bluuebunny/crossref_metadata_2025 huggingface dataset:
Body melanization and its adaptive role in thermoregulation and tolerance against desiccating conditions in drosophilids
Authors: RAJPUROHIT Subhash , PARKASH Ravi , RAMNIWAS Seema
Published: March 2008

Melanism seems to have evolved independently through diverse mechanisms in various taxa and different ecological factors could be responsible for selective responses. Increased body melanization at higher altitudes as well as latitudes is generally considered to be adaptive for thermoregulation. Physiological traits such as body melanization and desiccation resistance have been investigated independently in diverse insect taxa at three levels: within populations, between populations and among species. A substantial number ofDrosophilastudies have reported clinal variations in both these traits along latitude. A possible link between these traits had remained unexplored in wild and laboratory populations of ectothermic insect taxa, including drosophilids, to date. Simultaneous analysis of these traits in assorted darker and lighter phenotypes in each population in the present study showed parallel changes for body melanization and desiccation resistance. The mechanistic basis of evolving desiccation resistance was explained on the basis of differential rates of water loss per hour in darker versus lighter phenotypes in six populations ofDrosophila melanogasterfrom adjacent localities differing substantially in altitude all along the Indian subcontinent. Data on cuticular impermeability suggest a possible role of melanization in desiccation tolerance. However, substantial gaps remain in extending these results to other insect taxa and further exploring the physiological and molecular changes involved in melanization for conferring desiccation resistance.
Why study diapause?
Authors: DENLINGER David L.
Published: March 2008

This review highlights a number of reasons why insect diapause merits attention. Knowledge of diapause is essential for understanding the seasonal biology of an insect species, and such information is also required for the development of effective pest management strategies; manipulating domesticated species used in pollination and silk production; developing accurate predictive models used to forecast periods of pest abundance; and increasing the shelf‐life of parasitoids and predatory mites used in the biological control industry. Mechanisms used by diapausing insects to survive low temperature may provide tips for cryopreserving insect stocks, a vital need within the research community. Diapause also presents an interesting model for probing fundamental questions in development, and we are indebted to diapause studies for early insights into insect hormones. In addition, I argue that insect diapause may provide insights into questions on aging, obesity and disease transmission, and diapausing insects offer a potentially rich source of pharmaceutical agents that may contribute to improvement of human health.
Popular Culture (Islam, Early and Middle Periods)
Authors: Frenkel Yehoshua
Published: March 2008

This contribution dwells on popular culture in Mamluk Egypt and Syria. Following a short examination of this topic and of the sources, the study focuses on three themes: the cycle of life, the cycle of the year and sacred topography. Popular manners and customs provoked opposition from religious circles. A condensed delineation of these voices is provided at the closing part of the article.
Autoinducer‐2 Activity of Gram‐Negative Foodborne Pathogenic Bacteria and Its Influence on Biofilm Formation
Authors: Yoon Y. , Sofos J.N.
Published: March 2008

ABSTRACT:  This study evaluated whether autoinducer‐2 (AI‐2) activity would be associated with biofilm formation by Salmonella and Escherichia coli O157:H7 strains on food contact surfaces. In study I, a Salmonella Typhimurium DT104 strain and an E. coli O157:H7 strain, both AI‐2 positive, were individually inoculated into 50 mL of Luria–Bertani (LB) or LB + 0.5% glucose (LBG) broth, without or with stainless steel or polypropylene (Salmonella) coupons. At 0, 14 (Salmonella), 24, 48, and 72 h of storage (25 °C), cells in suspension and detached cells from the coupons, obtained by vortexing, were enumerated on tryptic soy agar. In study II, a Salmonella Thompson AI‐2‐positive strain and an AI‐2‐negative strain, and an E. coli O157:H7 AI‐2‐positive strain and an AI‐2‐negative strain were inoculated into LB broth with stainless steel coupons. Cells were enumerated as in study I. In both studies, AI‐2 activity was determined in cell‐free supernatants. Cell numbers of S. Typhimurium DT104 on biofilms were higher (P < 0.05) in LB than those in LBG, while the E. coli O157:H7 strain showed no difference (P≥ 0.05) in biofilm cell counts between LB and LBG after storage for 72 h. Both S. Typhimurium DT104 and E. coli O157:H7 strains produced higher (P < 0.05) AI‐2 activity in LBG than LB cell suspensions. Cell counts of AI‐2‐positive and‐negative S. Thompson and E. coli O157:H7 strains were not different (P≥ 0.05) within suspensions or coupons (study II). The results indicated that, under the conditions of this study, AI‐2 activity of the pathogen strains tested may not have a major influence on biofilm formation on food contact surfaces, which was similar between AI‐2‐positive and ‐negative strains.
Effect of Polymer Surface Modification on Polymer–Protein Interaction via Hydrophilic Polymer Grafting
Authors: Liu S.X. , Kim J.‐T. , Kim S.
Published: March 2008

