bluuebunny/crossref_metadata_2025 huggingface dataset:
Invariant glycines and prolines flanking in loops the strand β2 of various (α/β)8‐barrel enzymes: A hidden homology?
Authors: Janeček Stefan
Published: August 2010

The question of parallel (α/β)8‐barrel fold evolution remains unclear, owing mainly to the lack of sequence homology throughout the amino acid sequences of (α/β)8‐barrel enzymes. The “classical” approaches used in the search for homologies among (α/β)8‐barrels (e.g., production of structurally based alignments) have yielded alignments perfect from the structural point of view, but the approaches have been unable to reveal the homologies. These are proposed to be “hidden” in (α/β)8‐barrel enzymes. The term “hidden homology” means that the alignment of sequence stretches proposed to be homologous need not be structurally fully satisfactory. This is due to the very long evolutionary history of all (α/β)8‐barrels. This work identifies so‐called hidden homology around the strand 02 that is flanked by loops containing invariant glycines and prolines in 17 different (α/β)8‐barrel enzymes, i.e., roughly in half of all currently known (α/β)8‐barrel proteins. The search was based on the idea that a conserved sequence region of an (α/β)8‐barrel enzyme should be more or less conserved also in the equivalent part of the structure of the other enzymes with this folding motif, given their mutual evolutionary relatedness. For this purpose, the sequence region around the well‐conserved second β‐strand of α‐amylase flanked by the invariant glycine and proline (56_GFTAIWITP, Aspergillus oryzae α‐amylase numbering), was used as the sequence‐structural template. The proposal that the second β‐strand of (α/β)8‐barrel fold is important from the evolutionary point of view is strongly supported by the increasing trend of the observed β2‐strand structural similarity for the pairs of (α/β)8‐barrel enzymes: α‐amylase and the α‐subunit of tryptophan synthase, α‐amylase and mandelate racemase, and α‐amylase and cyclodextrin glycosyltransferase. This trend is also in agreement with the existing evolutionary division of the entire family of (α/β)8‐barrel proteins.
Botulinum Toxin Injection Versus Lateral Internal Sphincterotomy in the Treatment of Chronic Anal Fissure: A Randomized Controlled Trial
Authors: Nasr Maged , Ezzat Hussin , Elsebae Magdy
Published: August 2010

Background

Although lateral internal sphincterotomy has been the gold standard of treatment for chronic anal fissure, the main concern remains its effects on anal continence. Intrasphincteric injection of botulinum toxin seems to be a reliable option providing temporary alleviation of sphincter spasm and allowing the fissure to heal. The aim of the present prospective controlled randomized study was to compare the outcome of lateral internal sphincterotomy and botulinum toxin injection treatments in patients with uncomplicated chronic anal fissure.

Methods

Eighty consecutive patients with uncomplicated chronic anal fissure who had failed conservative treatment were randomized to receive either intrasphincteric injection of botulinum toxin (BT) or lateral internal sphincterotomy (LIS). Postoperative pain relief, healing of fissure, continence scores, and fissure relapse during 18 weeks of follow‐up were the outcomes assessed.

Results

There was a statistically significantly higher healing in the LIS group than the BT group (p = 0.0086 and 95% CI = 7.38–45.69%). In addition, LIS was associated with a high rate of anal incontinence as compared to BT (p = 0.0338 and 95% CI = −1.64–27.53%). The recurrence rate in the BT group was significantly higher statistically than that in the LIS group (p = 0.0111 and 95% CI = 6.68–46.13%).

Conclusions

Surgical internal sphincterotomy has a higher healing rate and a lower recurrence rate than intrasphincteric injection of botulinum toxin in the treatment of uncomplicated chronic anal fissure. Injection of botulinum toxin, however, is a simple noninvasive technique that avoids the greater risk of incontinence. It could be used as the first therapeutic approach in patients without clinical risk factors of recurrence.
International Preoperative Rectal Cancer Management: Staging, Neoadjuvant Treatment, and Impact of Multidisciplinary Teams
Authors: Augestad Knut M. , Lindsetmo Rolv‐Ole , Stulberg Jonah , Reynolds Harry , Senagore Anthony , Champagne Brad , Heriot Alexander G. , Leblanc Fabien , Delaney Conor P. ,   International Rectal Cancer Study Group (IRCSG)
Published: August 2010

Background

Little is known regarding variations in preoperative treatment and practice for rectal cancer (RC) on an international level, yet practice variation may result in differences in recurrence and survival rates.

Methods

One hundred seventy‐three international colorectal centers were invited to participate in a survey of preoperative management of rectal cancer.

