cssi/SciSciGPT-SciSciNet huggingface dataset:
Thermal history reconstruction by inversion of down-hole S2 pyrolysis data; synthetic studies and case histories

Abstract Thermal history reconstruction, as seen by buried kerogen samples, relies upon both a kinetic scheme for kerogen break down in the sub-surface as well as paleoheat flux information. A numerical model to invert S2 data from routine Rock-Eval pyrolysis was developed and tested against synthetic data sets and real data from two wells. The synthetic tests show that the S2 inverse model is sensitive to the present day heat flux (Q0, to parameters describing paleoheat flow, to the number of probability channels for activation energy, and to the range of activation energy. The synthetic tests also show that for a given S2 data set, there can be different sets of kinetic parameters which give not only the same degree of fit between the calculated and measured S2 values, but also similar S2 evolution patterns with burial paths, i.e. there is no unique kinetic solution for a given set of data. The applications of the S2 inverse model to two real well data sets show that the S2 data can be used as a thermal indicator to determine the paleoheat flow and that the results are as useful as those from other thermal indicators, provided high quality S2 data are available. For an S2 data set with a mixture of kerogen types, it is first necessary to perform an un-mixing procedure prior to using the inverse model in order to obtain equivalent single type kerogen contributions, or else results obtained will not be trustworthy.
Narratives, choices, alienation, and identity: learning from an elementary science teacher

As we contemplate on teacher identity research, there is a need to place a teacher’s narratives or story-lines at the center of that work. In this forum, in response to the insightful commentary from Stephen Ritchie and Maria Inez Mafra Goulart and Eduardo Soares, I place a greater emphasis on understanding Daisy’s narratives from an existing social identity framework. Narratives tell us intricate and complex actions that a teacher has taken both personally and professionally. Additionally, narratives help us see implicit nature of identity explicitly. Therefore, a greater focus has to be placed on interactions and utterances of a teacher to make sense of who they are and what they do as expressed by their own words (identity and action). Finally, I join with Ritchie and Goulart and Soares to advocate that identity research needs to include participants as co-researchers and co-authors as identities are very personal and complex to be fully understood by the outsiders (researchers).
Potential utility of plasma fatty acid analysis in the diagnosis of cystic fibrosis.

Background: An altered distribution of fatty acids in cells and tissues is found in patients with cystic fibrosis (CF). In this study, we assessed the potential role of plasma fatty acid analysis in the diagnosis of CF. Methods: In this 2-part study, we first used gas chromatography–mass spectrometry to analyze fatty acids in plasma from 13 CF patients and 11 controls without CF. We then used the fatty acid distribution data to identify the fatty acids or multiple fatty acid calculations most effective in identifying CF patients. Part 2 of the study was a blinded analysis of 10 CF patients and 9 controls to directly test the effectiveness of the diagnostic parameters for CF identified from the plasma fatty acid analysis. Results: In the nonblinded trial, the multiplication product of (18:2 n-6) × (22:6 n-3) (each as percentage of total plasma fatty acid) was the most effective indicator for distinguishing patients with CF from controls ( P = 0.0003). In part 2 (the blinded trial), this multiplication product was also the most effective indicator for distinguishing CF patients from controls ( P = 0.0008). Conclusions: The product of (18:2 n-6) × (22:6 n-3) is effective for distinguishing CF patients from persons without CF. This diagnostic marker may have value as an alternative to the sweat chloride test in selected patients being evaluated for CF.
A general theory of finite elements. I. Topological considerations

This paper presents a general theory of finite elements. The concept of finite elements is cast in a general topological framework valid for spaces of finite dimension. It is shown that the idea of finite element models can be developed in higher-dimensional spaces, independent of specific co-ordinate systems, for any type of continuous abstract function defined on the space. Generalizations of the familiar Lagrange and Hermite interpolation functions are presented as well as a general statement of the notion of generalized variables and conjugate fields. It is also shown that admissible finite elements can be developed for non-Euclidean spaces of finite dimension. Topological properties of finite element models are examined in Part I of the paper. Part II is devoted to certain applications.
UNIONISM AND THE JUDEO‐CHRISTIAN SOCIAL GOSPEL

Warren S. Stone, President of the Brotherhood of Locomotive Engineers, when asked, at the height of the anti‐union open shop movement of the 1920s, what labor thought of the churches, said “…labour does not think very much of Iabor.”
Laser flash photography of cold cavitation-driven ablation in tissues

