cssi/SciSciGPT-SciSciNet huggingface dataset:
Modeling the evolution of protein domain architectures using maximum parsimony.

Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture “neighbors” identified in this way may lead to new insights about the evolution of protein function.
Adsorption of HCN and H2O vapor mixtures by activated and impregnated carbons

Abstract Adsorption isotherms for HCN-H2O vapor mixtures have been determined on BPL grade activated carbon and on ASC whetlerite (impregnated) carbon. The results show that the adsorption of HCN by carbons which are already in equilibrium with high levels of water vapor is significant. Adsorption of HCN strongly dominates when HCN and H2O are simultaneously adsorbed from the vapor phase. Adsorbed HCN discourages additional adsorption of water vapor.
Studies of the interactions of an MRI system with the shielding in a combined PET/MRI scanner

A positron emission tomography (PET) system or 'insert' has been constructed for placement and operation in the bore of a small animal magnetic resonance imaging (MRI) scanner to allow simultaneous MR and PET imaging. The insert contains electronics, components with a variety of magnetic properties and large continuous sheets of metal—all characteristics of an object that should, by conventional wisdom, never be placed in the bore of an MR scanner, especially near the imaging volume. There are a variety of ways the two systems might be expected to interact that could negatively impact the performance of either or both. In this article, the interaction mechanisms, particularly the impact of the PET insert and shielding on MR imaging, are defined and explored. Additionally, some of the difficulties in quantifying errors introduced into the MR images as a result of the presence of the PET components are demonstrated. Several different approaches are used to characterize image artifacts and determine optimal placement of the shielding. Data are also presented that suggest ways the shielding could be modified to reduce errors and enable placement closer to the isocenter of the magnet.
502 NOSOCOMIAL SCABIES INFECTIONS: EPIDEMIOLOGY IN THE OUTPATIENT CLINIC

Scabies infestation appears to be increasing over the past few years. Nosocomial spread of this disease has been rarely reported. In October of 1978, 2 nurses and a medical student developed pruritic, papular eruptions on wrists, shoulders, neck and axillary areas. Scabies was diagnosed in each case by clinical and microscopic findings. Since all 3 of these individuals were assigned to the general pediatric outpatient clinic, an epidemiologic investigation was initiated. Both nurses and the medical student remembered prolonged close contact (during lumbar puncture procedure) with a 6-year-old child with aseptic meningitis and scabies. This index child had been diagnosed infested with scabies 24 hours previously, but had not received the prescribed treatment. A total of 41 persons who had both direct and indirect contact with the scabietic child were identified and examined. Scabies was diagnosed in 12 cases: 6 family members of the index child, 5 family members of the nurses, and a single child visiting one of the infested children. Topical application of 1% gamma benzene hexachloride was initiated for all diagnosed individuals and persons sharing living facilities were simultaneously treated to avoid reinfection. A re-education of staff, stressing the importance of proper handling of infected and suspected patients was initiated. Proper gowning and careful hand-washing between patients may have prevented this outbreak.
Molecular Modeling and Simulation of Conjugated Polymer Oligomers: Ground and Excited State Chain Dynamics of PPV in the Gas Phase

The ground and excited state dynamics of poly(p-phenylenevinylene) (PPV) chains is studied through an implementation of mixed quantum/classical molecular dynamics simulation. The model used in the simulations combines the semiempirical Pariser−Parr−Pople (PPP) Hamiltonian to treat the π molecular electronic structure with a mechanical force field capturing all other aspects. Nuclear degrees of freedom are treated classically. We first validate the model by simulating PPV chains of various length, and evaluate the absorption spectra. The thermal disorder contribution to the breadth of the first absorption band is estimated to be 0.2 eV at T = 300 K. To investigate the relationship between the emission and chain conformation, we simulate an isolated ten unit chain of PPV in the ground and the lowest excited state. The emission spectrum, red-shifted with respect to absorption of about 0.2 eV as found in experiments, shows a structured line shape that we relate to the photoinduced CC bond distortions. In acco...
Spatial and temporal variability of diurnal wind forcing in the coastal ocean

[1] Spatial and temporal variability of diurnal wind forcing and the coastal response is characterized for the New York Bight from February through May, 2005. This analysis demonstrates that diurnal wind forced motions are significant in the coastal ocean during the spring and summer months, near shore and as far as 100 km offshore. A doubling of diurnal current amplitudes is common in the spring compared to the winter months, associated with an increase in sea/land breeze days. Diurnal fluid motions due to sea/land breeze events can account for up 50% of the total kinetic energy during the spring.
The mechanisms of stress and immunosuppression