ABSTRACT:  Surface modification of flat sheet ultrafiltration membranes, polyethersulfone (PES), was investigated to improve the hydrophilicity of the membrane surface thereby reducing adsorption of the proteins onto the membrane. Grafting of hydrophilic polymers onto UV/ozone‐treated PES was used to improve the hydrophilicity of the commercial PES membranes. Hydrophilic polymers, that is, poly(vinyl alcohol) (PVA), polyethylene glycol (PEG), and chitosan, were employed to graft onto PES membrane surfaces because of their excellent hydrophilic property. The surfaces of modified PES membranes were characterized by contact angle measurement, FTIR, and AFM. The FTIR spectra indicated that PES membranes were successfully modified by grafting of the hydrophilic polymers. The modified PES membranes showed 20% to 50% reduction in contact angle measurements in comparison with those of the virgin PES membrane. The tapping mode AFM technique was employed to investigate the changes of surface topography, cross‐section, and root mean square roughness of the modified PES membrane surfaces. The modified PES membranes showed elevated roughness (ranging from 7.0 to 25.7 nm) compared with that of the virgin PES membrane (2.1 nm). It is concluded that grafting of PVA, PEG, or chitosan onto UV/ozone‐treated PES membranes increases hydrophilicity and lowers protein adsorption by 20% to 60% compared to the virgin PES membrane. Among the 3 hydrophilic polymers studied, PEG showed the most favorable result in terms of contact angle and protein adsorption.
Inactivation of Lymphocytes in Blood Products Using Riboflavin Photochemical Treatment with Visible Light
Authors: Cui Zhenling , Huang Yuwen , Mo Qin , Wang Xun , Qian Kaicheng
Published: March 2008

Immunocompetent lymphocytes present in blood products are an important cause of immune reactions following blood transfusion such as transfusion‐associated graft‐versus‐host disease (TA‐GVHD). In this study the effects of riboflavin photochemical treatment (RPT) on lymphocyte proliferation and cytokine production in vitro were measured to establish whether RPT of blood products can be used to prevent immune reactions resulting from transfused lymphocytes. Lymphocytes and riboflavin were added together in medical PVC transparent bags and then exposed to visible light. Control lymphocytes were exposed to light in the absence of riboflavin. Lymphocytes exposed to riboflavin photochemical treatment (RPT‐lymphocytes) and control lymphocytes were tested for the proliferative ability and the production of several cytokines upon stimulation with antigens. Upon stimulation by phytohemagglutinin (PHA) the proliferation of RPT‐lymphocytes was inhibited. Using flow cytometry it was shown that RPT‐lymphocytes were unable to enter the S‐phase of the cell cycle following PHA stimulation. The level of cytokines present in the supernatant of RPT‐lymphocytes after stimulation by antigens was significantly lower than those present in the corresponding supernatant of control lymphocytes. RPT with visible light inactivates lymphocytes, inhibits lymphocyte proliferation and the production of cytokines. It appears to be a promising method to prevent immune reactions such as TA‐GVHD.
The Lifetimes of Pharaonis Phoborhodopsin Signaling States Depend on the Rates of Proton Transfers—Effects of Hydrostatic Pressure and Stopped Flow Experiments†
Authors: Kikukawa Takashi , Saha Chabita K. , Balashov Sergei P. , Imasheva Eleonora S. , Zaslavsky Dmitry , Gennis Robert B. , Abe Takayuki , Kamo Naoki
Published: March 2008

Pharaonis phoborhodopsin (ppR), a negative phototaxis receptor of Natronomonas pharaonis, undergoes photocycle similar to the light‐driven proton pump bacteriorhodopsin (BR), but the turnover rate is much slower due to much longer lifetimes of the M and O intermediates. The M decay was shown to become as fast as it is in BR in the L40T/F86D mutant. We examined the effects of hydrostatic pressure on the decay of these intermediates. For BR, pressure decelerated M decay but slightly affected O decay. In contrast, with ppR and with its L40T/F86D mutant, pressure slightly affected M decay but accelerated O decay. Clearly, the pressure‐dependent factors for M and O decay are different in BR and ppR. In order to examine the deprotonation of Asp75 in unphotolyzed ppR we performed stopped flow experiments. The pH jump‐induced deprotonation of Asp75 occurred with 60 ms, which is at least 20 times slower than deprotonation of the equivalent Asp85 in BR and about 10‐fold faster than the O decay of ppR. These data suggest that proton transfer is slowed not only in the cytoplasmic channel but also in the extracellular channel of ppR and that the light‐induced structural changes in the O intermediate of ppR additionally decrease this rate.
What Mistakes Disclose: A Process Dissociation Approach to Automatic and Controlled Processes in Social Psychology
Authors: Payne B. Keith
Published: March 2008

Process dissociation is a model for separating automatic and controlled contributions to responses in a single task. Although it was developed to separate conscious and unconscious uses of memory, researchers have increasingly found the model useful to answer questions in social psychology. This article reviews process dissociation studies with a focus on social psychology. It emphasizes the model's conceptual definitions of automatic and controlled processing and how those relate to procedures for estimating them. Process dissociation is contrasted with task dissociation, in which automatic and controlled processes are identified with implicit and explicit tasks. Current trends and future directions are identified, including the use of model testing procedures to compare competing theories of how automatic and controlled processes interact.
Cultural Consumption in the Fine and Popular Arts Realms
Authors: Lizardo Omar , Skiles Sara
Published: March 2008

