sorokiniana , followed by acid digestion. The highest lipid content of C. curvatus was achieved at 47.3% through acid digestion, compared to sonication, bead‐beating and Soxhlet methods. This study suggests that acid digestion may be the most simple and effective method for lipid recovery from the tested species in terms of time and reaction temperature. Moreover, fatty acid profile analysis revealed that lipids extracted by acid digestion were similar to those from untreated microbial cells, indicating a favorable feedstock for use in biodiesel production. Practical applications: An effective cell disruption method is critical for not only enhancing the lipid recovery in a large scale but also reporting the accurate values of lipid contents of microorganisms in a lab scale. Different cell disruption methods have different effects on lipid extraction from different microorganisms. In this work, for the first time, we performed comparative investigations among yeast, fungus, and microalga to reveal the lipid recovery yields by cell disruption methods for microbial lipid extraction from different oleaginous microorganisms and identified their most effective methods for analytical lipid determination. An effective cell disruption method is critical for enhancing lipid recovery and reporting the accurate lipid contents of microorganisms. In this study, the authors performed comparative investigations among yeast, fungus, and microalga to determine the lipid recovery yields from these oleaginous micro organisms using various cell disruption methods. They identified the most effective cell disruption methods for analytical lipid determination in each microorganism.
General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations (2004)

Monte Carlo statistical mechanics simulations were used in combination with the extended linear response (ELR) approach to develop a model to predict the activities of kinase inhibitors. One hundred forty eight inhibitors of three protein kinases, cyclin-dependent kinase 2 (CDK2), lymphocyte-specific kinase (Lck), and p38 mitogen-activated protein kinase were considered. The inhibitor sets for the individual kinases were analyzed first, and ELR models using only three descriptors were obtained with correlation coefficients, r(2), of 0.7-0.8. Models for each pair of kinases were then developed and used to predict the activities of the inhibitors for the remaining kinase with resultant q(2) values of 0.71 (CDK2), 0.70 (Lck), and 0.54 (p38). Finally, the three datasets were combined to yield a general ELR model for kinase inhibition; with just three physically reasonable descriptors, EXX, DeltaHB(total), and DeltaSASA, the r(2) and leave-one-out q(2) are 0.69 and 0.67. The optimization of the model was confirmed using a genetic algorithm. The descriptors reflect the structural requirements for strong inhibition: good steric and electrostatic complementarities between inhibitor and protein, limited loss of hydrogen bonds for the inhibitor upon binding, and increased burial of surface area of the inhibitor.
Sepsis syndrome: a valid clinical entity. Methylprednisolone Severe Sepsis Study Group. (1989)

The sepsis syndrome represents a systemic response to infection and is defined as hypothermia (temperature less than 96 degrees F) or hyperthermia (greater than 101 degrees F), tachycardia (greater than 90 beat/min), tachypnea (greater than 20 breath/min), clinical evidence of an infection site and with at least one end-organ demonstrating inadequate perfusion or dysfunction expressed as poor or altered cerebral function, hypoxemia (PaO2 less than 75 torr), elevated plasma lactate, or oliguria (urine output less than 30 ml/h or 0.5 ml/kg body weight.h without corrective therapy). One hundred ninety-one patients with the sepsis syndrome were evaluated prospectively and comprised the placebo group of a multicenter trial of methylprednisolone in sepsis syndrome and septic shock. Forty-five percent of the patients were found to be bacteremic. Thirty-six percent of the patients were in septic shock (sepsis syndrome plus a systolic BP less than 90 mm Hg or a decrease from baseline in systolic BP greater than 40 mm Hg) on study entry. An additional 23% of the patients developed shock after admission with 70% doing so within 24 h of study entry. Shock reversal occurred with a 73% frequency. Twenty-five percent of the patients developed the adult respiratory distress syndrome (ARDS). Mortality for the patients with sepsis syndrome who did not develop shock was 13%. Mortality for the groups of patients with shock on admission and shock postadmission was 27.5% and 43.2%, respectively. Forty-seven percent of the bacteremic patients developed shock after study admission compared to 29.6% of the nonbacteremic patients (p less than .05).(ABSTRACT TRUNCATED AT 250 WORDS)
Nicotinamide-rich diet improves physical endurance by up-regulating SUR2A in the heart (2010)