Abstract The effects of stress on the central nervous system, endocrine balance, and immunity were observed in male Sprague-Dawley rats. Food and water were supplied in unlimited quantities. Extraneous odors were kept away from the control room by an exhaust fan in the adjacent room. At 70 days, experimentation occurred for 20 days. In the aspirin, parathroid, serotonin, and pineal groups, there was no significant difference between the undisturbed control and experimental groups. A significant reduction in both the pituitary and adrenal weights was seen in the melatonin experimental group and the undisturbed control group. The placebo control group showed a significant increase in both the pituitary and adrenal gland weights. Stress was blocked in the groups receiving aspirin, parathroid, serotonin, and pineal preparations. The melatonin group, however, very significantly blocked the stress in that both the pituitary and adrenal weights were significantly below the undisturbed control group. The aspirin blocked stress by inhibiting synthesis of prostaglandins. Melatonin works through the pituitary — adrenal axis to reduce adrenal secretion.
L-Histidinol phosphate aminotransferase from Salmonella typhimurium. Kinetic behavior and sequence at the pyridoxal-P binding site☆

Abstract A coupled assay with α-hydroxyglutarate dehydrogenase was used to analyze the kinetic behavior of histidinol phosphate aminotransferase from Salmonella typhymurium . Data obtained from studies of initial velocity, inhibition by products or substrate analogues, isotope exchange rates, and the determination of the equilibrium constant were consistent only with a Ping-Pong Bi Bi mechanism. Variations in inhibition patterns by different substrate analogues indicate that the microenvironment about the pyridoxal phosphate and the pyridoxamine phosphate forms of histidinol phosphate aminotransferase are different, and favor the presence of one active site with partially overlapping substrate-binding subsites for these 2 forms of the enzyme. Histidinol phosphate aminotransferase also catalyzes decomposition of β-chloro- L -alanine to pyruvate, NH 3 and Cl − ; no transamination of this substrate occurs and inactivation of the enzyme accompanies this reaction. After reduction of histidinol-P aminotransferase with [ 3 H]NaBH 4 , carboxymethylation and tryptic digestion, one major radioactive peptide absorbing at 325 nm was isolated. Its primary structure was determined to be TLSK ∗ AFALAGR, where K ∗ is the P-pyridoxyllysine residue. Although this peptide is only 30–40% homologous with the corresponding segment reported for other transaminases, all of these peptides are similar in placement of an hydroxyamino acid residue three residues upstream from the lysine residue, and in the cluster of hydrophobic amino acid residues immediately following the lysine residue.
Enhanced nitric oxide inactivation in aortic coarctation-induced hypertension

Enhanced nitric oxide inactivation in aortic coarctation-induced hypertension. Background Abdominal aortic coarctation above the renal arteries leads to severe hypertension (HTN) above the stenotic site. We have recently shown marked up-regulations of endothelial nitric oxide synthase (eNOS) in heart and thoracic aorta and of neuronal NOS (nNOS) in the brain of rats with severe aortic coarctation above the renal arteries. We hypothesize that the presence of severe regional HTN in the face of marked up-regulation of NO system may be partly due to enhanced NO inactivation by reactive oxygen species (ROS) leading to functional NO deficiency. Methods Tissue nitrotyrosine (which is the footprint of NO interaction with ROS) was determined by Western blot in sham-operated control and aortic-banded (above renal arteries) rats three weeks postoperatively. Intra-arterial pressure and tissue nitrotyrosine (Western blot) were measured. Results The banded group showed a marked rise in arterial pressure measured directly through a carotid cannula (203 ± 9 vs. 131 ± 2 mm Hg, P Conclusion Coarctation-induced HTN is associated with increased nitrotyrosine abundance in all tissues exposed to high arterial pressure, denoting enhanced ROS-mediated inactivation and sequestration of NO in these sites. This can, in part, account for severe regional HTN in this model. The normality of nitrotyrosine abundance in the abdominal aorta wherein blood pressure is not elevated points to the role of baromechanical factors as opposed to circulating humoral factors that were necessarily similar in both segments.
Inhibition of heparanase activity and heparanase-induced angiogenesis by suramin analogues.

Heparanase, a heparan sulfate-specific endo-beta-D-glucuronidase, plays an important role in tumor cell metastasis through the degradation of extracellular matrix heparan sulfate proteoglycans (ECM HSPG). Heparanase activity correlates with the metastatic propensity of tumor cells. Suramin, a polysulfonated naphthylurea, is an inhibitor of heparanase with suramin analogues shown to possess antiangiogenic and antiproliferative properties. We investigated the effects of selected suramin analogues (NF 127, NF 145 and NF 171) on heparanase activity and heparanase-driven angiogenesis. Studies of the ability of cellular extracts and purified heparanase from human, highly invasive and brain-metastatic melanoma (70W) cells revealed that heparanase expressed by these cells was effectively inhibited by suramin analogues in a dose-dependent manner. These analogues possessed more potent heparanase inhibitory activities than suramin: The concentrations required for 50% heparanase inhibition (IC(50)) were 20-30 microM, or at least 2 times lower than that for suramin. One hundred percent inhibition was observed at concentrations of 100 microM and higher. Of relevance, these compounds significantly decreased (i) the invasive capacity of human 70W cells by chemoinvasion assays performed with filters coated with purified HSPG or Matrigel trade mark, and (ii) blood vessel formation by in vivo angiogenic assays, thus linking their antiangiogenic properties with impedance of heparanase-induced angiogenesis. Specifically, inhibition of invasion by NF 127, NF 145 and NF 171 was found at 10 microM concentrations of compounds with a significant decrease of invasive values at concentrations as low as 1.5 microM. In addition, NF 127, NF 145 and NF 171 promoted nearly complete inhibition of heparanase-induced angiogenesis at values ranging from 236 microM (for NF 145) to 362 microM (for NF 127). These results further emphasize the importance of heparanase in invasive and angiogenic mechanisms and the potential clinical application of heparanase inhibitors such as suramin analogues in cancers and angiogenesis-dependent diseases.
Common muscle synergies for balance and walking

