cssi/SciSciGPT-SciSciNet huggingface dataset:
Arsenite retention mechanisms within estuarine sediments of pescadero, CA

Arsenic, a toxic metalloid, is commonly associated with sulfide minerals in anoxic sediments. Here we characterize arsenic(III) retention on sediments from a sulfidic estuarine marsh using a series of sorption experiments, and probe the structure of retained arsenite with X-ray absorption spectroscopy. Although the extent of sorption varied with sampling locations, several adsorption characteristics were apparent. A fraction of arsenite adsorbed over the entire pH range examined, although it was most extensive at pH greater than 7, and conformed to a Langmuir isotherm. Iron sulfide phases were responsible for As partitioning in these sediments. Initially, an FeAsS-like precipitate formed with a structure similar to those reported for As(III) sorbed on iron sulfides, a complex that is highly reactive. Following reaction for 21 d, much of the FeAsS-like precipitate was converted to As2S3. A drop in the redox potential accompanied this conversion, suggesting that the evolution of sulfide and other reduced sp...
Reconsidering heterogeneity in panel data estimators of the stochastic frontier model

This paper examines several extensions of the stochastic frontier that account for unmeasured heterogeneity as well as firm inefficiency. The fixed effects model is extended to the stochastic frontier model using results that specifically employ its nonlinear specification. Based on Monte Carlo results, we find that the incidental parameters problem operates on the coefficient estimates in the fixed effects stochastic frontier model in ways that are somewhat at odds with other familiar results. We consider a special case of the random parameters model that produces a random effects model that preserves the central feature of the stochastic frontier model and accommodates heterogeneity. We then examine random parameters and latent class models. In these cases, explicit models for firm heterogeneity are built into the stochastic frontier. Comparisons with received results for these models are presented in an application to the U.S. banking industry.
Nonlinear model predictive control of a fixed-bed water-gas shift reactor: An experimental study

Abstract This paper describes new results on the experimental application of nonlinear model-predictive control (NMPC) to a fixed-bed water-gas shift (WGS) reactor. The development and experimental validation of an appropriate first-principles WGS reactor model, and how it impacts controller performance is discussed. The implementation of NMPC is computationally intense, requiring that a large nonlinear program (NLP) be solved at each sampling period. The significant computational burden dictates that a relatively slow sampling rate be used. Infrequent sampling, however, diminishes disturbance rejection capabilities. To combat this problem, NMPC was implemented in a master- slave cascade configuration where a low-level liner controller, having a significantly faster sampling rate, was employed. The control study was performed using a PC-based distributed control system (DCS) . One of the three processors was dedicated to NMPC calculations. A complete and rigorous implementation strategy is described in the paper, and the performance of NMPC for set-point tracking of this nonlinear process is shown to be superior to adaptive or linear control. We also illustrate the ease with which NMPC accommodated feedforward control.
A Method for Continuous Measurement of Plasma Potential over a Range of 0-4 kV

A method is described for continuously measuring plasma potential over a 4-kV range using conventional components and equipment. The time resolution of the measurement is presently 1 msec, but could be made 0.1 msec without serious difficulty. The lithium-ion-beam transmission technique is used. The ion-beam energy is varied from 0 to 4 kV by a saw-tooth generator at a frequency of 1 kc/sec. A Faraday cup collects the ions which have acquired sufficient energy to overcome the plasma potential. When the current from the Faraday cup reaches a threshold level, the oscilloscope trace of the saw-tooth wave form is intensity-modulated, producing the desired plasma potential versus time relation.
Atriopeptins: a family of potent biologically active peptides derived from mammalian atria.

Abstract Extracts of rat atria are potent stimulators of sodium and urine excretion, and relax vascular and intestinal smooth muscle preparations. The structures of six biologically active peptides obtained from atrial extracts are reported here. Ion exchange chromatography of a low molecular weight fraction obtained by gel filtration of atrial extracts produced two natriuretic fractions: the first induced relaxation of intestinal smooth muscle strips only, whereas the second also relaxed vascular strips as well. From the first fraction four pure biologically active peptides obtained by reverse phase HPLC have been sequenced: the 21 amino acid peptide, designated atriopeptin I, and three homologs (des-ser 1 -, des-ser 1 -ser 2 -, and des-ser 21 -atriopeptin I). From the second fraction two pure biologically active peptides were obtained, which had C-terminal extensions of atriopeptin I: atriopeptins II (23 amino acid residues) and III (24 residues), having respectively phe-arg and phe-arg-tyr C-termini. These results suggest that this family of six peptides, sharing the same 17 membered ring formed by an internal cystine disulfide, is derived from a common high molecular weight precursor.
Session scribe notes for Twenty-First ACM Symposium on Operating Systems Principles

The following article is divided into nine sections, one for each of the sessions presented at SOSP 2007. For each session, two student volunteers took notes at the conference, capturing the questions and answers following each of the papers presented in that session. Note that the session order follows the program as given at the conference which, due to logistic necessity, differs slightly from the order in the proceedings.
Development of a vaginal delivery film containing EFdA, a novel anti-HIV nucleoside reverse transcriptase inhibitor.

