cssi/SciSciGPT-SciSciNet huggingface dataset:
Shape complementarity of protein–protein complexes at multiple resolutions

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein-protein complexes. Proteins often undergo conformational changes to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. Despite the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein-protein complexes represented by multiresolution blurred surfaces. Complexed and unbound structures are available for these protein-protein complexes. They are a subset of complexes from a nonredundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work, we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall-off coefficient, termed "blobbyness." Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness = -0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness = -0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein-protein docking.
Primary Steps in the Reaction of OH Radicals with Amino Acids at Low Temperatures in Laval Nozzle Expansions: Perspectives from Experiment and Theory

Recent work has focused on the damaging effects of free radicals on biological molecules. This study investigates the kinetics of the attack of OH radicals on L-alanine ethyl ester in the gas phase in cold beams of Laval nozzle expansions. Experiments and high-level theory are used to understand the preferred site of attack by the OH radical. Optimizations of L-alanine and L-alanine ethyl ester show that the essential transition state features for hydrogen abstraction off the C(alpha), C(beta), and N are similar. The energetics show that for L-alanine, the C(alpha)-site, C(beta)-site, and N-site transition states are all below the reactants level. For L-alanine ethyl ester, however, the energetics for hydrogen abstraction off the C(alpha) and N are the preferred site of reaction. These findings are supported by the observed negative temperature dependence of the rate constants of OH with alanine ethyl ester in Laval nozzle expansion experiments. More importantly, both the experiments and theory show that L-alanine ethyl ester provides a good model for gas phase studies of the amino acids such as L-alanine.
Are Matched Partner Trade Statistics a Usable Measure of Transportation Costs

Data on transportation costs are difficult to obtain. In the absence of good data, many researchers have turned to indirect measures of transportation costs constructed using matched partner c.i.f./f.o.b. ratios from IMF and UN data. We investigate whether these data are usable, by comparing their levels and variation to directly measured transport costs for the US and New Zealand. We find that IMF c.i.f./f.o.b. ratios are badly error-ridden in levels, and contain no useful information for time-series or cross-commodity variation. However, the IMF data do appear to reveal some meaningful cross-exporter variation that might be usefully exploited by researchers.
Energy savings in refrigeration systems

Resume Ce rapport passe en revenue quelques unes des methodes actuelles de conception des installations frigorifiques du point de vue de leur consommation annuelle d'energie. On donne des exemples du supplement d'energie attribue aux systemes a temperature de condensation constante en comparaison des systemes a temperature variable. De meme, l'augmentation de la consommation d'energie consommee par l'installation frigorifique modulaire est comparee a celle du type d'installation integreu toutes les surfaces d'echange de chaleur sont utilisees, de la charge minimale a la charge totale. On examine l'importance de l'optimisation des installations et l'on etudie des exemples des besoins d'energie des compresseurs, qui confirment la necessite d' effectuer la simulation par ordinateur sur l'aspiration et les clapets de refoulement du compresseur. L'utilisation d'eau pour le refroidissement du condenseur semble soulever des difficultes dans certains environments. On evalue donc les besoins d'energie des systemes frigorifiques a refroidissement d'air et a refroidissement d'eau. L'analyse tient compte des donnees meteorologiques variables. On indique aussi dans le rapport que la mise en oeuvre de procedes d'economie d'energie permet non seulement d'economiser des frais de fontionnement mais encore d'eviter, dans certains cas, le besoin de frais d'investissement pour assurer l'agrandissement de l'installation.
Bicyclic pyrazolidinones, a new class of antibacterial agent based on the β-lactam model

Abstract Several bicyclic pyrazolidinones were synthesized as γ-lactam analogs of the β-lactam antibiotics. Two of these compounds exhibited in vitro antibacterial activity, and thus constitute a new class of antibacterial agents.
Eyewitness Confidence and Accuracy Among Three Age Cohorts

The relation between eyewitness confidence and accuracy of 28 young (ages 18 to 35, M = 21.14), 33 young-old (ages 59 to 74, M = 67.73) and 29 old-old (ages 75 to 94, M = 80.66) persons was examined. After viewing a videotape of an ongoing crime, participants answered a multiple-choice questionnaire about the videotaped events and were asked to identify the suspectfrom a valid orfoil photographic line-up. Confidence in each answer was assessed using a 1-10 rating scale. Questionnaire performance declined across age groups but all groups performed poorly on the line-up task. Confidence and accuracy correlations were not signtficant for any group; however, confidence ratings were significantly higher for correct responses than for incorrect responses for all age groups. Thus age alone does not determine eyewitness competence.
Shape-memory polymer networks with Fe3O4 nanoparticles for remote activation