Little is known about the integration of neural mechanisms for balance and locomotion. Muscle synergies have been studied independently in standing balance and walking, but not compared. Here, we hypothesized that reactive balance and walking are mediated by common set of lower-limb muscle synergies. In humans, we examined muscle activity during multidirectional support-surface perturbations during standing and walking, as well as unperturbed walking at two speeds. We show that most muscle synergies used in perturbations responses during standing were also used in perturbation responses during walking, suggesting common neural mechanisms for reactive balance across different contexts. We also show that most muscle synergies using in reactive balance were also used during unperturbed walking, suggesting that neural circuits mediating locomotion and reactive balance recruit a common set of muscle synergies to achieve task-level goals. Differences in muscle synergies across conditions reflected differences in the biomechanical demands of the tasks. For example, muscle synergies specific to walking perturbations may reflect biomechanical challenges associated with single limb stance, and muscle synergies used during sagittal balance recovery in standing but not walking were consistent with maintaining the different desired center of mass motions in standing versus walking. Thus, muscle synergies specifying spatial organization of muscle activation patterns may define a repertoire of biomechanical subtasks available to different neural circuits governing walking and reactive balance and may be recruited based on task-level goals. Muscle synergy analysis may aid in dissociating deficits in spatial versus temporal organization of muscle activity in motor deficits. Muscle synergy analysis may also provide a more generalizable assessment of motor function by identifying whether common modular mechanisms are impaired across the performance of multiple motor tasks.
Growing a New Heart from the Old One

With the high rates of heart disease in the United States, one could expect to regularly hear a variation of the Tin Man’s musical lament: “If I only had a new heart.” Indeed, heart attack affects ~3% of Americans over the age of 20, and once present, the resulting scarring of the heart is irreversible and can lead to heart failure, dangerous arrhythmias, and death. Regeneration of new heart muscle has long been sought as a solution, but progress has been slow. Many prior efforts have centered on coaxing stem or progenitor cells to differentiate into new cardiac myocytes. But in a new approach, O’Meara et al. identify possible mechanisms by which mammalian cardiac myocytes can reenter the cell cycle and replicate directly. Currently, the only treatment for patients with severe heart-muscle damage is heart transplantation or implantation of mechanical assist pumps, both of which confer considerable health risks and high financial costs. In their innovative new work, investigators used an unusual mammalian model of myocardial regeneration to study reentry of heart cells into the cell cycle. Until one week of age, neonatal mouse hearts can fully regenerate after resection of the left ventricular apex. On the basis of genetic fate mapping studies, this phenomenon has been attributed to the division of existing cardiac myocytes. O’Meara et al. performed a detailed evaluation of changes in gene expression associated with regeneration of myocytes in neonatal mouse hearts. By comparing these data with genetic data from myocytes in tissue culture and in nonregenerating heart tissue, the authors identified genes potentially involved in cardiac regeneration. They then used computer modeling to predict upstream regulators of these genes and identified the most likely candidates on the basis of their demonstrated ability to promote myocardial DNA synthesis. The gene networks identified as important for neonatal mouse heart regeneration have known functions in cell cycling, mitosis, and RNA processing. The work by O’Meara et al. has important translational implications. If promoters of cardiac myocyte regeneration can be successfully tested in vivo, therapies could be designed to promote the reversal of otherwise progressive heart damage. Such therapies could improve patient outcomes and add important new tools for the management of heart disease. C. O’Meara et al ., Transcriptional reversion of cardiac myocyte fate during mammalian cardiac regeneration. Circ. Res . 10.1161/CIRCRESAHA.116.304269 (2014). [[Abstract]][1] [1]: http://circres.ahajournals.org/content/early/2014/12/04/CIRCRESAHA.116.304269.abstract?sid=700965e5-8f9d-4786-8eb4-4cad3ff39c81
Enhancing Recall and Recognition for Brand Names and Body Copy: A Mixed-Language Approach

