cssi/SciSciGPT-SciSciNet huggingface dataset:
Brief intervention protocol for assisting patients with tobacco cessation.

In recent years, educational efforts have been directed toward providing health care professionals with the necessary knowledge and skills to effectively counsel patients about tobacco cessation. By and large, these training programs have positioned the clinician as the sole provider of tobacco-
Radiation quality effects in the quenching of benzene fluorescence in pulsed proton and alpha particle irradiation

Abstract Alpha particle induced quenching of fluorescence from dilute solutions of benzene in cyclohexane was observed to depend on incident ion energy. For protons and alpha particles of the same mean stopping power, the amount of quenching is less for alpha excitation. Our present model of intratrack quenching by products of radiation does not fully explain these observations.
Drained and undrained response of deep tunnels subjected to far-field shear loading

Abstract An analytical solution for a rectangular opening in an infinite elastic medium subjected to far-field shear stresses has been derived for drained and undrained loading conditions. A number of numerical simulations has been conducted to determine the distortion of a rectangular structure in an infinite elastic medium under far-field shear stresses also for drained and undrained conditions and when there is full slip or no slip at the ground–structure interface. The results show that the shape of the opening has a minor influence on the structure’s deformations and that full-slip conditions result in lower deformations. Undrained conditions tend to reduce distortions when the structure is more flexible than the ground, but tend to increase them for stiffer structures. A comparison between results obtained for a rectangular lined opening and for a circular lined opening are presented, and show that deformations of a rectangular structure with no-slip can be estimated from equations derived for a circular opening with an incompressible liner and also with no-slip. The effects of flexibility, slip condition at the interface, and drained or undrained loading are different for circular tunnels than for rectangular tunnels.
Fusing object information and peer information

We consider the problem of information fusion, specifically the task of fusing information from two different categories, information which is directly about an object of interest (OBJOIN information) and information about related objects (peer information). We discuss the representation of these different types of information, the first in terms of a possibilistic distribution and the second in terms of a probability distribution. We introduce an approach to information fusion based upon the use of the fuzzy modeling technology. In this approach we represent the fusion function in terms of rules which indicate when to use the different types of information. Particularly notable here is the role of information quality as a guiding factor in the fusion process. © 2001 John Wiley & Sons, Inc.
Effect of Food Composition on the Heat Resistance of Yeast Ascospores

The ascospores of Saccharomyces cerevisiae were over 100-fold more resistant than vegetative cells of the same strain. The D60 of spores in apple juice was 6.1 min and the z value was 3.8°C; in a Chenin blanc wine the D55 was 0.57 min and the z value was 6.7°C. The presence of sugar in the heating medium increased spore resistance while alcohol reduced it; varying pH over the range 3.0 to 7.0 had little effect.
Setting Up a Sovereign Wealth Fund: Some Policy and Operational Considerations

This paper offers a policy and operational "roadmap" to policymakers considering setting up an SWF. It should also be of interest to policymakers in countries where SWFs are already in place, to review their existing policies and operations. Finally, it offers an opportunity to identify areas where research in macroeconomics and finance should give further answers as to the adequacy of existing practice related to the setting up and management of SWFs, an area where practical considerations often lead theoretical research. For instance, policymakers should optimally consider both their sovereign assets and liabilities together with their macroeconomic objectives, when setting up an SWF.
Study on the Dynamical Behavior of a Real-Time Distributed Simulation System

The typical time-critical distributed simulation system in military applications involves a large number of entities that interact with each other in real time. The dynamical behavior of this kind of system is very complicated. When there is a disturbance caused by, for example, time delay, the reaction of the system may not remain in the local area. Instead, it can propagate to a wide region and affect many entities. This paper uses a model called Self-Organized Criticality to ex plain the dynamical behavior of a real-time dis tributed simulation system. A generic war game program is used to simulate the real-time inter actions among the entities on a battlefield. The dynamical behavior of the war game is recorded after a large number of runs with randomly gen erated initial conditions. The results show that the system demonstrates the characteristics of Self-Organized Criticality.
Unite interventionnelle hybride multimodale : de la planification préopératoire au contrôle postopératoire immédiat