Shape-memory polymers (SMPs) have recently shown the capacity to actuate by remote heating via the incorporation of magnetic nanoparticles into the polymer matrix and exposure to an alternating magnetic field. In this study, methacrylate-based thermoset SMP networks were synthesized through free-radical polymerization with varying amounts of Fe3O4 magnetite (0, 1, and 2.5 wt %). Furthermore, the chemistry of the networks was controlled to maintain a constant glass transition temperature (Tg) while varying the degree of chemical crosslinking. Remote heating of the networks was shown to be a direct function of the nanoparticle concentration and independent of the chemistry. Magnetite reinforcement was shown to influence the thermomechanical properties of the networks; increasing Fe3O4 concentrations led to decreases in Tg and rubbery modulus. However, networks with a higher degree of crosslinking were more resistant to thermomechanical changes with respect to magnetite concentration. Strain to failure was shown to decrease with the addition of nanoparticles and the free-strain shape-memory cycle was investigated for all of the networks. Networks with lower degrees of crosslinking and high magnetite concentrations showed a significant amount of irrecoverable strain. Last, the use of remotely heated shape-memory materials is discussed in light of potential biomedical applications. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
High-Frequency Transformation of Undeveloped Plastids in Tobacco Suspension Cells

Although leaf chloroplast transformation technology was developed more than a decade ago, no reports exist of stable transformation of undeveloped plastids or other specialized plastid types, such as proplastids, etioplasts, or amyloplasts. In this work we report development of a dark-grown tobacco suspension cell model system to investigate the transformation potential of undeveloped plastids. Electron microscope analysis confirmed that the suspension cells carry plastids that are significantly smaller (approximately 50-fold less in volume) and have a very different subcellular localization and developmental state than leaf cell chloroplasts. Using antibiotic selection in the light, we demonstrated that both plastid and nuclear transformation of these cell suspensions is efficient and reproducible, with plastid transformation frequency at least equal to that of leaf chloroplast transformation. Homoplasmic plastid transformants are readily obtained in cell colonies, or in regenerated plants, providing a more consistent and versatile model than the leaf transformation system. Because of the uniformity of the cell suspension model, we could further show that growth rate, selection scheme, particle size, and DNA amount influence the frequency of transformation. Our results indicate that the rate-limiting steps for nuclear and plastid transformation are different, and each must be optimized separately. The suspension cell system will be useful as a model for understanding transformation in those plant species that utilize dark-grown embryogenic cultures and for characterizing the steps that lead to homoplasmic plastid transformation.
Immunological relationships among envelope antigens of avian tumor viruses.

Abstract The patterns of cross reaction in fluorescent antibody and neutralization tests with chicken immune sera indicate the existence of two antigenic subgroups, A and B, in the avian sarcoma and leukosis complex. Each subgroup consists of several distinct antigenic types. Type- and subgroup-specificity appear to be controlled by an antigen of the viral envelope. Antigenic types of subgroup A are stable over at least four undiluted tissue culture passages. Occasional instability of subgroup B virus under such conditions, resulting in the selection of subgroup A serotypes is ascribed to the slower growth rate of subgroup B as compared to subgroup A viruses. Subgroups A and B do not include all avian tumor viruses tested, and the finding of additional subgroups is to be expected.
Aspiration cytology of the collagenized variant of mammary myofibroblastoma: a case report with review of the literature.

Myofibroblastoma of the breast is a rare benign stromal neoplasm, which occurs primarily in men. Classical myofibroblastoma is a circumscribed, nonencapsulated tumor comprised of bipolar fusiform cells arranged randomly, or in fascicles alternating with broad collagenous bands. Additional histologic variants (the cellular, collagenized, infiltrative, and epitheloid types) have been described. Several case reports describe the cytopathologic features of the classical and cellular variants. We report on a 70-yr-old woman, who presented with a circumscribed mass in her left breast. Aspiration biopsy showed paucicellular smears with singly distributed atypical spindle-shaped cells and rare fragments of collagenized stroma, raising suspicion of a phyllodes tumor. Histologic examination revealed spindle-shaped cells distributed in a diffusely collagenized stroma. Some nuclear atypia was present. To the best of our knowledge, this is the first case reporting the cytologic features of the collagenized variant of myofibroblastoma. Although we believe a specific diagnosis of myofibroblastoma can be rendered in a male based on the typical cytologic and clinical findings in the classical type, the variant forms are difficult to classify accurately and require excision for a definitive diagnosis.
Discussion on road infrastructure asset management practices