As the inclusion of foreign languages in advertisements is a growing global trend, this research examines how language choice may influence important advertising outcome measures within a South Korean advertising context. Specifically, the study aims to explore how foreign and local languages influence recall and recognition for brand name and body copy messages. The interaction of using two languages in an advertisement, to convey different elements of the ad may secure varied levels of attention and comprehension. The findings suggest that recall and recognition are significantly affected by the language presented. An ad presenting a brand name in the foreign language (English Roman alphabet) with the body copy message in the local language (Hangul) is an effective strategy to enhance recall and recognition of the brand name and the ad message within the Korean youth market. The results of this study expand linguistic theory within an advertising context while also providing international advertisers wi...
Comparison of Two Methods for Ranking Applicants for Residency

Ranking radiology residency applicants is a complex process. Multiple factors, such as the variability in evaluation of candidates and the sometimes excessive subjectivity experienced, may influence the final outcome. To address inconsistencies, Yale University's selection committee integrated a mathematical model of ranking. The goal is to compare the mathematically generated rank list with the traditional committee-derived list to identify applicants with discrepancies between the two rank orders as a safety net to ensure that the final rank order list reflects true committee consensus. For three consecutive years, beginning with the 2006-2007 interview season, three rank order lists were compiled. The subjective list was developed by committee consensus on appropriate rank for each applicant. The mathematical list was developed using an equation to assign a score from each of an applicant's three interviewers, which were then averaged and arranged in descending order. These two lists were compared to identify applicants who had differences of 10 rank order positions. Identified applicants were reassessed and reassigned if necessary, forming the National Resident Matching Program (final) list submitted for the match. Over three years, 224 applicants were ranked in total, with 109 being reevaluated (49%) and 24 ultimately reassigned (11%). Discrepancies in rank on the two lists were identified and discussed. In some but not all cases, the discrepancies were remedied. Reasons for discrepancies are discussed. The mathematical method used in parallel with the subjective method has proved useful in identifying misplaced applicants and provided assurance that the final rank list reflects the committee's evaluation of each applicant.
Nonlinear dynamics of the atomic force microscope at the liquid-solid interface

The measurement of intermolecular forces at the liquid-solid interface is key to many studies of electrochemistry, wetting, catalysis, biochemistry, and mechanobiology. The atomic force microscope (AFM) is unique in its ability to measure and map these forces with nanometer resolution using the oscillating sharp tip of an AFM cantilever. These surface forces are only measured by observing the changes they induce in the dynamics of the resonant AFM probe. However, AFM cantilever dynamics at this interface can be significantly different when compared to air/vacuum environments due to the nature of nanoscale forces at the interface and the low-quality factors in liquids. In this work, we study the nonlinear dynamics of magnetically excited AFM microcantilevers on graphite and mica immersed in deionized water, high-concentration buffers, and methanol. By combining theory and experiments, a wealth of nonlinear dynamical phenomena such as superharmonic resonance, hysteretic jumps, and multimodal interactions are demonstrated and their dependence on hydration/solvation forces is clarified. These results are expected to aid ongoing efforts to link liquid-solid interface properties to cantilever dynamics and lead to accurate interpretation of data from experiments.
Pulsar Rotation and Dispersion Measures and the Galactic Magnetic Field.

Use of observations of pulsar polarization and pulse time of arrival at frequencies between 250 and 500 MHz to determine rotation and dispersion measures for 19 and 21 pulsars, respectively. These measurements have been used to calculate mean line-of-sight components of the magnetic field in the path to the pulsars. These and other observations show that there is probably no contribution to the observed rotation measure from the pulsar itself. Low-latitude, low-dispersion pulsars are observed to have strong field components, and a strong dependence of rotation-measure sign on galactic longitude has been found. The observations are consistent with a relatively uniform field of about 3.5 microgauss directed toward about l = 90 deg in the local region, but appear to be inconsistent with the helical model for the local field.
Deregulated expression of CD40 ligand in HTLV-I infection: Distinct mechanisms of downregulation in HTLV-I-transformed cell lines and ATL patients

HTLV-I infection is associated with the development of adult T cell leukemia (ATL) and the neuroinflammatory disease HAM/TSP. There are quantitative and qualitative differences in the antiviral cytotoxic T cell (CTL) response in ATL and HAM/TSP although the underlying mechanisms are unclear. Here, we demonstrate that the HTLV-I Tax trans-activating protein is a transcriptional activator of CD40 ligand (CD40L), a critical regulator of dendritic cell maturation and adaptive immunity. Tax activates CD40L expression via a cyclosporin A insensitive pathway that is also independent of NF-κB. Although Tax upregulates CD40L gene expression, CD40L expression is absent in Tax-expressing HTLV-I-transformed cell lines via an epigenetic mechanism involving methylation. T lymphocytes cultured ex vivo from ATL patients, but not HAM/TSP or normal controls, exhibit a potent block in the induction of CD40L, but not CD69. However, the CD40L gene is not silenced by methylation in ATL patients, thus CD40L is downregulated by distinct mechanisms in HTLV-I-transformed cell lines and ATL patients.
Measurements of eddy fluxes of momentum in the surface layer of the Gulf Stream

