cssi/SciSciGPT-SciSciNet huggingface dataset:
Efficient Solution of Two-Stage Stochastic Linear Programs Using Interior Point Methods

Solving deterministic equivalent formulations of two-stage stochastic linear programs using interior point methods may be computationally diflicult due to the need to factorize quite dense search direction matrices (e.g., AAT). Several methods for improving the algorithmic efficiency of interior point algorithms by reducing the density of these matrices have been proposed in the literature. Reformulating the program decreases the effort required to find a search direction, but at the expense of increased problem size. Using transpose product formulations (e.g., A*A) works well but is highly problem dependent, Schur complements may require solutions with potentially near singular matrices. Explicit factorizations of the search direction matrices eliminate these problems while only requiring the solution to several small, independent linear systems. These systems may be distributed across multiple processors. Computational experience with these methods suggests that substantial performance improvements are possible with each method and that, generally, explicit factorizations require the least computational effort.
A teacher's schoolyard tale: illuminating the vagaries of practicing participatory action research (par) pedagogy

This single case study, situated within a larger narrative inquiry project, closely examines the professional stories told by one Project Grow teacher. Project Grow is a 10‐year‐old collaborative i...
Multiplexing symbolic dynamics-based chaos communications using synchronization

A novel form of multiplexing information-bearing chaotic waveforms is demonstrated experimentally. This scheme dramatically increases the information carrying capacity of a chaotic communication system. In the transmitter, information is encoded in the chaotic waveforms of two electronic circuits using small perturbations to induce the symbolic dynamics to follow a prescribed symbol sequence. Waveforms from each of the drive oscillators are summed to form a single scalar signal that is transmitted to the receiver. Identical oscillators in the receiver synchronize to their counterparts in the drive system, effectively de-multiplexing the transmitted signal. The transmitted information in each channel is extracted from simple return maps of the receiver oscillators.
Characterization of a Wireless Potentiostat for Integration With a Novel Implantable Biotransducer

Wireless potentiostats are being developed and commercialized for use in the development of implantable electrochemical biosensors for the monitoring of physiological markers in a wide range of pathologies. The merits and drawbacks of the Pinnacle 8151 dual potentiostat were investigated for use with a novel implantable biotransducer, the dual responsive microdisc electrode array (MDEA 5037) of ABTECH Scientific. The potentiostat was evaluated with R and RC dummy cells and with MDEA transducers modified with polypyrrole-poly(2-hydroxyethyl methacrylate) electroconductive hydrogels that were all qualified by calibrated ac impedance spectroscopy. In a laboratory setting, the 8151 potentiostat maintained a steady and unbroken signal as far away as 75 ft (23 m), and when unobstructed, up to 100 ft (30 m). The error between the two channels was determined to be 6.4 (±0.3)% and 0.7 (±0.1)% for resistor-capacitor dummy cells ( RC=nominally 10 MΩ and 1 μF) and resistor dummy cells (R=nominally 10 MΩ), respectively. The intra-channel variability was judged to be too large for exacting analyte determinations.
Aggregative feeding of pipevine swallowtail larvae enhances hostplant suitability

Many hypotheses have been proposed to explain the adaptive significance of aggregative feeding in the Lepidoptera. One hypothesis that has received little attention is how induced plant responses may be influenced by aggregative feeding, as compared to feeding by solitary larvae. This study investigated the role of aggregative feeding of the pipevine swallowtail, Battus philenor, in California with special emphasis on the induced responses to herbivory of its hostplant. Here, I show that first-instar larvae develop faster when feeding in a large aggregation compared to solitary or small groups of larvae. Furthermore, I show that this effect is mediated by a larval-density-dependent response in the plant and is independent of prior larval experience and direct interaction among larvae. These results indicate that large groups of larvae can effectively enhance hostplant suitability. A separate experiment showed that larvae feeding on previously damaged leaves had a reduced growth rate. Thus, following initial damage a plant first goes through a period of increased suitability, followed by induced resistance against subsequent herbivory. Aggregative feeding in this system may be an adaptive strategy for larvae to manipulate hostplant suitability, adding a new dimension to the role of aggregative feeding for the Lepidoptera.
Horizontal variability in chlorophyll fluorescence and potential temperature