Plasma mediated ablation of collagen gels and porcine cornea was studied at various laser pulse durations in the range from 350 fs to 1 ns at 1053 nm wavelength. A time resolved stress detection technique was employed to measure transient stress profiles and amplitudes. Optical microscopy was used to characterize ablation craters qualitatively, while a wide band acoustic transducer helped to quantify tissue mechanical response and the ablation threshold. The ablation threshold was measured as a function of laser pulse duration and linear absorption coefficient. For nanosecond pulses the ablation threshold was found to have a strong dependence on the linear absorption coefficient of the material. As the pulse length decreased into the subpicosecond regime the ablation threshold became insensitive to the linear absorption coefficient. The ablation efficiency was found to be insensitive to both the laser pulse duration and the linear absorption coefficient. High quality ablation craters with no thermal or mechanical damage to surrounding material were obtained with 350 fs laser pulses. The mechanism of optical breakdown at the tissue surface was theoretically investigated. In the nanosecond regime, optical breakdown proceeds as an electron collisional avalanche ionization initiated by thermal seed electrons. These seed electrons are created by heating of the tissue by linear absorption. In the ultrashort pulse range, optical breakdown is initiated by the multiphoton ionization of the irradiated medium (6 photons in case of tissue irradiated at 1053 nm wavelength), and becomes less sensitive to the linear absorption coefficient. The energy deposition profile is insensitive to both the laser pulse duration and the linear absorption coefficient.
On Non-Glide Stresses and Their Influence on the Screw Dislocation Core in Body-Centred Cubic Metals II. The Core Structure

The change in core structure of the screw dislocation in a body-centred cubic lattice subjected to a general applied stress tensor is studied by means of computer simulation. The large variations observed are found not to be correlated with the applied stress, in that the same deformed core structure can be realized by many different combinations of stress components. Instead, the core structure is found to be characterized almost exclusively by the magnitude and orientation of the induced glide strain, with a much smaller dependence on the glide stress. This means that while the force acting on a dislocation is defined by the applied stress, it is the elastic strain within the lattice that determines the resistance to motion. This explains the anomalously large dependence of the Peierls stress upon non-glide components of the applied stress tensor. The Peierls stress varies strongly with the shape of the dislocation core, which depends upon the glide strain. However, the glide strain is in turn dependent on non-glide components of the applied stress by way of anisotropic elastic couplings. Therefore the Peierls stress is itself dependent on the non-glide stresses, to an extent governed by the elastic anisotropy. The possible origin of the strain-dependence of the core structure in elastic strain multiplet forces (equal and opposite generalized forces acting on the dislocation) is discussed briefly, as are implications for the phenomenon of ductile fracture.
Comparison of Plaque- and Flow Cytometry-Based Methods for Measuring Dengue Virus Neutralization

As dengue vaccines enter clinical trials, there is a need for rapid and quantitative assays to measure neutralization. We have developed flow-based neutralization assays which generated results similar to those generated by the established, plaque reduction neutralization test. The flow assays are an improvement, as they use human cells and allow for high-throughput screening.
Transcription and DNA damage: a link to a kink.

Abstract Living organisms are constantly exposed to a variety of naturally occurring and man-made chemical and physical agents that pose threats to health by causing cancer and other illnesses, as well as cell death. One mechanism by which these moieties can exert their toxic effects is by inducing modifications to the genome. Such changes in DNA often result in the formation of nucleotides not normally found in the double helix, bases containing covalent chemical alterations, single- and double-strand breaks, and interstrand and intrastrand cross-links. When these lesions are present during replication, mutations often result in the newly synthesized DNA. Likewise, when such damage occurs in a gene, transcription elongation, and hence expression, can be adversely affected because of pausing or arresting of the RNA polymerase at or near the altered site; this could result in the synthesis of a defective RNA molecule. It has become increasingly clear that transcription and DNA damage are intimately linked, since the removal of certain adducts from the genome is highly dependent on their location. When such lesions are present on the transcribed strand of actively expressed genetic loci, they are better cleared from that strand when compared to the complementary DNA or other quiescent regions. This process is called transcription-coupled DNA repair, and it modulates the mutagenic spectrum of many DNA-damaging agents. Furthermore, based upon evidence from systems in which it is absent, this process has a profound effect on ameliorating the adverse consequences of exposure to many environmentally relevant genotoxins. The precise cellular pathway that mediates the preferential clearance of DNA damage from active genetic loci has not yet been established, but it appears to be effected by a repertoire of proteins that are also involved in other DNA repair pathways and transcription as well as some factors that might be unique to it. Because a cellular process as indispensable as gene expression can be thwarted by the presence of DNA damage, an understanding of the mechanism underlying transcription-coupled DNA repair is relevant to the continued discernment of how environmental genotoxins endanger human health.
SENSITIVITY TO NOISE VARIANCE IN A SOCIAL NETWORK DYNAMICS MODEL

Abstract : The dynamics of social networks are modeled with a system of continuous Stochastic Ordinary Differential Equations (SODE). With the proper amount of noise input, the SODE model captures dynamic features that are lacking in the corresponding deterministic ODE model. Therefore, sensitivity to noise levels is investigated by considering four different regimes: essentially deterministic, noise-enriched, noise-enlarged, and noise-dominated. Each regime is defined based on the behavior of solutions of the SODE, and the geometry of the regimes is categorized with stochastic simulations.
Validation of a constraint satisfaction neural network for breast cancer diagnosis: new results from 1,030 cases