Further observations are reported, in which the action of eddies in the Florida Current produces a surface flux of momentum towards higher mean velocities. The results are thus in contrast to what would be expected if the eddies acted as a frictional dissipation mechanism. Furthermore, associated with the momentum flux is a surface transfer of kinetic energy from the eddies to the mean flow. The results from four locations along the length of the Florida Current are compared. The kinetic energy transfer between fluctuations and mean flow is found to be similar in magnitude at all locations and is restricted primarily to the zone of cyclonic shear of the mean surface velocity field. The flow of kinetic energy to the mean flow is sufficient to maintain the current against the dissipative actions of lateral eddy processes. Both the techniques used to measure surface velocities and the sampling method are examined. Neither appears to introduce any biases which might account for the observed momentum fluxes. DOI: 10.1111/j.2153-3490.1965.tb01415.x
Testing departure from additivity in Tukey's model using shrinkage: application to a longitudinal setting

While there has been extensive research developing gene-environment interaction (GEI) methods in case-control studies, little attention has been given to sparse and efficient modeling of GEI in longitudinal studies. In a two-way table for GEI with rows and columns as categorical variables, a conventional saturated interaction model involves estimation of a specific parameter for each cell, with constraints ensuring identifiability. The estimates are unbiased but are potentially inefficient because the number of parameters to be estimated can grow quickly with increasing categories of row/column factors. On the other hand, Tukey's one-degree-of-freedom model for non-additivity treats the interaction term as a scaled product of row and column main effects. Because of the parsimonious form of interaction, the interaction estimate leads to enhanced efficiency, and the corresponding test could lead to increased power. Unfortunately, Tukey's model gives biased estimates and low power if the model is misspecified. When screening multiple GEIs where each genetic and environmental marker may exhibit a distinct interaction pattern, a robust estimator for interaction is important for GEI detection. We propose a shrinkage estimator for interaction effects that combines estimates from both Tukey's and saturated interaction models and use the corresponding Wald test for testing interaction in a longitudinal setting. The proposed estimator is robust to misspecification of interaction structure. We illustrate the proposed methods using two longitudinal studies-the Normative Aging Study and the Multi-ethnic Study of Atherosclerosis.
Abnormal Spectral Behavior of Trivalent Neodymium Ions in Potassium Yttrium Fluoride Crystals

Nd3+ ions in KYF4 can occupy different sites. The energy transfer processes that take place between them are responsible for the unusual behavior of Nd3+. From the spectroscopic measurements at different temperatures we found an anomalous spectroscopic behavior in the low temperature range (20K - 100K). Based on an energy transfer model, we proposed an explanation to this abnormal behavior. We derived the formula to describe the deexcitation process and make a data fitting on our dynamic decay measurements.
Responses of Nicotiana tabacum to CO2 enrichment at low‐photon flux density

Effects of CO2 enrichment on photosynthesis and on dry matter allocation were examined in two tobacco (Nicotiana tabaum L.) genotypes. Samsun and W38. Plants were grown from seed in controlled environment chambers at a photosynthetic photon flux density of 450 μmol m−2 s−1. Averaged over the 9 day study, net photosynthesis rates were 14.2±0.5 and 13.0±0.4 μmol m−2 s−1 in elevated (70 Pa) and in ambient (35 Pal CO2 air. respectively, when measured at the irradiance and CO2 partial pressure employed for plant growth. However. photosynthesis rates of plants grown in elevated CO2 were 50% less than those of the ambient controls on the last day of treatment, when measured al 70 Pa CO2 air and an irradiance of 900 μmol m−2 s−1 Total plant dry weight and specific leaf weight were greater (P < 0.051 in enriched-CO2-grown than in ambient-CO2-grown plants. Leaf starch, measured during the first hour of the photoperiod. increased over 7 days of treatment in elevaled-CO2-grown but not in ambient-CO2-grown plants. Ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) activities of tobacco plants grown at 35 and 70 Pa CO2 air were 58.5±4.5 and 48.5±3.7 umol m−2 s−1. respectively, between days 0 and 9 of the study. Rubisco activation state. Rubisco protein concentration. soluble protein and total chlorophyll were unaffected by CO2 enrichment. The above findings demonstrated that photosynthesis was down regulated in tobacco plants after 7 to 9 days of CO2 enrichment at low photosynthetic photon flxu density, but less than at moderate irradiances.
Increased nodulation of soybean by a strain of Bradyrhizobium japonicum with altered tryptophan metabolism

A strain of Bradyrhizobium japonicum was isolated that accumulated anthranilic acid, indole, 3-indoleacetic acid, 3-indolelactic acid and 3-indolepyruvic acid in culture. Such accumulations are indicative of altered tryptophan metabolism. Soybean plants inoculated with these bacteria formed more nodules (349 vs 159 per plant) and had more nodule mass (3.9 vs 2.2 g wet wt per plant) than plants inoculated with the wild-type strain.
A hybrid replica control algorithm combining static and dynamic voting

