bluuebunny/crossref_metadata_2025 huggingface dataset:
Long‐Term Effect of Deslorelin Implant on Ovarian Pre‐Antral Follicles and Uterine Histology in Female Rats
Authors: Cetin Y , Alkis I , Sendag S , Ragbetli M , Akyol V , Ucar O , Wehrend A
Published: June 2012

Contents

The objective of the present study was to investigate the inhibitory effects of long‐term deslorelin implant administration on the ovarian and uterine structures of female rats. A total of 16 non‐pregnant female rats were randomly assigned to two groups, each consisting of eight animals. Animals in the implant group (DESL) received subcutaneously (s.c.) a single deslorelin implant (4.7 mg), an analogue of GnRH, while no treatment was applied to the control group (CON). A single adult male rat was introduced into the cages of both the DESL and CON females after 6 weeks of implant administration. After 1 year of implant administration, all animals were killed and follicular structures and volumes of ovaries and uterus were examined using stereological methods. Stereological observations showed that the mean ovarian total volume of the DESL group (0.28 ± 0.07 cm3) was lower than that of the CON group (1.55 ± 0.23 cm3) (p < 0.001). On the other hand, the total number of pre‐antral follicles in the ovaries of DESL (555.32 ± 151.47) females were significantly lower than the control group (1162.96 ± 189.19) (p < 0.001). In the DESL group, the mean volumes of epithelium, endometrium, myometrium and total volume of the uterus were significantly (p < 0.001) lower than in the control groups. In conclusion, these findings indicate that the long‐term deslorelin implant (i) interferes with the normal cyclicity of female rats and (ii) affects the pre‐antral follicle population. Further studies will be required to determine the effects of long‐term deslorelin treatment on the pre‐antral follicle numbers and future fertility in other species.
Is backdating executive stock options always costly to shareholders?
Authors: Grégoire Philippe , Glenn Hubbard Robert , Koehn Michael F. , Audenrode Marc Van , Royer Jimmy
Published: June 2012

We use a binomial model to investigate the cost to shareholders of backdating employee stock option (ESO) grants to award in‐the‐money rather than at‐the‐money options to a manager. When the expected return of the stock underlying an ESO is sufficiently close to the risk‐free rate, a backdating arrangement can always be structured to simultaneously improve shareholders’ wealth and the manager's utility. The smaller the manager's non‐option wealth, personal income tax rate or risk tolerance, the more likely a backdating arrangement can be welfare improving.
Bread matters: a national initiative to profile the genetic diversity of Australian wheat
Authors: Edwards David , Wilcox Stephen , Barrero Roberto A. , Fleury Delphine , Cavanagh Colin R. , Forrest Kerrie L. , Hayden Matthew J. , Moolhuijzen Paula , Keeble‐Gagnère Gabriel , Bellgard Matthew I. , Lorenc Michał T. , Shang Catherine A. , Baumann Ute , Taylor Jennifer M. , Morell Matthew K. , Langridge Peter , Appels Rudi , Fitzgerald Anna
Published: June 2012

The large and complex genome of wheat makes genetic and genomic analysis in this important species both expensive and resource intensive. The application of next‐generation sequencing technologies is particularly resource intensive, with at least 17 Gbp of sequence data required to obtain minimal (1×) coverage of the genome. A similar volume of data would represent almost 40× coverage of the rice genome. Progress can be made through the establishment of consortia to produce shared genomic resources. Australian wheat genome researchers, working with Bioplatforms Australia, have collaborated in a national initiative to establish a genetic diversity dataset representing Australian wheat germplasm based on whole genome next‐generation sequencing data. Here, we describe the establishment and validation of this resource which can provide a model for broader international initiatives for the analysis of large and complex genomes.
Urban vulnerability and displacement: a review of current issues
Authors: Pantuliano Sara , Metcalfe Victoria , Haysom Simone , Davey Eleanor
Published: June 2012

Urban displacement is frequently portrayed as a new and unfamiliar dilemma for the humanitarian sector, yet broad awareness of its characteristics and challenges has been developing since the 1970s. In the past decade, however, there has been greater attention to, and recognition of, the implications of rapid urbanisation in the developing world. This has led to some policy development and a mounting body of NGO (non‐governmental organisation) and think‐tank literature on the topic. Assuming displacement to be a key lens on urban vulnerability more broadly, this paper presents an overview of the historical development of debates on urban displacement since the 1970s. Drawing examples from the contributions in this special issue of Disasters, as well as from other sources of information on recent humanitarian responses in various contexts, it assesses the ramifications of urban vulnerability for humanitarian practitioners. The paper contends that the humanitarian sector has failed to galvanise on the issue, and has struggled therefore to employ existing knowledge and to adapt practice.
Jockeying for position in the humanitarian field: Iraqi refugees and faith‐based organisations in Damascus
Authors: Zaman Tahir
Published: June 2012