Abstract Chlorophyll fluorescence and temperature were measured with a horizontal resolution of 4 m on two isopycnals and two isobars along a 1000 km meridional transect in the eastern North Pacific. Probability density functions (PDFs) of the magnitude of fluctuations in temperature and fluorescence are compared at each of a large range of length scales. While they are nearly identical at larger scales, the shapes of the PDFs of fluorescence and temperature differ significantly at small scales (∼1 km and less). This difference may indicate that at these scales, temperature and fluorescence distributions are controlled by distinct mechanisms. By comparing the phase of wavelet transforms of each of these two tracers, the tendency for temperature and fluorescence gradients to line up is investigated over a large range of spatial scales. At horizontal length scales of order 10 km and larger, the wavelet phase difference between temperature and fluorescence tends to be close to 0° or 180°—that is, the gradients tend to align, either in phase or 180° out of phase. At smaller scales, the distribution of phase difference on isopycnals is uniform—there is no tendency for gradients to coincide. Simple stirring models demonstrate that the locations of enhanced gradients in all tracers would be expected to coincide where the strain has been greatest. However, the directions of enhanced gradients formed in this way may be either parallel or antiparallel, depending on initial conditions and on the direction of the strain. These analyses suggest the horizontal distributions of temperature and fluorescence at large scales were both governed by advective processes. At intermediate scales, of order 1–10 km, a renovating wave model suggests that gradient alignment could be destroyed by turbulent diffusion or by rapid local phytoplankton growth.
A different kind of social enterprise: social cooperatives and the development of civic capital in Italy

Viewed predominantly as service-based institutions, the contribution of social enterprises to civil society has not received much attention. In the discussion that follows, I draw from a variety of primary sources, including an in person survey of presidents and directors of 140 Italian social cooperatives, as well as in-depth interviews with leaders of the Italian Cooperative Movement, to investigate the capacity of social cooperatives to generate collective benefits for Italian civil society. Combining a social economy framework with emerging conceptual work on civic capital, I analyze the relationship between this unique form of social enterprise and two key challenges to community development in Italy: parochialism and clientelism. By combining systematic empirical research of Italian social cooperatives, as a novel though increasingly important form of social enterprise in Europe, with a conceptual framework which focuses on the solidaristic aspects of these organizations, for which there is very lit...
Quantitation of cell concentration using the flow cytometer

A simple procedure has been developed to simultaneously measure cell concentration and analyze marker positive cell populations using the flow cytometer. Fluorescent latex particles of known concentration are added to the sample to be analyzed. Marker positive cells and fluorescent particles are then analyzed using flow cytometric methods. Since the particle concentration is known, the number of particles that have accumulated gives the exact volume of the sample analyzed. The concentration of total and marker positive cells that were analyzed then can be calculated. The method will be illustrated using single, dual, and triple laser excitation of cells stained for DNA content in combination with green or red fluorescent spheres. The usefulness of the procedure is demonstrated by counting cells from highly necrotic tumors where large amounts of debris are present.
Multidimensional magic angle spinning NMR spectroscopy for site-resolved measurement of proton chemical shift anisotropy in biological solids.

The proton chemical shift (CS) tensor is a sensitive probe of structure and hydrogen bonding. Highly accurate quantum-chemical protocols exist for computation of 1H magnetic shieldings in the various contexts, making proton chemical shifts potentially a powerful predictor of structural and electronic properties. However, 1H CS tensors are not yet widely used in protein structure calculation due to scarcity of experimental data. While isotropic proton shifts can be readily measured in proteins even in the solid state, determination of the 1H chemical shift anisotropy (CSA) tensors remains challenging, particularly in molecules containing multiple proton sites. We present a method for site-resolved measurement of amide proton CSAs in fully protonated solids under magic angle spinning. The approach consists of three concomitant 3D experiments yielding spectra determined by either mainly 1H CSA, mainly 1H–15N dipolar, or combined 1H CSA and 1H–15N dipolar interactions. The anisotropic interactions are recoupl...
Coalescence model for induction growth behavior in high shear granulation

Abstract Complex wet granulation behavior is often dependent on process parameters and formulation properties simultaneously. Mathematical models of granulation need to account for the complex physics if they are to be predictive. In this paper, a physically-based coalescence model is evaluated for use in the three-dimensional volume-based framework. The Liu coalescence kernel [20] is calculated for the three-dimensional system as a function of (1) the solid, liquid and gas volumes that form the granule, (2) an empirical correlation for granule mechanical properties as they depend on the granule composition and strain rate, and (3) the process conditions. A complex but well characterized industrial formulation is used as a case study. For this formulation, the granule strength varies over an order of magnitude for a range of conditions that correspond to actual behavior during granulation as granules densify due to consolidation. The kernel predicts that most collisions will result in rebound early in the granulation. As granules densify they become stronger, but also surface wet, resulting in Type I coalescence for many collisions once the average granule porosity drops below a critical value of 0.37. A kernel sub-model that incorporates changes in granule mechanical properties as a function of composition can then describe classic induction time behavior. The model is compared to an experimental study in a 50 L horizontal axis high shear granulator. Measurements of the size, porosity and morphology are used to identify rate process mechanisms over the course of the wet granulation process. The proposed coalescence model successfully describes the experimentally observed induction behavior as a function of composition, based on comparison to the kernel regime map for this formulation. The experimental value of critical porosity corresponding to the observed induction time, and continued growth of surface wet granules well past 1 mm in size also match the micro-scale behavior predicted by the kernel. This comparison shows that the physically-based kernel can be used to predict complex granulation behavior such as induction growth.
Mesodermal development in mouse embryos mutant for fibronectin