A hybrid scheme that integrates the static voting protocol and dynamic voting with linearly ordered copies is proposed. A stochastic model is used to compare the file availability afforded by the proposed hybrid scheme with the availabilities of voting, dynamic voting, and dynamic voting with linearly ordered copies. The hybrid scheme has the most availability of these four algorithms for all reasonable repair/failure ratios tested. >
An effective approach to obtain model parameters for BJTS and FETS from data books

The authors address the problem of obtaining the values of small signal parameters of the high frequency hybrid- pi models of bipolar junction transistors (BJTs) and junction FETs (JFETs) for a given set of bias conditions from the data-book values. They also show the methods of determining the 'typical' values of the input parameters to be used in the model statements of circuit simulators, such as SPICE. >
A conservative semi‐Lagrangian method for multidimensional fluid dynamics applications

We describe a finite volume semi-Lagrangian method for the numerical approximation of conservation laws arising in fluid-dynamic applications. A discrete conservation relation is satisfied by using conservative interpolation for the material (or property) being conserved. The method was developed with a view to application in climate prediction. © 1995 John Wiley & Sons, Inc.
Regenerative healing following foetal myocardial infarction

Objectives:Theadult response to myocardialinfarctionresults in inflammation, scarformation,left ventriculardilatation, andloss of regional and global function. Regenerative scarless healing has been demonstrated in foetal dermis and tendon and is associated with diminished inflammation. We hypothesised that following foetal myocardial infarction, there would be minimal inflammation, regenerative healing, and preservation of function. Methods: Anteroapical myocardial infarction encompassing 20% of the left ventricle was created in adult or early gestation foetal sheep. Myocardial function was serially assessed using quantitative echocardiography. Infarct architecture was examined histologically for evidence of scar formation. Cellular inflammation, cellular proliferation, and apoptosis were assessed using immunohistochemistry. Results: In the adult sheep 4 weeks following myocardial infarction, there was a significant decline in ejection fraction (EF) (41 � 7.4% to 26 � 7.4%, p < 0.05), and the akinetic myocardial segment increased in size (6.9 � 0.8 cm to 7.9 � 1.1 cm, p < 0.05). By contrast, there was no decline in the foetal EF (53 � 8.1% to 55 � 8.8%) and no akinetic foetal myocardial segment 4 weeks post-infarction. The foetal infarcts lacked an inflammatory cell infiltrate and healed with minimal fibrosis, compared with the adults. Foetal infarcts also demonstrated 5-bromo-20deoxyuridine (BrdU)+ proliferating cells, including cardiomyocytes, within the infarct. Conclusions: These data demonstrate that the foetal response to myocardial infarction is dramatically different from the adult and is characterised by minimal inflammation, lack of fibrosis, myocardial proliferation and restoration of cardiac function. Diminished inflammation is associated with foetal regenerative cardiac healing following injury. Understanding the mechanisms involved in foetal myocardial regeneration may lead to applications to alter the adult response following myocardial infarction. # 2010 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.
Overview of High Throughput Sequencing Technologies to Elucidate Molecular Pathways in Cardiovascular Diseases

High throughput sequencing technologies have become essential in studies on genomics, epigenomics, and transcriptomics. Although sequencing information has traditionally been elucidated using a low throughput technique called Sanger sequencing, high throughput sequencing technologies are capable of sequencing multiple DNA molecules in parallel, enabling hundreds of millions of DNA molecules to be sequenced at a time. This advantage allows high throughput sequencing to be used to create large data sets, generating more comprehensive insights into the cellular genomic and transcriptomic signatures of various diseases and developmental stages. Within high throughput sequencing technologies, whole exome sequencing can be used to identify novel variants and other mutations that may underlie many genetic cardiac disorders, whereas RNA sequencing can be used to analyze how the transcriptome changes. Chromatin immunoprecipitation sequencing and methylation sequencing can be used to identify epigenetic changes, whereas ribosome sequencing can be used to determine which mRNA transcripts are actively being translated. In this review, we will outline the differences in various sequencing modalities and examine the main sequencing platforms on the market in terms of their relative read depths, speeds, and costs. Finally, we will discuss the development of future sequencing platforms and how these new technologies may improve on current sequencing platforms. Ultimately, these sequencing technologies will be instrumental in further delineating how the cardiovascular system develops and how perturbations in DNA and RNA can lead to cardiovascular disease.
A general theory of ecology