In this paper, we review recent sociological research dealing with the consumption of culture produced in the fine and popular arts realms. Most of the initial theoretical developments in the study of culture consumption were intended to explain audience segmentation in the fine arts realm under the ‘cultural capital’ paradigm developed by Pierre Bourdieu. This paradigm shift has led to the current dominance of the ‘omnivore thesis’ in the sociology of taste. The consumption of popular culture, however, remained for a long time dominated by the Birmingham ‘resistance’ and ‘subculture’ paradigms developed in the 1970s. Recent popular arts consumption research has moved beyond the limitations of the subculture paradigm by incorporating the theoretical legacy of the cultural capital paradigm in order to account for patterns in audience and producer differentiation in popular arts ‘scenes’. This has brought the study of popular and fine arts culture consumption under a single conceptual framework after a long period of theoretical disengagement.
Encouraging Cancer Patients to Talk to Their Physicians About Clinical Trials: Considering Patients' Information Needs1
Authors: Latimer Amy E. , Williams‐Piehota Pamela , Cox Ashley , Katulak Nicole A. , Salovey Peter , Mowad Linda
Published: March 2008

This study examined the effectiveness of detailed and nondetailed information for encouraging cancer patients to discuss clinical trials with their physicians. We hypothesized that detailed messages would lead to greater understanding of clinical trials and increased intentions and likelihood of broaching the topic with a physician, especially among individuals high in need for cognition (NFC). Participants (448 cancer patients) (a) completed a baseline assessment of understanding and intentions, (b) received either detailed or nondetailed messages, and (c) completed follow‐up assessments at Weeks 1 and 6. The detailed messages led to greater intentions to discuss clinical trials than nondetailed messages among low‐NFC participants. High‐NFC participants' understanding, intentions, and behavior were not differentially affected by the detailed message.
Self‐Objectification and Exercise Behaviors: The Mediating Role of Social Physique Anxiety
Authors: Melbye Lise , Tenenbaum Gershon , Eklund Robert
Published: March 2008

Self‐objectification (SO) and Social Physique Anxiety (SPA) were investigated in relation to reported exercise behaviors (EBs). A conceptual model was used in which SPA was posited as a mediating variable between SO and EBs categorized as protective or permissive. Two hundred and ninety‐one women (age range = 18–74 years) completed the SO, SPA, and EB questionnaires. Women lower in SO reported exercising more, wearing more concealing exercise apparel, and preferring outdoors locations. The models were found to fit the data adequately, but only the path from SO to SPA was significant. These results reaffirm the relationship between SO and SPA, but further understanding of the potential effects of SO on behaviors involving health, body, and exercise is required.
Effects of Directed Thinking on Exercise and Cardiovascular Fitness
Authors: Ten Eyck Laura L. , Gresky Dana P. , Lord Charles G.
Published: March 2008

Although it is well established that exercise aids in the prevention of disease, recent surveys suggest that many Americans do not engage in regular physical activity. The present experiment examined one possible technique for increasing regular exercise, in sedentary college students. Previous studies had shown that students who are directed to think about action strategies that would increase studying subsequently report greater intentions to study. The present experiment found that directed thinking about actions to increase a target exercise significantly increased time spent on exercising and cardiovascular fitness. The results are discussed in terms of theoretical perspectives on attitude processes.
Clinical productivity indicators for a dental general practice residency program
Authors: Boston Daniel W.
Published: March 2008

Management of clinical productivity is an essential activity in the dental general practice residency GPR program. Because productivity is a relative term, indicators of clinical productivity must be developed to evaluate current performance. This article presents a 3‐year study of clinical productivity in a two‐resident GPR program. Productivity indicators are developed and analyzed for this program and for application to other GPR programs.
Caries experience, periodontal treatment needs, salivary pH, and Streptococcus mutans counts in a preadolescent Down syndrome population
Authors: Stabholz Ayala , Mann Jonathan , Sela Michal , Schurr Dan , Steinberg Doron , Dori S. , Shapira Joseph
Published: March 2008

The prevalence of dental caries and periodontal treatment needs in an institutionalized population with Down syndrome was examined and the relationship between caries prevalence, salivary pH, and salivary levels of Streptococcus mutans was studied. Thirty‐two children with Down syndrome, aged 8 to 13, were compared with two control groups of similar age ranges: healthy children and non‐Down mentally retarded (MR) children living in the same institution as the Down syndrome population. The gender ratio mixtures in each group also matched the study sample. Caries experience as indicated by decayed, missing, and filled surfaces (DMF‐S) showed significantly lower mean scores for the Down syndrome group compared with both control groups. A similar pattern was found when evaluating the mean numbers of decayed surfaces. Streptococcus mutans counts, expressed as number of colony‐forming units on mitis salivarius agar plates among the Down syndrome group, were the lowest, although not statistically significant compared with the counts of the healthy children. Both groups had bacterial counts which were significantly lower than those of the MR group. Significant differences between the two institutionalized groups and the healthy group were recorded for the salivary pH levels. The periodontal treatment needs as evaluated by the Community Periodontal Index of Treatment Needs showed significant difference between the MR group versus both the healthy population and the Down syndrome group. On the whole, 84% of the Down syndrome children were cariesfree.
Symplectomorphism groups and embeddings of balls into rational ruled 4-manifolds
Authors: Pinsonnault Martin
Published: March 2008