Previously, we presented a Constraint Satisfaction Neural Network (CSNN) to predict the outcome of breast biopsy using mammographic and clinical findings. Based on 500 cases, the study showed that CSNN was able to operate not only as a predictive but also as a knowledge discovery tool. The purpose of this study is to validate the CSNN on a database of additional 1,030 cases. An auto-associative backpropagation scheme was used to determine the CSNN constraints based on the initial 500 patients. Subsequently, the CSNN was applied to 1,030 new patients (358 patients with malignant and 672 with benign lesions) to predict breast lesion malignancy. For every test case, the CSNN reconstructed the diagnosis node given the network constraints and the external inputs to the network. The activation level achieved by the diagnosis node was used as the decision variable for ROC analysis. Overall, the CSNN continued to perform well over this large dataset with ROC area of Az=0.81±0.02. However, the diagnostic performance of the network was inferior in cases with missing clinical findings (Az=0.80±0.02) compared to those with complete findings (Az=0.84±0.03). The study also demonstrated the ability of the CSNN to effectively impute missing findings while performing as a predictive tool.
Hepatic stellate cell lipid droplets: A specialized lipid droplet for retinoid storage

The majority of retinoid (vitamin A and its metabolites) present in the body of a healthy vertebrate is contained within lipid droplets present in the cytoplasm of hepatic stellate cells (HSCs). Two types of lipid droplets have been identified through histological analysis of HSCs within the liver: smaller droplets bounded by a unit membrane and larger membrane-free droplets. Dietary retinoid intake but not triglyceride intake markedly influences the number and size of HSC lipid droplets. The lipids present in rat HSC lipid droplets include retinyl ester, triglyceride, cholesteryl ester, cholesterol, phospholipids and free fatty acids. Retinyl ester and triglyceride are present at similar concentrations, and together these two classes of lipid account for approximately three-quarters of the total lipid in HSC lipid droplets. Both adipocyte-differentiation related protein and TIP47 have been identified by immunohistochemical analysis to be present in HSC lipid droplets. Lecithin:retinol acyltransferase (LRAT), an enzyme responsible for all retinyl ester synthesis within the liver, is required for HSC lipid droplet formation, since Lrat-deficient mice completely lack HSC lipid droplets. When HSCs become activated in response to hepatic injury, the lipid droplets and their retinoid contents are rapidly lost. Although loss of HSC lipid droplets is a hallmark of developing liver disease, it is not known whether this contributes to disease development or occurs simply as a consequence of disease progression. Collectively, the available information suggests that HSC lipid droplets are specialized organelles for hepatic retinoid storage and that loss of HSC lipid droplets may contribute to the development of hepatic disease.
A spectroscopic study of some oxometal ion complexes

The i.r. spectra (4000-250 cm−1) of Cs3[VO(CN)5], [(C2H5)4N]3[VO(NCS)5], and K3 [ReO2(CN)4·2H2O have been obtained and empirical band assignments made. From a study of the v (CN) frequency it was possible to ascertain that metal-cyanide π-bonding is probably more important in VO(CN)53− than ReO2(CN)43−. Infrared evidence confirms the presence of N-bonded thiocyanate in VO(NCS)53−. The electronic spectra of the mulled solidssuggest that the lowest-energy transition in symmetrical VO2+ and trans-ReO2+ systems is similar.
Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors

Recently a new algorithm for reverse engineering of biochemical networks was developed by Laubenbacher and Stigler. It is based on methods from computational algebra and finds most parsimonious models for a given data set. We derive mathematically rigorous estimates for the expected amount of data needed by this algorithm to find the correct model. In particular, we demonstrate that for one type of input parameter (graded term orders), the expected data requirements scale polynomially with the number n of chemicals in the network, while for another type of input parameters (randomly chosen lex orders) this number scales exponentially in n. We also show that, for a modification of the algorithm, the expected data requirements scale as the logarithm of n.
Detector effects on time-integrating correlator performance

Detector array effects are considered for a time-integrating acoustooptic correlator used for signal detection. Effects such as detector area integration, detector element, spatial response, and the location of the correlation peak within a detector element are included. General SNR, PD, and PFA expressions are derived as a function of various system and detector parameters. Quantitative data are provided for a Gaussian-Markov signal, and initial experimental confirmation is included.
Inheritance of partial rust resistance in pearl millet

Quantitative disease resistance should be exploited to complement the use of genes for qualitative or hypersensitive resistance. The expression and inheritance of partial rust resistance of pearl millet inbreds 700481-21-8 and 'ICMP 501' crossed to moderately susceptible 'Tift 383' were evaluated in seedling assays in the greenhouse and in generation mean and single-seed descent populations in the field. Uredinium sizes on seedling leaves of hybrids were generally intermediate to those of the parental inbreds and consistent differences could be discerned in uredinium lengths. Area under the disease progress curves (AUDPCs) of individual plants of the parents, F 1 , F 2 , and backcross F 1 s to each parent were determined from field trials. Broad-sense heritability estimates for both crosses were 43%. In generation mean analyses, additive genetic effects were significant in the cross of 700481-21-8 x 'Tift 383', whereas additive, dominance, and dominance x dominance epistatic effects were significant for 'ICMP 501' x 'Tift 383'. The number of genes conferring partial resistance was estimated to be two for 700481-21-8 and 2.5 for 'ICMP 501'. A hierarchical single-seed descent analysis revealed significant differences in AUDPC among F 3 -derived F 4 progenies in the F6 generation. Selection for progenies with greater resistance should be possible among F4 families. Higher levels of resistance were observed in progeny derived from 'ICMP 501'. Because segregation of resistance differed among progeny derived from 700481-21-8 and 'ICMP 501', the genetic basis for resistance probably differs between the two inbreds.
Kidney brush border membrane maltase: purification and properties.