The rise in the number of interventions by faith‐based organisations in the humanitarian field has reignited debate about the role of religion in the public sphere. This paper presents a nuanced examination of the part played by religious institutions and networks in the strategies of forced migrants in urban contexts. Furthermore, it considers how such organisations work to integrate displaced populations into their new surroundings. Drawing on two case studies and ethnographic fieldwork and in‐depth interviews with Iraqi refugees and refugee service providers in Damascus, Syria, carried out between March 2010 and March 2011, it evaluates how Iraqi refugees, as active social agents, utilise religious institutions and networks in conjunction with established international humanitarian organisations to produce a distinctive geography of exile. In addition, it draws attention to how the Syrian state exerts influence over religious actors and how ultimately this affects the decision‐making of forced migrants.
Mutualisms are not constraining cross‐continental invasion success of Acacia species within Australia
Authors: Birnbaum Christina , Barrett Luke G. , Thrall Peter H. , Leishman Michelle R.
Published: June 2012

Aim

Studying plant–soil interactions of introduced species in different parts of their global range could assist in managing biological invasions by elucidating the level of host specificity of key mutualists. We assessed the role of the soil microbial community (with an emphasis on symbiotic nitrogen‐fixing bacteria, collectively termed rhizobia) in determining cross‐continental invasion success of five woody legume species.

Location

Australia.

Methods

For each species, we compared growth of plants in soils from their native and non‐native ranges using a glasshouse study, a soil dilution method (most probable number) and T‐RFLP to assess rhizobial abundance and community composition, respectively.

Results

Acacia longifolia was the only species that had significantly larger above‐ground biomass when grown in soils from its non‐native range. Rhizobial abundance was equally high across species and ranges, indicating plants are unlikely to be limited by soil rhizobial abundance in non‐native ranges. Acacia cyclops, A. saligna and Paraserianthes lophantha formed associations with different rhizobial communities in non‐native vs. native range soils. Acacia longifolia and A. melanoxylon associated with similar rhizobial communities in their native and non‐native ranges, suggesting that rhizobia may have been accidentally introduced into their novel range with seeds or seedlings.

Main conclusions

Invasive success of these five legume species is not constrained by the abundance of rhizobia in novel ranges for established legume populations, at least within Australia. Although differences in rhizobial community composition were evident between the native and non‐native ranges for three of the five species, these were not associated with differences in plant growth. Increased above‐ground biomass of A. longifolia when grown in soil from its non‐native range suggests that invasive success of this species may be associated with differences in the non‐rhizobial components of soil microbial communities in the novel range. This information could assist in management practises by facilitating a more instructive and effective screening for invasiveness.
Policy Alienation of Public Professionals: The Construct and Its Measurement
Authors: Tummers Lars
Published: June 2012

Currently, there is an intense debate on the pressures facing public professionals during policy implementation. Frequently, professionals have difficulty identifying with new policies, resulting in diminished policy performance. The author examines this problem using the concept of “policy alienation” and develops and tests a scale for its measurement. Policy alienation is associated conceptually with five subdimensions: strategic powerlessness, tactical powerlessness, operational powerlessness, societal meaninglessness, and client meaninglessness. A policy alienation scale was using a survey of 478 Dutch health care professionals implementing a new financial policy, diagnosis related groups. The resulting 23‐item policy alienation scale demonstrated good psychometric qualities. A reliable and valid policy alienation scale can help in understanding and enhancing policy performance.
Public Service Motivation (PSM) and Support for Citizen Participation: A Test of Perry and Vandenabeele’s Reformulation of PSM Theory
Authors: Coursey David , Yang Kaifeng , Pandey Sanjay K.
Published: June 2012

This article examines how public service motivation (PSM) relates to public managers’ attitudes toward citizen participation. Perry and Vandenabeele suggest that PSM effects are moderated and/or mediated by self‐regulation and by the salience of an activity to self‐identity. Using data from Phase IV of the National Administrative Studies Project, latent model results suggest a direct, positive relationship between PSM and citizen participation evaluation. The relationship is not mediated by value congruence but rather is moderated by the perceived importance of the organization’s citizen participation efforts. The moderating effect has three interpretations: (1) PSM has a stronger relationship to evaluation as citizen participation becomes more important in the agency; (2) at low and medium PSM levels, the greater the importance of citizen participation, the lower its evaluation; or (3) at high PSM levels, the greater the importance of citizen participation, the higher its evaluation. This suggests that PSM is more germane for activities such as citizen participation, invoking relevant values as perceived organizational commitment increases.
Calorimetric Study of Glass Structure Modification Induced by α Decay
Authors: Maugeri Emilio Andrea , Peuget Sylvain , Staicu Dragos , Zappia Alessandro , Jegou Christophe , Wiss Thierry
Published: June 2012