Let Mμ0 denote S2×S2 endowed with a split symplectic form $\mu \sigma \oplus \sigma $ normalized so that μ≥1 and σ(S2)=1. Given a symplectic embedding $\iota :B_{c}\hookrightarrow M^0_{\mu }$ of the standard ball of capacity c∈(0,1) into Mμ0, consider the corresponding symplectic blow-up $\widetilde {M}^0_{\mu ,c}$. In this paper, we study the homotopy type of the symplectomorphism group ${\mathrm {Symp}}(\widetilde {M}^0_{\mu ,c})$ and that of the space $\Im {\mathrm {Emb}}(B_{c},M^0_{\mu })$ of unparametrized symplectic embeddings of Bc into Mμ0. Writing ℓ for the largest integer strictly smaller than μ, and λ∈(0,1] for the difference μ−ℓ, we show that the symplectomorphism group of a blow-up of ‘small’ capacity c<λ is homotopically equivalent to the stabilizer of a point in Symp(Mμ0), while that of a blow-up of ‘large’ capacity c≥λ is homotopically equivalent to the stabilizer of a point in the symplectomorphism group of a non-trivial bundle $\mathbb {C}P^2\#\,\overline {\mathbb {C}P^2}$ obtained by blowing down $\widetilde {M}^0_{\mu ,c}$. It follows that, for c<λ, the space $\Im {\mathrm {Emb}}(B_{c},M^0_{\mu })$ is homotopy equivalent to S2 ×S2, while, for c≥λ, it is not homotopy equivalent to any finite CW-complex. A similar result holds for symplectic ruled manifolds diffeomorphic to $\mathbb {C}P^2\#\,\overline {\mathbb {C}P^2}$. By contrast, we show that the embedding spaces $\Im {\mathrm {Emb}}(B_{c},\mathbb {C}P^{2})$ and $\Im {\mathrm {Emb}}(B_{c_{1}}\sqcup B_{c_{2}},\mathbb {C}P^{2})$, if non-empty, are always homotopy equivalent to the spaces of ordered configurations $F(\mathbb {C}P^{2},1)\simeq \mathbb {C}P^{2}$ and $F(\mathbb {C}P^{2},2)$. Our method relies on the theory of pseudo-holomorphic curves in 4 -manifolds, on the computation of Gromov invariants in rational 4 -manifolds, and on the inflation technique of Lalonde and McDuff.
Involvement of AMPA receptor desensitization in short‐term synaptic depression at the calyx of Held in developing rats
Authors: Koike‐Tani Maki , Kanda Takeshi , Saitoh Naoto , Yamashita Takayuki , Takahashi Tomoyuki
Published: March 2008

Paired‐pulse facilitation (PPF) and depression (PPD) are forms of short‐term plasticity that are generally thought to reflect changes in transmitter release probability. However, desensitization of postsynaptic AMPA receptors (AMPARs) significantly contributes to PPD at many glutamatergic synapses. To clarify the involvement of AMPAR desensitization in synaptic PPD, we compared PPD with AMPAR desensitization, induced by paired‐pulse glutamate application in patches excised from postsynaptic cells at the calyx of Held synapse of developing rats. We found that AMPAR desensitization contributed significantly to PPD before the onset of hearing (P10–12), but that its contribution became negligible after hearing onset. During postnatal development (P7–21) the recovery of AMPARs from desensitization became faster. Concomitantly, glutamate sensitivity of AMPAR desensitization declined. Single‐cell reverse transcription‐polymerase chain reaction (RT‐PCR) analysis indicated a developmental decline of GluR1 expression that correlated with speeding of the recovery of AMPARs from desensitization. Transmitter release probability declined during the second postnatal week (P7–14). Manipulation of the extracellular Ca2+/Mg2+ ratio, to match release probability at P7–8 and P13–15 synapses, revealed that the release probability is also an important factor determining the involvement of AMPAR desensitization in PPD. We conclude that the extent of involvement of AMPAR desensitization in short‐term synaptic depression is determined by both pre‐ and postsynaptic mechanisms.
Distinct receptors underlie glutamatergic signalling in inspiratory rhythm‐generating networks and motor output pathways in neonatal rat
Authors: Ireland M. F. , Lenal F. C. , Lorier A. R. , Loomes D. E. , Adachi T. , Alvares T. S. , Greer J. J. , Funk G. D.
Published: March 2008

Despite the enormous diversity of glutamate (Glu) receptors and advances in understanding recombinant receptors, native Glu receptors underlying functionally identified inputs in active systems are poorly defined in comparison. In the present study we use UBP‐302, which antagonizes GluR5 subunit‐containing kainate (KA) receptors at ≤ 10 μm, but other KA and AMPA receptors at ≥ 100 μm, and rhythmically activein vitropreparations of neonatal rat to explore the contribution of non‐NMDA receptor signalling in rhythm‐generating and motor output compartments of the inspiratory network. At 10 μm, UBP‐302 had no effect on inspiratory burst frequency or amplitude. At 100 μm, burst amplitude recorded from XII, C1 and C4 nerve roots was significantly reduced, but frequency was unaffected. The lack of a frequency effect was confirmed when local application of UBP‐302 (100 μm) into the pre‐Bötzinger complex (preBötC) did not affect frequency but substance P evoked a 2‐fold increase. A UBP‐302‐sensitive (10 μm), ATPA‐evoked frequency increase, however, established that preBötC networks are sensitive to GluR5 activation. Whole‐cell recordings demonstrated that XII motoneurons also express functional GluR5‐containing KA receptors that do not contribute to inspiratory drive, and confirmed the dose dependence of UBP‐302 actions on KA and AMPA receptors. Our data provide the first evidence that the non‐NMDA (most probably AMPA) receptors mediating glutamatergic transmission within preBötC inspiratory rhythm‐generating networks are pharmacologically distinct from those transmitting drive to inspiratory motoneurons. This differential expression may ultimately be exploited pharmacologically to separately counteract depression of central respiratory rhythmogenesis or manipulate the drive to motoneurons controlling airway and pump musculature.
Influence of Staggering Angle of a Rotating Rod on Flow Past a Circular Cylinder
Authors: Ayyappan T. , Vengadesan S.
Published: March 2008