Abstract Brush border membrane maltase was purified from rat kidney by a procedure that included papain hydrolysis, ammonium sulfate fractionation, gel filtration, and affinity chromatography in which Tris, an inhibitor of maltase, served as the ligand. The pure enzyme had a specific activity of 42 μmol/min · mg protein; this represented a 1200-fold purification relative to the activity in the cortex homogenate. The enzyme was found to be a glycoprotein, containing 17.5% hexoses. The native enzyme was an aggregate of four monomers or subunits, each with a molecule weight of 335,000 daltons, as judged by SDSpolyacrylamide gel electrophoresis. The K m for maltose was 1.6 m m , and the K i for Tris was 3.4 m m . Monospecific antibody produced in rabbits against the rat enzyme did not cross-react with dog kidney maltase. Unlike the intestinal enzyme, the renal maltase was specific for maltose and did not hydrolyze starch or other disaccharides.
Fludarabine and cytarabine in patients with acute myeloid leukemia refractory to two different courses of front-line chemotherapy.

Abstract The most effective regimen for acute myeloid leukemia (AML) patients who do not achieve complete remission (CR) after two different courses of front-line chemotherapy has not been established. We therefore evaluated the efficacy, toxicity, and prognostic factors for achieving CR following treatment with fludarabine and cytarabine in 25 newly diagnosed AML patients who did not respond to initial therapy with idarubicin and cytarabine followed by mitoxantrone and etoposide. CR was achieved in 32% of patients; in 55% of patients with intermediate-risk karyotype and in 14% with unfavorable-risk. Eight percent died of infectious complications. Median duration of overall survival was 6.6 months (95% CI 3.4 months to ∞); 3.4 months (95% CI 0.8–8.6 months) for patients with an unfavorable-risk karyotype and 18.1 months (95% CI 5.0 months to ∞) with an intermediate-risk karyotype ( p = 0.02). Our data suggest that poor-risk karyotype patients are unlikely to benefit from third course treatment with fludarabine–cytarabine, and that this regimen merits further investigation in AML patients with good or intermediate-risk karyotype that have persistent leukemia after two courses of front-line chemotherapy.
Teacher choice and effects of classroom resource utilization in a technological intervention on rate and proportionality

SimCalc MathWorlds™ (SMW) is a piece of educational software that supports dynamic graph creation and manipulation. The Scaling Up SimCalc study is a controlled, randomized experiment investigating the hypothesis that the students of a wide variety of teachers could benefit from the package of SMW plus curriculum and teacher professional development more than those who were given an alternative, highly rated teaching option. The first year of the study has been completed, and researchers found that students who used the SimCalc package gained significantly more than those in the control group. While this result demonstrates the successful use of technology in class settings, a number of questions still remain. In particular, how do different ways of implementing SimCalc affect students' access to learning resources? I plan to explore the differences between classrooms that have successfully implemented the SimCalc curriculum through a series of case studies.
Academic workforce trends in community hospitals.

Introduction: Obstetrician-gynecologist faculty workforce studies have been limited to faculty at university training programs. Not much is known about the obstetrician-gynecologist faculty workforce at community programs. Method: This study assessed the obstetrician-gynecologist faculty workforce in community training programs via administering surveys to the department chairs. The questionnaire assessed number of current faculty by degree, work status (part-time/full-time), rank, and sub-specialty. Out of 125 programs, 65 responded (52% response rate). Results: The mean number of full-time faculty per department in community hospitals was 17 faculty. Two-thirds of community department chairs anticipated an increase in full-time faculty and 43% anticipated an increase in part-time faculty. Like university programs, sub-specialists and Professors (compared to generalists and assistant professors) were more likely to be male. Conclusion: There are similarities between the community and university faculty workforce, many of the community program faculty are involved in research. Given the evolving clinical, educational, and research demands on community faculty, it is important to continue to monitor and study community program faculty. Keywords: Workforce; community hospital; ob-gyn; faculty; gender; university (Published: 30 April 2012) Citation: Journal of Community Hospital Internal Medicine Perspectives 2012, 2 : 17361 - http://dx.doi.org/10.3402/jchimp.v2i1.17361
Shrinkage and Orthogonal Decomposition

. The problem of estimating the mean of a multivariate normal distribution when the parameter space allows an orthogonal decomposition is discussed. Risk functions and lower bounds for a class of shrinkage estimators that includes Stein’s estimator are derived, and an improvement on Stein’s estimator that takes advantage of the orthogonal decomposition is introduced. Uniform asymptotics related to Pinsker’s minimax risk is derived and we give conditions for attaining the lower risk bound. Special cases including regression and analysis of variance are discussed.
Oxysterol-induced endothelial cell dysfunction in culture.