Results

One hundred twenty‐three (71%) responded, with a majority of respondents from North America, Europe, and Asia. Ninety‐three percent have more than 5 years’ experience with rectal cancer surgery. Fifty‐five percent use CT scan, 35% MRI, 29% ERUS, 12% digital rectal examination and 1% PET scan in all RC cases. Seventy‐four percent consider threatened circumferential margin (CRM) an indication for neoadjuvant treatment. Ninety‐two percent prefer 5‐FU‐based long‐course neoadjuvant chemoradiation therapy (CRT). A significant difference in practice exists between the US and non‐US surgeons: poor histological differentiation as an indication for CRT (25% vs. 7.0%, p = 0.008), CRT for stage II and III rectal cancer (92% vs. 43%, p = 0.0001), MRI for all RC patients (20% vs. 42%, p = 0.03), and ERUS for all RC patients (43% vs. 21%, p = 0.01). Multidisciplinary team meetings significantly influence decisions for MRI (RR = 3.62), neoadjuvant treatment (threatened CRM, RR = 5.67, stage II + III RR = 2.98), quality of pathology report (RR = 4.85), and sphincter‐saving surgery (RR = 3.81).

Conclusions

There was little consensus on staging, neoadjuvant treatment, and preoperative management of rectal cancer. Regular multidisciplinary team meetings influence decisions about neoadjuvant treatment and staging methods.
Influence of foraging behavior and host spatial distribution on the localized spread of the emerald ash borer,Agrilus planipennis
Authors: Mercader Rodrigo J. , Siegert Nathan W. , Liebhold Andrew M. , McCullough Deborah G.
Published: August 2010

Management programs for invasive species are often developed at a regional or national level, but physical intervention generally takes place over relatively small areas occupied by newly founded, isolated populations. The ability to predict how local habitat variation affects the expansion of such newly founded populations is essential for efficiently targeting resources to slow the spread of an invasive species. We assembled a coupled map lattice model that simulates the local spread of newly founded colonies of the emerald ash borer (Agrilus planipennisFairmaire), a devastating forest insect pest of ash (Fraxinusspp.) trees. Using this model, we investigated the spread ofA. planipennisin environments with differentFraxinusspp. distributions, and explored the consequences of ovipositional foraging behavior on the local spread ofA. planipennis. Simulations indicate that increased larval density, resulting from lower host tree density or higher initial population sizes, can increase the spread rate during the first few years after colonization by increasing a density‐dependent developmental rate and via host resource depletion. Both the radial spread rate and population size were greatly influenced by ovipositional foraging behavior. Two known behaviors of ovipositingA. planipennisfemales, attraction towards areas with high ash tree density and attraction to stressed trees, had opposing effects on spread. Results from this model illustrate the significant influence of resource distribution and foraging behavior on localized spread, and the importance of these factors when formulating strategies to monitor and manage invasive pests.
Reporter gene expression at single‐cell level characterized with real‐time RT‐PCR, chemiluminescence, fluorescence, and electrochemical imaging
Authors: Shiku Hitoshi , Okazaki Daisuke , Suzuki Junya , Takahashi Yasufumi , Murata Tatsuya , Akita Hidetaka , Harashima Hideyoshi , Ino Kosuke , Matsue Tomokazu
Published: August 2010

mRNA from single cells was quantified using real‐time RT‐PCR after recording the address and reporter protein activity with chemiluminescence, fluorescence, and electrochemical techniques, using luciferase, green fluorescent protein, and secreted alkaline phosphatase. mRNA copy number ranging from below 103 to 107 in single cells showed a lognormal distribution for both externally introduced reporter genes and internally expressed genes. The fluctuation in the gene expression decreased with the increase of the number of cells picked but did not decrease with the increase of mRNA copy number per cell. We found that the correlation coefficients for mRNA and protein expression in logarithmic plot at single‐cell level were much lower than 1.00.
Feminine to smell but masculine to touch? Multisensory congruence and its effect on the aesthetic experience
Authors: Krishna Aradhna , Elder Ryan S. , Caldara Cindy
Published: August 2010

We draw upon literature examining cross‐modal sensory interactions and congruence to explore the impact of smell on touch. In line with our predictions, two experiments show that smell can impact touch in meaningful ways. Specifically, we show that multisensory semantic congruence between smell and touch properties of a stimulus enhances haptic perception and product evaluation. We explore this relationship in the context of two properties of touch, namely texture and temperature, and demonstrate that both smell and touch can have semantic associations, which can affect haptic perception and product evaluation depending on whether they match or not. In study 1, we focus on the semantic association of smell and touch (texture) with gender and in study 2 with temperature. Our results extend prior work on smell and touch within consumer behavior, and further contribute to emerging literature on multisensory interactions.
Role of manufacturing flexibility in managing duality of formalization and environmental uncertainty in emerging firms
Authors: Patel Pankaj C.
Published: August 2010

