gebhart/patrepeval huggingface dataset:
Trace Element Speciation in Poultry Litter (2003)

Trace elements are added to poultry feed for disease prevention and enhanced feed efficiency. High concentrations are found in poultry litter (PL), which raises concerns regarding trace element loading of soils. Trace metal cation solubility from PL may be enhanced by complexation with dissolved organic carbon (DOC). Mineralization of organo-As compounds may result in more toxic species such as As(III) and As(V). Speciation of these elements in PL leachates should assist in predicting their fate in soil. Elemental concentrations of 40 PL samples from the southeastern USA were determined. Water-soluble extractions (WSE) were fractionated into hydrophobic, anionic, and cationic species with solid-phase extraction columns. Arsenic speciation of seven As species, including the main As poultry feed additives, roxarsone (ROX; 3-nitro-4-hydroxyphenylarsonic acid) and p-arsanilic acid (p-ASA; 4-aminophenylarsonic acid), was performed by ion chromatography-inductively coupled plasma-mass spectrometry (IC-ICP-MS). Total As concentrations in the litter varied from 1 to 39 mg kg(-1), averaging 16 mg kg(-1). Mean total Cu, Ni, and Zn concentrations were 479, 11, and 373 mg kg(-1), respectively. Copper and Ni were relatively soluble (49 and 41% respectively) while only 6% of Zn was soluble. Arsenic was highly soluble with an average of 71% WSE. Roxarsone was the major As species in 50% of PL samples. However, the presence of As(V) as the major species in 50% of the PL samples indicates that mineralization of ROX had occurred. The high solubility of As from litter and its apparent ready mineralization to inorganic forms coupled with the large quantity of litter that is annually land-applied in the USA suggests a potential detrimental effect on soil and water quality in the long term.
Abilities of some antioxidants to stabilize soybean oil in industrial use conditions (2002)

Abstract Antioxidants, chelators, and alcohols were screened at 0.01 and 1.28% by weight for their ability to delay viscosity increase in soybean oil in the presence of metallic colloidal copper and iron at 105°C with air flowing through the sample. Most substances did not significantly enhance the effect of the natural tocopherols in the soybean oil at 0.01%. A few substances were mildly prooxidant, and a few delayed the increase in viscosity significantly. TBHQ at 0.01% was the best antioxidant of those tested. At 1.28% ascorbyl palmitate, BHT, hydroquinone, and TBHQ increased the stability significantly. Again, TBHQ was the most effective. As measured by viscosity increase to 150 CP, TBHQ increased stability about five times over that of soybean oil controls.
Live cell imaging using confocal microscopy induces intracellular calcium transients and cell death (2003)

Isolated chondrocytes stained with fluo 4-AM and visualized using standard confocal microscopy techniques exhibited Ca2- transients and oscillations. Decreasing the power of the laser light decreased the percent-age of cells exhibiting these Ca2+ signals. Treatment with the antioxidant ascorbate reduced the Ca2+ response, suggesting that it was mediated by light-induced release of reactive oxygen species (ROS). Cell viability 24 h after the 1-h confocal imaging period was approximately 90% for cells that were neither fluorescently stained nor subjected to laser excitation. By contrast, fluorescently stained cells imaged for 1 h exhibited greatly reduced viability. Treatment with ascorbate reduced the level of cell death, suggesting that the effect was mediated by release of exogenous ROS associated with the interaction of light and the fluorochrome. Ca2+ oscillations were not always associated with cell death, suggesting that separate light-sensitive pathways mediate the two processes. Light-activated Ca2+ signaling may trigger alterations in numerous cell processes and thereby represent an important and hitherto overlooked artifact in fluorescent microscopy of viable cells.
Learning causal networks using inducible transcription factors and transcriptome‐wide time series (2020)