The objective of this study is to discuss and compare the practices of Road Infrastructure Asset Management System (RIAMS) adopted in different countries. This discussion mainly focuses on the pavement management system. Internationally, the RIAMS approach is moving from the condition-based towards the service-based approach focusing on the customer-driven priorities. This service-based approach needs to be balanced with the budget constraints, level of service and risk tolerance. The transportation agencies have not yet addressed the integrated land use and transportation modelling, the comparison of the relative advantages between capital and operating investments, the risk-based estimation, and the identification of a range of costs associated with the failure within the RIAMS. The transportation agencies should develop a performance-based RIAMS ensuring the serviceability, accountability, stewardship, long-term financial plans, and transparent investments. The RIAMS is still emerging and needs to incorporate the local mission, budget and other constraints within the scope of the local context.
Ion Bombardment Magnetron Furnace for Atomic Spectroscopy

Positive-ion bombardment of a graphite cathode in a low-pressure glow discharge is used to heat the cathode to temperatures in excess of 2000°C. A magnetic field of a few hundred Gauss used in a magnetron configuration reduces lamp voltage and permits operation at less than 1 kV with cathode current densities greater than 350 mA/cm2. A solution residue sample deposited on the 1.6-mm-diameter graphite cathode is atomized in about one second. The atomic vapor is excited in the glow discharge near the cathode surface. The effects of pressure and magnetic field strength on furnace performance are described. At low furnace temperature, plasma current conduction is by electrons produced by positive ion bombardment of the cathode surface. At higher temperatures, current conduction is largely by thermionic electrons.
Edge Preserving Image Enhancement Using Anisotropic Diffusion

Enhancing an image in such a way that maintains image edges is a difficult problem. Many current methods for image enhancement either smooth edges on a small scale while improving contrast on a global scale or enhance edges on a large scale while amplifying noise on a small scale. One method which has been proposed for overcoming this is anisotropic diffusion, which views each image pixel as an energy sync which interacts with the surrounding pixels based upon the differences in pixel intensities and conductance values calculated from local edge estimates. In this paper, we propose a novel image enhancement method which makes use of these smoothed images produced by diffusion methods. The basic steps of this algorithm are: a) decompose an image into a smoothed image and a difference image, for example by using anisotropic diffusion or as in Lee's Algorithm [14]; b) apply two image enhancement algorithms, such as alpha rooting [7] or logarithmic transform shifting [15]; c) fuse these images together, for example by weighting the two enhanced images and summing them for the final image. Computer simulations comparing the results of the proposed method and current state-of-the-art enhancement methods will be presented. These simulations show the higher performance, both on the basis of subjective evaluation and objective measures, of the proposed method over current methods.
THE EFFECT OF RACTOPAMINE AND INTRAMUSCULAR FAT CONTENT ON SENSORY ATTRIBUTES OF PORK FROM PIGS OF SIMILAR GENETICS

The objective of this research was to determine how marbling influences sensory properties of pork. Fresh boneless pork loins were collected from 229 barrows of the same genetic line over a 2-day period from a commercial slaughter facility. Live phase treatments included a control diet and the control diet supplemented with ractopamine (RAC) at 5 ppm for the final 28 days. Multiple 2.54-cm chops were cut for determination of proximate composition, cook loss, Warner–Bratzler shear force and sensory analysis. RAC minimally affected pH and objective color, but had no effect on other pork quality measurements. Additionally, the relationship between extractable lipid and sensory properties or shear force was weak. These results suggest that the level of intramuscular fat has little to do with the eating quality in this population of pigs. PRACTICAL APPLICATIONS The interest in highly marbled pork is based upon historical research that indicated increased marbling was beneficial to shear force values and sensory properties. Our research demonstrates that within a single genetic line, marbling does not dramatically affect sensory properties. Research of this type will help guide both consumers and the pork industry in a positive direction to determine factors that affect palatability and ultimately consumer satisfaction.
Secondary Sexual Characteristics in Boys: Estimates From the National Health and Nutrition Examination Survey III, 1988-1994

Background Descriptive data on pubertal stages for a representative population of racially and ethnically diverse boys in the United States have not been published to our knowledge. Objective To determine at what ages boys in the United States reach each of the 5 sexual maturity stages for genital and pubic hair growth. Design and Setting Cross-sectional survey from the National Health and Nutrition Examination Survey III (NHANES III), 1988-1994. Participants A population-based sample of 2114 boys aged 8 to 19 years representing 16 575 753 boys according to NHANES III sampling strategies. The sample included white, African American, and Mexican American boys. Main Outcome Measures Sexual maturity stages for genital maturation and pubic hair growth. Results The median (equivalent mean) ages at stage 2 for pubic hair development of white, African American, and Mexican American boys were 12.0 (95% confidence interval [CI], 11.7-12.3), 11.2 (95% CI, 10.9-11.4), and 12.3 (95% CI, 12.1-12.6) years, respectively, and at stage 2 for genital growth were 10.1 (95% CI, 9.6-10.6), 9.5 (95% CI, 8.9-10.0), and 10.4 (95% CI, 9.6-11.1) years, respectively. All 3 groups were significantly taller and heavier than boys in previous NHANES reports and showed earlier genital maturation and pubic hair growth than previous studies based on Tanner staging. Statistically significant differences among the 3 racial/ethnic groups were found in the median ages of onset of pubic hair growth and genital development at stage 5 with and without controlling for height and weight, indicating an earlier age of attainment for the African American boys. Conclusions The median (mean) ages at the onset of genital and pubic hair growth were younger than in past studies. Additional studies are required to further evaluate these findings and to explore the public health implications.
Comparison of Validated Instruments Measuring Sexual Function in Men