The influence of the staggering position of a rotating rod on flow past a main circular cylinder is investigated numerically. The rod is rotated at a constant speed ratio of 3. The effect of the diameter ratio of the rotating rod is studied by considering two different diameter ratios. The investigation is carried out at a fixed pitch length of 1. The study is carried out for two Reynolds number, viz., 100 and 500. The momentum injection from the rod is found to alter the flow characteristics behind the main cylinder. For a certain arrangement of stagger angle and diameter ratio, the vortex shedding behind the main cylinder gets suppressed. The corresponding configuration for which minimum drag coefficient is achieved is suggested from this study.
Cavitation Analogy to Gasdynamic Shocks: Model Conservativeness Effects on the Simulation of Transient Flows in High-Pressure Pipelines
Authors: Ferrari Alessandro , Manno Michele , Mittica Antonio
Published: March 2008

A comparison between conservative and nonconservative models has been carried out for evaluating the influence of conservativeness on the prediction of transient flows in high-pressure pipelines. For the numerical tests, a pump-line-nozzle Diesel injection system was considered because the pipe flow presented interesting cases of cavitation. The validity of a conservative model in the simulation of cavitating transient flows was substantiated by the comparison between computed pressure time histories and experimental results at two pipeline locations in the injection system. Although nonconservative models can assure satisfactory accuracy in the evaluation of the wave propagation phenomena, they introduce fictitious source terms in the discretized equations. Such terms are usually negligible, but can play a significant role in the presence of acoustic cavitation, i.e., pressure-wave-induced cavitation, producing errors in the pressure-wave speed prediction. A theoretical analysis based on unsteady characteristic lines was carried out, showing that the cavitation desinence is a shock gas-dynamic-like event, whereas cavitation inception is a supersonic expansion. The Rankine–Hugoniot jump conditions were applied to evaluate the shock wave speed in the presence of cavitation. Analytical relations to calculate the flow property variations across the cavitation-induced discontinuities were also derived. A previously published analytical expression of the sound speed in a homogeneous two-phase flow model was also derived from the eigenvalues of the Euler flow equations for the two distinct phases and a comparison was made with Wallis’ formula, which is commonly applied to cavitating flow simulation in transmission lines. Finally, a novel algorithm for calculating the shock speed, as is predicted by nonconservative models, was presented and applied to Burgers’ equation, pointing out the contribution of internal fictitious fluxes in the shock-speed wrong estimation.
Hydrodynamics and Sound Generation of Low Speed Planar Jet
Authors: Suponitsky Victoria , Avital Eldad , Gaster Mike
Published: March 2008

Hydrodynamics and sound radiation of a low speed planar jet with Re=3000 have been studied by large eddy simulation combined with Lighthill’s acoustic analogy. Jets evolving from both well-developed (parabolic) and undeveloped (top-hat) mean velocity profiles have been simulated. The results showed the following: (i) initial domination of a symmetrical mode for jets evolving from top-hat profiles and prevailing of an antisymmetrical mode resulting in a sinuous distortion of the potential core for jets evolving from parabolic profiles, and (ii) shape of a mean velocity profile has some effect on mean flow characteristics; however, the major differences were observed in the development of the fluctuations. Velocity fluctuations were significantly higher for jets evolving from a parabolic profile in the region beyond the end of the potential core before the flow reached a self-preserving state. To calculate the basic sound radiation, the sources in Lighthill’s equation were treated either as compact in all directions or as noncompact in the spanwise direction. The spanwise length of the computational domain was found to have a little effect on the results obtained with compact in all directions solution provided that spanwise length exceeds the correlation length. Results showed that the majority of sound was generated by the region beyond the end of the potential core.
Computational physics with particles
Authors: Hoover Wm. G. , Hoover Carol G.
Published: March 2008

Microscopic and macroscopic particle simulation techniques are useful introductions to computational physics. These techniques make it possible to simulate complex problems in fluid and solid mechanics, including laminar and turbulent flows, shockwaves, as well as fracture and failure in solids. We illustrate several particle-based techniques with several examples.
Synaptic Theory of Working Memory
Authors: Mongillo Gianluigi , Barak Omri , Tsodyks Misha
Published: March 2008

It is usually assumed that enhanced spiking activity in the form of persistent reverberation for several seconds is the neural correlate of working memory. Here, we propose that working memory is sustained by calcium-mediated synaptic facilitation in the recurrent connections of neocortical networks. In this account, the presynaptic residual calcium is used as a buffer that is loaded, refreshed, and read out by spiking activity. Because of the long time constants of calcium kinetics, the refresh rate can be low, resulting in a mechanism that is metabolically efficient and robust. The duration and stability of working memory can be regulated by modulating the spontaneous activity in the network.
Predators Induce Cloning in Echinoderm Larvae
Authors: Vaughn Dawn , Strathmann Richard R.
Published: March 2008