Ecologists bemoan the dearth of theory in ecolo- gy, in particular, the lack of an overarching, general theory. These complaints largely are unjustified. The components of a general theory of ecology have existed for the past half century; ecologists simply have failed to explicitly recognize them. We present a general theory of ecology and show how it relates to ecology's numerous constituent theories and models. The general theory consists of a description of the domain of ecology and a set of fundamental principles. The domain of ecology is the spatial and temporal patterns of the distribution and abundance of organisms, including causes and consequences. Fundamental principles are broad statements about the patterns that exist and the processes that operate within a domain. The seven fundamental principles of the theory of ecology are: the heterogeneous distribution of organisms, interactions of organisms, contingency, envi- ronmental heterogeneity, finite and heterogeneous resources, the mortality of organisms, and the evolutionary cause of ecological properties. These principles are the necessary and sufficient elements for a general theory of ecology. The propositions of any constituent theory of ecology can be shown to be a consequence of these fundamental principles along with principles from other science domains. The general theory establishes relationships among constituent theories through shared fundamental principles. The next challenge is to develop and integrate unified, constituent theories and to establish the relationships among them within the framework established by the general theory.
Rimonabant’s Reductive Effects on High Densities of Food Reinforcement, but not Palatability, in Lean and Obese Zucker Rats

Rationale Cannabinoid antagonists purportedly have greater effects in reducing the intake of highly palatable food compared to less palatable food. However, this assertion is based on free-feeding studies in which the amount of palatable food eaten under baseline conditions is often confounded with other variables, such as unequal access to both food options and differences in qualitative features of the foods.
High frequency scattering by a conducting circular cylinder coated with a lossy dielectric of non uniform thickness

Parrikar et al. (1991) obtained a series solution for the scattering by an impedance cylinder embedded in a nonconcentric dielectric cylinder. Later, Raghep et al. (1988, 1991) studied the elliptic cylinder coated by a nonconfocal dielectric coating. These solutions are rapidly converging only for cylinder sizes comparable to or smaller than the wavelength. For electrically larger cylinders asymptotic solutions are required. The present paper gives an analytical solution to high frequency scattering by a conducting circular cylinder coated with a lossy dielectric of nonuniform thickness. It is assumed that the coating is thin.
Multiport VNA measurement uncertainty - Signal integrity applications

Vector network analyzer (VNA) measurements are often stated without an indication of the estimated uncertainty. Understanding the uncertainty can lead to understanding the sources of uncertainty and targeting improvements in the metrology to address the largest sources. Connector repeatability in manually probed measurements can be a primary source of uncertainty with this metrology. A measurement capability assessment provides the method for evaluating the total uncertainty. Evaluation of the probe launch and cable movement provided substantial opportunities to improve the capability. Implementing improvements identified through the measurement capability assessment (MCA) process has resulted in a doubling of the highest frequency where the metrology is deemed capable.
Feedback inhibition of the cholesterol biosynthetic pathway in patients with Smith-Lemli-Opitz syndrome as demonstrated by urinary mevalonate excretion.

Smith-Lemli-Opitz syndrome (SLOS) is a genetic disorder characterized by low plasma cholesterol and high 7-dehydrocholesterol (7-DHC). Synthesis of cholesterol and 7-DHC and its metabolites is regulated by HMG-CoA reductase, whose activity can be measured by 24-h excretion of its product mevalonate. We devised a simple, non-invasive method for collecting 24-h urine in our subjects. With a background of a very low cholesterol diet, mean mevalonate excretion did not differ between controls and SLOS children, indicating that SLOS subjects have normal HMG-CoA reductase activity. In a short term feeding study, the effects of a high cholesterol diet in SLOS subjects include a significant 55% increase in plasma cholesterol levels and 39% decrease in mevalonate excretion and no change in plasma 7-DHC levels. However, in four SLOS subjects, fed a high cholesterol diet for 2–3 years, plasma cholesterol levels continued to increase, urinary mevalonate excretion remained low and total 7-DHC decreased significantly, likely from decreased total sterol synthesis. Thus, in SLOS subjects, HMG-CoA reductase activity was normal and was subject to normal cholesterol induced feedback inhibition. However, total sterol synthesis in SLOS may still be decreased because of increased diversion of mevalonate into the shunt pathway away from sterol synthesis.
Cylinder Test Correction for Copper Work Hardening and Spall

As a basis for the corrections to be discussed, an analytical equation is first presented for calculating detonation energy densities from copper wall velocities in the Cylinder test. Steinberg-Guinan work hardening is sufficient for the Cylinder problem, between 1 and 60 GPa, with a change of Yo to 0.10 kJ cm−3 for annealed copper. An air gap correction was the first to be applied, which is a function of the initial air gap width and the tilt angle of the cylinder. Irreversible heat loss was also found to be a small error. Spall is calibrated using new copper gun shot data and this energy is also small. The model up through work hardening agrees with the code, which does not contain heat loss or spall, both of which equal the error of repetitive calculation. The effect of the many additions to the original Gurney energy is shown.
Phase behavior and density of polysulfone in binary fluid Mixtures of tetrahydrofuran and carbon dioxide under high pressure: Miscibility windows