Objectives There is no universally accepted instrument to measure sexual function (SF) in men. We compare validated SF measures in a single cohort. Methods We compare the Sexual Health Inventory for Men (SHIM), Expanded Prostate Cancer Index Composite SF domain (EPIC-SF), and a reconstructed University of California Los Angeles Prostate Cancer Index SF domain (PCI-SF) in 856 men scheduled for radical prostatectomy. We define potency thresholds for the PCI-SF and EPIC-SF. Results Mean age, body mass index, Gleason sum, and PSA were 57 years, 26.7 kg/m2, 6.3, and 5.9 ng/mL, respectively. Mean instrument scores were as follows: SHIM 20.1; EPIC-SF 65; PCI-SF 71. All instruments were significantly intercorrelated (r = 0.99 for EPIC-SF vs PCI-SF, r = 0.75 for SHIM vs EPIC-SF, r = 0.77 for SHIM vs PCI-SF, all P < .001). The SHIM had the greatest negative skew and ceiling effect (P < .001). Although high scores on either the EPIC-SF or PCI-SF translated reliably to high SHIM scores, the reverse was not true. Subjects who reported no erectile dysfunction (ED) on the SHIM (≥22) had diverse overall SF, whereas those who scored highly on the EPIC-SF or PCI-SF had both excellent erectile function (potency) and overall SF (including orgasmic function, erectile function, and sexual desire). EPIC-SF scores ≥65 and PCI-SF scores ≥75 define men that are both potent and have good SF. Conclusions The SHIM is intended as an instrument to assess ED. It is, however, inadequate as a measure of overall SF. The EPIC-SF and PCI-SF capture gradations of both sexual and erectile function and may also be used to define potency more comprehensively.
The Relation Between Multiple Sleep Latency Test Findings and the Frequency of Apneic Events in REM and Non-REM Sleep

Study objectives A recent study of 34 patients with mild obstructive sleep apnea syndrome (OSAS) suggested that the number of apneas and hypopneas per hour of sleep (apnea/hypopnea index [AHI]) may show a stronger correlation with sleepiness, as measured by the Multiple Sleep Latency Test (MSLT), when calculated for rapid eye movement (REM) sleep alone (AHIR) as opposed to the entire night. We sought to reexamine this possibility in a larger group of similar patients and in patients who had a wider range of OSAS severity. Design Retrospective and observational. Setting A large, accredited, academic sleep disorders center where a database of sleep study results is maintained. Patients We studied 1,146 persons who had polysomnography and MSLTs for clinical indications. Results In linear regression models, the AHI explained 11.0% of the variance in MSLT results, AHIN (AHI during non-REM sleep) explained 10.8%, and AHIR explained only 6.0% (p≤0.0001 for each). Among subjects with AHI Conclusions We conclude that apneic events during REM and non-REM sleep probably contribute equally to sleepiness as measured by the MSLT.
Vision-Based Spacecraft Relative Navigation Using Sparse-Grid Quadrature Filter

In this paper, vision-based relative navigation of two spacecraft is addressed using the sparse-grid quadrature filter. The relative navigation provides the estimates of the relative orbit and relative attitude as well as the gyro biases. It is a challenging problem because of its high nonlinearity and dimensionality. The extended Kalman filter (EKF) and the unscented Kalman filter (UKF) have been used in the past to solve this problem. However, these filters are not accurate enough in the presence of large initial uncertainties or high nonlinearities. Moreover, although other filters, such as the Gauss-Hermite quadrature filter and the particle filter, can be more accurate than the EKF and UKF, they are hard to use in this high-dimensional estimation problem since a large number of quadrature points or particles are required and therefore the computation complexity is prohibitive. It is shown in this paper that the new sparse-grid quadrature filter can achieve much higher estimation accuracy than EKF, UKF, and the cubature Kalman filter without excessive computation load.
Seasonal variation in American Indian suicide.

The distribution of American Indian and Alaska Native suicides in 1980 peaked in the fall but did not differ significantly from chance.
Polyglutaraldehyde: a new reagent for coupling proteins to microspheres and for labeling cell-surface receptors.