Increased firm formalization helps emerging firms develop stable routines and processes to increase their chances of survival. However, uncertain and dynamic task environments of emerging firms require more flexible organizational structures. Such duality of structural prescriptions stems from competing demands of task and institutional environments. We propose that manufacturing flexibility could help decouple activities required in task environments from those required in institutional environments, thereby mitigating the conflict of adopting flexible and rigid structures at the same time. An emerging venture could meet demands of institutional environments through formalized structures, and use manufacturing flexibility to address needs of task environment in order to mitigate liabilities of newness. Using a sample of 167 high‐technology manufacturing firms in the UK, we use a moderated polynomial regression approach to test the proposed framework. Results indicate that formalized structures in conjunction with manufacturing flexibility lead to enhanced performance. The findings extend literature on organizational structures in operations management and entrepreneurship.
Brain tumor stem cells: The cancer stem cell hypothesis writ large
Authors: Dirks Peter B.
Published: August 2010

Brain tumors, which are typically very heterogeneous at the cellular level, appear to have a stem cell foundation. Recently, investigations from multiple groups have found that human as well as experimental mouse brain tumors contain subpopulations of cells that functionally behave as tumor stem cells, driving tumor growth and generating tumor cell progeny that form the tumor bulk, but which then lose tumorigenic ability. In human glioblastomas, these tumor stem cells express neural precursor markers and are capable of differentiating into tumor cells that express more mature neural lineage markers. In addition, modeling brain tumors in mice suggests that neural precursor cells more readily give rise to full blown tumors, narrowing potential cells of origin to those rarer brain cells that have a proliferative potential. Applying stem cell concepts and methodologies is giving fresh insight into brain tumor biology, cell of origin and mechanisms of growth, and is offering new opportunities for development of more effective treatments. The field of brain tumor stem cells remains very young and there is much to be learned before these new insights are translated into new patient treatments.
Effect of Low‐flow Anesthesia Education on Knowledge, Attitude and Behavior of the Anesthesia Team
Authors: Hanci Volkan , Yurtlu Serhan , Ayoğlu Hilal , Okyay Rahşan Dilek , Erdoğan Gülay , Abduşoğlu Mustafa , Sayin Esin , Turan Işil Özkoçak
Published: August 2010

The aim of this study was to evaluate the effect of education on the knowledge, attitude and behavior of anesthesiology staff and residents towards low‐flow anesthesia. The staff and residents in the Department of Anesthesia and Reanimation, Zonguldak Karaelmas University were given theoretical and practical training in delivering low‐flow anesthesia. To evaluate their attitudes and behaviors toward low‐flow anesthesia, we collected data during the 6 months before training, during the first 3 months after training, and at 4–6 months after training. Anesthesia follow‐up records, operation time, volatile anesthetic agent used, and the amount (in liters) of fresh gas low mid‐anesthesia were recorded in all three stages. A total of 3,158 patients received general anesthesia and inhalation anesthesia was used in 3,115 of these patients. Our study group consisted of 2,752 patients who had no absolute or relative contraindications to low‐flow anesthesia. While the mean fresh gas flow was 4.00 ± 0.00 L/min before training, this level dropped to 2.98 L/min in the first 3 months after training, and to 3.26 L/min in the following 3 months. The mean fresh gas flow was significantly lower at the two post‐training assessments than before training (p < 0.05). In conclusion, low‐flow anesthesia may be used more frequently if educational seminars are provided to anesthetists. The use of low‐flow anesthesia may increase further by allocating more time to this technique in anesthesia training programs provided at regular intervals.
Method of Retention Control for Compromised Periodontal Bone Support Abutment of Conical Crown Retained Denture
Authors: Wang Chau‐Hsiang , Lee Huey‐Er , Lan Ting‐Hsun , Igarashi Yoshimasa
Published: August 2010