Asexual propagation (cloning) is a widespread reproductive strategy of plants and animals. Although larval cloning is well documented in echinoderms, identified stimuli for cloning are limited to those associated with conditions favorable for growth and reproduction. Our research shows that larvae of the sand dollar Dendraster excentricus also clone in response to cues from predators. Predator-induced clones were smaller than uncloned larvae, suggesting an advantage against visual predators. Our results offer another ecological context for asexual reproduction: rapid size reduction as a defense.
Caribbean Reef Development Was Independent of Coral Diversity over 28 Million Years
Authors: Johnson Kenneth G. , Jackson Jeremy B. C. , Budd Ann F.
Published: March 2008

The relationship between natural variations in coral species diversity, reef development, and ecosystem function on coral reefs is poorly understood. Recent coral diversity varies 10-fold among geographic regions, but rates of reef growth are broadly similar, suggesting that diversity is unimportant for reef development. Differences in diversity may reflect regional differences in long-term biotic history in addition to environmental conditions. Using a combination of new and published fossil and stratigraphic data, we compared changes in coral diversity and reef development within the tropical western Atlantic over the past 28 million years. Reef development was unrelated to coral diversity, and the largest reef tracts formed after extinction had reduced diversity by 50%. High diversity is thus not essential for the growth and persistence of coral reefs.
Gate-Variable Optical Transitions in Graphene
Authors: Wang Feng , Zhang Yuanbo , Tian Chuanshan , Girit Caglar , Zettl Alex , Crommie Michael , Shen Y. Ron
Published: March 2008

Two-dimensional graphene monolayers and bilayers exhibit fascinating electrical transport behaviors. Using infrared spectroscopy, we find that they also have strong interband transitions and that their optical transitions can be substantially modified through electrical gating, much like electrical transport in field-effect transistors. This gate dependence of interband transitions adds a valuable dimension for optically probing graphene band structure. For a graphene monolayer, it yields directly the linear band dispersion of Dirac fermions, whereas in a bilayer, it reveals a dominating van Hove singularity arising from interlayer coupling. The strong and layer-dependent optical transitions of graphene and the tunability by simple electrical gating hold promise for new applications in infrared optics and optoelectronics.
A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit
Authors: Xiao Han , Jiang Ning , Schaffner Erin , Stockinger Eric J. , van der Knaap Esther
Published: March 2008

Edible fruits, such as that of the tomato plant and other vegetable crops, are markedly diverse in shape and size.
SUN
, one of the major genes controlling the elongated fruit shape of tomato, was positionally cloned and found to encode a member of the IQ67 domain–containing family. We show that the locus arose as a result of an unusual 24.7-kilobase gene duplication event mediated by the long terminal repeat retrotransposon
Rider
. This event resulted in a new genomic context that increased
SUN
expression relative to that of the ancestral copy, culminating in an elongated fruit shape. Our discovery demonstrates that retrotransposons may be a major driving force in genome evolution and gene duplication, resulting in phenotypic change in plants.
Nutritional Control of Reproductive Status in Honeybees via DNA Methylation
Authors: Kucharski R. , Maleszka J. , Foret S. , Maleszka R.
Published: March 2008

Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly–like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA–treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in
Apis
is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status.
The Late Pleistocene Dispersal of Modern Humans in the Americas
Authors: Goebel Ted , Waters Michael R. , O'Rourke Dennis H.
Published: March 2008

When did humans colonize the Americas? From where did they come and what routes did they take? These questions have gripped scientists for decades, but until recently answers have proven difficult to find. Current genetic evidence implies dispersal from a single Siberian population toward the Bering Land Bridge no earlier than about 30,000 years ago (and possibly after 22,000 years ago), then migration from Beringia to the Americas sometime after 16,500 years ago. The archaeological records of Siberia and Beringia generally support these findings, as do archaeological sites in North and South America dating to as early as 15,000 years ago. If this is the time of colonization, geological data from western Canada suggest that humans dispersed along the recently deglaciated Pacific coastline.
Fresh Renderings of Physics
Authors: Kaiser David
Published: March 2008

Reading Popular Physics
. Disciplinary Skirmishes and Textual Strategies.
By Elizabeth Leane
. Ashgate, Aldershot, Hampshire, England, 2007. 208 pp. $99.95, £50. ISBN 9780754658504.

Viewing popular science as the presentation of science content through the techniques of literature, the author explores popular presentations of quantum mechanics, the big bang, chaos, and complexity.
Synthesis of Macrocyclic Copolymer Brushes and Their Self-Assembly into Supramolecular Tubes
Authors: Schappacher Michel , Deffieux Alain
Published: March 2008