Abstract The aim of this work was to develop a fast-dissolving film formulation containing EFdA for potential use as a topical vaginal microbicide for prevention of HIV sexual transmission. Solid state compatibility approaches were used to screen commonly used polymers for formulation development. Factorial design and desirability function were used to investigate the effect of two variables, the ratio of the polymers and the concentration of selected plasticizer on four mechanical responses including tensile strength, elongation at break, toughness and elastic modulus for optimization of the film formulation. Assessments of EFdA-loaded films included physicochemical characteristics, in vitro cytotoxicity, epithelia integrity, ex vivo permeability and bioactivity test. The optimal placebo film was composed of PVA, HPMC E5 and propylene glycol (7:3:3, w/w), and its mechanical characteristics were comparable to those of VCF® film (a commercial vaginal film product). Permeability studies using human ectocervical explants showed that there was no significant difference in cumulative permeated amount of EFdA between EFdA film and free EFdA. The results of in vitro cytotoxicity and bioactivity testing showed that 50% cytotoxic concentration (CC50) was several orders of magnitude higher than 50% effective concentration (EC50) of EFdA. Furthermore, epithelial integrity study showed that EFdA-loaded film had a much lower toxicity to HEC-1A cell monolayers as compared to VCF®. Therefore, EFdA-loaded vaginal film may be considered as a promising vaginal microbicide for HIV prevention.
Estrogen replacement therapy: effects on the endogenous androgen milieu.

Abstract Objective: To review the impact of exogenous estrogen replacement therapy (ERT) on the production, binding, and metabolism of ovarian and adrenal androgens. Design: Review of the scientific literature from January 1966 through June 2001 using MEDLINE. Conclusion(s): Although no precipitous drop in androgen production is apparent at the time of the menopause, androgens decrease slowly and progressively from early adulthood until old age. The impact of aging and of estrogen replacement therapy, particularly oral ERT, significantly reduces androgen bioavailability after menopause. The combined effects of reduced production with aging and the pharmacologic effects of oral ERT dramatically reduce the endogenous bioavailable androgen milieu. These changes may have adverse clinical implications for susceptible individuals.
Wickedness, reflexivity, and dialogue: toward a multivalent bioenergy

Bioenergy development is intensifying and is often accompanied by contentious social issues. This article provides a reflexive account of scholarship intended to advance citizen engagement around bioenergy through the practice of deliberative dialogue. Using a case from our work in Michigan, USA, we conceptualize bioenergy as a wicked problem – one that is ill-structured, socially complex, tentative, and eschews a definitive way forward that avoids clear outcomes. Problems are made ‘tame’, however, when complexity, diversity, and indeterminancy are obscured. Simultaneously holding in tension the diversity of meanings and values held by actors can reduce the likelihood of taming wicked problems, which is central to a democratic science. Thus, we argue for a multivalent approach to bioenergy. Deliberative dialogue is one technique that can engage citizens and achieve multivalency, yet, it, like any method, requires rigorous reflexivity. This reflexive exercise demonstrates how the normative biases of resear...
Chemical and mechanical instability in hot isospin-asymmetric nuclear matter

Abstract Using phenomenological equations of state, we study the chemical and mechanical instabilities in hot isospin-asymmetric nuclear matter. Both instabilities are found to depend strongly on the isospin asymmetry of the nuclear matter. For chemically and mechanically stable asymmetric nuclear matter, a lower neutron excess is found in the liquid phase than in the gas phase. Furthermore, the neutron excess in the mixed phase at densities between that of the liquid and the gas phases is limited by a certain maximum value. Also, for the nuclear equations of state considered here the boundary of chemical instability in the pressure-density plane is found to be more extended than that of mechanical instability. However, the locations of these boundaries depend sensitively on both the bulk compressibility of nuclear matter and the density dependence of the symmetry energy.
Mott transition in Ga-doped MgxZn1-xO: A direct observation

Abstract This paper reports the direct evidence for Mott transition in Ga-doped Mg x Zn 1− x O thin films. Highly transparent Ga-doped Mg x Zn 1− x O thin films were grown on c-plane sapphire substrates using pulsed laser deposition. 0.1 at.%, 0.5 at.% and 1 at.% Ga-doped Mg 0.1 Zn 0.9 O films were selected for resistivity measurements in the temperature range from 250 K to 40 mK. The 0.1 at.% Ga-doped Mg 0.1 Zn 0.9 O thin film showed typical insulator-like behavior and the 1 at.% Ga-doped Mg 0.1 Zn 0.9 O thin film showed typical metal-like behavior. The 0.5 at.% Ga-doped Mg 0.1 Zn 0.9 O film showed increasing resistivity with decreasing temperature; resistivity was saturated with a value of 1.15 × 10 −2 Ω cm at 40 mK, which is characteristic of the metal–insulator transition region. Temperature-dependent conductivity σ ( T ) in the low temperature range revealed that the electron-electron scattering is the dominant dephasing mechanism. The inelastic scattering time is found to vary as T −3/2 .
A method to facilitate and monitor expression of exogenous genes in the rat kidney using plasmid and viral vectors