Three independent mutations were made by homologous recombination in two different regions of the fibronectin (FN) gene; all three appeared to be functional null mutations. The embryonic lethal phenotypes of these mutations were indistinguishable; all three FN mutant strains show mesodermal defects and fail to develop notochord or somites. Nevertheless analysis with lineage markers (Brachyury, sonic hedgehog, Notch-1, and mox-1) showed that both the notochord and the somite lineages were induced at the correct times and places. Furthermore, notochord precursor cells showed extensive cell migration in the absence of FN. However, neither notochord nor somites condensed properly in the absence of FN. These results show that specification of notochordal and somitic mesodermal lineages and significant cell migration are independent of fibronectin but that correct morphogenesis of these structures is FN-dependent.
A Saline Conductivity Method for Detection of Cardiac Shunts by Indicator-Dilution Technic

A new method for cardiovascular shunt detection is described using the indicator-dilution principle applied to blood conductivity changes produced by 5 per cent saline. It possesses these distinct advantages over the Evans blue technic: (1) an unlimited number of determinations can be made without an increasing blood dye background or bluish discoloration of the patient, (2) oximetric determination of blood oxygen saturation is not interferred with, and (3) a simple modification of the carrier amplifiers of commonly used recording systems supplies most of the necessary instrumentation.
Attitudes toward Empathy in Domestic Dogs and Cats

Summary This exploratory study included 524 undergraduate students (360 women, Mage = 21.1 yr., SD = 6.1; and 164 men, Mage = 20.0 yr., SD = 3.6) enrolled in introductory psychology sections who completed the Empathy in Pet Dogs and Cats Scale to assess their attitudes regarding how much domestic dogs and cats show vicarious experiencing of the thoughts, feelings, or attitudes of their owners. A principal components analysis followed by varimax rotation extracted five factors accounting for 60.85% of the total variance as follows: (1) Pets' empathy for owner, (2) Cats' empathy for owner, (3) Dogs' empathy for owner, (4) Souls in humans and pets, (5) Owners' empathy for pets. Women gave significantly higher ratings than men regarding dogs' and cats' knowing when their owners are happy, sad, or angry. Women also gave significantly higher ratings than men regarding dogs' and cats' feeling love and compassion for their owners. Specific instances of empathy in pets underscore the need for contemporary research...
Linear Integral Equations for Relativistic Multichannel Scattering

A set of three-dimensional coupled linear integral equations is presented for relativistic scattering and production processes. The new equations seem more amenable to numerical analysis than the standard Bethe-Salpeter equations. In addition one may discuss multiparticle scattering and hence inelastic processes. As a numerical example we discuss low-energy pion-pion scattering in the simplest approximation. We find that there are no self-consistent values for the mass and width of the $\ensuremath{\rho}$ meson if one takes into account only the elastic and $\ensuremath{\pi}\ensuremath{-}\ensuremath{\omega}$ channels.
The analysis of the semi-infinite cylinder problem

Abstract A semi-infinite cylinder with fixed short end is considered. Normal loads far away from the fixed end are prescribed. An exact formulation of the problem in terms of a singular integral equation is provided by using an integral transform technique. Stresses along the rigid end and stress intensity factors are computed numerically and are presented graphically.
Near-haploid cell line in the blastic crisis of chronic myelogenous leukemia: A possible marker for lymphoid malignancy☆

Abstract The blast cells of a 14-year-old patient in the blastic phase of chronic myelogenous leukemia (CML) were studied. Cellular morphology, presence of the enzyme terminal deoxynucleotidyl transferase (TdT), and reactivity to the common acute lymphoblastic leukemia antiserum (CALLA) substantiated a lymphoid blast cell line. Immunologic surface markers were nonreactive for E-rosette (T) cells and immunoglobulin-bearing (B) cells. Cytogenetic studies revealed persistance of the Philadelphia chromosome and a near-haploid cell line, i.e., 28,XY,t(9;22),+14,+15,+21,+22(GTG). The patient responded to chemotherapy with vincristine, prednisone, and l -asparaginase, first line drugs used for remission-induction of acute lymphoblastic leukemia in childhood. We suggest that severe hypodiploidy or near-haploidy, along with TdT and CALLA, may provide more accurate prognostic information in patients with CML and the lymphoid blastic crisis.
Differential Nitrogen‐15 Labeling of Dairy Manure Components for Nitrogen Cycling Studies