Cholesterol oxidation products (oxysterols), such as cholestan-3 beta,5 alpha,6 beta-triol (Triol), may be atherogenic by altering the barrier function of the vascular endothelium. We have shown that incubation of endothelial cell monolayers with Triol increased transendothelial albumin transfer (i.e., decreased barrier function) in a concentration- and time-dependent manner. Such dysfunction of endothelium could result from alterations in membrane characteristics, including changes in membrane-associated enzyme activities. To test this hypothesis, endothelial monolayers were treated with 20 microM Triol and the activities of selected membrane enzymes were measured at 0, 2, 4, 6, 12 and 24 hours. Calcium-adenosine triphosphatase (Ca(++)-ATPase) and sodium, potassium, magnesium-adenosine triphosphatase (Na+, K+, Mg(++)-ATPase) activities were significantly increased after 4 or 2 hours incubation with 20 microM Triol, respectively. 5'-nucleotidase activity was significantly elevated only after a 24-hour exposure to Triol, whereas there was no change in angiotensin-converting enzyme (ACE) activity in response to 20 microM Triol treatment at any time studied. Compared with all concentrations tested 40 microM Triol increased Ca(++)-ATPase activity most markedly, with a significant increase already after a 2-hour exposure. No major morphological changes were noted until 12 hours of exposure to 20 microM Triol; obvious cellular damage was observed by 24 hours. Cultures treated with Triol for 24 hours showed significant signs of toxicity, measured by an elevated [3H]adenine release, compared with control cultures. These data demonstrate that Triol alters the activity of certain membrane-bound enzymes, particularly Na+, K+, Mg(++)-ATPase and Ca(++)-ATPase.(ABSTRACT TRUNCATED AT 250 WORDS)
Adrenocorticotropin — A central trigger in immune responsiveness: Tonal inhibition of immune activation

Adrenocorticotropin is known for its key role in mediating neuroendocrine responses, especially in response to stress. Recently, it has been recognized to have direct immunomodulatory actions, most of which are suppressive. This is a widely conserved action which occurs in invertebrates and vertebrates. This conservation illustrates the fundamental nature of adrenocorticotropin's immunomodulatory action. Such a mechanism of action helps explain why the immunocytes themselves can serve as a source of adrenocorticotropin. Regulation of adrenocorticotropin production and action is complex and the result is an integration of multiple mechanisms. Serum adrenocorticotropin levels fluctuate in response to stimulatory and inhibitory factors. Further, peptidases can specifically process adrenocorticotropin into smaller active fragments, inactive peptides or into peptides with different activities. These proteolytic enzymes have a differential tissue and cellular distribution. Immune stimulating factors such as interleukin-1 can overcome adrenocorticotropin inhibition and secondarily, block adrenocorticotropin production through the release of corticosteroids. With an endogenous presence and complex regulation it has been difficult to characterize adrenocorticotropin's role in the immune system. Here, we propose that adrenocorticotropin is a tonis regulator of immune response, i.e. it tonally inhibits immunocytes which undergo disinhibition as the result of exposure to stimulatory signals, e.g. cytokines, neuropeptides, etc. Thus, adrenocorticotropin appears to set the threshold for immunoactivation by controlling the degree of immunoexcitability.
Energy of a Boson Fluid with Lennard-Jones Potentials

A more powerful version of a numerical method published before is given which permits the integration of the Schr\"odinger equation for a large ensemble of particles. A new method for obtaining quantum expectation values is outlined. Numerical results are tabulated for the energy of the ground state of a system of 32 bosons interacting by Lennard-Jones potentials and with periodic boundary conditions. This is a commonly used model of liquid ${\mathrm{He}}^{4}$. The present results are substantially lower and closer to experiment than variational estimates based on a Jastrow-type wave function.
Routes of Zn2+ entry in ischemia

Synaptic release of Zn2+ and its translocation into postsynaptic hippocampal pyramidal neurons may contribute to their degeneration in epilepsy or ischemia. Culture studies have revealed that of the three major routes of divalent cation entry [NMDA channels, voltage sensitive Ca2+ channels (VSCC) and Ca-A/K channels], Ca-A/K channels exhibit the highest permeability to exogenously applied Zn2+. Until recently, there has been little information about routes through which synaptically released Zn2+ enters postsynaptic neurons. In a recent study employing mouse hippocampal slice preparations subjected to brief oxygen and glucose deprivation (OGD), we found a Ca-A/K channel antagonist, but not combined NMDA and VSCC antagonism, to attenuate both Zn2+ accumulation in CA3 and CA1 pyramidal neurons and their subsequent injury. While overall Zn2+ accumulation appears to reflect a combination of translocation and release from intracellular stores, present results suggest that Zn2+ influx through Ca-A/K channels may play a critical role in Zn2+ dependent ischemic injury.
Analysis of Error Response of Amplitude Modulated Reticles

A method is described for calculating the error response of optical-reticle systems used to convert line-of-sight angle into an electrical signal. The calculation is carried out in the frequency domain and relates optical aberrations as expressed in terms of a spot diagram, and the reticle pattern which is characterized by a reticle phase function, to the amplitudes and phases of the significant harmonics in the output waveform. The procedure is easily programmed for a computer and permits the rapid evaluation of reticle and optical designs and design changes.
Mutagenesis and Modeling to Predict Structural and Functional Characteristics of the Staphylococcus aureus MepA Multidrug Efflux Pump