Resume Introduction La chirurgie assistee par ordinateur s’est developpee ces dernieres annees grâce a l’essor de la navigation et des techniques d’imagerie 3D et de fusion d’image. Plus recemment est apparue la technologie du cone-beam scanner (CBCT) a detecteur plat, qui permet d’obtenir des images osseuses de haute resolution et de qualite comparable a celles d’un scanner classique. La combinaison de ces deux technologies dans une unite interventionnelle hybride multimodale permet de faire converger les etapes pre-, per-, et postoperatoires, en une procedure ininterrompue assistee par ordinateur afin d’optimiser la precision, la previsibilite et la qualite des resultats, d’un traitement chirurgical. Elle doit permettre une reduction des couts et de la duree operatoire et eviter les reprises chirurgicales. Note technique L’unite hybride comprend 1) une salle d’operation (65 m2) equipee d’un flux laminaire horizontal, un systeme mobile de CBCT sur arceau monoplan a suspension au plafond avec detecteur plat et un systeme de navigation sans fil, 2) une salle de commande separee de la salle d’operation par une vitre plombee consistant en deux stations de travail distinctes pour l’integration et le traitement tridimensionnels des images et 3) une salle de preparation des chirurgiens (17 m2) pour le lavage chirurgical des mains. Le protocole operatoire comprend les etapes suivantes : 1) elaboration du plan du traitement et simulation informatique a partir des images acquises en preoperatoire ou en peroperatoire, 2) reglage du guidage peroperatoire par navigation, 3) intervention chirurgicale, 4) controle scanner peroperatoire, 5) fermeture.
Using “fresh” to determine a source

Abstract Water scarcity is a problem facing the arid southwest portion of the United States. Compounding the scarcity issue is the fact that much of the water is also of poor quality. In recent years, the quest for sources of fresh water has intensified as the realization of the potential for long-term water shortages becomes a reality. This paper examines the definition of “fresh” water as a function of the end use of the water, i.e. human consumption, environmental release, or reuse for industrial or municipal applications. It is within this context that a discussion of the term “fresh” is evaluated as a defining criterion for potential sources. The technology to produce good quality water from poor quality sources exists. However, factors other than technology often control the decision making as to whether to treat a water source of poor quality, or continue to look for a source of higher quality. Some of these factors are: public acceptance, environmental impact, regulations, economics, human health risks, regional issues, political issues. The specific case discussed here uses a wastewater source that is highly controversial by its very nature, as it contains radionuclides and other industrial contaminants. The factors leading to this source being considered are as follows: (1) the municipal water production wells are 1500–2000 ft. 457.5–610 m) below the surface making production costly; (2) the groundwater quantity is limited and recharge is extremely slow; and, (3) the groundwater has a high level of naturally occurring silica (80–120 mg/l The case facility, located in western portion of the United States, treats an average of 15,000 gpd (57 m 3 /d through the use of chemical precipitation, sand filtration, ultrafiltration, ion exchange and reverse osmosis. The secondary waste (reject or concentrate) from this treatment process is further treated with electrodialysis-reversal and mechanical evaporation. The product from this facility is currently discharged, by regulatory permit, to the environment. The product water is being considered for reuse primarily for industrial applications.
Total synthesis of (±)-monomorine

Abstract An efficient, two-operation synthesis of the trail ant pheromone (±)-monomorine is reported. The synthesis features an aqueous Claisen-Schmidt condensation followed by the stereocontrolled installation of the three resident stereocenters in a single operation.
RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle.
The flucose effect in rat liver: Studies of δ-aminolevulinate synthase and tyrosine amino-transferase

1. 1. Studies of the repression by carbohydrate of the induction of hepatic δ-aminolevulinate synthase (succinyl-CoA: glycine C-succinyltransferase (decarboxylating), EC 2.3.1.37) and tyrosine aminotransferase (L-tyrosine: 2-oxoglutarate aminotransferase, EC 2.6.1.5) (the glucose effect) have been performed in rats. These included changes in enzyme induction produced by administration of hexoses and certain other metabolites and by alterations of carbohydrate metabolism resulting from 2-deoxy-D-glucose, diazoxide, and experimental diabetes. 2. 2. Cyclic AMP and N6, O2′-dibutyryl cyclic AMP could not be shown to induce δ-aminolevulinate synthase as they are known to do for tyrosine aminotransferase. 3. 3. Both 2-deoxyglucose and diazoxide induce tyrosine aminotransferase to high levels. There are distinct differences between the two, however, in that the induction by 2-deoxyglucose is additive with that of allylisopropylacetamide and is repressed by carbohydrate, whereas for the induction by diazoxide, neither of these is true. 4. 4. Allylisopropylacetamide exerts a pronounced synergistic effect on the production of hyperglycemia by diazoxide in the starved rat. A less marked synergism obtains in fasted rats treated with allylisopropylacetamide and 2-deoxy-D-glucose. 5. 5. The data indicate a divergent behavior in the response of the two enzymes to a variety of manipulations and provide evidence that the glucose effect on the two may operate by different mechanisms. 6. 6. The data seem most compatible with the concept that carbohydrate repression of δ-aminolevulinate synthase is mediated by glucose or glucose 6-phosphate.
IASM: An Integrated Attribute Similarity for complex networks generation

Complex networks are seen in different real life disciplines. They are characterized by a scale-free power-law degree distribution, a small average path length (small world phenomenon), a high average clustering coefficient, and the emergence of community structure. Most proposed complex networks models did not incorporate all of the four common properties of complex networks. Models have also neglected incorporating the heterogeneous nature of network nodes. In this paper, we propose two generation models for heterogeneous complex networks. We introduce the Integrated Attribute Similarity Model (IASM). IASM uses preferential attachment to connect nodes based on their attributes similarities integrated with node's structural popularity (normalized degree or Eigen vector centrality). IASM proposed model is modified to increase their clustering coefficient using a triad formation step.
Ribosome binding to the endoplasmic reticulum: a 180-kD protein identified by crosslinking to membrane-bound ribosomes is not required for ribosome binding activity.

