gebhart/patrepeval huggingface dataset:
Understanding Nucleic Acid–Ion Interactions (2014)

Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
Inflated Test Score Gains: Is the Problem Old Norms or Teaching the Test? (1990)

What explanations have been provided for spurious test score gains? Are states and districts narrowing the curriculum and teaching the test? What effect does teaching the test have on the norms themselves? What alternatives must be sought to protect the integrity of instruction and the validity of scores?
Airway Exposure Levels of Lipopolysaccharide Determine Type 1 versus Type 2 Experimental Asthma (2007)

Allergic asthma is characterized by airway inflammation initiated by adaptive immune responses to aeroallergens. Recent data suggest that severe asthma may be a different form of asthma rather than an increase in asthma symptoms and that innate immune responses to LPS can modulate adaptive immune responses to allergens. In this study, we evaluated the hypothesis that airway exposure to different doses of LPS induces different form of asthma. Our study showed that neutrophilic inflammation and IFN-gamma expression were higher in induced sputum from severe asthma patients than from mild to moderate asthmatics. Animal experiments indicated that allergen sensitization with low-dose LPS (0.1 microg) induced type 2 asthma phenotypes, i.e., airway hyperresponsiveness, eosinophilic inflammation, and allergen-specific IgE up-regulation. In contrast, allergen sensitization with high-dose LPS (10 microg) induced asthma phenotypes, i.e., airway hyperresponsiveness and noneosinophilic inflammation that were not developed in IFN-gamma-deficient mice, but unaffected in the absence of IL-4. During the allergen sensitization period, TNF-alpha expression was found to be enhanced by both low- and high-dose LPS, whereas IL-12 expression was only enhanced by high-dose LPS. Interestingly, the asthma phenotypes induced by low-dose LPS, but not by high-dose LPS, were completely inhibited in TNF-alpha receptor-deficient mice, whereas the asthma phenotypes induced by high-dose LPS were abolished in the homozygous null mutation of the STAT4 gene. These findings suggest that airway exposure levels of LPS induces different forms of asthma that are type 1 and type 2 asthma phenotypes by high and low LPS levels, respectively.
[Acute changes in intracerebral vascular resistance after application of dihydrogenated ergot alkaloids (author's transl)]. (1980)

Measurements of total cerebrovascular resistance (CVR) before and after administration of dihydrogenated ergot alkaloids are performed using a decoupling extracorporeal bypass system in rabbits. From the experiments there is clear evidence that the application of dihydroergotoxine-mesylate (28 micrograms/ml intracarotid.) or dihydroergocristine-methansulfonate (Decme, DHEC, 27 micrograms/ml) is followed by a significant drop in total CVR during 5--6 min. In addition, DHEC shows other, more differentiated effects within the cerebrovascular system. At comparable concentrations within the cerebrovascular system, the vasodilatory effect of DHEC seems to be a function of the initial CVR before administration of the drug (range of the initial CVR-values: 1.1--2.0 kPa-min/ml). During very low initial CVR-values (CVR less than 1.1. kPa-min/ml) the application of DHEC is followed by an increase in CVR. There are indications that DHEC acts as a vasoconstrictor in the cerebral vascular bed if the initial CVR-values are quite low. This bivalent effect of DHEC on CVR may cause favourable redistributions of regional blood flow under certain circumstances (e.g., if focal hypoperfusion is combined with perifocal hyperemia).
Photoluminescence and reflectance spectroscopy of excitonic transitions in high-quality homoepitaxial GaN films (1999)