Current estimates of dairy manure nitrogen availability to crops are based on indirect measures and vary greatly. The objective of this study was to differentially label dairy manure N components with the stable isotope 15 N for direct measurement of manure N cycling in soils and availability to crops. Dairy urine and fecal N components (microbial and undigested feed N) were differentially labeled by feeding either 15 N-enriched forage or urea to mature dry dairy cows (Bos taurus). Nitrogen-15-enriched ammonium sulfate was used to label alfalfa (Medicago sativa L.) hay and corn (Zea mays L.) silage. These 15 N-enriched forages or either single or multiple doses of 15 N-enriched urea were fed for 2 to 3 d, and feces and urine were collected separately for 8 d after the initiation of 15 N feeding. For both labeling techniques, 15 N appeared first in urine followed by fecal microbial and undigested feed N. For the forage method, the proportionate combination of feces excreted before and after peak 15 N excretion levels would achieve uniform labeling of fecal N components. For the urea method, no undigested feed N in feces was labeled since 15 N-enriched forage N was not fed. The choice of which labeling method to use depends on the intended use of labeled manure. Manure enriched using the forage method and high levels of manure 15 N enrichments should be used for long-term manure N cycling studies. Manure enriched using the urea method and lower 15 N enrichments could be used in shorter-term studies.
Diffusion and Exchange of Non-Integral Membrane Associated Fluorophores During Fluorescence Recovery After Photobleaching with the Confocal Laser Scanning Microscope: ROI Size Analysis of EGFP:Ras2 Plasma Membrane Diffusion in Saccharomyces cerevisiae

Binding, lateral diffusion and exchange are fundamental dynamic processes involved in protein localization in cellular membranes. In this study, we developed numerical simulations of lateral diffusion of a fluorophore in a membrane with arbitrary bleach geometry and exchange of the fluorophore with cytosol during Fluorescence Recovery after Photobleaching (FRAP) experiments. Based on our model simulations, we designed and performed FRAP experiments with varying bleach region sizes on plasma-membrane localized EGFP:Ras2 in live yeast cells to investigate the mobility and the presence of any exchange processes operating in the time scale of our experiments. Model parameters estimated from a 1 micron x 1 micron bleach region-of-interest (ROI) size successfully predicted the 0.5 micron x 0.5 micron bleach ROI experiment without additional fitting. Successful prediction of the second experiment without data fitting shows the agreement of the experiment with the theory and excluded alternative models including both diffusion and binding, which were also tested against the experimental data. We also performed Fluorescence Correlation Spectroscopy (FCS) experiments as an independent method to measure the mobility of EGFP:Ras2. We show that simulation of FRAP experiments based on the mobilities and fluorophore fractions derived from FCS model fits enables the validation of the FCS model. The methods developed in this study are generally applicable for studying diffusion and exchange of membrane associated fluorophores using FRAP on widely available commercial confocal laser scanning microscopes.
ELECTROPHORESIS COMBINED WITH NOVEL MASS SPECTROMETRY TECHNIQUES : POWERFUL TOOLS FOR THE ANALYSIS OF PROTEINS AND PROTEOMES

Analytical and preparative electrophoresis separation techniques have been essential tools in protein biochemistry and the biological sciences in general. The combination of high resolution electrophoresis techniques with high performance analytical procedures has dramatically enhanced analytical protein biochemistry. In this report we describe the combination of electrophoretic separation techniques with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). A series of different techniques, consisting of automated high performance liquid chromatography (HPLC)-MS/MS, capillary-HPLC-MS/MS, and solid phase extraction (SPE)-capillary zone electrophoresis (CZE)-MS/MS, are described in the context of the identification of high pmol to the low fmol amounts of proteins. Application of these powerful new tools for the analysis of proteins on a large proteome-wide scale is presented. Furthermore, the combination of orthogonal separation techniques, such as immobilized metal affinity chromatography (IMAC) with SPE-CZE-MS/MS, and IMAC followed by HPLC, and by SPE-CZE-MS/MS, are presented for the detailed investigation of post-translational modifications of specific proteins.
Histopathology of Neodymium:YAG Laser Iridectomy in Humans

Abstract Fifteen peripheral iridectomy specimens were obtained, with informed consent, from patients with primary narrow angle glaucoma, after previous neodymium:YAG (Nd:YAG) laser iridectomy. The iridectomies were performed three hours to ten weeks after laser application. Iridectomy specimens were examined by scanning and/or transmission electron microscopy. Early effects of the Nd: YAG laser on the iris were mild hemorrhage and fibrinous aggregates. There were no inflammatory cell infiltrates. At later time intervals (up to 2 months postlaser treatment) the holes showed irregular thickness of iris pigment epithelium at the margins, and tissue atrophy limited to the immediate margins of the hole. Elsewhere the iris was structurally intact. The diameter of the holes varied from 60 to 500 μm. The larger holes corresponded to cases that had received more application shots.
Malnutrition, Altered Immune Function, and the Risk of Infection in Maintenance Hemodialysis Patients