We have used the membrane-impermeable, thiol-cleavable, crosslinker 3,3'-dithio bis (sulfosuccinimidylpropionate) to identify proteins that are in the vicinity of membrane-bound ribosomes of the RER. A specific subset of RER proteins was reproducibly crosslinked to the ribosome. Immunoblot analysis of the crosslinked products with antibodies raised against signal recognition particle receptor, ribophorin I, and the 35-kD subunit of the signal sequence receptor demonstrated that these translocation components had been crosslinked to the ribosome, but each to a different extent. The most prominent polypeptide among the crosslinked products was a 180-kD protein that has recently been proposed to be a ribosome receptor (Savitz, A.J., and D.I. Meyer, 1990. Nature (Lond.). 346: 540-544). RER membrane proteins were reconstituted into liposomes and assayed with radiolabeled ribosomes to determine whether ribosome binding activity could be ascribed to the 180-kD protein. Differential detergent extraction was used to prepare soluble extracts of microsomal membrane vesicles that either contained or lacked the 180-kD protein. Liposomes reconstituted from both extracts bound ribosomes with essentially identical affinity. Additional fractionation experiments demonstrated that the bulk of the ribosome binding activity present in detergent extracts of microsomal membranes could be readily resolved from the 180-kD protein by size exclusion chromatography. Taken together, we conclude that the 180-kD protein is in the vicinity of membrane bound ribosomes, yet does not correspond to the ribosome receptor.
Application of a priori established gene sets to discover biologically important differential expression in microarray data

We thank Joseph Nevins, Bala Balakumarin, Geoffrey Ginsburg, and Alessandro Porrello for their careful review of this Commentary. P.G.F. is a Damon Runyon Cancer Research Foundation Clinical Investigator and receives additional support from National Institutes of Health Grant CA-089031 and the Prostate Cancer Foundation.
Maternal Support Networks, Maternal Cognitions, and Young Children's Social and Cognitive Development.

The relations among maternal support networks, maternal perceptions of parenting, maternal attributions for parenting situations, and children's social development, as indexed by peer acceptance, and cognitive performance, as indexed by the PPVT-R and PSI, were examined in a sample of 69 mothers and their preschool-age children. Network characteristics directly predicted cognitive performance and indirectly predicted peer acceptance through effects on maternal perceptions and attributions. Parent cognitions as mediators of network effects on children's development are discussed, addressing variation due to network dimensions, types of parent cognitions, and domain of children's development.
Changes in FaRP-like peptide levels during development of eggs from the plant-parasitic cyst nematode, Heterodera glycines

The plant-parasitic cyst nematode Heterodera glycines requires a host plant to complete its life cycle, which involves hatching of infective juveniles that parasitize through root entry. A laboratory population of H. glycines grown on soybean, Glycine max, undergoes a sharp increase in maturity between 5 and 6 weeks in culture, as measured by the proportion of eggs containing well developed pre-hatch juveniles (late development eggs) versus eggs without visible juveniles (early development eggs). The median percent of eggs classified as late development, representing all samples taken from 4 to 7 weeks in culture, was 61%. For all samples taken up to 5 weeks, 80% scored below the median. In samples taken after 5 weeks, 15% scored below the median. This shift in population maturity was accompanied by a significant increase (P < 0.01) in the number of hatched juveniles present in each sample. There was also a significant increase (P < 0.02) in amount of FaRP-like peptide detected by specific ELISA. Total FaRP levels increased from 0.18 +/- 0.07 fMol FLRFamide equivalents per ng protein in early development eggs to 0.40 +/- 0.17 in late development eggs. The level remained high in hatched juveniles. HPLC/ELISA detected as many as nine potential FaRPs in H. glycines, two of which were specifically increased (P < 0.005) in hatched juveniles. The association of FaRPs with maturing eggs and the possible involvement of these neuropeptides with juvenile hatching and motility are discussed.
Mixture in the distribution of haloperidol-induced oral dyskinesias in the rat supports an animal model of tardive dyskinesia.