We report on highly resolved photoluminescence (PL) and reflectance (RF) spectra of a homoepitaxial GaN layer grown by metal-organic vapor phase epitaxy. This sample exhibits narrow linewidths of several PL emission peaks, down to $\ensuremath{\approx}100\ensuremath{\mu}\mathrm{eV}$ full width at half maximum for some bound exciton transitions. As a consequence, we have detected new PL features as, e.g., a fivefold fine structure of the donor-bound exciton line at $\ensuremath{\approx}3.471\mathrm{eV},$ and other known PL transitions could be determined with high precision. In RF measurements, the extraordinary quality of the epitaxial layer allowed observation of weakly damped excitonic ground-state transitions and of narrow excited exciton transitions with high signal-to-noise ratio.
Super resolution in a magneto-optical disk with an active mask (1991)

The cut-off frequency was extended by a factor of more than two using a magneto-optical disk with thermally induced mask.
Comparison of antifungal activity of amphotericin B deoxycholate suspension with that of amphotericin B cholesteryl sulfate colloidal dispersion (1992)

Complexing amphotericin B (AmB) with lipids or entrapping it in liposomes may increase its efficacy by reducing toxicity and affecting distribution. However, depending on the lipids involved, interference with antifungal activity has been shown. We compared the in vitro activity of AmB colloidal dispersion by cholesteryl sulfate (ABCD) to the standard AmB deoxycholate suspension (ABDS) against 41 isolates of 15 pathogenic species. Broth dilution MIC and minimum fungicidal concentration (MFC) ranges were similar, and the same number of isolates had lower MICs and MFCs with one drug as with the other. Differences between species were noted. In less than a third of comparisons, there were large (fourfold or more) decreases in ABCD activity relative to that of ABDS, and in approximately 1/10, there were large increases. Thus, ABCD complexing variably affects AmB activity. As ABCD pharmacokinetics and toxicology differ from those of ABDS, the significance of these results for in vivo activity needs to be determined.
The DEN and CCl<sub>4</sub>‐Induced Mouse Model of Fibrosis and Inflammation‐Associated Hepatocellular Carcinoma (2014)

Abstract Human hepatocellular carcinoma (HCC) develops most often as a complication of fibrosis or cirrhosis. While most human studies of HCC provide crucial insights into the molecular signatures of HCC, seldom do they address the etiology of HCC. Mouse models are essential tools for investigating the pathogenesis of HCC; however, the overwhelming majority of cancer models in rodents do not feature liver fibrosis. Detailed in this unit is a protocol for an experimental mouse model of HCC that arises in association with advanced liver fibrosis. The disease model is induced by a single injection of N ‐nitrosodiethylamine (DEN) followed by repeated administration of carbon tetrachloride (CCl 4 ). A dramatic potentiation of liver tumor incidence is observed following administration of DEN and CCl 4 , with100% of mice developing liver tumors at 5 months of age. This model can be employed for studying the molecular mechanisms of fibrogenesis and HCC development, and in cancer hazard/chemotherapy testing of drug candidates. Curr. Protoc. Pharmacol . 66:14.30.1‐14.30.10. © 2014 by John Wiley & Sons, Inc.
A quantum theory of molecular structure and its applications (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA quantum theory of molecular structure and its applicationsRichard F. W. BaderCite this: Chem. Rev. 1991, 91, 5, 893–928Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/cr00005a013https://doi.org/10.1021/cr00005a013research-articleACS PublicationsRequest reuse permissionsArticle Views9817Altmetric-Citations5572LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Matching of tomographic slices for interpolation (1992)

An automatic method that can transform a sequence of tomographic image slices into an isotropic volume data set is described. In this method, correspondence is established between points in consecutive slices, and then this correspondence is used to estimate data between the slices by linear interpolation. The method takes advantage of the fact that consecutive slices have small geometric differences, and carries out the search in predicted small neighborhoods. Only points with high gradient magnitudes are used in the search process to increase the reliability of the correspondences. Mismatches that occur are detected and corrected using the continuity constraint in the correspondences. Experimental results showing the matching and interpolation of magnetic resonance slices and computed tomography slices are presented.
Crystallization-Induced Charge-Transfer Change in TiOPc Thin Films Revealed by Resonant Photoemission Spectroscopy (2011)