Gene therapy has been proposed as a novel alternative to treat kidney disease. This goal has been hindered by the inability to reliably deliver transgenes to target cells throughout the kidney, whi...
Periodicity and boundedness for the integer solutions to a minimum-delay difference equation

In this paper, we study periodicity and boundedness for the integer solutions to a minimum-delay difference equations. As an application, a recent theorem regarding absolute-difference equations is extended.
A locally formed deep ocean canyon system along the Blanco Transform, Northeast Pacific

A dissected terrain resembling a shelf-edge canyon system with individual canyons up to 100 m in relief, 3 km in width, and 10 km in length is found along the south flank of the Cascadia Channel within the central Blanco Transform zone. The channels apparently formed from a combination of downcutting from turbidity currents off the Blanco Ridge and from backcutting due to mass-wasting. The relationships between the transform tectonics and the formation of the canyon are presented in a model which proposes both a direct link via triggering of slides from earthquakes and an indirect link associated with lowering the local base level of Cascadia Channel, thalweg downcutting, and wall-steepening leading to increased mass-wasting.
The incomplete fixation measure

In this paper we evaluate several of the most popular algorithms for segmenting fixations from saccades by testing these algorithms on the scanning patterns of toddlers. We show that by changing the parameters of these algorithms we change the reported fixation durations in a systematic fashion. However, we also show how choices in analysis can lead to very different interpretations of the same eye-tracking data. Methods for reconciling the disparate results of different algorithms as well as suggestions for the use of fixation identification algorithms in analysis, are presented.
Flocculation of Bacteria by Protozoa

IN view of the recent discussion1,2 of the possible importance of certain Protozoa in the flocculation of bacteria in sewage sludge, it may be of interest to record a clear-cut instance of flocculating activity on the part of a protozoan.
Differential Potentiation by Nystatin of the Effect of Antibiotics on Yeast and Mammalian Cells

The effect of the polyene antibiotic nystatin, used in combination with several other antibiotics, on the membranes of Candida albicans SC#8169 (yeast) cells and of Chinese hamster ovary and 3T3 (mammalian) cells was investigated. It was concluded from determinations of the viability of the yeast cells and from measurements of deoxyribonucleic acid synthesis by the mammalian cells that nystatin acts synergistically with several antibiotics on yeast cells, but not on CHO and 3T3 cells. This selective action of nystatin may prove useful in chemotherapy.
Hegel's Morals

Opponents of Hegel's philosophy traditionally support their arguments against his metaphysics and dialectical methodology by implying that the lack of an ethics in his system has unfortunate consequences for personal and political life. In rebuttal, defenders of Hegel then block the ad hominem charges by pointing out examples of sound moral and political behavior in Hegel's own life and by arguing that amoral or immoral conduct is not entailed by Hegel's dialectical reasoning. The success of this defense of the biographical Hegel has not yet been matched, however, by a systematic explanation of the nature of morality based on Hegel's philosophical writings themselves. Instead of supplying an alternative to Kant's conception of morality, Hegel's texts indeed seem to involve the devious strategy of attacking Kantian morality and then abruptly moving on to another topic. The shift of discussion to religion or the state appears to force commentators to conclude either that his philosophy lacks a systematic moral philosophy (Marcuse) or that it surreptitiously preserves an essentially Kantian ethics (Knox). In the former case his system apparently permits immoral conduct (for the sake of historical progress), and in the latter the philosopher merely deceives us with a dialectical sleight of hand. In either case, Hegel's morals are still in doubt.
Intravenous nitroglycerin infusion inhibits cyclic blood flow responses caused by periodic platelet thrombus formation in stenosed canine coronary arteries.

BACKGROUNDNitroglycerin and other clinically relevant organic nitrate derivatives have been shown to inhibit platelet aggregation in vitro. This antithrombotic effect of nitrates is potentiated by reduced thiol. To determine the potential relevance of this mechanism of action in vivo, we examined the effect of intravenous nitroglycerin infusion on periodic platelet thrombus formation in a canine model of coronary artery stenosis.METHODS AND RESULTSWe used a canine model of coronary artery stenosis associated with cyclic reductions in coronary blood flow that have been shown to depend on periodic platelet thrombus formation. We quantified the frequency of cycles per 40-minute observation period and monitored the effect of a continuous infusion of intravenous nitroglycerin on the cycle frequency. The administration of 10-15 micrograms/kg/min nitroglycerin reduced cyclic platelet thrombus formation significantly and did so without a significant change in coronary artery blood flow. Pretreatment with the redu...
Monte Carlo Renormalization Group Calculations for Polymers