R7T7‐type glass samples doped with different concentrations of 244Cm and stored for different time periods to produce different levels of accumulated radiation damage were analyzed by differential scanning calorimetry to better understand the structural evolution of R7T7 nuclear glass due to the accumulation of α radiation damage. The stored energy and fictive temperature were observed to increase as a function of the α decay dose. The stored energy saturates at about 1018 α decays·g−1, whereas the fictive temperature continues to increase and saturates at about 6–7 × 1018 α decays·g−1. This discrepancy was interpreted in terms of different effects of energy lost during α decay on the glass structure due to electronic stopping and nuclear stopping. This study demonstrates that the stored energy is affected by both phenomena, whereas the fictive temperature variation depends mainly on elastic collisions. The increase of fictive temperature with the cumulative α dose is direct evidence that the energy lost by recoil nuclei induces the formation of a new structure similar to a fast‐quenched glass.
Oral human β‐defensin 2 in HIV‐infected subjects with long‐term use of antiretroviral therapy
Authors: Nittayananta Wipawee , Kemapunmanus Marisa , Amornthatree Korntip , Talungchit Sineepat , Sriplung Hutcha
Published: June 2012

Background:  The objectives of this study were to determine (i) oral hBD2 expression in HIV‐infected subjects compared with non‐HIV controls, (ii) the expression of oral hBD2 in HIV‐infected subjects with antiretroviral therapy (ART) compared with those without ART, and (iii) factors associated with the expression of oral hBD2.

Methods:  Oral examination and punched biopsy on buccal mucosa were performed in HIV‐infected subjects with and without ART, and non‐HIV individuals. The expression of hBD2 mRNA was determined by quantitative real‐time PCR. Saliva samples of both un‐stimulated and stimulated saliva were collected and analyzed for hBD2 levels using ELISA. Student’s t‐test and nonparametric multi‐way ANOVA test were used for comparison of measurements between or among groups.

Results:  One hundred and fifty‐seven HIV‐infected subjects were enrolled: 99 on ART (age range, 23–57 years; mean 39 years), 58 not on ART (age range, 20–59 years; mean 34 years), and 50 non‐HIV controls (age range, 19–59 years; mean 36 years). The most common ART regimen was two nucleoside reverse transcriptase inhibitors + one non‐nucleoside reverse transcriptase inhibitor. Salivary levels of hBD2 were significantly increased in HIV infection (P < 0.001). The levels of hBD2 in stimulated saliva were also found to be significantly different between HIV‐infected subjects who were and were not on ART (P < 0.001). No significant difference was observed with the expression of hBD2 mRNA.

Conclusion:  Oral innate immunity is affected by HIV infection and use of ART. Salivary hBD2 levels may be the useful biomarkers to monitor those on long‐term ART who are at risk of developing oral infections and malignant transformation.
Additive effects of the dopamine D2 receptor and dopamine transporter genes on the error‐related negativity in young children
Authors: Meyer A. , Klein D. N. , Torpey D. C. , Kujawa A. J. , Hayden E. P. , Sheikh H. I. , Singh S. M. , Hajcak G.
Published: June 2012

The error‐related negativity (ERN) is a negative deflection in the event‐related potential that occurs approximately 50ms following the commission of an error at fronto‐central electrode sites. Previous models suggest dopamine plays a role in the generation of the ERN. We recorded event‐related potentials (ERPs) while 279 children aged 5–7 years completed a simple Go/No‐Go task; the ERN was examined in relation to the dopamine D2 receptor (DRD2) and dopamine transporter (DAT1) genes. Results suggest an additive effect of the DRD2 and DAT1 genotype on ERN magnitude such that children with at least one DRD2 A1 allele and children with at least one DAT1 9 allele have an increased (i.e. more negative) ERN. These results provide further support for the involvement of dopamine in the generation of the ERN.
Thomas Aquinas’ Metaphysics of ‘Relation’ and ‘Participation’ and Contemporary Trinitarian Theology
Authors: Awad Najeeb
Published: June 2012

This paper is an attempt at proposing Thomas Aquinas’ metaphysics of ‘relationship’ and ‘participation’ as a corrector of a contemporary theological trend that conflates ‘person’ with ‘relation’ in its understanding of the trinity, turning God, eventually, from a self-existing, particular personal Being into an idealist expression of a network of relational movements reflective of what the human personhood means. Thomas Aquinas’ theology of relation and participation invites contemporary theology to retrieve a theology that keeps ‘transcendence’ characteristic of God's personal being in order not to turn the participation of God in the finite's realm of existence into a panentheist or one-sidedly, human-centered relationality.
Scientism and its Challenge to Humanism
Authors: Haldane John
Published: June 2012

Viewed from the perspective of the nineteenth century there is little in the details of contemporary political life that would seem special. Tensions between great powers, ethnic and religious divisions, trade rivalries, economic recessions, currency crises, civil unrest, etc. are all part of the fabric of the modern world. Social life in the West has been marked by the dissolution of families and communities into voluntary and market associations of individuals; but while that was a distinctive feature of the twentieth century and has extended into the twenty-first, it is a continuation of trends well-established in previous times principally through industrialisation and urbanisation.
WhiB2/Rv3260c, a cell division‐associated protein of Mycobacterium tuberculosis H37Rv, has properties of a chaperone
Authors: Konar Monica , Alam Md. Suhail , Arora Chandni , Agrawal Pushpa
Published: June 2012