T HE RISK of infection is increased during maintenance hemodialysis (MHO) treatment. 1 One well recognized risk factor for infection is the vascular access. 2 It provides a direct portal of entry to the circulation, and a local site favorable for bacterial colonization. Another potential risk factor for infection is altered immune function. 3 Immune alterations have been recognized for sometime in patients with chronic renal failure, and in the past these alterations have usually been attributed to uremia. 4•5 With the recent application of more sophisticated tests of immune function, an increasing variety of immune alterations have been documented in MHO patients, and predisposing causes other than uremia are being sought to explain these alterations. Protein-calorie malnutrition may be one such cause; it is associated both with altered immune function and an increased risk of infection. 6.7 Recently malnutrition has been recognized as a relatively common complication in MHO patients.8 Its recognition has been facilitated by a wider appreciation of the importance of nutrition in a variety of chronic diseases, by a more agressive approach to treatment, and by earlier diagnosis as a consequence of the more routine use of standardized nutritional assessment criteria. 9 In addition, malnutrition is probably more prevalent in MHO patients today than in their counterparts of several years ago; one reason for this is that the acceptance criteria for MHO treatment in patients with end-stage renal disease (ESRO) have gradually broadened since federal financial support became available in 1973. As a result, the average age of MHO patients is steadily increasing and patients with a variety of chronic diseases are now being accepted for treat-
Embryogenesis meets tumorigenesis.

Transplantation of metastatic melanoma cells into zebrafish embryo disrupts development—and identifies a potential new drug target for this deadly cancer ( pages 925 – 932 ).
Direct nuclear excitation of a 3He‐CO2 gas mixture

Probe measurements using a continuous wave CO2 laser have been carried out on a 3He‐CO2 gas mixture directly excited by the 3He(n,p)3H reaction. At a gas pressure of 1 atm and thermal neutron flux up to 1×1017 n/cm2 sec, total extinction of the probe beam was observed. Addition of N2 to the gas mixture (up to 20%) produced a media such as is used in electric discharge CO2 lasers. However, this mixture produced the same results as the 3He‐CO2 mixture. Absorption of the laser beam indicates that with direct nuclear excitation, it is the lower laser level which is excited. Therefore direct nuclear pumping of a CO2 laser does not appear feasible.
Evaporative spray cooling of plain and microporous coated surfaces

Experiments were performed on air and evaporative spray cooling of plain and microporous coated surfaces on flat and cylindrical heaters. Micron-size aluminum particles were used to build the microporous structures on the heated surfaces. To analyze the evaporative cooling, heat transfer curves were obtained in the form of the wall temperature difference versus heat flux. The heat transfer coefficients were also determined as a function of heat flux. Three water flow rates (1.25, 1.75 and 2.40 ml/min) were tested for the flat heater and one rate (3.0 ml/min) for the cylindrical heater, maintaining the air pressure of 7 psig (48 kPa) at the inlet of the nozzle. The effect of different particle sizes in the coating was also tested to optimize the microporous coating technique. Spraying water droplets on the microporous coating surface enhanced the heat removal due to the capillary pumping phenomenon through the microporous cavities connecting each other. The evaporative spray cooling increased the heat transfer coefficient by up to 400% relative to that of the uncoated surface cooled by dry air, and this enhancement was maintained at high heat fluxes by using microporous surfaces.
Cancer prevention with freeze-dried berries and berry components

Our laboratory is developing a food-based approach to the prevention of esophageal and colon cancer utilizing freeze-dried berries and berry extracts. Dietary freeze-dried berries were shown to inhibit chemically induced cancer of the rodent esophagus by 30-60% and of the colon by up to 80%. The berries are effective at both the initiation and promotion/progression stages of tumor development. Berries inhibit tumor initiation events by influencing carcinogen metabolism, resulting in reduced levels of carcinogen-induced DNA damage. They inhibit promotion/progression events by reducing the growth rate of pre-malignant cells, promoting apoptosis, reducing parameters of tissue inflammation and inhibiting angiogenesis. On a molecular level, berries modulate the expression of genes involved with proliferation, apoptosis, inflammation and angiogenesis. We have recently initiated clinical trials; results from a toxicity study indicated that freeze-dried black raspberries are well tolerated in humans when administered orally for 7 days at a dose of 45 g per day. Several Phase IIa clinical trials are underway in patients at high risk for esophagus and colon cancer; i.e., Barrett's esophagus, esophageal dysplasia and colonic polyps, to determine if berries will modulate various histological and molecular biomarkers of development of these diseases.
CD of ethidium bromide complexes with normal and electrophoretically anomalous DNA restriction fragments.