Mixtures of tetrahydrofuran (THF) and carbon dioxide (CO2) were identified as new solvent systems for polysulfone. The miscibility and density of polysulfone in binary fluid mixtures of THF and CO2 were investigated from 300 to 425 K at pressures up to 70 MPa. The influence of the CO2 and polysulfone concentrations was studied, with the concentrations of the other two components kept constant. At a 4.5 wt % polymer concentration, the demixing pressures in a 10 wt % CO2 and 90 wt % THF mixture increased with temperature (310–425 K) from 15 to 40 MPa. With increasing CO2 concentration (from ca. 10 to 14 wt %), a significant increase (from 15 to 70 MPa at 310 K) was observed in the demixing pressures. Furthermore, with an increasing amount of CO2, the nature of the phase boundary shifted from lower critical solution temperature behavior to upper critical solution temperature behavior. The influence of the polymer concentration was studied in the 0–5 wt % range at two CO2 levels, with solvent compositions of 10 wt % CO2 and 90 wt % THF and 13 wt % CO2 and 87 wt % THF. The system with a higher level of CO2 (13 wt %) showed highly unusual phase behavior: on pressure–composition and temperature–composition diagrams, the system displayed two distinct regions of miscibility. In the system with 10 wt % CO2, the distinct regions of miscibility that were observed in the system with 13 wt % CO2 partially overlapped and led to a W-shape phase boundary. The densities of the polymer solutions were measured from the one-phase region through the demixing point into the two-phase region at a constant temperature. No significant change in density was found around the phase boundary; this indicated that the coexisting phases had similar densities, as is often the case with liquid–liquid phase separation in polymer solutions under high pressure. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 2357–2362, 2002
Towards a Just Solar Radiation Management Compensation System: A Defense of the Polluter Pays Principle

!! ! ! ! ! ! ! ! ! ! ! ! ! In their ‘Ethical and Technical Challenges in Compensating for Harm Due to Solar Radiation Management Geoengineering’ (2014), Toby Svoboda and Peter Irvine (S&I) argue that there are significant technical and ethical challenges that stand in the way of crafting a just solar radiation management (SRM) compensation system. My aim here is to contribute to the project of addressing these problems. I will do so by focusing on one of S&I’s important ethical challenges, their claim that thepolluter pays principle(PPP) is too problematic to be useful in determining responsibility for SRM compensation. Their argument for the latter claim consists in a series of allegations, mostly in the form of questions, that are thought to indicate serious difficulties standing in the way of using the PPP to craft a just compensation system. I will argue that S&I fail to substantiate these allegations: the PPP is not as problematic as S&I suggest, and moreover, is a viable candidate for determining responsibility for SRM compensation. S&I raise five allegations against the PPP. I will discuss each in turn.
Skeletal muscle contractile activity in vitro stimulates mitogen-activated protein kinase signaling.

Physical exercise is a potent stimulator of mitogen-activated protein (MAP) kinase signaling. To determine if this activation is secondary to systemic responses to exercise or due to muscle contrac...
Waves of actin and microtubule polymerization drive microtubule-based transport and neurite growth before single axon formation

Many developing neurons transition through a multi-polar state with many competing neurites before assuming a unipolar state with one axon and multiple dendrites. Hallmarks of the multi-polar state are large fluctuations in microtubule-based transport into and outgrowth of different neurites, although what drives these fluctuations remains elusive. We show that actin waves, which stochastically migrate from the cell body towards neurite tips, direct microtubule-based transport during the multi-polar state. Our data argue for a mechanical control system whereby actin waves transiently widen the neurite shaft to allow increased microtubule polymerization to direct Kinesin-based transport and create bursts of neurite extension. Actin waves also require microtubule polymerization, arguing that positive feedback links these two components. We propose that actin waves create large stochastic fluctuations in microtubule-based transport and neurite outgrowth, promoting competition between neurites as they explore the environment until sufficient external cues can direct one to become the axon.
Thermodynamic Analysis of Blanket and Selective Epitaxy of Sic on Si and SiO2 Masked Si

Thermodynamic analysis was conducted to determine the conditions necessary for the selective epitaxial growth (SEG) of SiC on SiO 2 masked Si substrates, and these results were compared to blanket SiC epitaxy on plain Si. For blanket SiC epitaxy, proper deposition conditions leading to single phase SiC without Si or graphite codeposition were found. For SiC SEG, the additional constraint that no significant SiO 2 mask etching should occur, was considered. Taken in combination, both the SiC deposition and the Si0 2 etching processes were analyzed to ensure meaningful subsequent experiments. All process parameters, i.e., temperature, C/Si, CI/Si and H 2 /Si in the gas mixture significantly affect the growth conditions when epitaxy is possible. Either providing more carbon than silicon in the gas sources or adding HCl helps to suppress Si codeposition. For SiC SEG, lower deposition temperature (e.g. less than 1400 K) should be used to avoid damaging the SiO 2 mask.