SUR2A is an ATP-binding protein that serves as a regulatory subunit of cardioprotective ATP-sensitive K(+) (K(ATP) ) channels. Based on signalling pathway regulating SUR2A expression and SUR2A role in regulating numbers of fully assembled K(ATP) channels, we have suggested that nicotinamide-rich diet could improve physical endurance by stimulating SUR2A expression. We have found that mice on nicotinamide-rich diet significantly improved physical endurance, which was associated with significant increase in expression of SUR2A. Transgenic mice with solely overexpressed SUR2A on control diet had increased physical endurance in a similar manner as the wild-type mice on nicotinamide-rich diet. The experiments focused on action membrane potential and intracellular Ca(2+) concentration have demonstrated that increased SUR2A expression was associated with the activation of sarcolemmal K(ATP) channels and steady Ca(2+) levels in cardiomyocytes in response to β-adrenergic stimulation. In contrast, the same challenge in the wild-type was characterized by a lack of the channel activation and rise in intracellular Ca(2+) . Nicotinamide-rich diet was ineffective to increase physical endurance in mice lacking K(ATP) channels. This study has shown that nicotinamide-rich diet improves physical endurance by increasing expression of SUR2A and that this is a sole mechanism of the nicotinamide-rich diet effect. The obtained results suggest that oral nicotinamide is a regulator of SUR2A expression and has a potential as a drug that can improve physical endurance in conditions where this effect would be desirable.
Molecular Mechanisms of Aldehyde Toxicity: A Chemical Perspective (2014)

Aldehydes are electrophilic compounds to which humans are pervasively exposed. Despite a significant health risk due to exposure, the mechanisms of aldehyde toxicity are poorly understood. This ambiguity is likely due to the structural diversity of aldehyde derivatives and corresponding differences in chemical reactions and biological targets. To gain mechanistic insight, we have used parameters based on the hard and soft, acids and bases (HSAB) theory to profile the different aldehyde subclasses with respect to electronic character (softness, hardness), electrophilic reactivity (electrophilic index), and biological nucleophilic targets. Our analyses indicate that short chain aldehydes and longer chain saturated alkanals are hard electrophiles that cause toxicity by forming adducts with hard biological nucleophiles, e.g., primary nitrogen groups on lysine residues. In contrast, α,β-unsaturated carbonyl derivatives, alkenals, and the α-oxoaldehydes are soft electrophiles that preferentially react with soft nucleophilic thiolate groups on cysteine residues. The aldehydes can therefore be grouped into subclasses according to common electronic characteristics (softness/hardness) and molecular mechanisms of toxicity. As we will discuss, the toxic potencies of these subgroups are generally related to corresponding electrophilicities. For some aldehydes, however, predictions of toxicity based on electrophilicity are less accurate due to inherent physicochemical variables that limit target accessibility, e.g., steric hindrance and solubility. The unsaturated aldehydes are also members of the conjugated type-2 alkene chemical class that includes α,β-unsaturated amide, ketone, and ester derivatives. Type-2 alkenes are electrophiles of varying softness and electrophilicity that share a common mechanism of toxicity. Therefore, exposure to an environmental mixture of unsaturated carbonyl derivatives could cause "type-2 alkene toxicity" through additive interactions. Finally, we propose that environmentally derived aldehydes can accelerate diseases by interacting with endogenous aldehydes generated during oxidative stress. This review provides a basis for understanding aldehyde mechanisms and environmental toxicity through the context of electronic structure, electrophilicity, and nucleophile target selectivity.
Transport-of-intensity approach to differential interference contrast (TI-DIC) microscopy for quantitative phase imaging (2010)

Differential interference contrast (DIC) microscopy is an inherently qualitative phase-imaging technique. What is obtained is an image with mixed phase-gradient and amplitude information rather than a true linear mapping of actual optical path length (OPL) differences. Here we investigate an approach that combines the transport-of-intensity equation (TIE) with DIC microscopy, thus improving direct visual observation. There is little hardware modification and the computation is noniterative. Numerically solving for the propagation of light in a series of through-focus DIC images allows linear phase information in a single slice to be completely determined and restored from DIC intensity values.
Metal-Organic Frameworks for Sensing Applications in the Gas Phase (2009)

Several metal-organic framework (MOF) materials were under investigated to test their applicability as sensor materials for impedimetric gas sensors. The materials were tested in a temperature range of 120 °C - 240 °C with varying concentrations of O(2), CO(2), C(3)H(8), NO, H(2), ethanol and methanol in the gas atmosphere and under different test gas humidity conditions. Different sensor configurations were studied in a frequency range of 1 Hz -1 MHz and time-continuous measurements were performed at 1 Hz. The materials did not show any impedance response to O(2), CO(2), C(3)H(8), NO, or H(2) in the gas atmospheres, although for some materials a significant impedance decrease was induced by a change of the ethanol or methanol concentration in the gas phase. Moreover, pronounced promising and reversible changes in the electric properties of a special MOF material were monitored under varying humidity, with a linear response curve at 120 °C. Further investigations were carried out with differently doped MOF materials of this class, to evaluate the influence of special dopants on the sensor effect.