We report on an efficient route to design large macrocyclic polymers of controlled molar mass and narrow dispersity. The strategy is based on the synthesis of a triblock copolymer A
B
C, in which the long central block
B
is extended by two short A and C sequences bearing reactive antagonist functions. When reacted under highly dilute conditions, this precursor produces the corresponding macrocycle by intramolecular coupling of the A and C blocks. Chloroethyl vinyl ether was selected as the monomer for the central block
B
, because it can be readily derivatized into brushlike polymers by a grafting process. The corresponding macrocyclic brushes were decorated with polystyrene or randomly distributed polystyrene and polyisoprene branches. In a selective solvent for the polyisoprene branches, the macrocyclic brushes self-assemble into cylindrical tubes of up to 700 nanometers.
Enhanced Protection against Bovine Tuberculosis after Coadministration ofMycobacterium bovisBCG with a Mycobacterial Protein Vaccine-Adjuvant Combination but Not after Coadministration of Adjuvant Alone
Authors: Wedlock D. Neil , Denis Michel , Painter Gavin F. , Ainge Gary D. , Vordermeier H. Martin , Hewinson R. Glyn , Buddle Bryce M.
Published: March 2008

Current efforts are aimed at optimizing the protective efficacy ofMycobacterium bovisBCG by the use of vaccine combinations. We have recently demonstrated that the protection afforded by BCG alone is enhanced by vaccinating cattle with a combination of vaccines comprising BCG and a protein tuberculosis vaccine, namely, culture filtrate proteins (CFPs) fromM. bovisplus an adjuvant. In the current study, three different adjuvant systems were compared. The CFP was formulated with a depot adjuvant, dimethyldioctadecyl ammonium bromide (DDA), together with one of three different immunostimulants: monophosphoryl lipid A (MPL), a synthetic mycobacterial phosphatidylinositol mannoside-2 (PIM2), and a synthetic lipopeptide (Pam3Cys-SKKKK [Pam3CSK4]). Groups of cattle (n= 10/group) were vaccinated with BCG-CFP-DDA-PIM2, BCG-CFP-DDA-MPL, or BCG-CFP-DDA-Pam3CSK4. Two additional groups (n= 10) were vaccinated with BCG alone or BCG-adjuvant (DDA-MPL), and a control group was left unvaccinated. Protection was assessed by challenging the cattle intratracheally withM. bovis. Groups of cattle vaccinated with BCG-CFP-DDA-PIM2, BCG-CFP-DDA-MPL, BCG-CFP-DDA-Pam3CSK4, and BCG alone showed significant reductions in three, three, five, and three pathological and microbiological disease parameters, respectively, compared to the results for the nonvaccinated group. Vaccination with the combination of BCG and the DDA-MPL adjuvant alone abrogated the protection conferred by BCG alone. The profiling of cytokine gene expression following vaccination, prior to challenge, did not illuminate significant differences which could explain the latter result. Vaccination of cattle with a combination of BCG and protein tuberculosis vaccine enhances protection against tuberculosis.
Specificity of Subcapsular Antibody Responses in Ethiopian Patients following Disease Caused by Serogroup A Meningococci
Authors: Norheim Gunnstein , Aseffa Abraham , Yassin Mohammed Ahmed , Mengistu Getahun , Kassu Afework , Fikremariam Dereje , Tamire Wegene , Merid Yared , Høiby E. Arne , Caugant Dominique A. , Fritzsønn Elisabeth , Tangen Torill , Melak Berhanu , Berhanu Degu , Harboe Morten , Kolberg Jan , Rosenqvist Einar
Published: March 2008

Dissecting the specificities of human antibody responses following disease caused by serogroup A meningococci may be important for the development of improved vaccines. We performed a study of Ethiopian patients during outbreaks in 2002 and 2003. Sera were obtained from 71 patients with meningitis caused by bacteria of sequence type 7, as confirmed by PCR or culture, and from 113 Ethiopian controls. Antibody specificities were analyzed by immunoblotting (IB) against outer membrane antigen extracts of a reference strain and of the patients' own isolates and by enzyme-linked immunosorbent assay for immunoglobulin G (IgG) levels against lipooligosaccharide (LOS) L11 and the proteins NadA and NspA. IB revealed that the main antigens targeted were the proteins PorA, PorB, RmpM, and Opa/OpcA, as well as LOS. MenA disease induced significant increases in IgG against LOS L11 and NadA. The IgG levels against LOS remained elevated following disease, whereas the IgG anti-NadA levels returned to acute-phase levels in the late convalescent phase. Among adults, the anti-LOS IgG levels were similar in acute-phase patient sera as in control sera, whereas anti-NadA IgG levels were significantly higher in acute-phase sera than in controls. The IgG antibody levels against LOS and NadA correlated moderately but significantly with serum bactericidal activity against MenA strains. Future studies on immune response during MenA disease should take into account the high levels of anti-MenA polysaccharide IgG commonly found in the population and seek to clarify the role of antibodies against subcapsular antigens in protection against MenA disease.
LiveMycobacterium aviumsubsp.paratuberculosisand a Killed-Bacterium Vaccine Induce Distinct Subcutaneous Granulomas, with Unique Cellular and Cytokine Profiles
Authors: Lei Liying , Plattner Brandon L. , Hostetter Jesse M.
Published: March 2008