A simple method based on Wilson's renormalization group ideas is applied to calculate the dynamical critical exponentz for polymer chains in different dynamical regimes. It is shown that the Doi-Edwards reptating chain does not belong to the same dynamical universality class as the Rouse chain. The earlier results based on e(4 −d, d ∼ space dimensionality) expansion for chains with excluded volume effect are recovered without any e expansion. When combined with the Monte Carlo techniques, this method results in a simple scheme for calculating the static and dynamic exponents for a polymer chain with a prescribed dynamics. Numerical results suggest that the slithering snake model of Wall and Mandel for the dynamics is in a different dynamic universality class than the Rouse chain.
Gas chromatography of urinary vanilmandelic acid in pheochromocytoma.

Abstract The properties and suitability of six different volatile derivatives of 3-methoxy-4-hydroxymandelic acid (VMA) were established on a non-polar and three polar columns, and the optimum conditions for determination of VMA by gas chromatography were established for a patient with pheochromocytoma. The method was then applied to eight other patients with pheochromocytoma. In all patients, VMA was significantly elevated. The advantages and disadvantages of the method are compared briefly with other methods reported in the literature.
Robotic light source failure and recovery: an innovative solution to an uncommon problem

Since 2003 the increasing use of robotic-assisted laparoscopic prostatectomy has been accompanied by the need to be prepared for a new set of problems in the operating room. Operative complications unique to the robot and its components are rare but can lead to case conversion and procedural abandonment. We describe an innovative solution to the uncommon problem of intraoperative robotic light source failure. Surgeons carrying out such procedures should be aware of this complication and be able to substitute a comparable light source. Possession of an appropriate type of low-cost alternative light source could prevent unnecessary procedural abandonment or open conversion in the setting of mid-operative light source failure.
Interactions between the secreted protein Amalgam, its transmembrane receptor Neurotactin and the Abelson tyrosine kinase affect axon pathfinding.

Two novel dosage-sensitive modifiers of the Abelson tyrosine kinase ( Abl ) mutant phenotype have been identified. Amalgam (Ama) is a secreted protein that interacts with the transmembrane protein Neurotactin (Nrt) to promote cell:cell adhesion. We have identified an unusual missense ama allele, ama M109 , which dominantly enhances the Abl mutant phenotype, affecting axon pathfinding. Heterozygous null alleles of ama do not show this dominant enhancement, but animals homozygous mutant for both ama and Abl show abnormal axon outgrowth. Cell culture experiments demonstrate the Ama M109 mutant protein binds to Nrt, but is defective in mediating Ama/Nrt cell adhesion. Heterozygous null alleles of nrt dominantly enhance the Abl mutant phenotype, also affecting axon pathfinding. Furthermore, we have found that all five mutations originally attributed to disabled are in fact alleles of nrt . These results suggest Ama/Nrt-mediated adhesion may be part of signaling networks involving the Abl tyrosine kinase in the growth cone.
Downstream targets of altered sphingolipid metabolism in response to inhibition of ENOX2 by phenoxodiol

Phenoxodiol, an ENOX2 inhibitor, alters cytosolic NADH levels to initiate a regulatory cascade linking sphingolipid metabolism and the PI3K/Akt pathway to programmed cell death. Specifically, the pyridine nucleotide products of plasma membrane redox, NAD+ and NADH, directly modulate in a recriprocal manner two key plasma membrane enzymes. NADH stimulation of sphingomyelinase and NADH inhibition of sphingosine kinase potentially lead to G1 arrest (increase in ceramide) and apoptosis (loss of sphingosine-1-phosphate). The findings link plasma membrane electron transport and the anticancer action of several clinically-relevant anticancer agents targeted to ENOX2 such as phenoxodiol. Growth inhibition by phenoxodiol is unaffected by inhibitors of protein or mRNA synthesis. Findings with okadiaic acid, an inhibitor of serine/threonine phosphatases, suggest that hyperphosphorylation of intracellular substrates does not affect the action of phenoxodiol on ENOX2. Our findings and those of others are consistent with operation of the FAS signaling pathway of apoptosis and its suppression by sphingosine-1-phosphate. The prevailing hypothesis is that products of Akt activation, c-FLIP and XIAP, which exhibit anticaspase activities to block FAS signaling when sphingosine-1-phospate is elevated, are down regulated to permit apoptosis when sphingosine-1-phosphate is decreased by inhibition of sphingosine kinase under conditions of elevated cytosolic NADH associated with anticancer drug inhibition of ENOX2.
Yeast Rad51 Recombinase Mediates Polar DNA Strand Exchange in the Absence of ATP Hydrolysis