Glutaraldehyde polymerized in basic aqueous solutions was found to react with low molecular weight amines, immunoglobulins and hemoglobin. The polyglutaraldehyde was covalently bound to hydrophilic microspheres. The rate of addition of proteins to the polyglutaraldehyde-derivatized microspheres was investigated spectrophotometrically as a function of pH and temperature. The reaction of polyglutaraldehyde was found to be faster than that of the monomer. The findings led to successful labeling of human lymphocyte subpopulations.
Radiation of Energy from Nonzonal Ocean Currents, Nonlinear Regime. Part II: Interactions between Waves

Abstract This article continues the study of the radiation of energy from nonzonal ocean currents in the nonlinear regime. The effects of the interactions between different waves in the initial spectrum on the radiating properties in the model are studied. The process is modeled by three numerical experiments, each initialized with a pair of waves. One wave is typically less radiative than the other. The development of radiation by an initially nonradiating set of modes is observed. The radiative response in the far field is dominated by the waves with a spatial scale longer than the jet width. A brief comparison of the results to the data in the North Atlantic is presented at the end.
Great Circle Rayleigh and Love Wave Dispersion from 100 to 900 Seconds

Rayleigh and Love wave phase velocities for great circle paths from ordinary seismograms of World Wide Standard Seismographic Network /WWSSN/ stations
Using Macromolecular Dynamics Simulations to Interpret Experiments

The use of molecular dynamics simulations to study the internal motions and structural flexibility of proteins and nucleic acids has received a great deal of attention in recent years. The attraction of the method is, in part, its potential for studying detailed properties of biological macromolecules that are only indirectly accessible to experiment. Equally important is the use of the method to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques are emphasized: (1) nuclear magnetic resonance relaxation spectroscopy; (2) refinement of macromolecular X-ray structures; and (3) vibrational spectroscopy.
Caregiver personality predicts rate of cognitive decline in a community sample of persons with Alzheimer’s disease. The Cache County Dementia Progression Study

Background: Environmental influences on the rate of Alzheimer's disease (AD) progression have received little attention. Our objective was to test hypotheses concerning associations between caregiver personality traits and the rate of AD progression. Methods: Care receivers (CR) were 161 persons with AD from a population-based dementia progression study; 55 of their caregivers were spouses and 106 were adult children. Cognitive status of the CR was measured with the Mini-Mental State Examination every six months, over an average of 5.6 (range: 1–14) years. Linear mixed models tested rate of cognitive decline as a function of caregiver personality traits from the NEO Five-Factor Inventory. Results: Significantly faster cognitive decline was observed with higher caregiver Neuroticism overall; however, in stratified models, effects were significant for adult child but not spouse caregivers. Neuroticism facets of depression, anxiety, and vulnerability to stress were significantly associated with faster decline. Higher caregiver Extraversion was associated with slower decline in the CR when caregivers were adult children but not spouses. Conclusions: For adult child caregivers, caregiver personality traits are associated with rate of cognitive decline in CRs with AD regardless of co-residency. Results suggest that dementia caregiver interventions promoting positive care management strategies and ways to react to caregiving challenges may eventually become an important complement to pharmacologic and other approaches aimed at slower rate of decline in dementia.
An Examination of the Scholarly Productivity of Social Work Journal Editorial Board Members and Guest Reviewers

This article reports findings on the scholarly productivity of editorial boards and guest reviewers for selected social work journals. This is the first study to analyze the scholarly productivity of those who serve as guest reviewers for social work journals. Scholarly productivity was defined by the number of citation counts and articles published by editorial board members and guest reviewers for the years 1987 through 1990. As reported in prior studies, many editorial board members appeared to have modest levels of scholarly productivity as defined by citation counts and numbers of articles published. Similar findings are reported for guest reviewers. The researchers conclude that these findings are notable and have serious implications for the academic and professional credibility of social work.
Influence of pH on Terminal Carbon Metabolism in Anoxic Sediments from a Mildly Acidic Lake.

The carbon and electron flow pathways and the bacterial populations responsible for transformation of H2-CO2, formate, methanol, methylamine, acetate, glycine, ethanol, and lactate were examined in sediments collected from Knaack Lake, Wis. The sediments were 60% organic matter (pH 6.2) and did not display detectable sulfate-reducing activity, but they contained the following average concentration (in micromoles per liter of sediment) of metabolites and end products: sulfide, 10; methane, 1,540; CO2, 3,950; formate, 25; acetate, 157; ethanol, 174; and lactate, 138. Methane was produced predominately from acetate, and only 4% of the total CH4 was derived from CO2. Methanogenesis was limited by low environmental temperature and sulfide levels and more importantly by low pH. Increasing in vitro pH to neutral values enhanced total methane production rates and the percentage of CO2 transformed to methane but did not alter the amount of 14CO2 produced from [2-14C]acetate (∼24%). Analysis of both carbon transformation parameters with 14C-labeled tracers and bacterial trophic group enumerations indicated that methanogenesis from acetate and both heterolactic- and acetic acid-producing fermentations were important to the anaerobic digestion process.
Decentralized Local Failure Detection in Dynamic Distributed Systems