whiB‐like genes have been found in all actinomycetes sequenced so far. The amino‐acid sequences of WhiB proteins of Mycobacterium tuberculosis H37Rv are highly conserved and participate in several cellular functions. Unlike other WhiB proteins of M. tuberculosis that have properties of protein disulfide reductases, WhiB2 showed properties like a chaperone as it suppressed the aggregation of several model substrates (e.g. citrate synthase, rhodanese and luciferase). Suppression of aggregation of the model substrates did not require ATP. Four cysteine residues of WhiB2 form two intramolecular disulfide bonds; however, chaperone function was unaffected by the redox state of the cysteines. WhiB2 also restored the activity of chemically denatured citrate synthase and did not require either ATP or a co‐chaperone for refolding. The results indicate that WhiB2, which has been shown to be associated with cell division in mycobacteria and streptomyces, has evolved independently of other WhiBs, although it retains basic properties of this group of proteins. This is the first report to show that a WhiB protein has chaperone‐like function; therefore, this report will have major implications in attempts to understand the role of WhiB proteins in mycobacteria, particularly in cell division.
Effects of Dietary β‐1,3‐Glucan on Expression of Immune‐related Genes of Litopenaeus vannamei Exposed to Nitrite‐N
Authors: Zhao Hong‐Xia , Cao Jun‐Ming , Wang An‐Li , Huang Yan‐Hua , Li Guo‐Li , Lan Han‐Bing
Published: June 2012

The effects of β‐1,3‐glucan on growth and expression of immune‐related genes in muscle were evaluated by a 84‐d feeding trial in white shrimp, Litopenaeus vannamei, fed diets containing 0, 250, 500, and 1000 mg/kg β‐1,3‐glucan, respectively. After the feeding trial, the shrimp were exposed to nitrite‐N (20 mg/L) for 120 h. The transcript abundance of hemocyanin, LPS/b‐glucan binding protein (LGBP), Penaeidin‐3, prophenoloxidase (proPO), Serine proteinase, and superoxide dismutase (SOD) was quantified by real‐time PCR. The results showed that during 84‐d feeding trial, 250 mg/kg β‐1,3‐glucan group showed significantly higher weight gain rate than control. There were no significant differences of survival rate between groups, but survival rate correlated inversely with dietary β‐1,3‐glucan levels (r2 = 0.96). Significantly upregulated LGBP were observed in 500 mg/kg β‐1,3‐glucan group compared to control. After 120 h nitrite stress, the expression level of hemocyanin, LGBP, proPO, Serine proteinase, and SOD in shrimp fed with 500 or 1000 mg/kg β‐1,3‐glucan were significantly higher than those in shrimp fed with other diets. Together, in this 84‐d feeding trial, 250 mg/kg β‐1,3‐glucan improved growth, whereas 500 mg/kg β‐1,3‐glucan preferentially improved nitrite resistance, probably through upregulating expression of immune‐related genes.
Androgen receptor polyglutamine repeat number: models of selection and disease susceptibility
Authors: Ryan Calen P. , Crespi Bernard J.
Published: June 2012

Variation in polyglutamine repeat number in the androgen receptor (AR CAGn) is negatively correlated with the transcription of androgen‐responsive genes and is associated with susceptibility to an extensive list of human disease. Only a small portion of the heritability for many of these diseases is explained by conventional SNP‐based genome‐wide association studies, and the forces shaping AR CAGn among humans remains largely unexplored. Here, we propose evolutionary models for understanding selection at the AR CAG locus, namely balancing selection, sexual conflict, accumulation‐selection, and antagonistic pleiotropy. We evaluate these models by examining AR CAGn‐linked susceptibility to eight extensively studied diseases representing the diverse physiological roles of androgens, and consider the costs of these diseases by their frequency and fitness effects. Five diseases could contribute to the distribution of AR CAGn observed among contemporary human populations. With support for disease susceptibilities associated with long and short AR CAGn, balancing selection provides a useful model for studying selection at this locus. Gender‐specific differences AR CAGn health effects also support this locus as a candidate for sexual conflict over repeat number. Accompanied by the accumulation of AR CAGn in humans, these models help explain the distribution of repeat number in contemporary human populations.
Pathogenesis, virulence factors and virulence regulation of vibrios belonging to the Harveyi clade
Authors: Darshanee Ruwandeepika Hettipala Arachchige , Sanjeewa Prasad Jayaweera Thotawaththage , Paban Bhowmick Patit , Karunasagar Indrani , Bossier Peter , Defoirdt Tom
Published: June 2012

The Harveyi clade or core group of the Vibrio genus includes both pathogenic and non‐pathogenic bacteria. Some of the species belonging to the clade, such as Vibrio harveyi, Vibrio alginolyticus, Vibrio campbellii and Vibrio parahaemolyticus, include serious pathogens of aquatic organisms. Importantly, within these species, some strains are pathogenic, whereas others are not. Other members of the clade, such as Vibrio natriegens and Vibrio mytili are reported to be non‐pathogenic. As bacteria belonging to the Harveyi clade show a high diversity with respect to virulence and as the virulent members cause high mortalities in the aquaculture sector, it is important to understand which gene products are responsible for the pathogenicity of the bacteria and how expression of these virulence factors is regulated. This knowledge will ultimately allow for the development of biocontrol measures that aim to reduce the severe losses that are currently faced in the aquaculture sector as a result of vibriosis. In this review, we discuss the pathogenesis of bacteria belonging to the Harveyi clade, their impact on the aquaculture sector, the virulence factors that are involved in pathogenicity and their regulation.
Broadly Reactive Polymerase Chain Reaction for Pathogen Detection in Canine Granulomatous Meningoencephalomyelitis and Necrotizing Meningoencephalitis
Authors: Barber R.M. , Porter B.F. , Li Q. , May M. , Claiborne M.K. , Allison A.B. , Howerth E.W. , Butler A. , Wei S. , Levine J.M. , Levine G.J. , Brown D.R. , Schatzberg S.J.
Published: June 2012