MepA is a multidrug and toxin extrusion (MATE) family protein and the only MATE protein encoded within the Staphylococcus aureus genome. Structural data for MATE proteins are limited to a single high-resolution example, NorM of Vibrio cholerae. Substitution mutations were created in MepA using gradient plates containing both a substrate and reserpine as an efflux pump inhibitor. Site-directed mutagenesis of plasmid-based mepA was used to reproduce these mutations, as well as unique or low-frequency mutations identified in mepA-overexpressing clinical strains, and to mutagenize conserved acidic residues. The effect of these changes on protein function was quantitated in a norA-disrupted host strain by susceptibility testing with and without inhibitors and by determining the proficiency of ethidium efflux. Up-function substitutions clustered in the carboxy half of MepA, near the cytoplasmic face of the protein. Repeated application of the same gradient plate conditions frequently reproduced identical substitution mutations, suggesting that individual residues are required for interaction with specific substrates. Acidic residues critical to protein function were identified in helices 4 and 5. In silico modeling revealed an outward-facing molecule, with helices 1, 2, 4, 7, 8, and 10 having contact with a central cavity that may represent a substrate translocation pathway. Functionally important residues within this cavity included S81, A161, M291, and A302. These data provide a critical starting point for understanding how MATE multidrug efflux proteins function and will be useful in refining crystallographic data when they are available.
Electron–Phonon-Induced Superconductivity

Some background regarding the evolution of calculations, predictions, and approaches to understand and increase Tc for phonon-mediated superconductivity is presented. This is followed by a description of a successful “after the fact” theoretical study of MgB2 and a description of current thinking about the relationship between phonon renormalization and Tc. It is then argued that in the search for high Tcs the evolution has gone from searching for high density of states materials to high electron–phonon couplings described by λ. Finally, it is suggested that the focus on finding large λ can be supplemented by a search for large electronic spring constants η. This is expected to be particularly relevant for the highest Tc materials in this class of superconductors.
Fine-scale vertical distributions of microbial biomass and activity in California Borderland sediments

Vertical distributions of total organic carbon (TOC), porosity, adenosine triphosphate (ATP), and rates of nucleic acid synthesis were measured at millimeter depth intervals in basin sediments from the California Borderland. Within the upper 5 mm, large gradients were measured in sediment microbial biomass (ATP) and nucleic acid synthesis rates, especially deoxyribonucleic acid (DNA) synthesis. A subsurface secondary maximum in specific growth rate (extrapolated from DNA synthesis and ATP biomass measurements) was also observed and may be associated with the onset of sulfate reduction. Carbon production rates integrated over the top 40 mm of the sediment profile in San Pedro Basin (160 to 220 mg carbon m−2 day−1) suggest that the central portion of the basin receives larger inputs of organic carbon than would be predicted from surface water primary production rates and a simple one-dimensional vertical settling model. Lateral transport of carbon from the shallower portions of the basin to the center is the most likely source of this carbon.
Focal Salabrasion for Removal of Linear Tattoos

The use of a power-driven, cotton-tipped, wooden applicator permits precision salabrasion of small or linear tattoos. Such focal salabrasion is facilitated by prior removal of the overlying epidermis by means of a rotating dental burr.
A New Host Diagnosed with a Strain of Sugarcane mosaic virus in Florida: Red-Veined Prayer Plant (Maranta leuconeura erythroneura).

Prayer plants (Maranta spp.), which are indigenous to Brazil, are commercially produced in nurseries mainly to be sold as potted houseplants. However, in frost-free areas, they are also used as a g...
Unitary Ca2+ Current through Mammalian Cardiac and Amphibian Skeletal Muscle Ryanodine Receptor Channels under Near-physiological Ionic Conditions

Ryanodine receptor (RyR) channels from mammalian cardiac and amphibian skeletal muscle were incorporated into planar lipid bilayers. Unitary Ca2+ currents in the SR lumen-to-cytosol direction were recorded at 0 mV in the presence of caffeine (to minimize gating fluctuations). Currents measured with 20 mM lumenal Ca2+ as exclusive charge carrier were 4.00 and 4.07 pA, respectively, and not significantly different. Currents recorded at 1–30 mM lumenal Ca2+ concentrations were attenuated by physiological [K+] (150 mM) and [Mg2+] (1 mM), in the same proportion (∼55%) in mammalian and amphibian channels. Two amplitudes, differing by ∼35%, were found in amphibian channel studies, probably corresponding to α and β RyR isoforms. In physiological [Mg2+], [K+], and lumenal [Ca2+] (1 mM), the Ca2+ current was just less than 0.5 pA. Comparison of this value with the Ca2+ flux underlying Ca2+ sparks suggests that sparks in mammalian cardiac and amphibian skeletal muscles are generated by opening of multiple RyR channels. Further, symmetric high concentrations of Mg2+ substantially reduced the current carried by 10 mM Ca2+ (∼40% at 10 mM Mg2+), suggesting that high Mg2+ may make sparks smaller by both inhibiting RyR gating and reducing unitary current.
Bulk magnetic susceptibility effects on the assessment of intra- and extramyocellular lipids in vivo