A failure detector is an important building block when constructing fault-tolerant distributed systems. In asynchronous distributed systems, failed processes are often indistinguishable from slow processes. A failure detector is an oracle that can intelligently suspect processes to have failed. Different classes of failure detectors have been proposed to solve different kinds of problems. Almost all of this work is focused on global failure detection, and moreover, in systems that do not contain mobile nodes or include dynamic topologies. In this paper, we present diamPm l - a local failure detector that can tolerate mobility and topology changes. This means that diamPm l can distinguish between a failed process and a process that has moved away from its original location. We also establish an upper bound on the duration for which a process wrongly suspects a node that has moved away from its neighborhood. We support our theoretical results with experimental findings from an implementation of this algorithm for sensor networks
Spatial variations in growth rate within Klebsiella pneumoniae colonies and biofilm

The use of acridine orange to visualize and quantify spatial variations in growth rate within Klebsiella pneumoniae colonies and biofilm was investigated. Bacterial colonies supported on polycarbonate filter membranes were grown on R2A agar plates. Some colonies were sampled for cell enumeration, while others were cryoembedded, sectioned, and stained with the fluorescent nucleic acid stain acridine orange. Spatial patterns of fluorescent color and intensity with depth in the colony were quantified using confocal microscopy and image analysis of stained cross sections. Colonies sampled in the midexponential phase were thin (20 microns), had high average specific growth rates (> 1 h-1), and had all the cells stained bright orange. Colonies sampled after more than 24 h of growth were thick (> 200 microns) and were growing slowly (mu < 0.15 h-1). These older colonies were characterized by distinct bands of orange at the colony edges and a dark green center. Stained biofilm cross sections displayed a similar orange band at the biofilm-bulk fluid interface and a green interior. Colony-average specific growth rates, determined by calculating the local slope of the cell accumulation versus time data, were correlated with colony-average fluorescence intensities. There was no correlation between average specific growth rate and orange or green intensity individually, but growth rate did correlate with the orange:green intensity ratio (r2 = 0.57). The resulting regression was used to predict specific growth rate profiles within colonies. These profiles indicated that bacteria were growing rapidly near the air and agar interfaces and more slowly in the center of the colonies when thicker than about 30 microns. The dimension of the orange bands ranged from 10 to 30 microns, which may indicate the thickness of growing regions. The inherent variability associated with this technique suggests that it is best applied in single species systems and that the results should be regarded as qualitative in nature.
Expression of Nitric Oxide Svnthase Isoforms after Miocardial Infarction in Humans

The present study is concerned with the expression of inducible (iNOS) and constutive nitric oxide synthase (cNOS) in human myocardial infarction. This investigation is based on previous studies which showed a time related activation of iNOS derived from infiltrating macrophages in infarcted rabbit myocardium. Specific monoclonal antibodies to both human isoforms were used in order to localize iNOS and cNOS in tissue sections from 6 patients who died on days 2, 7 and 25 after myocardial infarction. In addition, infiltrating macrophages were identified using a monoclonal antibody against human macrophages (CD68). Results showed that, comparable to the animal model, iNOS was primarily located in macrophages infiltrating the infarcted region; this was observed at days 7 and 25 after clinical diagnosis. iNOS was also found in non-necrotic cardiomyocytes within or close to the infarcted region and closely associated with the intercalated discs (IC). In all infarcts, cNOS was expressed in endothelial cells of p...
New Software Metrics for Evaluation and Comparison of Advanced Power Management Systems

A set of software metrics for the evaluation of power management systems (PMSs) is presented. Such systems for managing power need to be autonomous, scalable, low in complexity, and comprised of portable algorithms in order to be well applied across the varying implementations that utilize power systems. Although similar metrics exist for software in general, their definitions do not readily lend themselves to the unique characteristics of power management systems or systems of similar architecture.
The Yogi Project: Software Property Checking via Static Analysis and Testing

We present Yogi , a tool that checks properties of C programs by combining static analysis and testing. Yogi implements the Dash algorithm which performs verification by combining directed testing and abstraction. We have engineered Yogi in such a way that it plugs into Microsoft's Static Driver Verifier framework. We have used this framework to run Yogi on 69 Windows Vista drivers with 85 properties. We find that the new algorithm enables Yogi to scale much better than Slam , which is the current engine driving Microsoft's Static Driver Verifier.
Efficient Insertion Heuristics for Vehicle Routing and Scheduling Problems