Background

Granulomatous meningoencephalomyelitis (GME) and necrotizing meningoencephalitis (NME) are common inflammatory conditions of the central nervous system of dogs. Infectious pathogens, particularly viruses, are suspected to contribute to the etiopathogenesis ofGMEandNME.

Hypothesis

Broadly reactivePCRmight aid in the identification of infectious agents inGMEandNME.

Animals

Sixty‐eight client‐owned dogs evaluated by necropsy at 1 university referral hospital.

Methods

A mixed prospective/retrospective case‐control study was performed. Brain tissue prospectively collected at necropsy fromGME,NME, and control cases was evaluated by broadly reactive polymerase chain reaction (PCR) for adenoviruses, bunyaviruses, coronaviruses, enteroviruses, flaviviruses, herpesviruses, paramyxoviruses, and parechoviruses. In addition, these tissues were retrospectively evaluated for the presence of mycoplasmas byPCR, culture, and immunohistochemistry (IHC).

Results

Brain tissue was collected from 11GMEand 27NMEcases and 30 controls. Viral nucleic acids were not identified in the 6GMEcases, 25NMEcases, and 2 controls evaluated by viralPCR.Mycoplasma caniswas identified byMycoplasmagenusPCRin 1/5GMEand 4/25NMEcases and subsequently was cultured from 4/5GMEand 4/8NMEcases as well as 2/9 controls. TheIHCdid not detectM. canisin any of the 11GMEand 27NMEcases or 14 controls evaluated with strainPG14 polyclonal antiserum.

Conclusions and Clinical Importance

The negative results suggest that viral pathogens are not common in the brain tissue of dogs withGMEandNME. Further investigation is warranted to determine the importance ofM. canisin cases ofGMEandNME.
Behavior of Unsteady Turbulent Starting Round Jets
Authors: Abani Neerav , Ghandhi Jaal B.
Published: June 2012

Turbulent starting jets with time-varying injection velocities were investigated using high-speed schlieren imaging. Two solenoid-controlled injectors fed a common plenum upstream of an orifice; using different upstream pressures and actuation times, injection-rate profiles with a step increase or decrease in injection velocity were tested. The behavior of the jet was found to be different depending on the direction of the injection-velocity change. A step increase in injection velocity resulted in an increased rate of penetration relative to the steady-injection case, and a larger increase in injection velocity resulted in an earlier change in the tip-penetration rate. The step-increase data were found to be collapsed by scaling the time by a convective time scale based on the tip location at the time of the injection-velocity change and the difference in the injection velocities. A sudden decrease in injection velocity to zero was found to cause a deviation from the corresponding steady-pressure case at a time that was independent of the initial jet velocity, i.e., it was independent of the magnitude of the injection-velocity change. Two models for unsteady injection from the literature were tested and some deficiencies in the models were identified.
Effect of Impeller Speed Perturbation in a Rushton Impeller Stirred Tank
Authors: Roy Somnath , Acharya Sumanta
Published: June 2012

Flow inside an unbaffled Rushton-impeller stirred tank reactor (STR) is perturbed using a time dependent impeller rotational speed. Large eddy simulation (LES) revealed that the perturbation increased the width of impeller jet compared to the constant rotational speed cases. The turbulent fluctuations were also observed to be enhanced in the perturbed flow and showed higher values of production and convection of turbulent kinetic energy. Changes in the mean flow-field during the perturbation cycle are investigated. The trailing edge vortices were observed to propagate farther both in the radial and azimuthal direction in the perturbed case. Production of turbulent kinetic energy is observed to be related to the breakup of the impeller jet in the perturbed case. Dissipation of turbulent kinetic energy is augmented due to the perturbation ensuring a better mixing at the molecular scale.
Asymptotic Effect of Initial and Upstream Conditions on Turbulence
Authors: George William K.
Published: June 2012