The equilibrium binding of ethidium bromide (EB) to two small 147 base-pair (bp) DNA restriction fragments, which exhibit different mobilities in polyacrylamide gels, was investigated by CD. Two larger DNA restriction fragments and calf thymus DNA were also studied for comparison. Difference spectra were calculated by subtracting the spectrum of the pure DNA from the spectra of its DNA–EB complexes. The D/P ratios ranged from 0.03 to 1.0. The difference CD spectra of all fragments are characterized by bands with maxima near 310, 275, and 207 nm, and minima near 290, 253, 225, and 190 nm. The band near 310 nm, which has a shoulder at about 335 nm, has zero intensity at D/P ≤ 0.05, and rises to a plateau value, different for each fragment, at D/P ≃ 0.3 for large fragments (≥ 1400 bp), and D/P ∼ 0.7 for the two small 147 bp fragments. The minimum near 290 nm is markedly blue shifted with increasing D/P, the wavelength of the extremum corresponding approximately to the wavelength of the uv absorption maximum of the DNA–EB complex. The negative amplitude of this band at D/P = 1.0 depends on the molecular weight of the DNA. The difference CD maximum near 275 nm is positive at low D/P ratios, increases and goes through a maximum at D/P = 0.06–0.1, and then becomes increasingly negative with increasing D/P. The amplitude of the negative ellipticity per added dye is constant at high D/P ratios, suggesting that the transition can be attributed to outside-bound EB molecules. The ellipticities at 310, 290, and 253 nm increase in absolute magnitude with increasing D/P at approximately the same rate, suggesting that all three bands are associated with the same optical and/or conformational transition. For the two small 147 bp fragments the fractional increases in amplitude of these bands parallel the fractional increase in length of the DNA upon binding EB, determined by electric birefringence measurements. The titration of the restriction fragments with EB was also followed by optical absorption. Two end points are observed, the first at a D/P ratio of ∼ 0.1, reflecting the transition between intercalated and outside-bound dye molecules, and the second at D/P ≃ 1.0, the equivalence point of the titration.
Theophylline-induced upregulation of A1-adenosine receptors associated with reduced sensitivity to convulsants.

Abstract Chronic administration of theophylline (50 mg kg twice daily for 14 consecutive days) significantly increased the specific binding of [3H]CHA in membranes of the cerebral cortex and cerebellum of the rat, but not in membranes derived from the hippocampus or diencephalon. To characterize further the upregulation of A1 = adenosine receptors induced by theophylline, saturation analysis with [3H]CHA was performed in membranes of the cerebral cortex and cerebellum. In both saline- and theophylline-treated cortical membranes the binding isotherms for (3H]CHA could be resolved into receptor affinity states having respectively high (KH) and low (KL) affinity for [3H]CHA. The high and low affinity dissociation constants obtained from theophylline-exposed membranes of the cerebral cortex were 1.14 nM and 25.2 nM and did not differ significantly from the corresponding values in saline-treated animals. Chronic exposure to theophylline did, however, produce significant increases in the densities of both the high and low affinity forms of A1-adenosine receptors in the cerebral cortex. Qualitatively and quantitatively similar results were observed in cerebellar membranes. These results suggest that chronic exposure to theophylline increases the density of A1-receptor in the cerebral cortex and cerebellum with no concomitant changes in the ability of [3H]CHA to distinguish separate agonist affinity states of the receptor. The physiological significance of theophylline-induced upregulation was assessed by determining seizure thresholds for convulsants in rats treated chronically with saline or theophylline. Chronic exposure to theophylline resulted in significant increases in the doses of pentylenetetrazol, bicuculline and picrotoxinin required to elicit a clonic convulsion. Thus, these results suggest that the reduced susceptibility to seizures induced by change in convulsant animals treated chronically with theophylline represents a functional change.
Microsatellites of the self-compatible nemertean Prosorhochmus americanus (Hoplonemertea)

Thousands of microsatellite loci were identified in the nemertean Prosorhochmus americanus through enrichment-isolation and next-generation sequencing protocols. We tested 48 loci for amplification and subsequently genotyped 17 loci in 30 individuals from three North American populations. Most loci were polymorphic within and across populations; six were monomorphic. The number of alleles per locus ranged from 1 to 9 (mean 4.35, SD 2.37). Cross-species amplification in four nemertean species revealed extended marker utility. These loci will enable investigations of colonization potential and natural history in this selfing, putatively introduced species.
Prioritizing intrusion analysis using Dempster-Shafer theory