Insertion heuristics have proven to be popular methods for solving a variety of vehicle routing and scheduling problems. In this paper, we focus on the impact of incorporating complicating constraints on the efficiency of insertion heuristics. The basic insertion heuristic for the standard vehicle routing problem has a time complexity ofO( n 3 ). However, straightforward implementations of handling complicating constraints lead to an undesirable time complexity ofO( n 4 ). We demonstrate that with careful implementation it is possible, in most cases, to maintain theO( n 3 ) complexity or, in a few cases, increase the time complexity toO( n 3logn). The complicating constraints we consider in this paper are time windows, shift time limits, variable delivery quantities, fixed and variable delivery times, and multiple routes per vehicle. Little attention has been given to some of these complexities (with time windows being the notable exception), which are common in practice and have a significant impact on the feasibility of a schedule as well as the efficiency of insertion heuristics.
Instabilities of Ideal Fluids and Related Topics: Plenary Lecture, presented at the Annual GAMM Conference, Braunschweig 1994

Wir beschreiben ein Verfahren zur Stabilitatsanalyse von dreidimensionalen, nicht notwendig stationaren Stromungen idealer Flussigkeiten. In unserem Verfahren kommen Ideen aus der geometrischen Optik zur Anwendung. Anders als bei Methoden, in denen das Spektrum eines linearisierten Operators oder die Energiefunktion des Systems betrachtet wird, ist unser Verfahren speziell darauf ausgerichtet, die Instabilitat beliebiger Stromungen gegenuber Storungen mit kurzer Wellenlange zu studieren (ahnlich den von Rayleigh and Taylor untersuchten zentrifugalen Instabilitaten). Im vorliegenden Artikel benutzen wir unsere Methode, um die Stabilitat von Stromungen inkompressibler Flussigkeiten, nichtrelativistisch-adiabatischer Flussigkeiten sowie relativistisch-adiabatischer Flussigkeiten zu untersuchen. Insbesondere studieren wir die Stabilitat von Wirbelringen. Wir weisen nach, das Wirbelringe im generischen Fall instabil sind. A geometrical optics method which is capable of probing the stability of general non-steady three-dimensional flows is described Unlike the normal mode and energy stability methods the geometrical optics stability method is specifically designed for studying short-wave instabilities (akin to the centrifugal instabilities of Rayleigh-Taylor) for arbitrary background flows In the present paper it is used to study the stability of flows of incompressible fluids, nonrelativistic adiabatic fluids, and special relativistic adiabatic fluids. As a particular example the stability of vortex rings is studied. It is shown that all generic vortex rings are unstable.
Low molecular weight iron in guinea pig reticulocytes

The low molecular weight iron found in the guinea pig reticulocyte has been partially characterized. On thin layer chromatography it is distinguishable from the iron complexes of a variety of nucleotides, sugars, and amino acids. On paper chromatography it comigrates with a 250-nm absorbing, orcinol-positive material. The eluted count peak contains phosphorus. Approximately 1 microgram of iron is recovered from 1 ml of hemolyzed red cells. Preparation under nitrogen improves recovery of low molecular weight iron, suggesting that the iron is in the ferrous oxidation state.
Characterization of Low-Level Winds of Southern and Coastal Delaware

AbstractWinds across the Delaware Peninsula transport pollutants, modify the temperature, and play a critical role within the state’s agricultural and tourism industries. The low-level winds inland and near Delaware’s coastline are characterized using observations from eight meteorological stations operated by the Delaware Environmental Observing System and the National Data Buoy Center from 2005 through 2012. The low-level winds have pronounced dominant directions during the summer (southwest/southeast) and winter (northwest) seasons, with the greatest spatial and temporal variability occurring in the summer. This inhomogeneity was further investigated with a set of simulations of the low-level winds over the Delaware Bay and surrounding landmass using the Weather Research and Forecasting Model for a subset of days from 2006 through 2012. The model was run with three nests, with the inner nest having a 2-km horizontal resolution. The randomly selected days were organized by synoptic type and season. Meso...
Democratic Leadership Doesn't Just Happen:

The professional behavior of most educational ad ministrators can be classified as "authoritarian," contends this author, who believes that a "demo cratic" administrative style is more effective, and details a strategy for developing a democratic leadership style.
Brazil’s Pension Fund Developmentalism

Lula’s government in Brazil fostered an engagement with local pension funds that have become key state levers for long-term investment, particularly in large and politically salient infrastructure projects. This process, here called pension fund developmentalism, describes more than specific investment choices; it grounds Brazil’s current growth strategy on relationships between the government and a particular set of prominent players, shedding light on the state’s more forceful re-engagement as a promoter of development at a time when aspirations for global economic integration have been matched by the commitment to growth through the expansion of local sources of funding.
Constrained spectral clustering for regionalization: Exploring the trade-off between spatial contiguity and landscape homogeneity