Saccharomyces cerevisiae RAD51 gene is required for genetic recombination and recombinational repair of DNA strand breaks. Rad51 protein has a DNA-dependent ATPase activity, and it catalyzes ATP-dependent pairing and strand exchange between homologous DNA molecules. We show here that the rad51 Arg-191 protein, which is devoid of ATPase activity, mediates the pairing and strand exchange reaction upon binding ATP. In addition, the wild type Rad51 protein can catalyze pairing and strand exchange in the presence of the nonhydrolyzable ATP analogues adenylyl-imidodiphosphate and adenosine 5′-O-thiotriphosphate. Thus, homologous pairing and the unidirectional transfer of greater than 5 kilobases of DNA can occur efficiently without the need for nucleotide hydrolysis. Consistent with the results from the biochemical analyses, expression of the rad51 Arg-191 protein in a rad51 null mutant confers normal cellular resistance to the DNA damaging agent methylmethane sulfonate, suggesting that nucleotide binding by Rad51 is sufficient for biological function.
A GTPase-activating protein for the G protein Gα(z). Identification, purification, and mechanism of action

A GTPase-activating protein (GAP) specific for Galphaz was identified in brain, spleen, retina, platelet, C6 glioma cells, and several other tissues and cells. Gz GAP from bovine brain is a membrane protein that is refractory to solubilization with most detergents but was solubilized with warm Triton X-100 and purified up to 50,000-fold. Activity is associated with at least two separate proteins of Mr approximately 22,000 and 28,000, both of which have similar specific activities. In an assay that measures the rate of hydrolysis of GTP pre-bound to detergent-soluble Galphaz, the GAP accelerates hydrolysis over 200-fold, from 0.014 to 3 min -1 at 15 degrees C, or to >/=20 min-1 at 30 degrees C. It does not alter rates of nucleotide association or dissociation. When co-reconstituted into phospholipid vesicles with trimeric Gz and m2 muscarinic receptor, Gz GAP accelerates agonist-stimulated steady-state GTP hydrolysis as predicted by its effect on the hydrolytic reaction. In the single turnover assay, the Km of the GAP for Galphaz-GTP is 2 nM. Its activity is inhibited by Galphaz-guanosine 5'-O-thiotriphosphate (Galphaz-GTPgammaS) or by Galphaz-GDP/AlF4 with Ki approximately 1.5 nM for both species; Galphaz-GDP does not inhibit. G protein betagamma subunits inhibit Gz GAP activity, apparently by forming a GTP-Galphazbetagamma complex that is a poor GAP substrate. Gz GAP displays little GAP activity toward Galphai1 or Galphao, but its activity with Galphaz is competitively inhibited by both Galphai1 and Galphao at nanomolar concentrations when they are bound to GTPgammaS but not to GDP. Neither phospholipase C-beta1 (a Gq GAP) nor several adenylyl cyclase isoforms display Gz GAP activity.
Kinetic studies of l-valine and glycyl-l-valine uptake by Leuconostoc mesenteroides

Abstract When nongrowing but actively respiring cell suspensions of Leuconostoc mesenteroides were incubated under appropriate conditions with l -valine-1-C 14 , rapid uptake of the labeled amino acid occurred. This accumulation of valine-1-C 14 was much greater from glycyl- l -valine-1-C 14 than from the free amino acid form. By following the kinetics of valine uptake from the two sources, l -valine and glycyl- l -valine, specific uptake systems were found, and these systems followed Michaelis-Menten kinetics for enzymes. The apparent association constant, K , for valine uptake from glycyl- l -valine was 3.26 × 10 3 and was significantly greater than the K (1.60 × 10 3 ) observed for l -valine. Subsequent kinetic studies with combinations of labeled and unlabeled amino acids and peptides showed that the system which accumulated valine from glycyl- l -valine or other l -valine dipeptides was independent of the one operative with the free amino acid. These uptake systems were energy dependent as shown by the need for glucose as an energy source and by the effect of 2,4-dinitrophenol, which inhibited the uptake of the valine. Previously unrecognized was the stimulatory effect of unlabeled glycyl- l -valine and other l -valine dipeptides on the uptake of l -valine-1-C 14 . In the kinetic studies, K for the uptake of l -valine-1-C 14 was increased from 1.60 × 10 3 to 3.25 × 10 3 by the presence of unlabeled glycyl- l -valine. d -Valine peptides did not cause the same effect nor did other peptides which did not contain valine. Protein synthesis during the uptake studies did not appear to be necessary or associated with the uptake processes because chloramphenicol did not affect the uptake of valine or the stimulatory effect of the l -valine dipeptides.
Does addition of pramlintide to basal insulin improve glycemic control in type 2 diabetes mellitus

Does addition of pramlintide to basal insulin improve glycemic control in type 2 diabetes mellitus?
Quantitative high-performance liquid chromatography analysis of plant phospholipids and glycolipids using light-scattering detection