More than two decades ago the first strong experimental results appeared suggesting that turbulent flows might not be asymptotically independent of their initial (or upstream) conditions (Wygnanski et al., 1986, “On the Large-Scale Structures in Two-Dimensional Smalldeficit, Turbulent Wakes,” J. Fluid Mech., 168, pp. 31–71). And shortly thereafter the first theoretical explanations were offered as to why we came to believe something about turbulence that might not be true (George, 1989, “The Self-Preservation of Turbulent Flows and its Relation to Initial Conditions and Coherent Structures,” Advances in Turbulence, W. George and R. Arndt, eds., Hemisphere, New York, pp. 1–41). These were contrary to popular belief. It was recognized immediately that if turbulence was indeed asymptotically independent of its initial conditions, it meant that there could be no universal single point model for turbulence (George, 1989, “The Self-Preservation of Turbulent Flows and its Relation to Initial Conditions and Coherent Structures,” Advances in Turbulence, W. George and R. Arndt, eds., Hemisphere, New York, pp. 1–41; Taulbee, 1989, “Reynolds Stress Models Applied to Turbulent Jets,” Advances in Turbulence, W. George and R. Arndt, eds., Hemisphere, New York, pp. 29–73) certainly consistent with experience, but even so not easy to accept for the turbulence community. Even now the ideas of asymptotic independence still dominate most texts and teaching of turbulence. This paper reviews the substantial additional evidence - experimental, numerical and theoretical - for the asymptotic effect of initial and upstream conditions that has accumulated over the past 25 years. Also reviewed is evidence that the Kolmogorov theory for small scale turbulence is not as general as previously believed. Emphasis has been placed on the canonical turbulent flows (especially wakes, jets, and homogeneous decaying turbulence), which have been the traditional building blocks for our understanding. Some of the important outstanding issues are discussed; and implications for the future of turbulence modeling and research, especially LES and turbulence control, are also considered.
Real-Time Combustion Phase Detection Using Central Normalized Difference Pressure in CRDI Diesel Engines
Authors: Lim Jongsuk , Oh Seungsuk , Chung Jeasung , Sunwoo Myoungho
Published: June 2012

To develop eco-friendly diesel engines, accurate combustion phase control is important due to its significant effects on harmful emissions and fuel efficiency. In order to accurately control the combustion phase, the detection of the combustion phase should precede control system design. Currently, combustion phase detection is done by the location of 50% mass fraction burned (MFB50), because of its close correlation with emissions and fuel efficiency. However, this method is not easily implemented in real-time applications because the calculation of MFB50 requires a large amount of in-cylinder pressure data and an excessive computational load. For this reason, a combustion phase indicator with a simple algorithm is required for real-time combustion control. In this study, we propose a new combustion phase indicator, called the “Central normalized difference pressures (CNDP).” The CNDP indicates the center of the two crank angles where the normalized difference pressure between firing pressure and motoring pressure (NDP) reaches 90% of the maximum value before peak (NDPbp90), and 70% of the maximum value after peak (NDPap70). The NDPbp90 and NDPap70 are highly correlated with MFB50 and the correlation is enhanced as the center between the two points obtained. The CNDP is represented by a fixed quadratic polynomial with MFB50 that robust to changes in various engine operating conditions such as engine speed, main injection timing, injected fuel quantity, fuel-rail pressure, exhaust gas recirculation (EGR) rate and boost pressure. Furthermore, in performance evaluation, the CNDP requires remarkably fewer in-cylinder pressure data samples, calculation steps and less computation time compared to MFB50. These results show great potential for the CNDP to be a substitute for the MFB50 since the proposed combustion phase detection algorithm can be used effectively for real-time combustion phase detection and control.
Designing Compliant Spine Mechanisms for Climbing
Authors: Asbeck Alan T. , Cutkosky Mark R.
Published: June 2012

This paper presents design principles for compliant mechanisms used to support and load spines used in climbing rough vertical surfaces. The design principles ensure that constraints associated with spine/surface interactions are satisfied and that when multiple spines are placed in contact with a surface they share the load without premature failures or spine overloading. The design principles are demonstrated with a compliant mechanism that has been used for robotic and human climbing on surfaces such as brick, stucco and concrete.
A Novel Degree of Observability Used for Measurement Selections in Gas Path Diagnostics
Authors: Pu Xingxing , Liu Shangming , Jiang Hongde , Yu Daren
Published: June 2012

A novel method for measurement selections of gas path diagnostics has been developed. This method is based on the singular value decomposition of the observability matrix of linear systems, which are a good approximation of the nonlinear ones for small deviations. It also employs the concept of the degree of observability to formulate the criteria. The states with high degree of observability and the measurement sets with high overall degree of observability result in high estimation accuracy in gas path diagnostics. A heavy-duty gas turbine model is used to validate this method. The influence of the gas turbine nonlinearity, the measurement noise, and the overdetermined measurement on degree of observability is analyzed. The overall degree of observability is calculated for different measurement sets of heavy-duty gas turbine. The gas path diagnostics simulations with different measurement sets using the weighted least-squares estimation method and the extended Kalman filter are conducted. The quality of gas path diagnostics simulation with different measurement sets is assessed and the results demonstrate the capability of the developed method for measurement selections in gas path diagnostics.
Assessment of Residual Mass Estimation Methods for Cylinder Pressure Heat Release Analysis of HCCI Engines With Negative Valve Overlap
Authors: Ortiz-Soto Elliott A. , Vavra Jiri , Babajimopoulos Aristotelis
Published: June 2012