Organic semiconductors usually demonstrate crystal structure dependent electronic properties, and through precise control of film structure, the performance of novel organic electronic devices can be greatly improved. Understanding the crystal structure dependent charge-transfer mechanism thus becomes critical. In this work, we have prepared amorphous titanyl phthalocyanine films by vacuum molecular beam evaporation and have further crystallized them through vacuum annealing. In the crystalline phase, an excited electron is rapidly transferred into neighboring molecules; while in the amorphous phase, it is mainly localized and recombines with the core hole as revealed by resonant photoemission spectroscopy (RPES). The fast electron transfer time is determined to be around 16 fs in the crystalline film, which is in good agreement with the charge-transfer hopping time estimated from the best device performance reported. The crystallized film shows more p-type characteristics than the amorphous with all the energy levels shifting toward the vacuum level. However, the greatly improved charge transfer is assigned to the molecular orbital coupling rather than this shift. From density functional theory and RPES, we specify the contribution of two differently coordinated nitrogen atoms (N2c and N3c) to the experimental results and illustrate that the N3c related orbital has experienced a dramatic change, which is keenly related to the improved charge transfer.
Optimal implementation strategies for critical peak pricing (2009)

Critical peak pricing (CPP) is an important means of demand response in electricity markets. As a flexible tariff mechanism, making rational CPP implementation strategies and selecting suitable critical days are crucial to its successful implementation. Based on an analysis of tariff scheme and implementation process of CPP, customer response to CPP is described by a price elasticity matrix of demand, and electricity prices are forecasted by a hybrid electricity price model. Furthermore, a CPP decision model which considers the interests of both customers and load serving entity (LSE) is introduced and then solved by 0-1 integer programming. Numerical results are finally used to prove the effectiveness of the proposed model, which is beneficial to saving customer electricity bills, reducing electricity purchase cost of LSE, hedging against electricity purchasing risk for LSE in wholesale market, and realizing multi-party win.
Solar Hydrogen Generation from Lignocellulose (2017)

Photocatalytic reforming of lignocellulosic biomass is an emerging approach to produce renewable H<sub>2</sub> . This process combines photo-oxidation of aqueous biomass with photocatalytic hydrogen evolution at ambient temperature and pressure. Biomass conversion is less energy demanding than water splitting and generates high-purity H<sub>2</sub> without O<sub>2</sub> production. Direct photoreforming of raw, unprocessed biomass has the potential to provide affordable and clean energy from locally sourced materials and waste.
The prevalence of food hypersensitivity in an unselected population of children and adults (2005)

A rising prevalence of food hypersensitivity (FHS) and severe allergic reactions to food has been reported the last decade. To estimate the prevalence of FHS to the most common allergenic foods in an unselected population of children and adults. We investigated a cohort of 111 children <3 yr of age, 486 children 3 yr of age, 301 children older than 3 yr of age and 936 adults by questionnaire, skin prick test, histamine release test and specific immunoglobulin E followed by oral challenge to the most common allergenic foods. In total, 698 cases of possible FHS were recorded in 304 (16.6%) participants. The prevalence of FHS confirmed by oral challenge was 2.3% in the children 3 yr of age, 1% in children older than 3 yr of age and 3.2% in adults. The most common allergenic foods were hen's egg affecting 1.6% of the children 3 yr of age and peanut in 0.4% of the adults. Of the adults, 0.2% was allergic to codfish and 0.3% to shrimp, whereas no challenges with codfish and shrimp were positive in the children. The prevalence of clinical reactions to pollen-related foods in pollen-sensitized adults was estimated to 32%. This study demonstrates the prevalence of FHS confirmed by oral challenge to the most common allergenic foods in an unselected population of children and adults.
Offspring sex ratio is related to paternal train elaboration and yolk corticosterone in peafowl (2005)