Spontaneous adventitious oral movements which are produced in rats by very chronic (6- month) neuroleptic treatment have some phenomenologic and pharmacologic characteristics in common with tardive dyskinesia in humans. However, since not all of the features match, this putative model has been questioned and further support is warranted. Data from several laboratories support dichotomizing these neuroleptic-induced rat oral movements into “low”or “not TD-like” movements and “high”or “TD-like” movements, similar to the division of neuroleptic-induced involuntary movements in humans. Here, we have used mixture analysis to test this proposal statistically in 185 haloperidol-treated and 127 water-treated animals. Rats from several different studies were grouped together to form these two cohorts. The haloperidol dose, route of administration, rating technique, and balanced experimental groups were held constant across all experiments. Results show that two distinct groups of rat movements are induced by very chronic haloperidol treatment (1.5 mg/kg per day). The “low” vacuous chewing movement (VCM) group of rats had an average of 3.6 VCMs/5 min, and the “high” VCM group had an average of 16.1 VCMs/5 min; the conrol group, with a median VCM rate of 2.0 VCMs/5 min, demonstrated a single distribution. These data suggest that rats, like humans, dichotomize into two groups either expressing or not expressing “high” VCM dyskinesias with very chronic haloperidol treatment.
Feedback mechanisms for improving probabilistic memory prefetching

This paper presents three techniques for improving the effectiveness of the recently proposed Adaptive Stream Detection (ASD) prefetching mechanism. The ASD prefetcher is a standard stream buffer that takes a probabilistic feedback-based probabilistic approach to identifying streams. Its strength lies in its ability to effectively prefetch streams that are as short as two consecutive cache lines, which allows it to exploit spatial locality even for programs that have irregular access patterns.
Effect of prolactin on phosphate transport and incorporation in mouse mammary gland explants.

Inorganic phosphate is present in milk at a concentration that is severalfold higher than in maternal plasma. In cultured mammary tissues from 12- to 14-day-pregnant mice, the intracellular concent...
A new strategy to enhance cavitational tissue erosion using a high-intensity, initiating sequence

Our previous studies have shown that pulsed ultrasound can physically remove soft tissue through cavitation. A new strategy to enhance the cavitation-induced erosion is proposed wherein tissue erosion is initiated by a short, high-intensity sequence of pulses and sustained by lower intensity pulses. We investigated effects of the initiating sequence on erosion and cavitation sustained by lower intensity pulses. Multiple three-cycle pulses at a pulse repetition frequency of 20 kHz delivered by a 788-kHz focused transducer were used for tissue erosion. Fixing the initiating sequence at ISPPA of 9000 W/cm2, 16 combinations of different numbers of pulses within the initiating sequence and different sustaining pulse intensities were tested. Results showed: the initiating sequence increases the probability of erosion occurrence and the erosion rate with only slight overall increases in propagated energy; the initiating sequence containing more pulses does not increase the sustained cavitation period; and if extinguished and reinitiated, the sustained cavitation period becomes shorter after each initiation, although the waiting time between adjacent cavitation periods is random. The high-intensity, initiating sequence enhances cavitational tissue erosion and enables erosion at intensities significantly lower than what is required to initiate erosion
Have Business Communication Instructors Changed Their Perception Of Business Ethics? A Comparative Study With Implications For Teaching

The purpose of this study was to determine the opinions of communication instructors in the Southeastern and Southwestern Regions of the Association for Business Communication concerning the teaching of ethics.
Classification of Agents Used in Serotonin Research

Due to a lack of site-selective serotonergic ligands, and a need to develop novel agents with greater selectivity, an attempt is made to catalog serotonergic agents from a structural perspective. Not surprisingly, it would appear that the same structure-types are associated with multiple populations of 5-HT receptors. Selectivity seems to be more a matter of what substituents are present in a molecule, rather than overall structure-type.
Alcohol and Drug Use Problems Among Older Adults

Alcohol and drug use among older adults is an area of increasing public health concern, and one which is timely to explore from the perspective of psychological research and practice. Many people reduce substance use as they get older. Yet a substantial percentage drink at hazardous levels or use illegal drugs, over-the-counter medications, or prescription medications in ways that put them at risk for health and psychosocial problems. This review examines the epidemiological literature on substance use patterns, including age-associated changes, risk factors for the development of alcohol and drug use problems, and strategies for screening, assessment, and diagnosis. It also describes approaches to intervention across a range of problem severity, highlighting issues especially relevant to psychologists working with older adults.
Insulin Detemir—A New Basal Insulin Analog