Increased residual levels in homogeneous charge compression ignition (HCCI) engines employing valve strategies such as recompression or negative valve overlap (NVO) imply that accurate estimation of residual gas fraction (RGF) is critical for cylinder pressure heat release analysis. The objective of the present work was to evaluate three residual estimation methods and assess their suitability under naturally aspirated and boosted HCCI operating conditions: (i) the simple state equation method employs the ideal gas law at exhaust valve closing (EVC); (ii) the Mirsky method assumes isentropic exhaust process; and (iii) the Fitzgerald method models in-cylinder temperature from exhaust valve opening (EVO) to EVC by accounting for heat loss during the exhaust process and uses measured exhaust temperature for calibration. Simulations with a calibrated and validated “virtual engine” were performed for representative HCCI operating conditions of engine speed, fuel-air equivalence ratio, NVO and intake pressure (boosting). The state equation method always overestimated RGF by more than 10%. The Mirsky method was most robust, with average errors between 3–5%. The Fitzgerald method performed consistently better, ranging from no error to 5%, where increased boosting caused the largest discrepancies. A sensitivity study was also performed and determined that the Mirsky method was most robust to possible pressure and temperature measurement errors.
Thermal Pyrolysis of Polyethylene in Fluidized Beds: Review of the Influence of Process Parameters on Product Distribution
Authors: Suresh Kumar Reddy K. , Kannan Pravin , Al Shoaibi Ahmed , Srinivasakannan C.
Published: June 2012

The present work is an attempt to compile and analyze the most recent literature pertaining to thermal pyrolysis of plastic waste using fluidized bed reactors. The review is short owing to the small number of work reported in the open literature in particular to the fluidized beds. Although works on pyrolysis are reported in fixed beds, autoclaves, and fluidized beds, vast majority of them address to the utilization of fluidized bed due to their advantages and large scale adaptability. The pyrolysis temperature and the residence time are reported to have major influence on the product distribution, with the increase in pyrolysis temperature favoring gas production, with significant reduction in the wax and oil. The pyrolysis gas generally contains H2, CO, CO2, CH4, C2H4, C2H6 while liquid product comprises benzene, toluene, xylene, styrene, light oil, heavy oil, and gasoline with the variations depending on process conditions. The effects of other process parameters, namely fuel feed rate, fuel composition, and fluidizing medium have been reviewed and presented.
Effects of Relative Humidity and Spraying Medium on UV Decontamination of Filters Loaded with Viral Aerosols
Authors: Woo Myung-Heui , Grippin Adam , Anwar Diandra , Smith Tamara , Wu Chang-Yu , Wander Joseph D.
Published: June 2012

Although respirators and filters are designed to prevent the spread of pathogenic aerosols, a stockpile shortage is anticipated during the next flu pandemic. Contact transfer and reaerosolization of collected microbes from used respirators are also a concern. An option to address these potential problems is UV irradiation, which inactivates microbes by dimerizing thymine/uracil in nucleic acids. The objective of this study was to determine the effects of transmission mode and environmental conditions on decontamination efficiency by UV. In this study, filters were contaminated by different transmission pathways (droplet and aerosol) using three spraying media (deionized water [DI], beef extract [BE], and artificial saliva [AS]) under different humidity levels (30% [low relative humidity {LRH}], 60% [MRH], and 90% [HRH]). UV irradiation at constant intensity was applied for two time intervals at each relative humidity condition. The highest inactivation efficiency (IE), around 5.8 logs, was seen for DI aerosols containing MS2 on filters at LRH after applying a UV intensity of 1.0 mW/cm
2
for 30 min. The IE of droplets containing MS2 was lower than that of aerosols containing MS2. Absorption of UV by high water content and shielding of viruses near the center of the aggregate are considered responsible for this trend. Across the different media, IEs in AS and in BE were much lower than in DI for both aerosol and droplet transmission, indicating that solids present in AS and BE exhibited a protective effect. For particles sprayed in a protective medium, RH is not a significant parameter.
A Novel Glycosylphosphatidylinositol-Anchored Glycoside Hydrolase from Ustilago esculenta Functions in β-1,3-Glucan Degradation
Authors: Nakajima Masahiro , Yamashita Tetsuro , Takahashi Machiko , Nakano Yuki , Takeda Takumi
Published: June 2012