Application of the evaporative light-scattering principle to quantitative high-performance liquid chromatography (HPLC) analyses of plant membrane lipids has received little study. Light-scattering detection response curves were generated for nine classes of plant membrane phospholipid and glycolipids. Quantitative results obtained by HPLC/light-scattering detection and conventional lipid analytical methods (thin-layer chromatography and lipid-P assay) were in close agreement, confirming the reliability of HPLC/evaporative light-scattering detection (ELSD) analyses. Only three of the nine plant lipid classes gave linear detector response functions above 10 μg injected lipid mass. This finding contradicts earlier precepts involving light-scattering detection of lipids. At a given mass, appreciable variation in ELSD signal intensity and detection limit was found to exist among the various plant membrane lipid classes. The variation in detector response among plant lipid classes is an important consideration in achieving accurate quantitative results in plant lipid analyses.
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. We applied this method to two isolates of the phytopathogenic bacteria Pseudomonas syringae. Sequencing and reassembly of the well-studied tomato and Arabidopsis pathogen, Pto(DC3000), facilitated development and testing of our method. Sequencing of a distantly related rice pathogen, Por(1_)(6), demonstrated our method's efficacy for de novo assembly of novel genomes. Our assembly of Por(1_6) yielded an N50 scaffold size of 531,821 bp with >75% of the predicted genome covered by scaffolds over 100,000 bp. One of the critical phenotypic differences between strains of P. syringae is the range of plant hosts they infect. This is largely determined by their complement of type III effector proteins. The genome of Por(1_6) is the first sequenced for a P. syringae isolate that is a pathogen of monocots, and, as might be predicted, its complement of type III effectors differs substantially from the previously sequenced isolates of this species. The genome of Por(1_6) helps to define an expansion of the P. syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species.
Minimax rates of convergence for high-dimensional regression under ℓ q -ball sparsity

Consider the standard linear regression model y = Xs∗ + w, where y ∊ Rn is an observation vector, X ∊ Rn×d is a measurement matrix, s∗ ∊ Rd is the unknown regression vector, and w ~ N (0, σ2Ι) is additive Gaussian noise. This paper determines sharp minimax rates of convergence for estimation of s∗ in l 2 norm, assuming that β∗ belongs to a weak l b -ball B q (n q ) for some q ∊ [0,1]. We show that under suitable regularity conditions on the design matrix X, the minimax error in squared l 2 -norm scales as R q (log d ÷ n)1 −q÷2. In addition, we provide lower bounds on rates of convergence for general l p norm (for all p ∊ [l,+∞], p ≠ q). Our proofs of the lower bounds are information-theoretic in nature, based on Fano's inequality and results on the metric entropy of the balls B q (R q ). Matching upper bounds are derived by direct analysis of the solution to an optimization algorithm over B q (R q ). We prove that the conditions on X required by optimal algorithms are satisfied with high probability by broad classes of non-i.i.d. Gaussian random matrices, for which RIP or other sparse eigenvalue conditions are violated. For q = 0, t 1 -based methods (Lasso and Dantzig selector) achieve the minimax optimal rates in t 2 error, but require stronger regularity conditions on the design than the non-convex optimization algorithm used to determine the minimax upper bounds.
Geometric correction through complex interpolation

A method for the correction of images that are subject to spatial warping is presented. The correction method applies to two-dimensional images and employs the construction of a complex-valued interpolating polynomial. The construction is based on defining a set of points in an image whose desired location is known. The coefficients of the polynomial are shown to satisfy a recursion relation that simplifies implementation and improves evaluation efficiency. Results are presented for a two-dimensional slice from a magnetic resonance image.
Cost effectiveness of periodontal services

This paper presents the combined use of decision trees and cost-effectiveness analysis to determine on which patients new diagnostic tests can be useful, and whether they can change the dentist's decision to provide different services and thus improve patient outcomes in 5 different categories of patients. A decision tree is constructed in which the primary decision branches are "test" and "no test". The treatment and outcome branches in the test branch are affected by the results of the test which is then either negative or positive. In contrast, the treatment and outcome branches in the no-test branch represent pathways for patient therapy when the new (or additional) test is not used. Results show that even with excellent test efficacy parameters (sensitivity 0.87 and specificity 0.84) it is not cost effective to use a diagnostic test in the general population or for adults under age 45 years. However for adults > 45 years, patients referred to a periodontist, and patients with a history of periodontal disease, the test would change treatment decisions and improve patient care outcomes.
Computable visually observed phenotype ontological framework for plants