OBJECTIVE:To review the pharmacology, pharmacokinetics, clinical trial data, adverse effects, and role in therapy of insulin detemir.DATA SOURCES:Articles and meeting abstracts were identified through searches of MEDLINE (1996–June 2004), EMBASE (1980–June 2004), and International Pharmaceutical Abstracts (1970–June 2004) databases, and unpublished information was provided by the manufacturer.STUDY SELECTION AND DATA EXTRACTION:All available studies relating to insulin detemir's pharmacology were selected. Only human studies were used for pharmacokinetic, drug interaction, efficacy, and safety data.DATA SYNTHESIS:Insulin detemir is a basal insulin analog that has been shown to improve glycemic control in patients with type 1 and type 2 diabetes.CONCLUSIONS:Insulin detemir offers some benefits over NPH for use as basal insulin in patients with type 1 and type 2 diabetes.
Geniotubercle advancement with a uvulopalatal flap and its effect on swallow function in obstructive sleep apnea

Objectives/Hypothesis Evaluate swallowing characteristics before and after geniotubercle advancement (GTA) with a uvulopalatal flap (UPF). Study Design Prospective case control series in an academic military practice. Methods Fourteen patients with apnea-hypopnea index (AHI) >10 scheduled for GTA were enrolled consecutively, eight of whom completed all aspects of the study for evaluation. Video fluoroscopic swallow study was performed preoperatively and 4 months postoperatively. National Institute of Health freeware ImageJ64 software was used to measure hyolaryngeal elevation and displacement. Video recordings assessed vallecular pooling, aspiration, and bolus movement. Studies were reviewed by a speech pathologist and an otolaryngologist. Results Preoperatively, the mean AHI was 48.3 ± 48.45 events per hour, with a median of 48.5 (range, 12.4–76). Postoperatively the mean AHI was 11.6 ± 10.7 events per hour, with a median of 10.75 (range, 3.8–29) (P = .003). There was no reported pre- or postoperative dysphagia or aspiration. No radiographic evidence of silent aspiration was seen. Hyolaryngeal movements were measured as a percentage of C2–C4 reference distance. The superior elevations were pre- and postoperatively 40% and 37% (P = .85), anterior displacement changes 18.9% and 18.8% (P = .23), and total motion 49% and 42% (P = .26), respectively. Conclusions GTA with UPF surgery did not significantly affect the hyolaryngeal function of patients. Level of Evidence 4. Laryngoscope, 125:758–761, 2015
β-Catenin Links Hepatic Metabolic Zonation with Lipid Metabolism and Diet-Induced Obesity in Mice

β-catenin regulates the establishment of hepatic metabolic zonation. To elucidate the functional significance of liver metabolic zonation in the chronically overfed state in vivo, we fed a high-fat diet (HFD) to hepatocyte-specific β-catenin transgenic (TG) and knockout (KO) mice. Chow-fed TG and KO mice had normal liver histologic findings and body weight. However, HFD-fed TG mice developed prominent perivenous steatosis with periportal sparing. In contrast, HFD-fed KO mice had increased lobular inflammation and hepatocyte apoptosis. HFD-fed TG mice rapidly developed diet-induced obesity and systemic insulin resistance, but KO mice were resistant to diet-induced obesity. However, β-catenin did not directly affect hepatic insulin signaling, suggesting that the metabolic effects of β-catenin occurred via a parallel pathway. Hepatic expression of key glycolytic and lipogenic genes was higher in HFD-fed TG and lower in KO mice compared with wild-type mice. KO mice also exhibited defective hepatic fatty acid oxidation and fasting ketogenesis. Hepatic levels of hypoxia inducible factor-1α, an oxygen-sensitive transcriptional regulator of glycolysis and a known β-catenin binding partner, were higher in HFD-fed TG and lower in KO mice. KO mice had attenuated perivenous hypoxia, suggesting disruption of the normal sinusoidal oxygen gradient, a major determinant of liver carbohydrate and liver metabolism. Canonical Wnt signaling in hepatocytes is essential for the development of diet-induced fatty liver and obesity.
An Asset Allocation Primer

This paper serves as a general guide to asset allocation. It answers the following questions: (1) What is asset allocation? (2) What are asset classes? (3) What is a normal allocation? (4) When should an allocation deviate from the norm?
Younger Dryas in southern South America