Localized proton spectroscopy provides a novel method for noninvasive measurement of lipid content in skeletal muscle. It has been suggested that the chemical shift difference between lipid signals from distinct compartments in skeletal muscle might be caused by bulk magnetic susceptibility (BMS) differences from lipids stored in intra- (IMCL) and extramyocellular (EMCL) compartments. Direct evidence is provided to confirm the theoretical prediction that compartment symmetry is responsible for discrimination between resonances of IMCL and EMCL. Phantoms imitating lipids in skeletal muscle were constructed using soybean oil to represent EMCL, and IntralipidTM, an intravenous fat emulsion of fine droplets, to represent IMCL. It was found that the chemical shift of IntralipidTM is independent of the BMS effects, while the resonance of soybean oil shifts in a predictable manner determined by the geometry of the compartment.
Searching for high baryon density at the AGS with ARC

Abstract A relativistic cascade ARC is used to analyse heavy ion experiments at the AGS. In particular predictions from ARC for Au on Au at 11.6 GeV c have proved to be remarkably accurate. Going to lower energies and inserting a phenomenological equation of state into the cascade should lead to information about the interesting region of high baryon density.
Retrospective case series of the clinical features, management and outcomes of patients with autoimmune epilepsy

A B S T R A C T Purpose: Analyze clinical and electrographic characteristics of patients with autoimmune epilepsy, and evaluate the effect of early diagnosis and treatment on reduction of seizure frequency. Methods: Observational retrospective case series, conducted using electronic medical data from two teaching hospitals. Clinical data was collected from 2008 to 2013. Cases of new onset seizures were selected based on the presence of laboratory evidence of autoimmunity. Results: 34 hospitalized patients who presented predominantly due to seizures with concern for autoimmune etiology were identified. Mean age of patients was 44.94 years and 64.7% were males. Autoimmune antibodies were detected in 76.5% (26) of patients as follows: VGKc (8); NMDA-R (7); antithyroid (5); GAD (4); GABAB (2). 22 patients had unilateral temporal lobe onset and 4 had bilateral temporal lobe onset, while 8 had extra-temporal onset/multiple ictal foci. Median number of seizures during initial prolonged vEEG monitoring was 8 (range 0–48); median number of anti-seizure medications used was 2 (range 1–5). 9 patients had an underlying malignancy. 94.1% (32) patients received immunomodulation, as follows: high dose corticosteroids (96.8%), plasmapheresis (62.5%), IVIG (34.4%), rituximab (21.8%), mycophenolate (15.6%), cyclophosphamide (12.5%). 63.3% (19) participants achieved 50% seizure reduction (Responder Rate) at first clinic visit. Patients without malignancy had better seizure control (p < 0.05). Time from symptom onset to diagnosis (p < 0.005) and symptom onset to immunomodulation (p < 0.005) was significantly lower among patients who achieved responder rate (RR). Conclusion: This study highlights certain important clinical and electrographic aspects of autoimmune epilepsy, and the significance of early diagnosis and initiation of immunomodulatory therapy.
Lattice sums and madelung constants

Abstract A new method for the evaluation of classical or quantum-mechanical lattice sums is illustrated by the calculation of Madelung constants. The method is more rapid than the standard technique for evaluating Madelung sums.
Within-compound associations between taste and contextual stimuli

When rats are presented with a compound conditioned stimulus (CS) made up of two taste elements, they are able to form a within-compound association between the individual elements of the CS compound. The present experiment demonstrates that when a taste stimulus is presented in a distinctive context, subjects are able to form a within-compound association between taste and contextual stimuli. These data suggest that within-compound learning represents a general process by which subjects are able to associate stimuli from a variety of modalities. Implications of these data for explanations of taste-potentiated contextual aversions are discussed.
Schistosomiasis Vaccines: What Parasitology can do for Immunology

In response to B. Gryseels article on schistosomiasis vaccines1xSchistosomiasis vaccines: a devils’ advocate view. Gryseels, B. Parasitol. Today. 2000; 16: 46–48Abstract | Full Text | Full Text PDF | PubMed | Scopus (27)See all References1, I suggest that it is ‘not what immunology can do for parasitology but what parasitology can do for immunology’ (Roland Terry, pers. commun.). This is especially applicable to the development of a schistosomiasis vaccine, which has done much to support the field of immunology, but which, in reality, has done little to alleviate the disease.The 1974 Edna McConnell Clark Foundation meeting was followed by a strategic plan to have a vaccine ready by 1984. Between the Clark Foundation, the National Institute of Health (NIH) and the Tropical Disease Research initiative of WHO, a conservative estimate of US$100 million must have been spent on schistosomiasis vaccine research. One could argue that this amount is far from adequate as vaccine development is an expensive area of research and companies often spend far in excess of this before a single product can be marketed.There is no doubt that new concepts and ideas in vaccine development and basic immunology will allow for a major breakthrough in schistosomiasis vaccine development. However, the crucial question is do we really need a vaccine?I consider schistosome population genetic structure (see Curtis and Minchella2xSchistosome population genetic structure: when clumping worms is not just splitting hairs. Curtis, J. and Minchella, D.J. Parasitol. Today. 2000; 16: 68–71Abstract | Full Text | Full Text PDF | PubMed | Scopus (47)See all References2) to be a more important area of schistosome research than is vaccine development. Understanding the basic genetic structure of schistosome populations will allow a much more rational approach towards developing more effective strategies for drug usage and the design and development of a vaccine than would direct vaccine research. Knowing the genetic structure and the genetic/biochemical mechanisms of the parasite that allow it to evade the immune system of the host, will be much more productive than taking the ‘black box’ approach of developing drugs and vaccines without this information.
Computer graphics education directory