A glycoside hydrolase responsible for laminarin degradation was partially purified to homogeneity from a
Ustilago esculenta
culture filtrate by weak-cation-exchange, strong-cation-exchange, and size-exclusion chromatography. Three proteins in enzymatically active fractions were digested with chymotrypsin followed by liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis, resulting in the identification of three peptide sequences that shared significant similarity to a putative β-1,3-glucanase, a member of glucoside hydrolase family 16 (GH16) from
Sporisorium reilianum
SRZ2. A gene encoding a laminarin-degrading enzyme from
U. esculenta
,
lam16A
, was isolated by PCR using degenerate primers designed based on the
S. reilianum
SRZ2 β-1,3-glucanase gene. Lam16A possesses a GH16 catalytic domain with an N-terminal signal peptide and a C-terminal glycosylphosphatidylinositol (GPI) anchor peptide. Recombinant Lam16A fused to an N-terminal FLAG peptide (Lam16A-FLAG) overexpressed in
Aspergillus oryzae
exhibited hydrolytic activity toward β-1,3-glucan specifically and was localized both in the extracellular and in the membrane fractions but not in the cell wall fraction. Lam16A without a GPI anchor signal peptide was secreted extracellularly and was not detected in the membrane fraction. Membrane-anchored Lam16A-FLAG was released completely by treatment with phosphatidylinositol-specific phospholipase C. These results suggest that Lam16A is anchored in the plasma membrane in order to modify β-1,3-glucan associated with the inner cell wall and that Lam16A is also used for the catabolism of β-1,3-glucan after its release in the extracellular medium.
Expansion of a Plasmid Classification System for Gram-Positive Bacteria and Determination of the Diversity of Plasmids in Staphylococcus aureus Strains of Human, Animal, and Food Origins
Authors: Lozano Carmen , García-Migura Lourdes , Aspiroz Carmen , Zarazaga Myriam , Torres Carmen , Aarestrup Frank Møller
Published: June 2012

An expansion of a previously described plasmid classification was performed and used to reveal the plasmid content of a collection of 92
Staphylococcus aureus
strains of different origins.
rep
genes of other genera were detected in
Staphylococcus
. S1 pulsed-field gel electrophoresis (PFGE) hybridizations were performed with 18 representative
S. aureus
strains, and a high number of plasmids of different sizes and organizations were detected.
High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses
Authors: Quigley Lisa , O'Sullivan Orla , Beresford Tom P. , Ross R. Paul , Fitzgerald Gerald F. , Cotter Paul D.
Published: June 2012

Here, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, including
Faecalibacterium
,
Prevotella
, and
Helcococcus
and, for the first time, detected the presence of
Arthrobacter
and
Brachybacterium
in goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence on
Lactobacillus
populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of
Lactococcus
species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.
Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite
Authors: Shelobolina Evgenya , Xu Huifang , Konishi Hiromi , Kukkadapu Ravi , Wu Tao , Blöthe Marco , Roden Eric
Published: June 2012

Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 10
7
cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.
Real-Time PCR Detection of Paenibacillus spp. in Raw Milk To Predict Shelf Life Performance of Pasteurized Fluid Milk Products
Authors: Ranieri Matthew L. , Ivy Reid A. , Mitchell W. Robert , Call Emma , Masiello Stephanie N. , Wiedmann Martin , Boor Kathryn J.
Published: June 2012

Psychrotolerant sporeformers, specifically
Paenibacillus
spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While
Paenibacillus
spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of
Paenibacillus
spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect
Paenibacillus
spp. in fluid milk and to discriminate between
Paenibacillus
and other closely related spore-forming bacteria. Specificity was confirmed using 16
Paenibacillus
and 17
Bacillus
isolates. All 16
Paenibacillus
isolates were detected with a mean cycle threshold (

C
T

) of 19.14 ± 0.54. While 14/17
Bacillus
isolates showed no signal (

C
T

> 40), 3
Bacillus
isolates showed very weak positive signals (

C
T

= 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 × 10
1
CFU/ml using total genomic DNA extracted from raw milk samples inoculated with
Paenibacillus
. Application of the TaqMan PCR to colony lysates obtained from heat-treated and enriched raw milk provided fast and accurate detection of
Paenibacillus
. Heat-treated milk samples where
Paenibacillus
(≥1 CFU/ml) was detected by this colony TaqMan PCR showed high bacterial counts (>4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of
Paenibacillus
that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product.
Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae
Authors: Lee Sun-Mi , Jellison Taylor , Alper Hal S.
Published: June 2012

The heterologous expression of a highly functional xylose isomerase pathway in
Saccharomyces cerevisiae
would have significant advantages for ethanol yield, since the pathway bypasses cofactor requirements found in the traditionally used oxidoreductase pathways. However, nearly all reported xylose isomerase-based pathways in
S. cerevisiae
suffer from poor ethanol productivity, low xylose consumption rates, and poor cell growth compared with an oxidoreductase pathway and, additionally, often require adaptive strain evolution. Here, we report on the directed evolution of the
Piromyces
sp. xylose isomerase (encoded by
xylA
) for use in yeast. After three rounds of mutagenesis and growth-based screening, we isolated a variant containing six mutations (E15D, E114G, E129D, T142S, A177T, and V433I) that exhibited a 77% increase in enzymatic activity. When expressed in a minimally engineered yeast host containing a
gre3
knockout and
tal1
and
XKS1
overexpression, the strain expressing this mutant enzyme improved its aerobic growth rate by 61-fold and both ethanol production and xylose consumption rates by nearly 8-fold. Moreover, the mutant enzyme enabled ethanol production by these yeasts under oxygen-limited fermentation conditions, unlike the wild-type enzyme. Under microaerobic conditions, the ethanol production rates of the strain expressing the mutant xylose isomerase were considerably higher than previously reported values for yeast harboring a xylose isomerase pathway and were also comparable to those of the strains harboring an oxidoreductase pathway. Consequently, this study shows the potential to evolve a xylose isomerase pathway for more efficient xylose utilization.