Two high resolution pollen records, Caunahue from mid-latitudes and Harberton from high latitudes, illustrate the issues in defining the Younger Dryas episode in records from southern South America. At mid-latitudes in the Chilean lake region, previous claims for the existence of a substantially cooler and wetter episode between 11,000 and 10,000 BP can no longer be supported by new pollen records with high temporal and paleoenvironmental resolution, such as Caunahue. The transition from glacial to interglacial conditions occurred in several steps, one shortly after 13,000 BP, when open Nothofagus woodland was replaced by cool-temperate North Patagonian forest, and one at 9,500 BP, when warmtemperate Validivian forest elements replaced the North Patagonian elements. At high latitudes, on the other hand, high resolution records do show marked short-term changes during the late-glacial, inclding the 11,000 to 10,000 BP Interval. However, neither the exact timing nor the duration of these changes is synchronous for specific taxa, neither within one record nor between different records. One of the two intervals of low pollen influx that has been singled out as evidence for a cooler episode is consistently dated between 11,000 and 12,000 BP, while the other interval dates between 10,800 and 9,000 BP. Based on all this information I believe that there is no evidence of Younger Dryas episode for the midlatitudes. For the high latitudes, on the other hand, the overall high paleoenvironmental variability in the records offers multiple choices for a Younger Dryas-type interval if specific taxa are selected without considering the overall context. However, the lack of synchroneity between short-term changes of specific taxa between different records suggests primarily a response to local disturbances, rather than a response to a global forcing.
Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration

Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services. We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info . A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST). The need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high priority data from local, independent, idiosyncratic data schemas to common shared concepts as implemented in web-accessible ontologies. These mappings are then amenable for use in semantic web services. Our implementation of approximately two dozen services means that biological data at three large information resources (Gramene, SoyBase, and LIS) is available for programmatic access, semantic searching, and enhanced interaction between the separate missions of these resources.
Global patterning of the vertebrate mesoderm.

We describe recent advances in the understanding of patterning in the vertebrate post-cranial mesoderm. Specifically, we discuss the integration of local information into global level information that results in the overall coordination along the anterioposterior axis. Experiments related to the integration of the axial and appendicular musculoskeletal systems are considered, and examples of genetic interactions between these systems are outlined. We emphasize the utility of the terms primaxial and abaxial as an aid to understanding development of the vertebrate musculoskeletal system, and hypothesize that the lateral somitic frontier is a catalyst for evolutionary change. Developmental Dynamics 236:2371–2381, 2007. © 2007 Wiley-Liss, Inc.
Hereditary properties of the class of closed sets of uniqueness for trigonometric series

It is shown that theσ-idealU 0 of closed sets of extended uniqueness inT is hereditarily non-Borel, i.e. every “non-trivial”σ-ideal of closed setsI⊆U 0 is non-Borel. This implies both the result of Solovay, Kaufman that bothU 0 andU (theσ-ideal of closed sets of uniqueness) are not Borel as well as the theorem of Debs-Saint Raymond that every Borel subset ofT of extended uniqueness is of the first category. A further extension to ideals contained inU 0 is given.
Construction and characterization of recombinant vaccinia viruses co-expressing a respiratory syncytial virus protein and a cytokine.

Recombinant vaccinia viruses are well-characterized tools that can be used to define novel approaches to vaccine formulation and delivery. While vector co-expression of immune mediators has enormous potential for optimizing the composition of vaccine-induced immune responses, the impact on antigen expression and vector antigenicity must also be considered. Co-expression of IL-4 increased vaccinia virus vector titres, while IFN-γ co-expression reduced vaccinia virus replication in BALB/c mice and in C57BL/6 mice infected with some recombinant viruses. Protection against respiratory syncytial virus (RSV) challenge was similar in mice immunized with vaccinia virus expressing RSV G glycoprotein and IFN-γ, even though the replication efficiency of the vector was diminished. These data demonstrate the ability of vector-expressed cytokine to influence the virulence of the vector and to direct the development of selected immune responses. This suggests that the co-expression of cytokines and other immunomodulators has the potential to improve the safety of vaccine vectors while improving the immunogenicity of vaccine antigens.
Fluoride Model Systems: IV, The Systems LiF‐BeF2 and PbF2‐BeF2

Additional information on phase equilibria in the subsolidus region of the system LiF-BeF2 was obtained and a study was made of the system PbF2–BeF2. In the system LiF-BeF2 the compound LiBeF3 occurs; it decomposes below the solidus at 300° C. to yield Li2BeF4 and the quartz form of BeF2. An additional subsolidus compound having the probable composition LiBe2F5 forms below 275°C. No evidence was found for the existence of the alleged compound LiBe2F5. In the system PbF2-BeF2 two compounds occur: 3PbF2.BeF2 and PbF2-BeF2; the former melts congruently at 482°± 5°C. and the latter at 585°± 5°C. Extensive solid solution exists between PbF2.BeF2 and BeF2. The cristobalite form of BeF2 crystallizes from glasses of high BeF2 content at temperatures of 450°C. or lower but is converted to the quartz form by heating at higher temperatures or in the presence of liquid.
OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Motivation: Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the sequencing-by-synthesis and signal acquisition processes. This drives the search for accurate, scalable and computationally tractable base calling algorithms capable of accounting for such imperfections. Results: Relying on a statistical model of the sequencing-by-synthesis process and signal acquisition procedure, we develop a computationally efficient base calling method for Illumina's sequencing technology (specifically, Genome Analyzer II platform). Parameters of the model are estimated via a fast unsupervised online learning scheme, which uses the generalized expectation–maximization algorithm and requires only 3 s of running time per tile (on an Intel i7 machine @3.07GHz, single core)—a three orders of magnitude speed-up over existing parametric model-based methods. To minimize the latency between the end of the sequencing run and the generation of the base calling reports, we develop a fast online scalable decoding algorithm, which requires only 9 s/tile and achieves significantly lower error rates than the Illumina's base calling software. Moreover, it is demonstrated that the proposed online parameter estimation scheme efficiently computes tile-dependent parameters, which can thereafter be provided to the base calling algorithm, resulting in significant improvements over previously developed base calling methods for the considered platform in terms of performance, time/complexity and latency. Availability: A C code implementation of our algorithm can be downloaded from http://www.cerc.utexas.edu/OnlineCall/ Contact: ude.saxetu.ece@olakivh Supplementary information: Supplementary data are available at Bioinformatics online.
Reduced Bias Autocorrelation Estimation:Three Jackknife Methods:

The effectiveness of jackknife methods in reducing bias in the estimation of the lag-I autocorrelation parameter Pi was evaluated. A Monte Carlo investigation was carried out to study the empirical bias, mean-square error, and variance properties of three jackknife estimators using sample sizes that ranged from 6 through 500. The results demonstrated that these estimators are far less biased in the small sample case than are many other estimators that have been recently investigated. Results on the mean-squared error revealed that the advantage of greatly reduced bias associated with the jackknife estimators does not overcome the disadvantage of increased error variance. Three previously investigated estimators yield smaller mean-squared error than do the jackknife estimators or the conventional estimator at most sample sizes.
Heterogeneity in Lipid Composition of the Outer Membrane and Cytoplasmic Membrane of Pseudomonas BAL-31

Abstract The outer membranes and cytoplasmic membranes of the marine bacterium Pseudomonas BAL-31 were separated by washing the cells three times in 0.5 M NaCl and twice in 0.5 M sucrose. Electron microscopy during the removal of membranes revealed that the outer membranes fragmented in a regular manner to give rise to fairly uniform vesicles measuring approximately 140 nm in diameter. Isolated outer membranes had a buoyant density in sucrose of 1.230 g per cm3, whereas the cytoplasmic membranes had a density of 1.194 g per cm3. The removal of the outer membrane during the application of this procedure was monitored by measuring the release of 2-keto-3-deoxyoctulosonic acid and phospholipid. The cells lost 85.5% of their 2-keto-3-deoxyoctulosonic acid and 47.3% of their phospholipid during this treatment. Complete recovery of outer membrane material could be achieved. The removal of 25.5% of the 2-keto-3-deoxyoctulosonic acid and 0.9% of the phospholipid rendered the cells sensitive to lysis with Triton X-100. The phospholipid composition of the outer membrane was calculated to be 78.9% phosphatidylethanolamine and 16.1% phosphatidylglycerol. The phospholipid composition of the cytoplasmic membrane proved to be 71.5% phosphatidylethanolamine and 23.5% phosphatidylglycerol. The fatty acid composition was also found to be quantitatively heterogeneous between the two membranes.
Providing hepatitis B vaccination to injection drug users: Referral to health clinics vs on-site vaccination at a syringe exchange program

Injection drug users (IDUs) are at very high risk for infection with hepatitis B virus (HBV) through multiperson use of injection equipment and through unprotected sexual contact. Although a safe and efficacious vaccine exists for hepatitis B, there are multiple problems in vaccinating IDUs in the United States, including (1) discrimination against drug users by health care providers, (2) the need to reach IDUs before they are exposed to HBV, (3) paying for the vaccinations, and (4) difficulties in completing the 3-injection vaccination series. We compared 2 methods for delivering free hepatitis B vaccination to IDUs: (1) referral by research staff to local health care providers and (2) on-site vaccination at a syringe exchange program.
Efficient Hybrid Security Mechanisms for Heterogeneous Sensor Networks

Many applications that make use of sensor networks require secure communication. Because asymmetric-key solutions are difficult to implement in such a resource-constrained environment, symmetric-key methods coupled with a priori key distribution schemes have been proposed to achieve the goals of data secrecy and integrity. These approaches typically assume that all nodes are similar in terms of capabilities and, hence, deploy the same number of keys in all sensors in a network to provide the aforementioned protections. In this paper, we demonstrate that a probabilistic unbalanced distribution of keys throughout the network that leverages the existence of a small percentage of more capable sensor nodes can not only provide an equal level of security, but also reduce the consequences of node compromise. To fully characterize the effects of the unbalanced key management system, we design, implement, and measure the performance of a complementary suite of key establishment protocols known as LIGER. Using their predeployed keys, nodes operating in isolation from external networks can securely and efficiently establish keys with each other. Should resources such as a backhaul link to a key distribution center (KDC) become available, networks implementing LIGER automatically incorporate and benefit from such facilities. Detailed experiments demonstrate that the unbalanced distribution in combination with the multimodal LIGER suite offers a robust and practical solution to the security needs in sensor networks
Spermatozoa Bound to Solid State Hyaluronic Acid Show Chromatin Structure With High DNA Chain Integrity: An Acridine Orange Fluorescence Study