This is SIGGRAPH's second directory of college-level computer graphics education, covering courses in computer graphics in a broad spectrum of disciplines. This directory is a single source of computer graphics course information. If you are a student entering college or considering a change of studies, a professional considering broadening your skills, or an educator seeking broader contacts in graphics among your peers, this directory is designed for you.The directory was compiled from the first directory and responses to a questionnaire sent out last spring. These responses were divided up by topic according to information received on the questionnaire and our perception of the course's audience. The placement of some courses may not be precise, so you may be advised to use more than one directory list in your search. For example, someone interested in graphics for architects would consult the Arts, Architecture, and Design listings, but might also find useful information in the list on Engineering, CAD/CAM, and Drafting. All interesting entries should be followed up by direct contact with the school for the many details of schedule, cost, and admission which are not included here.The courses we received were placed in individual lists by the following criteria. The Concepts and Systems list consists of courses covering general concepts in computer graphics and systems for producing graphics; such courses are often found in Computer Science or EECS programs and have no particular application orientation. The Engineering, CAD/CAM, and Drafting list contains courses which seem to be oriented toward applications in these areas. For CAD/CAM and Drafting courses, this is rather easy to tell, while the engineering orientation is inferred from a location in an Engineering program with no other information, or from a title such as "Engineering Computer Graphics." Many Engineering programs, however, have courses which seem to fit the Concepts and Systems category most closely and so are listed there. The other lists are fairly easily categorized, except for some problems determining where to place courses in Design; here the home program is usually the determining factor.
The excitotoxicity of heterocyclic dicarboxylic acids in rat hippocampal slices: structure-activity relationships

The structural resemblance of certain heterocyclic dicarboxylates to aspartate and glutamate led investigators to study their potency as agonists and antagonists of the N-methyl-D-aspartate (NMDA) receptor. The sensitivity of hypoxic rat hippocampal slices to NMDA ligands is several fold greater than that of normoxic slices. In the present study, the excitotoxic potency of heterocyclic dicarboxylates was assessed electrophysiologically by measuring their ability to enhance hypoxic and hypoglycemic neuronal damage in the rat hippocampal slice preparation. Four compounds were tested: quinolinate (QUIN), 4,5-imidazole-dicarboxylate (IZDA), 1,2,3-triazole-4,5-dicarboxylate (TZDA), and 2,3-pyrazinedicarboxylate (PZDA). QUIN was the most toxic drug in enhancing both hypoxic and hypoglycemic neuronal damage. IZDA and TZDA were slightly less toxic than QUIN, while PZDA was innocuous. The effect of the 3 active drugs was blocked by the NMDA competitive antagonist DL-2-amino-5-phosphonovalerate. The sequence -N-CH(COOH)-CH(COOH)- appears to be a prerequisite for a heterocyclic dicarboxylate to exert NMDA-type agonistic properties. A 5-membered ring heterocyclic compound which contains more than one nitrogen atom in its ring retains its NMDA-type toxicity while a 6-membered ring with more than one nitrogen atom (PZDA) does not.
Anomalous enhancement of negative sputtered ion emission by oxygen

Abstract Enhancement of negative sputtered ion yields by oxygen (either O + 2 bombardment or O 2 gas with Ar + bombardment) is demonstrated for Si − , As − , P − , Ga − , Cu − and Au − , sputtered from a variety of matrices. Because oxygen also enhances positive ion yields of the same species, this effect cannot be simply explained on the basis of existing sputtered ion emission models. To rationalize these phenomena, a surface polarization model is developed which invokes localized electron emissive or electron retentive sites associated with differently oriented surface dipoles in the oxygenated surface. Such sites are considered to dominate the emission of negative and positive ions respectively. The model is shown to correctly predict that Au + and Au − ion yields are much more strongly enhanced by oxygen in dilute Au-Al alloys than in pure gold.
Watching Sausage Being Made: Lessons learned from the co-production of governance in a behavioural health system

AbstractWe draw out lessons from a multi-level governance system implemented to create more consumer oversight and involvement in the governance of behavioural health services. Through two rounds of interviews, we identified key areas of design that were difficult to implement, resulting in the system continuing to operate as a top-down environment rather than a flatter arrangement. Although new governance structures can be implemented, the underlying culture of government has to shift to allow real buy-in. Until this happens, multi-level governance systems will remain single-layered and command and control systems. The patina of change will cause frustration and animosity among participants.