The ability to search for and precisely compare similar phenotypic appearances within and across species has vast potential in plant science and genetic research. The difficulty in doing so lies in the fact that many visual phenotypic data, especially visually observed phenotypes that often times cannot be directly measured quantitatively, are in the form of text annotations, and these descriptions are plagued by semantic ambiguity, heterogeneity, and low granularity. Though several bio-ontologies have been developed to standardize phenotypic (and genotypic) information and permit comparisons across species, these semantic issues persist and prevent precise analysis and retrieval of information. A framework suitable for the modeling and analysis of precise computable representations of such phenotypic appearances is needed. We have developed a new framework called the Computable Visually Observed Phenotype Ontological Framework for plants. This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in a machine-interpretable form. This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery. The framework was applied to two different plant species with semantic rules mined and an ontology constructed. Rule quality was evaluated and showed high quality rules for most semantics. This framework also facilitates automatic annotation of phenotype images and can be adopted by different plant communities to aid in their research. The Computable Visually Observed Phenotype Ontological Framework for plants has been developed for more efficient and accurate management of visually observed phenotypes, which play a significant role in plant genomics research. The uniqueness of this framework is its ability to bridge the knowledge of informaticians and plant science researchers by translating descriptions of visually observed phenotypes into standardized, machine-understandable representations, thus enabling the development of advanced information retrieval and phenotype annotation analysis tools for the plant science community.
EFFICACY OF FAMILY THERAPY FOR DRUG ABUSE: PROMISING BUT NOT DEFINITIVE

Drug abuse is an enormous public health problem with consequences not only for individuals using drugs but also for families, communities, and society. Moreover, research evidence and clinical experience agree that drug abuse is one of the more difficult problems to treat. Despite considerable research on the connection between family factors and drug use, and the existence of family therapy models for drug abuse, comparatively few controlled efficacy studies have been conducted. This article presents a critical review of controlled treatment outcome research in the area of family therapy for drug abuse in both adults and adolescents. A number of studies from different clinical research groups demonstrate that different versions of family intevention can engage and retain drug users and their families in treatment, significantly reduce drug use and other related problem behaviors, and enhace particular domains of prosocial functioning. Moreover, a smaller number of comparative efficacy studies have shown family therapy to be more effective than nonfamily therapies. Family therapy of adolescent drug abuse is more developed at present than family therapy of adult drug abuse. Although the results of the reviewed studies are promising, a blanket confirmation of family therapy's efficacy for drug abuse cannot be made at this time because of the relatively small number of studies and the noted methodological limitations of the studies published to date. Nonetheless, substantial progress in this clinical research area has occurred, and if research and funding support continue or can expand, significant breakthroughs in the treamtment of drug abuse with family-based treatments are possible.
Response of Chicks to Graded Concentrations of Cane Final Molasses

Abstract CANE final molasses is cheap, plentiful, and easily mixed into chicken rations. Despite these commendable attributes, it is rarely incorporated into present-day rations; and, when fed, it is mixed in low concentrations. If molasses can be fed at comparatively high levels, this should benefit greatly the poultry and cane sugar industries, and enhance their positions economically. The following studies and reviews have contributed to the generally held belief that for best results chickens should not be fed comparatively high levels of cane final molasses. Ewing (1951) recommended that not more than 2.5 percent be fed on a year-round basis. Scott (1953), following a more comprehensive review of the literature, concluded that levels of 4 to 5 percent molasses in starting and growing rations produced results which were “at least equivalent to those obtained with similar rations without molasses.” This conclusion was based on the results and interpretation of data reported …
Predation by Introduced Fishes on Endangered Humpback Chub and other Native Species in the Little Colorado River, Arizona

Abstract Fishes in the Little Colorado River in the Grand Canyon, Arizona, were sampled monthly from July 1991 to June 1995 as part of a study of the ecology of endangered humpback chub Gila cypha. Diets of five introduced predatory fish species were examined. Stomach contents varied among species and were low in diversity and dominated by algae (primarily Cladophora), aquatic insects, and fishes. Humpback chub plus other native species were a significant component of the diet (13.7% frequency of occurrence among 219 of 408 stomachs that contained food). Predation mortality from introduced fishes may significantly affect the native species by depleting numbers and reducing recruitment.
Sulforaphane enhances proteasomal and autophagic activities in mice and is a potential therapeutic reagent for Huntington's disease

The ubiquitin proteasome system (UPS) is impaired in Huntington's disease, a devastating neurodegenerative disorder. Sulforaphane, a naturally occurring compound, has been shown to stimulate UPS activity in cell cultures. To test whether sulforaphane enhances UPS function in vivo, we treated UPS function reporter mice ubiquitously expressing the green fluorescence protein (GFP) fused to a constitutive degradation signal that promotes its rapid degradation in the conditions of a healthy UPS. The modified GFP is termed GFP UPS reporter (GFPu). We found that both GFPu and ubiquitinated protein levels were significantly reduced and the three peptidase activities of the proteasome were increased in the brain and peripheral tissues of the mice. Interestingly, sulforaphane treatment also enhanced autophagy activity in the brain and the liver. To further examine whether sulforaphane promotes mutant huntingtin (mHtt) degradation, we treated Huntington's disease cells with sulforaphane and found that sulforaphane not only enhanced mHtt degradation but also reduced mHtt cytotoxicity. Sulforaphane-mediated mHtt degradation was mainly through the UPS pathway as the presence of a proteasome inhibitor abolished this effect. Taken together, these data indicate that sulforaphane activates protein degradation machineries in both the brain and peripheral tissues and may be a therapeutic reagent for Huntington's disease and other intractable disorders. Accumulation of mutant huntingtin (mHtt) protein causes Huntington's disease (HD). Sulforaphane (SFN), a naturally occurring compound, increased proteasome and autophagy activities in vivo and enhanced mHtt turnover and cell survival in HD cell models. SFN-mediated mHtt degradation is mainly through the proteasome pathway. These data suggest that SFN can be a therapeutic reagent for treating HD and other intractable disorders.
Aerosol Container-Related Eye Injuries in the United States: 1997-2009