Intrusion analysis and incident management remains a difficult problem in practical network security defense. The root cause of this problem is the large rate of false positives in the sensors used by Intrusion Detection System (IDS) systems, reducing the value of the alerts to an administrator. Standard Bayesian theory has not been effective in this regard because of the lack of good prior knowledge. This paper presents an approach to handling such uncertainty without the need for prior information, through the Dempster-Shafer (DS) theory. We address a number of practical but fundamental issues in applying DS to intrusion analysis, including how to model sensors' trustworthiness, where to obtain such parameters, and how to address the lack of independence among alerts. We present an efficient algorithm for carrying out DS belief calculation on an IDS alert correlation graph, so that one can compute a belief score for a given hypothesis, e.g. a specific machine is compromised. The belief strength can be used to sort incident-related hypotheses and prioritize further analysis by a human analyst of the hypotheses and the associated evidence. We have implemented our approach for the open-source IDS system Snort and evaluated its effectiveness on a number of data sets as well as a production network. The resulting belief scores were verified through both anecdotal experience on the production system as well as by comparing the belief rankings of hypotheses with the ground truths provided by the data sets we used in evaluation, showing thereby that belief scores can be effective in mitigating the high false positive rate problem in intrusion analysis.
Why Are There No Spinsters in Japan

The Western European folk model of spinsterhood portrays the spinster as a woman who eschews marriage because of economic difficulties or who deliberately chooses a career other than marriage. How does this model fare in other societies? Using population registers covering a single village in Japan in the preindustrial period (1671-1871), this paper finds that spinsters are rare. There are few economic bars to marriage, but, more importantly, there are no careers for unmarried women. They do not serve as domestic servants or as sur rogates in other roles in the household; they do not occupy specialist helping roles, and they do not become religieuses. On the contrary, even women whose prospects are slim are deliberately placed in households as married women. Hence, spinsterhood in Western Europe is an anomaly. Its existence must be ex plained, not assumed.
Evidence for Misaligned Disks in the T Tauri Triple System: 10 μm Superresolution with MMTAO and Markov Chains

Although T Tauri is one of the most studied young objects in astronomy, the nature of its circumstellar environment remains elusive, due in part to the small angular separation of its three components (North-South and South a-b are separated by 0.68'' and 0.12'', respectively). Taking advantage of incredibly stable, high Strehl ratio point-spread functions (PSFs) obtained with mid-IR adaptive optics at the 6.5 m MMT, we are able to resolve the system on and off the 10 μm silicate dust feature (8.7, 10.55, and 11.86 μm; 10% bandwidth), and broad N. At these wavelengths, South a-b are separated by only ~0.3λ/D. This paper describes a robust Markov chain Monte Carlo technique to separate all three components astrometrically and photometrically, for the first time, in the mid-IR. Our results show that the silicate feature previously observed in the unresolved T Tau South binary is dominated by T Tau Sa's absorption, while Sb does not appear to have a significant feature. This suggests that a large circumbinary disk around Sa-Sb is not likely the primary source of cool dust in our line of sight, and that T Tau Sa is enshrouded by a nearly edge-on circumstellar disk. Surprisingly, T Tau Sb does not appear to have a similarly oriented disk.
Alchemical prediction of hydration free energies for SAMPL

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not.
Robust control design for uncertain flexible-joint manipulators: a singular perturbation approach

A robust composite control law is proposed for flexible-joint manipulators which contain uncertainties. The uncertainty considered is nonlinear and (possibly fast) time-varying. Therefore, the uncertain factors such as imperfect modeling, friction, payload change, and external disturbances are all addressed. Based only on the possible bound of the uncertainty, a robust control law is constructed for the rigid counterpart of the flexible-joint robot. A velocity feedback control term is then added to the robust control law to stabilize the elastic vibrations at the joint. To show that the proposed robust composite control law is indeed applicable to flexible-joint robots, a singular perturbation approach for the stability study is proposed. Practical stability is proven. The size of the uniform ultimate boundedness ball can be manipulated to be arbitrary small. >
MODELING SHAPES AND DYNAMICS OF CONFINED BUBBLES

We review mathematical models of confined bubbles, emphasizing physical mechanisms as expressed in simple geometries. Molecular interactions between liquid, gas, and the confining solid are all important and are described through the disjoining pressure concept. Methods for finding static shapes are considered. The static solution is a springboard for discussing pressure-driven and surface-tension-driven flows, both of which involve viscous effects and macroscopic films entrained near apparent contact lines. We next discuss vapor bubbles produced by thermal effects. Vaporization localized near contact lines and condensation distributed in colder parts of the interface lead to steady vapor bubbles. Their size is determined through global constraints. Unsteady vapor bubbles are discussed and we end with thoughts on open problems.
A New Biometric Identity Based Encryption Scheme

In this paper, we present a new and efficient biometric identity based encryption scheme (BIO-IBE) using the Sakai Kasahara key construction and prove its security in the random oracle model based on the well-exploited k-BDHI computational problem. Our new scheme achieves better efficiency in terms of the key generation and decryption algorithms compared to the existing fuzzy IBE schemes. The main difference of the new BIO-IBE scheme is the structure of the key generation algorithm, where a unique biometric identity string ID obtained from the biometric attributes is used instead of picking a different polynomial for each user as in other fuzzy IBE schemes.
Okazaki Fragment Metabolism