Several recent experimental studies have provided strong evidence for the ability of birds to manipulate the sex ratio of their offspring prior to laying. Using a captive population of peafowl (Pavo cristatus), we tested experimentally the effects of paternal attractiveness on offspring sex ratio, and related sex ratio deviations to egg-yolk concentrations of testosterone, 17beta-estradiol and corticosterone. When females were mated to males whose attractiveness had been experimentally reduced by removing prominent eyespot feathers from their trains, they produced significantly more female offspring, had significantly higher yolk corticosterone concentrations and tended to have lower levels of yolk testosterone than when mated to the same males with their full complement of feathers. Concentrations of 17beta-estradiol did not vary consistently with sex ratio biases. These findings add to the small number of studies providing experimental evidence that female birds can control the primary sex ratio of their offspring in response to paternal attractiveness, and highlight the possibility that corticosterone and perhaps testosterone are involved in the sex manipulation process in birds.
P‐glycoprotein regulates a volume‐activated chloride current in bovine non‐pigmented ciliary epithelial cells. (1996)

1. The whole-cell patch clamp technique was used to investigate the swelling-activated currents in bovine non-pigmented ciliary epithelial (NPCE) cells. 2. Exposure to hypotonic solution activated a current that was blocked by 5-nitro-2-(3-phenylpropylamino)benzoic acid (NPPB). The I-V relationship was shifted in the direction expected for a Cl- current when the external Cl- was replaced by gluconate (permeability ratio P(gluconate)/PCl = 0.17). The inhibition of the current evoked by voltage clamp steps of +80 mV yielded an IC50 for NPPB of 13.4 microM. 3. The current was found to be dependent on ATP. With ATP in the patch pipette the current could be repeatedly activated by exposure to hypotonic solution but when ATP was omitted the current ran down with time. 4. The development of this current was associated with visible cell swelling and inhibitors of regulatory volume decrease in these cells, e.g. tamoxifen, 4-acetamido-4'-isothiocyanatostilbene-2,2'-disulphonic acid (SITS) and 4,4'-diisothiocyanostilbene-2,2'-disulphonic acid (DIDS), also inhibited this current. 5. The volume-activated current was additionally blocked by NPPB, verapamil, quinidine and dideoxyforskolin. 6. The current was independent of external calcium and exhibited slight outward rectification and time-dependent inactivation at strong depolarizing potentials. 7. Disrupting the cytoskeleton and microtubules with cytochalasin B and colchicine had no effect on the activation of the Cl- current. 8. An antibody (C219) to the MDR1 gene product, P-glycoprotein, caused a functional block of the swelling-activated Cl- current when added to the patch pipette. 9. Immunofluorescence studies using the monoclonal antibodies C219 and JSB-1 demonstrated the presence of P-glycoprotein in the ciliary epithelial cells. The immunofluorescence was stronger on the non-pigmented than on the pigmented cells. 10. It is concluded that swelling in NPCE cells activates a Ca(2+)-independent, ATP-dependent Cl- current and that the activity of this current is associated with P-glycoprotein. 11. It is suggested that this Cl- current contributes to regulatory volume decrease and may participate in the secretory activity of these cells.
The <i>Mycobacterium tuberculosis ino1</i> gene is essential for growth and virulence (2003)

Inositol is utilized by Mycobacterium tuberculosis in the production of its major thiol and of essential cell wall lipoglycans. We have constructed a mutant lacking the gene encoding inositol-1-phosphate synthase (ino1), which catalyses the first committed step in inositol synthesis. This mutant is only viable in the presence of extremely high levels of inositol. Mutant bacteria cultured in inositol-free medium for four weeks showed a reduction in levels of mycothiol, but phosphatidylinositol mannoside, lipomannan and lipoarabinomannan levels were not altered. The ino1 mutant was attenuated in resting macrophages and in SCID mice. We used site-directed mutagenesis to alter four putative active site residues; all four alterations resulted in a loss of activity, and we demonstrated that a D310N mutation caused loss of the active site Zn2+ ion and a conformational change in the NAD+ cofactor.
Treatment of experimental breast cancer using interleukin-12 gene therapy combined with anti–vascular endothelial growth factor receptor-2 antibody (2004)