A regionalization system delineates the geographical landscape into spatially contiguous, homogeneous units for landscape ecology research and applications. In this study, we investigated a quantitative approach for developing a regional-ization system using constrained clustering algorithms. Unlike conventional clustering, constrained clustering uses domain constraints to help guide the clustering process towards finding a desirable solution. For region delineation, the adjacency relationship between neighboring spatial units can be provided as constraints to ensure that the resulting regions are geographically connected. However, using a large-scale terrestrial ecology data set as our case study, we showed that incorporating such constraints into existing constrained clustering algorithms is not that straightforward. First, the algorithms must carefully balance the trade-off between spatial contiguity and landscape homogeneity of the regions. Second, the effectiveness of the algorithms strongly depends on how the spatial constraints are represented and incorporated into the clustering framework. In this paper, we introduced a truncated exponential kernel to represent spatial contiguity constraints for region delineation using constrained spectral clustering. We also showed that a Hadamard product approach that combines the kernel with landscape feature similarity matrix can produce regions that are more spatially contiguous compared to other baseline algorithms.
Working to Awaken

Two kindergarteners are squabbling at their desk when the teacher comes over. One of them says to the teacher, “It’s not fair, she took all the red ones!” In a teacher education course, in discussing that while “race” is not a biological category, it is still important to collect data using racial categories so we can recognize where social injustices exist. A student argues that collecting and using this data only further perpetuates social stereotypes, and is thus a poor strategy.
A Hyperbolic System of Conservation Laws in Modeling Endovascular Treatment of Abdominal Aortic Aneurysm

In this paper we present modeling of endovascular treatment of abdominal aortic aneurysm. We describe a simple, one-dimensional model, discuss the well posedness of the corresponding initial-boundary value problem, and present numerical simulations, which suggest an improvement in the design of stents used in treatment.
Day and night glycaemic control with a bionic pancreas versus conventional insulin pump therapy in preadolescent children with type 1 diabetes: a randomised crossover trial

Summary Background The safety and efficacy of continuous, multiday, automated glycaemic management has not been tested in outpatient studies of preadolescent children with type 1 diabetes. We aimed to compare the safety and efficacy of a bihormonal bionic pancreas versus conventional insulin pump therapy in this population of patients in an outpatient setting. Methods In this randomised, open-label, crossover study, we enrolled preadolescent children (aged 6–11 years) with type 1 diabetes (diagnosed for ≥1 year) who were on insulin pump therapy, from two diabetes camps in the USA. With the use of sealed envelopes, participants were randomly assigned in blocks of two to either 5 days with the bionic pancreas or conventional insulin pump therapy (control) as the first intervention, followed by a 3 day washout period and then 5 days with the other intervention. Study allocation was not masked. The autonomously adaptive algorithm of the bionic pancreas received data from a continuous glucose monitoring (CGM) device to control subcutaneous delivery of insulin and glucagon. Conventional insulin pump therapy was administered by the camp physicians and other clinical staff in accordance with their established protocols; participants also wore a CGM device during the control period. The coprimary outcomes, analysed by intention to treat, were mean CGM-measured glucose concentration and the proportion of time with a CGM-measured glucose concentration below 3·3 mmol/L, on days 2–5. This study is registered with ClinicalTrials.gov, number NCT02105324. Findings Between July 20, and Aug 19, 2014, 19 children with a mean age of 9·8 years (SD 1·6) participated in and completed the study. The bionic pancreas period was associated with a lower mean CGM-measured glucose concentration on days 2–5 than was the control period (7·6 mmol/L [SD 0·6] vs 9·3 mmol/L [1·7]; p=0·00037) and a lower proportion of time with a CGM-measured glucose concentration below 3·3 mmol/L on days 2–5 (1·2% [SD 1·1] vs 2·8% [1·2]; p vs five [0–14]; p=0·037). No episodes of severe hypoglycaemia were recorded. Medium-to-large concentrations of ketones (range 0·6–3·6 mmol/dL) were reported on seven occasions in five participants during the control period and on no occasion during the bionic pancreas period (p=0·063). Interpretation The improved mean glycaemia and reduced hypoglycaemia with the bionic pancreas relative to insulin pump therapy in preadolescent children with type 1 diabetes in a diabetes camp setting is a promising finding. Studies of a longer duration during which children use the bionic pancreas during their normal routines at home and school should be done to investigate the potential for use of the bionic pancreas in real-world settings. Funding The Leona M and Harry B Helmsley Charitable Trust and the US National Institute of Diabetes and Digestive and Kidney Diseases.