Replication of cellular chromosomal DNA is initiated by the multienzyme replisome machinery, which unwinds the DNA helix to create a replication fork. The antiparallel structure of double-helical DNA and the 3′ end extension specificity of all DNA polymerases confine the mechanisms that can be used by the cell for DNA duplication. One copied strand, called leading, can conveniently be extended in a continuous manner in the same direction that the helix must open to allow exposure of templates for polymerization. The other, or lagging strand, must be periodically extended away from the opening helix. This can only be accomplished if the strand is made discontinuously (Kornberg and Baker 1992). The strand is synthesized in short segments, named Okazaki fragments, after their discoverer (Sakabe and Okazaki 1966; Okazaki et al. 1968) and the segments are then joined. This requirement has two fundamental consequences: (1) The lagging strand must have evolved priming and fragment joining mechanisms involving many additional steps and reactions than needed for leading-strand extension. (2) Mechanisms of lagging-strand replication must have developed means of avoiding mutagenesis while handling the necessary strand manipulations.
Syndromic Surveillance: Hospital Emergency Department Participation During the Kentucky Derby Festival

Introduction Electronic syndromic surveillance may have value in detecting emerging pathogens or a biological weapons release. Hospitals that have an agile process to evaluate chief complaints of patients seeking emergency care may be able to more quickly identify subtle changes in the community's health. An easily adaptable prototype system was developed to monitor emergency department patient visits during the Kentucky Derby Festival in Louisville, Kentucky, from April 16–May 14, 2002. Use of the system was continued during the same festival periods in 2003 and 2004. Method Twelve area hospitals in Louisville, Kentucky, participated in a prospective analysis of the chief symptoms of patients who sought care in the emergency department during the Kentucky Derby Festival during 2002. Six hospitals were classified as computer record groups (CRG) and used their existing computerized record capabilities. The other 6 hospitals used a personal digital assistant (PDA) with customized software (PDA group). Data were evaluated by the health department epidemiologist using SaTScan, a modified version of a cancer cluster detection program, to look for clusters of cases above baseline over time and by Zip code. Results All 12 hospitals were able to collect and provide data elements during the study period. The 6 CRG hospitals were able to perform daily data transmission; however, 3 CRG hospitals were unable to interpret their data because it was transmitted in pure text format. In contrast, data from all 6 PDA group hospitals were interpretable. Real-time data analysis was compared with postevent data, and it was found that the real-time evaluation correctly identified no unusual disease activity during the study period. Conclusions The 12 hospitals participating in this study demonstrated that community-wide surveillance using computerized data was possible and that the 6 study hospitals using a PDA could quickly interpret emergency department patients' chief complaints. The emergency department chief complaints group could serve as a disease sentinel for the community.
Histocompatibility: Clarifying Fusion Confusion

In the colonial tunicate Botryllus schlosseri, a co-dominant trait determines the capacity of adjacent colonies to fuse or reject. An innovative RNA sequencing approach has now identified the gene that predicts the outcomes of this naturally occurring allograft.
Mechanism of Inhibition of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase by d4TTP: an Equivalent Incorporation Efficiency Relative to the Natural Substrate dTTP

Among the clinically used nucleoside analogue inhibitors that target human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), there is little detailed mechanistic information on the interactions of 2*,3*-didehydro-2*,3*-dideoxythymidine-5*-triphosphate (d4TTP) with the enzyme z primer-template complex and how these interactions compare with those of the natural substrate, dTTP. Using a pre-steady-state kinetic analysis, we found that d4TTP was incorporated by HIV-1 RT just as efficiently as dTTP during both DNA- and RNA-dependent DNA synthesis. To our knowledge, these results represent the first observation of a 3*-modified nucleoside triphosphate analogue that has an incorporation efficiency comparable to that observed for the natural substrate during DNA synthesis by HIV-1 RT. This information provides a mechanistic basis for understanding the inhibition of HIV-1 RT by d4TTP as well as insight into the clinically observed lack of d4T resistance mutations in HIV-1 RT isolated from AIDS patients. The replication of human immunodeficiency virus (HIV), which causes AIDS, requires the virally encoded enzyme reverse transcriptase (RT). RT converts the single-stranded HIV RNA genome to a double-stranded DNA copy by catalyzing both DNA-dependent and RNA-dependent DNA polymerization as well as RNase H cleavage activity to remove the RNA template once the DNA has been synthesized. Because of its unique catalytic properties, RT has been the target enzyme for many antiviral therapeutic agents used in the treatment of AIDS, including nucleoside and nonnucleoside analogues (2‐4, 8, 26). The nucleoside analogues that are used clinically