We have shown previously that interleukin-12 (IL-12) gene therapy induced strong antitumor effects in several syngeneic murine tumor models including 4T1 mammary adenocarcinoma. Antiangiogenic treatment with a monoclonal antibody (mAb) directed against the vascular endothelial growth factor receptor-2 (VEGFR-2) is another promising treatment approach that can cause transient suppression of tumor growth. We hypothesized that the combination of IL-12 gene therapy and anti-VEGFR-2 mAb will achieve better antitumor and antimetastatic effects against 4T1 adenocarcinoma than each treatment alone via implementation of different mechanisms. Administration of anti-VEGFR-2 mAb into BALB/c mice bearing s.c. 4T1 tumors induced significant suppression of tumor growth, as did intratumoral administration of naked IL-12 DNA. The combined treatment with anti-VEGFR-2 mAb and IL-12 DNA resulted in significantly enhanced inhibition of tumor growth as compared with each treatment alone. This combination was also effective against spontaneous lung metastases. In T-cell-deficient nude mice, both IL-12 DNA and anti-VEGFR-2 mAb were effective in suppressing tumor growth. In T-cell- and natural killer cell-deficient scid/beige mice, only anti-VEGFR-2 mAb was effective, suggesting that natural killer cells are involved in the antitumor effects induced by IL-12 DNA. In both types of immunodeficient mice, the combination of anti-VEGFR-2 mAb and IL-12 DNA was as effective in suppressing 4T1 tumor growth as anti-VEGFR-2 mAb alone. Antitumor effects of anti-VEGFR-2 mAb were associated with the inhibition of angiogenesis within the tumors, whereas the antiangiogenic effect of IL-12 gene therapy was not detected. Our results show a therapeutic benefit of combining IL-12 gene therapy and anti-VEGFR-2 mAb for cancer treatment.
Novel Method to Evaluate Angular Stiffness of Prosthetic Feet From Linear Compression Tests (2013)

Lower limb amputee gait during stance phase is related to the angular stiffness of the prosthetic foot, which describes the dependence of ankle torque on angular progression of the shank. However, there is little data on angular stiffness of prosthetic feet, and no method to directly measure it has been described. The objective of this study was to derive and evaluate a method to estimate the angular stiffness of prosthetic feet using a simple linear compression test. Linear vertical compression tests were performed on nine configurations of an experimental multicomponent foot (with known component stiffness properties and geometry), which allowed for parametric adjustment of hindfoot and forefoot stiffness properties and geometries. Each configuration was loaded under displacement control at distinct pylon test angles. Angular stiffness was calculated as a function of the pylon angle, normal force, and center of pressure (COP) rate of change with respect to linear displacement. Population root mean square error (RMSE) between the measured and predicted angular stiffness values for each configuration of the multicomponent foot was calculated to be 4.1 N-m/deg, dominated by a bias of the estimated values above the predicted values of 3.8 ± 1.6 N-m/deg. The best-fit line to estimated values was approximately parallel to the prediction, with R2 = 0.95. This method should be accessible for a variety of laboratories to estimate angular stiffness of experimental and commercially available prosthetic feet with minimal equipment.
<title>Optical characteristics of wavelength-optimized reflective FLC SLMs</title> (1998)

we demonstrate that with a single manufacturing process and custom FLC materials, individual reflective FLC SLMs can be optimized for a wide range of chosen wavelength regions. One lot of 256 X 256 SLM cells were prepared from a single silicon wafer. These cells were filed wit five different FLC materials having birefringence spanning a range from 0.129 to 0.218. The resulting retardance variation allowed SLM characteristics to be tailored to give optimized performance in any wavelength region from 400nm to 1000nm.