During human spermiogenesis, the elongated spermatids undergo a plasma membrane remodeling step that facilitates formation of the zona pellucida and hyaluronic acid (HA) binding sites. Various biochemical sperm markers indicated that human sperm bound to HA exhibit attributes similar to that of zona pellucida-bound sperm, including minimal DNA fragmentation, normal shape, and low frequency of chromosomal aneuploidies. In this work, we tested the hypothesis that HA-bound sperm would be enhanced in sperm of high DNA chain integrity and green acridine orange fluorescence (AOF) compared with the original sperm in semen. Sperm DNA integrity in semen and in their respective HA-bound sperm fractions was studied in 50 men tested for fertility. In the semen samples, the proportions of sperm with green AOF (high DNA integrity) and red AOF (DNA breaks) were 54.9% ± 2.0% and 45.0% ± 1.9%, whereas in the HA-bound sperm fraction, the respective proportions were 99% and 1.0%, respectively. The data indeed demonstrated that HA shows a high degree of selectivity for sperm with high DNA integrity. These findings are important from the points of view of human sperm DNA integrity, sperm function, and the potential efficacy of HA-mediated sperm selection for intracytoplasmic sperm injection.
Vector Competence of Culicoides sonorensis (Diptera: Ceratopogonidae) for Vesicular Stomatitis Virus

To determine the vector competence of Culicoides sonorensis Wirth & Jones midges for vesicular stomatitis virus (VSV)-New Jersey, insects were experimentally infected per os and sampled over time. Viral replication, as determined by in situ hybridization, was seen in epithelial, neural, and hemolymph cell types throughout the insect. Spatial and temporal distribution of virus was determined by immunohistochemical examination of sequentially sampled insects. Tissues of the alimentary canal were infected in a temporal pattern that paralleled the route of digestion/absorption: foregut and midgut by day 1, surrounding hemolymph and Malpighian tubules by day 3, and finally the midgut/hindgut junction, hindgut, and rectal region by day 5. The circulation of virus in the hemolymph by day 3 coincided with infection of the dermis and fat bodies, the salivary glands, eyes, cerebral and subthoracic ganglia, and the ovaries. Oviduct epithelium and ovarial sheaths were infected by day 3, followed by infection of the developing oocytes by day 5. Interestingly, neural infections were seen in the subabdominal ganglia innervating the midgut in 33% of insects by 1 d postfeeding in the absence of positive staining in the hemolymph or surrounding tissues. A retrograde axonal transport infection route for these ganglia is discussed. The disseminated, productive, noncytolytic infection in Culicoides is consistent with that of an efficient biological vector for VSV. Virus readily replicated throughout the insect, passing both midgut and salivary gland infection barriers and reaching transmission-related organs in 3 d. Establishing the competence of this insect vector for VSV provides the foundation for animal transmission studies in the future. The possibility of horizontal, transovarial, and mechanical transmission is discussed.
Flammability and volatility attributes of binary mixtures of some practical multi-component fuels

Abstract Gasoline compression ignition (GCI) engines could be more efficient than most advanced SI engines while running on lower octane fuel. GCI engines may utilize a mixture of different fuels and fuel components such as gasoline and diesel or diesel and naphtha. The risks and hazards associated with such mixtures must be studied to ensure safe fuel storage, shipping and dispensing. In this work, flash point and vapor pressure measurements of different binary multi-component hydrocarbon mixtures are presented along with calculated lower and upper flammability limits. An equation has been developed to correlate flash point with other fuel properties. The flash point of a mixture approaches the flash point of the more volatile component, falling rapidly in some cases, as the more volatile component concentration increases. Vapor pressure is inversely related to flash point for a given mixture. Diesel/light straight run naphtha mixtures and diesel/gasoline mixtures exhibit similar flash point versus vapor pressure trends. Flammability limits were calculated using Le Chatelier’s Mixing Rule and modified Burgess–Wheeler Law. Hydrocarbon mixtures have similar lower and upper flammability limits over a range of temperatures. The vapor pressure of fuels and fuel blends has been used to determine the safe operating region as a function of blending formula and temperature. This work demonstrates that normal butane can be used to formulate blends of gasoline and naphtha with diesel, which are safe to handle and meet seasonal vapor pressure requirements.