We present IDEA (the Induction Dynamics gene Expression Atlas), a dataset constructed by independently inducing hundreds of transcription factors (TFs) and measuring timecourses of the resulting gene expression responses in budding yeast. Each experiment captures a regulatory cascade connecting a single induced regulator to the genes it causally regulates. We discuss the regulatory cascade of a single TF, Aft1, in detail; however, IDEA contains > 200 TF induction experiments with 20 million individual observations and 100,000 signal-containing dynamic responses. As an application of IDEA, we integrate all timecourses into a whole-cell transcriptional model, which is used to predict and validate multiple new and underappreciated transcriptional regulators. We also find that the magnitudes of coefficients in this model are predictive of genetic interaction profile similarities. In addition to being a resource for exploring regulatory connectivity between TFs and their target genes, our modeling approach shows that combining rapid perturbations of individual genes with genome-scale time-series measurements is an effective strategy for elucidating gene regulatory networks.
Wild-Type MIC Distributions and Epidemiological Cutoff Values for Caspofungin and Aspergillus spp. for the CLSI Broth Microdilution Method (M38-A2 Document) (2011)

Clinical breakpoints have not been established for mold testing. Epidemiologic cutoff values (ECVs) are available for six Aspergillus spp. and the triazoles, but not for caspofungin. Wild-type (WT) minimal effective concentration (MEC) distributions (organisms in a species-drug combination with no acquired resistance mechanisms) were defined in order to establish ECVs for six Aspergillus spp. and caspofungin. The number of available isolates was as follows: 1,691 A. fumigatus, 432 A. flavus, 192 A. nidulans, 440 A. niger, 385 A. terreus, and 75 A. versicolor isolates. CLSI broth microdilution MEC data gathered in five independent laboratories in Canada, Europe, and the United States were aggregated for the analyses. ECVs expressed in μg/ml that captured 95% and 99% of the modeled wild-type population were for A. fumigatus 0.5 and 1, A. flavus 0.25 and 0.5, A. nidulans 0.5 and 0.5, A. niger 0.25 and 0.25, A. terreus 0.25 and 0.5, and A. versicolor 0.25 and 0.5. Although caspofungin ECVs are not designed to predict the outcome of therapy, they may aid in the detection of strains with reduced antifungal susceptibility to this agent and acquired resistance mechanisms.
Quantitative analysis of the inelastic background in surface electron spectroscopy (1988)

Abstract Recent progress, in the quantitative analysis of the distortion of surface electron spectra, resulting from inelastic electron scattering, is reviewed. A physical model for the problem is formulated and based on this, basic deconvolution formulae are found. In the formulae, detailed information on the differential inelastic electron scattering cross‐section K is essential. Methods to determine, K are studied and developed. One method is based on a dielectric response calculation. Furthermore, it is found that for the noble and transition metals, K is sufficiently similar that a simple ‘universal’ cross‐section can be defined. In addition, methods for experimental determination of cross‐sections are found and in particular a formula is derived which allows the extraction of direct quantitative cross‐section information through a simple analysis of REELS spectra. The importance of proper background correction is investigated for model electron spectra. Experimental XPS spectra are also studied and it is found that for both the simple and the noble metals, the primary excitation spectra extend 2–3 inelastic scattering events, i.e. ∼50 eV, below the peak energy. Beyond this energy, the spectra are of zero intensity over a wide energy range. Besides, experimental spectra are analysed on the basis of experimentally determined cross‐sections and the results are discussed, in relation to the analysis based on theoretical cross‐sections. The importance of defining simple procedures for routine analysis of spectra is stressed and it is demonstrated that the proposed ‘universal’ cross‐section provides a very simple method for approximate spectral analysis. Finally, some important issues to be considered in the near future are pointed out.
Domain control by spark ablation (1985)

The power loss of grain oriented electrical steel can be usefully reduced by refinement of the ferromagnetic domain structure in cases where overlarge grains support widely spaced domains. Artificial grain boundaries can be produced by laying down lines of ablated spots on the steel surface to generate a stress and atomic disruption pattern which pins domain walls and leads to a smaller wall spacing. A high voltage electrical discharge from capacitors or otherwise can be used to give high enough energy rates and spatial densities to achieve suitably ablated spots on the metal surface. The method is readily adaptable to a production situation.
Relation of composition of polyvinyl acetals to their physical properties. I. Acetals of saturated aliphatic aldehydes (1952)