Type II (lepromatous) granulomas are characterized by a lack of organization, with large numbers of macrophages heavily burdened with bacilli and disorganized lymphocyte infiltrations. Type II granulomas are a characteristic feature of the enteric lesions that develop during clinicalMycobacterium aviumsubsp.paratuberculosisinfection in the bovine. Considering the poor organization and function of these granulomas, it is our hypothesis that dendritic cell (DC) function within the granuloma is impaired during initial infection. In order to test our hypothesis, we used a subcutaneousM. aviumsubsp.paratuberculosisinfection model to examine early DC function withinM. aviumsubsp.paratuberculosis-induced granulomas. In this model, we first characterized the morphology, cellular composition, and cytokine profiles of subcutaneous granulomas that develop 7 days after subcutaneous inoculation with either vaccine or liveM. aviumsubsp.paratuberculosis. Second, we isolated CD11c+cells from within granulomas and measured their maturation status and ability to induce T-cell responses. Our results demonstrate thatM. aviumsubsp.paratuberculosisor vaccine administration resulted in the formation of distinct granulomas with unique cellular and cytokine profiles. These distinct profiles corresponded to significant differences in the phenotypes and functional responses of DCs from within the granulomas. Specifically, the DCs from theM. aviumsubsp.paratuberculosis-induced granulomas had lower levels of expression of costimulatory and chemokine receptors, suggesting limited maturation. This DC phenotype was associated with weaker induction of T-cell proliferation. Taken together, these findings suggest thatM. aviumsubsp.paratuberculosisinfection in vivo influences DC function, which may shape the developing granuloma and initial local protection.
Evaluation of 16S rRNA Gene-Based PCR Assays for Genus-Level Identification of
Helicobacter
Species
Authors: Moyaert H. , Pasmans F. , Ducatelle R. , Haesebrouck F. , Baele M.
Published: March 2008

The inclusivity, exclusivity, and detection limit of six 16S rRNA gene-based
Helicobacter
genus-specific PCR assays were examined. Five out of six assays were 100% inclusive, but the tests varied considerably in their exclusivity (9.1 to 95.5%). The clinical detection limit varied between 10
3
and 1 viable bacterial cell per reaction mixture.
Comparison of Neo-Sensitabs Tablet Diffusion Assay with CLSI Broth Microdilution M38-A and Disk Diffusion Methods for Testing Susceptibility of Filamentous Fungi with Amphotericin B, Caspofungin, Itraconazole, Posaconazole, and Voriconazole
Authors: Espinel-Ingroff A. , Canton E.
Published: March 2008

We compared the Neo-Sensitabs tablet assay to both reference M38-A broth microdilution and disk diffusion methods for testing the susceptibility of 183 filamentous isolates to amphotericin B, caspofungin, itraconazole, posaconazole, and voriconazole. Neo-Sensitabs and disk assay inhibition zone diameters, in millimeters, were obtained on nonsupplemented Mueller-Hinton agar at 16 to 48 h. The reproducibility of zone diameters (i.e., the percentage of replicate zone diameters that were within 2 standard deviations of the means), their correlation with either MICs or minimum effective concentrations (for caspofungin only), and the categorical agreement were similar between tablet and disk assays (93 to 100% [
R
, >0.70] and 79 to 96%, respectively) with four of the five agents. The exceptions were the results for posaconazole tablets (
R
, 0.686; disk, 0.757; 84% categorical agreement for tablet and 96% for disk). These data suggest the potential value of the Neo-Sensitabs assay for testing 5-μg caspofungin and 1-μg voriconazole posaconazole tablets against all mold isolates, 8-μg itraconazole and 5-μg tablets against all mold isolates except zygomycetes, and 10-μg amphotericin B tablets against zygomycete isolates only.
Novel Wide-Range Quantitative Nested Real-Time PCR Assay for
Mycobacterium tuberculosis
DNA: Clinical Application for Diagnosis of Tuberculous Meningitis
Authors: Takahashi Teruyuki , Tamura Masato , Asami Yukihiro , Kitamura Eiko , Saito Kosuke , Suzuki Tsukasa , Takahashi Sachiko Nonaka , Matsumoto Koichi , Sawada Shigemasa , Yokoyama Eise , Takasu Toshiaki
Published: March 2008

Although the “gold standard” for diagnosis of tuberculous meningitis (TBM) is bacterial isolation of
Mycobacterium tuberculosis
, there are still several complex issues. Recently, we developed an internally controlled novel wide-range quantitative nested real-time PCR (WR-QNRT-PCR) assay for
M. tuberculosis
DNA in order to rapidly diagnose TBM. For use as an internal control calibrator to measure the copy number of
M. tuberculosis
DNA, an original new-mutation plasmid (NM-plasmid) was developed. Due to the development of the NM-plasmid, the WR-QNRT-PCR assay demonstrated statistically significant accuracy over a wide detection range (1 to 10
5
copies). In clinical applications, the WR-QNRT-PCR assay revealed sufficiently high sensitivity (95.8%) and specificity (100%) for 24 clinically suspected TBM patients. In conditional logistic regression analysis, a copy number of
M. tuberculosis
DNA (per 1 ml of cerebrospinal fluid) of >8,000 was an independent risk factor for poor prognosis for TBM (i.e., death) (odds ratio, 16.142; 95% confidence interval, 1.191 to 218.79;
P
value, 0.0365). In addition, the copy numbers demonstrated by analysis of variance statistically significant alterations (
P
< 0.01) during the clinical treatment course for 10 suspected TBM patients. In simple regression analysis, the significant correlation (
R
2
= 0.597;
P
< 0.0001) was demonstrated between copy number and clinical stage of TBM. We consider the WR-QNRT-PCR assay to be a useful and advanced assay technique for assessing the clinical treatment course of TBM.