PURPOSE: To quantify and characterize eye injuries related to aerosol container consumer products treated in United States hospital emergency departments (EDs) from 1997 through 2009. DESIGN: Retrospective study. METHODS: Descriptive analysis of aerosol container-related eye injury data derived from the National Electronic Injury Surveillance System, a stratified probability sample of hospital-affiliated United States EDs. Data collected included demographic variables (gender and age), locale, diagnoses, and hospital disposition associated with aerosol container-related eye injuries treated in United States EDs from 1997 through 2009. Products associated with injury and mechanisms of injury also were extracted and analyzed. RESULTS: There were an estimated 10 765 (95% confidence interval [CI], 9842 to 11 688) visits to United States EDs for aerosol container-related eye injuries during the study period; 6756 (95% CI, 5771 to 7742; 63%) patients were male; 5927 (95% CI, 4956 to 6897; 55%) injuries occurred in children (age Language: en
Challenges in EGFRvIII detection in head and neck squamous cell carcinoma.

Objective Head and neck squamous cell carcinoma (HNSCC) accounts for more than 5% of all cancers worldwide. The mortality rate of HNSCC has remained unchanged (approximately 50%) over the last few decades. Ubiquitous overexpression of wild type EGFR in many solid tumors has led to the development of EGFR targeted therapies. EGFR can be constitutively activated via several mechanisms including the truncated, EGFR variant III isoform (EGFRvIII). EGFRvIII lacks exons 2–7 and has been reported to be present in up to 20– 40% of HNSCC. EGFRvIII has been shown to contribute to cetuximab resistance. The mechanisms leading to EGFRvIII expression in HNSCC are unknown. The present investigation was undertaken to determine the etiology of EGFRvIII in HNSCC.
Impact of an online educational program on pharmacy students' knowledge of folic acid and neural tube defects.

Purpose: Pharmacy students must receive adequate training regarding folic acid for the prevention of neural tube defects (NTDs). Pharmacy students’ knowledge should be evaluated and effective metho...
Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota

The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial species or phylotypes revealed by molecular approaches. Although recent new technologies such as metagenomics and metatranscriptomics can provide more functionality information about the microbial communities, it is still important to develop the capacity to isolate and cultivate individual microbial species or strains in order to gain a better understanding of microbial physiology and to apply isolates for various biotechnological applications. We have developed a new system to cultivate bacteria in an array of droplets. The key component of the system is the microbe observation and cultivation array (MOCA), which consists of a Petri dish that contains an array of droplets as cultivation chambers. MOCA exploits the dominance of surface tension in small amounts of liquid to spontaneously trap cells in well-defined droplets on hydrophilic patterns. During cultivation, the growth of the bacterial cells across the droplet array can be monitored using an automated microscope, which can produce a real-time record of the growth. When bacterial cells grow to a visible microcolony level in the system, they can be transferred using a micropipette for further cultivation or analysis. MOCA is a flexible system that is easy to set up, and provides the sensitivity to monitor growth of single bacterial cells. It is a cost-efficient technical platform for bioassay screening and for cultivation and isolation of bacteria from natural environments.
Malate dehydrogenase in Ascaris suum: characterization, ontogeny, and genetic control.

Abstract Whole body and tissue homogenates of Ascaris suum exhibit four major bands of malate dehydrogenase (MDH) activity by the method of starch gel electrophoresis: one, a cathodal form which predominates in mitochondria, and the other three, anodal forms which are located primarily in the supernatant fraction of the cells. Physico-chemical studies, including thermostability, pH optima, K m 's, substrate inhibition curves, and reactivity with coenzyme analogs demonstrated differences between the mitochondrial and supernatant enzymes similar to those reported for other species. In addition the three supernatant isozymes differed in their thermostability and pH optima curves, the middle isozyme exhibiting properties intermediate to those of the other two isozymes. Observations on the ontogeny and tissue distribution of the supernatant isozymes, dissociation and recombination experiments, and the detection of an electrophoretic variant suggest that Ascaris supernatant MDH isozymes are dimers composed of subunits under separate genetic control. The functional significance of the different forms of MDH in Ascaris is discussed.