Abstract Polyvinyl alcohol was condensed with straight and branched chain aldehydes (C n H 2 n O, n = 2 to 8) to varying degrees of completion. Measurements on resins and plasticized compositions included apparent modulus of elasticity at various temperatures, brittle temperature, tensile strength and elongation, and solubility. From these measurements it is concluded that: ( 1 ) Increasing degree of acetalization results in lowered transition temperature, lower stiffness at transition, narrower transition range, higher brittle temperature, decreased tensile strength, and shift in solubility toward solvents of lower dielectric constant. ( 2 ) Acetals of higher normal aldehydes have lower transition and brittle temperatures, lower tensile strength, and more limited solubility. ( 3 ) Branched chain aldehydes have higher transition and brittle temperatures than their normal isomers.
Catalytically synergistic effects of novel LaMnO<sub>3</sub> composite metal oxide in intumescent flame‐retardant polypropylene system (2014)

The newly prepared LaMnO 3 was introduced as a novel perovskite composite metal oxide catalyst for the first time to improve the flame retardancy of flame‐retarded (FR) polypropylene with intumescent flame‐retardant (IFR) system consisting of ammonium polyphosphate (APP), pentaerythritol (PER), and melamine (MA). The synergistic effects of LaMnO 3 catalyst on the performance of IFR PP composites as well as the corresponding catalytically synergistic FR mechanism were investigated. The experimental results show that the incorporated LaMnO 3 catalyst plays an excellently catalytic and synergistic part in improvement of the flame retardancy of FR PP system. Compared with FR system without LaMnO 3 , the incorporation of only 0.5 wt% LaMnO 3 into PP FR system could obviously improve the UL‐94 level from failure to V‐0 rating and decrease the micro‐scale calorimetry parameters peak heat release rate and heat release capacity. The remarkable improvement in flammability can be ascribed to the catalytic carbonization effect of LaMnO 3 on the intumescent flame retardant PP system. The incorporation of appropriate amount of LaMnO 3 , on one hand, could improve the thermal stability of FR PP material, and on the other hand, could also act as nuclei to induce formation of the continuous, compact and smooth condensed phase intumescent charred layer with radialized spherulite‐like structure. As a result, the char yield and also the quality of the formed condensed phase charred layers are correspondingly enhanced remarkably, which is beneficial to improvement of the FR properties. POLYM. COMPOS., 35:2390–2400, 2014. © 2014 Society of Plastics Engineers
Assessment of quality of life using three activity questionnaires in heart failure patients after monthly, intermittent administration of levosimendan during a six-month period. (2009)

Levosimendan treatment improved both objective echocardiographic measurements and the subjective QOL questionnaires. LIhFE and LVD36 show a significant improvement in QOL in heart failure patients after a 6-month period of monthly intermittent administration of levosimendan. The SAQ showed a very small improvement, because it describes more strenuous activity, a situation unusual for these patients, who are severely symptom limited.
Immunogenicity and Therapeutic Efficacy of a Dual-Component Genetic Cancer Vaccine Cotargeting Carcinoembryonic Antigen and HER2/ <i>neu</i> in Preclinical Models (2013)

Several cancer vaccine efforts have been directed to simultaneously cotarget multiple tumor antigens, with the intent to achieve broader immune responses and more effective control of cancer growth. Genetic cancer vaccines based on in vivo muscle electro-gene-transfer of plasmid DNA (DNA-EGT) and adenoviral vectors represent promising modalities to elicit powerful immune responses against tumor-associated antigens (TAAs) such as carcinoembryonic antigen (CEA) and human epidermal growth factor receptor-2 (HER2)/neu. Combinations of these modalities of immunization (heterologous prime-boost) can induce superior immune reactions as compared with single-modality vaccines. We have generated a dual component-dual target genetic cancer vaccine consisting of a DNA moiety containing equal amounts of two plasmids, one encoding the extracellular and transmembrane domains of HER2 (ECD.TM) and the other encoding CEA fused to the B subunit of Escherichia coli heat-labile toxin (LTB), and of an adenoviral subtype 6 dicistronic vector carrying the same two tumor antigens gene constructs. The CEA/HER2 vaccine was tested in two different CEA/HER2 double-transgenic mouse models and in NOD/scid-DR1 mice engrafted with the human immune system. The immune response was measured by enzyme-linked immunospot assay, flow cytometry, and ELISA. The CEA/HER2 vaccine was able to break immune tolerance against both antigens. Induction of a T cell and antibody immune response was detected in immune-tolerant mice. Most importantly, the vaccine was able to slow the growth of HER2/neu⁺ and CEA⁺ tumors. A significant T cell response was measured in NOD/scid-DR1 mice engrafted with human cord blood cells. In conclusion, the CEA/HER2 genetic vaccine was immunogenic and able to confer significant therapeutic effects. These data warrant the evaluation of this vaccination strategy in human clinical trials.
Similar and differential behaviour between the nectin‐afadin‐ponsin and cadherin‐catenin systems during the formation and disruption of the polarized junctional alignment in epithelial cells (1999)

These results indicate that the NAP and cadherin-catenin systems show similar and differential behaviour during the formation and disruption of the polarized junctional alignment in epithelial cells.
A new pick up and release method by heating for micromanipulation (2002)

Micro manipulation is required for assembly and maintenance of micro machines and their parts. In this paper, we propose a new pick up and release method for micromanipulation. The proposed method utilizes the pressure change based on the temperature change inside micro holes made on an end-effector surface. In order to pick up the micro object, the end-effector temperature is increased to exceed room temperature before touching the object. After contact with the object, its temperature decreases and negative pressure is generated inside the micro holes to pick it up. To effect release, the end-effector temperature is increased again. This method realizes quick response due to its scale advantage. We made a prototype end-effector by Si surface micromachining. We analyzed the static performance of this end-effector and conducted experiments. The effectiveness of the proposed method is shown.
Prevention of Left Ventricular Remodeling With Granulocyte Colony-Stimulating Factor After Acute Myocardial Infarction (2005)

Background— Experimental and clinical evidence has recently shown that pluripotent stem cells can be mobilized by granulocyte colony-stimulating factor (G-CSF) and may enhance myocardial regeneration early after primary percutaneous coronary intervention (PCI) management of acute myocardial infarction. Sustained or long-term effects of mobilized CD34-positive mononuclear stem cells, however, are unknown. Methods and Results— Thirty consecutive patients with ST-elevation myocardial infarction undergoing primary PCI with stenting and abciximab were selected for the study 85±30 minutes after PCI; 15 patients were randomly assigned to receive subcutaneous G-CSF at 10 μg/kg body weight for 6 days in addition to standard care including aspirin, clopidogrel, an angiotensin-converting enzyme inhibitor, β-blocking agents, and statins. In patients with comparable demographics and clinical and infarct-related characteristics, G-CSF stimulation led to sustained mobilization of CD34 positive mononuclear cells (MNC CD34+ ), with a 20-fold increase (from 3±2 at baseline to 66±54 MNC CD34+ /μL on day 6; P <0.001); there was no evidence of leukocytoclastic effects, accelerated restenosis rate, or any late adverse events. Within 4 months, G-CSF–induced MNC CD34+ mobilization led to enhanced resting wall thickening in the infarct zone of 1.16±0.29 mm ( P <0.05 versus control), which was sustained at 1.20±0.28 after 12 months ( P <0.001 versus control). Similarly, left ventricular ejection fraction improved from 48±4% at baseline to 54±8% at 4 months ( P <0.005 versus control) and 56±9% at 12 months ( P <0.003 versus control and paralleled by sustained improvement of wall-motion score index from 1.70±0.22 to 1.42±0.26 and 1.33±0.21 at 4 and 12 months, respectively), after G-CSF ( P <0.05 versus baseline and P <0.03 versus controls). Accordingly, left ventricular end-diastolic diameter showed no remodeling and stable left ventricular dimensions after G-CSF stimulation, whereas left ventricular end-diastolic diameter in controls revealed enlargement from 55±4 mm at baseline to 58±4 mm ( P <0.05 versus baseline) at 12 months after infarction and no improvement in diastolic function. Conclusion— Mobilization of MNC CD34+ by G-CSF after primary PCI may offer a pragmatic strategy for improvement in ventricular function and prevention of left ventricular remodeling 1 year after acute myocardial infarction.
Thermodynamic and Structural Studies of Cavity Formation in Proteins Suggest That Loss of Packing Interactions Rather Than the Hydrophobic Effect Dominates the Observed Energetics<sup>,</sup> (2000)

The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine. Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments. The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in DeltaC(p)() and positive values of both DeltaDeltaH degrees and DeltaDeltaS of folding. Enthalpic effects were dominant, and the sign of DeltaDeltaS is the opposite of that expected from the hydrophobic effect. Values of DeltaDeltaG degrees and DeltaDeltaH degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.
Segmentation and mapping of user-driven geospatial web data (2010)

The Internet has penetrated to every aspect of our daily life. Users are feeding their georeferenced knowledge, preference, consumer patterns and behaviors, likes and dislikes, and living patterns to the Web. Proper understanding of these user-provided georeferenced Web data is of great importance. This article combines Web 2.0 and Geospatial Web to retrieve and map user-driven data, and mixes clustering and segmentation to identify informative cluster weighted areas of influence. Case studies are provided to illustrate the working principle of proposed framework, to show how the framework can be applied to many different scenarios, and to demonstrate the usefulness and applicability of the proposed framework.
The embryonic origins of avian cephalic and cervical muscles and associated connective tissues (1983)

The objective of these experiments was to determine the embryonic origins of craniofacial and cervical voluntary muscles and associated connective tissues in the chick. To accomplish this, suspected primordia, including somitomeres 3-7, somites 1-7, and cephalic neural crest primordia have been transplanted from quail into chick embryos. Quail cells can be detected by the presence of a species-specific nuclear marker. The results are summarized as follows: (table; see text) These results indicate that muscles associated with branchial arch skeletal structures are derived from paraxial mesoderm, as are all other voluntary muscles in the vertebrate embryo. Thus, theories of vertebrate ontogeny and phylogeny based in part on proposed unique features of branchiomeric muscles must be critically reappraised. In addition, many of these cephalic muscles are composites of two separate primordia: the myogenic stem cells of mesodermal origin and the supporting and connective tissues derived from the neural crest or lateral plate mesoderm. Defining these embryonic origins is a necessary prerequisite to understanding how the mesenchymal primordia of cephalic muscles and connective tissues interact to form patterned, species-unique musculoskeletal systems.
Analysis of cache replacement-algorithms (1985)

This thesis describes a model used to analyze the replacement decisions made by LRU and OPT (Least-Recently-Used and an optimal replacement-algorithm). The model identifies a set of lines in the LRU cache that are dead, that is, lines that must leave the cache before they can be rereferenced. The model shows that the majority of the cache misses that OPT avoids over LRU come from the most-recently-discarded lines of the LRU cache. Also shown is that a very small set of lines account for the majority of the misses that OPT avoids over LRU. OPT requires perfect knowledge of the future and is not realizable, but our results lead to three realizable near-optimal replacement algorithms. These new algorithms try to duplicate the replacement decisions made by OPT. Simulation results, using a trace-tape and cache simulator, show that these new algorithms achieve up to eight percent fewer misses than LRU and obtain about 20 percent of the miss reduction that OPT obtains. Also presented in the thesis are two new trace-tape reduction techniques. Simulation results show that reductions in trace-tape length of two orders of magnitude are possible with little or no simulation error introduced.