Conical crown‐retained dentures (CCRD) show a higher survival rate and greater patient satisfaction than transitional removable partial dentures during long‐term follow‐up. However, unsustainable denture retention force on supporting abutments after initial delivery and loss retention are frequently seen in long‐term follow‐up of clinical cases. The main causes are insufficient information concerning denture retention designs and the retention‐tolerance of the supporting abutments. Monitoring by dental technicians of the quality of dental prostheses is critical. This case report describes an optimal method for CCRD construction that determines and distributes an optimal denture retention force on the supporting abutments to allow the patient to easily remove the denture while ensuring that the CCRD remains in place during physiologic activities. Oral rehabilitation with CCRD should consider the condition of the abutment periodontal support, the interarch occlusal relationship, supplemental fatigue of the terminal abutment, and patient's estimated bite force. The effects of friction on the abutment's inner crown were based on an optimal a angle. The dental laboratory used these measurements to fabricate a CCRD using a Koni‐Meter to adjust the retention of the inner crown. This method protects the abutments and reduces the wear between the inner and outer crowns. The CCRD achieved good esthetic results and physiologic functions. Periodic long‐term follow‐up of the patient and CCRD after initial placement is recommended.
The Flood Last Time: “Muck” and the Uses of History in Kara Walker's “Rumination” on Katrina
Authors: BIBLER MICHAEL P.
Published: August 2010

Kara Walker describes her book After the Deluge (2007) as “rumination” on Hurricane Katrina structured in the form of a “visual essay.” The book combines Walker's own artwork and the works of other artists into “a narrative of fluid symbols” in which the overarching analogy of “murky, toxic waters” holds the potential to “become the amniotic fluid of a potentially new and difficult birth.” This essay considers Walker's use of history within this collection of images to show how the book opens up ways to interrogate Katrina's particular significance as a wholly new, and yet eerily familiar, historical “event.” Nuancing a reading of Walker's book with reference to James Baldwin's The Fire Next Time (1963), to which After the Deluge implicitly alludes, the essay examines Walker's artistic challenge to the notion that history is a narratable account of a past that precedes the present and demonstrates how that challenge encourages us to think about the potential uses of history within civil rights discourse after Katrina.
Free at Last: Post-Katrina New Orleans and the Future of Conspiracy
Authors: GRAHAM ALLISON
Published: August 2010

In the first year following Hurricane Katrina and the breaking of the New Orleans levees, the New Orleans-based Alliance of Guest Workers for Dignity and the Southern Poverty Law Center filed a lawsuit on behalf of eighty-two workers from South and Central America who were stranded in the city. By 2008, the consequences of the regional reliance on slavecatchers began attracting global attention, most notably in the case of the eighty-nine Indian workers at Signal International's Pasacagoula, Mississippi shipyard. This essay explores the invocation of the American civil rights movement in contemporary transcultural dramas and the fact that another “universal” movement has been marching alongside new protesters, and demonstrates that the Free Trade movement in the US has been not only the cause of many current civil rights struggles, but also the beneficiary of the older struggle's very definition of its “cause.” New laborers in the Deep South – Latin Americans and Asians – find themselves not just homeless, but placeless post-Katrina. Black Americans who were shipped out of the city in 2005 to provide a “cleansed” urban area open to new demographics now find themselves in permanent exile, as placeless as their replacements.
Reflections on The American Scene: Prints from Hopper to Pollock, British Museum, London; Djanogly Art Gallery, Nottingham; Brighton Museum and Art Gallery; Whitworth Art Gallery, Manchester, April 2008–December 2009
Authors: TALLACK DOUGLAS
Published: August 2010

It is tempting to regard the remarkable success of this exhibition of works from the British Museum's American prints collection, as it toured England, as a response to the demise of the Bush Administration and the election of Barack Obama. However, George W. Bush was in the White House throughout the period when these prints were on display at the British Museum from April to September 2008.
Three-dimensional simulations of premixed hydrogen/air flames in microtubes
Authors: PIZZA G. , FROUZAKIS C. E. , MANTZARAS J. , TOMBOULIDES A. G. , BOULOUCHOS K.
Published: August 2010

The dynamics of fuel-lean (equivalence ratio φ = 0.5) premixed hydrogen/air atmospheric pressure flames are investigated in open cylindrical tubes with diameters ofd= 1.0 and 1.5 mm using three-dimensional numerical simulations with detailed chemistry and transport. In both cases, the inflow velocity is varied over the range where the flames can be stabilized inside the computational domain. Three axisymmetric combustion modes are observed in the narrow tube: steady mild combustion, oscillatory ignition/extinction and steady flames as the inflow velocity is varied in the range 0.5 ≤UIN≤ 500 cm s−1. In the wider tube, richer flame dynamics are observed in the form of steady mild combustion, oscillatory ignition/extinction, steady closed and open axisymmetric flames, steady non-axisymmetric flames and azimuthally spinning flames (0.5 ≤UIN≤ 600 cm s−1). Coexistence of the spinning and the axisymmetric modes is obtained over relatively wide ranges ofUIN. Axisymmetric simulations are also performed in order to better understand the nature of the observed transitions in the wider tube. Fourier analysis during the transitions from the steady axisymmetric to the three-dimensional spinning mode and to the steady non-axisymmetric modes reveals that them= 1 azimuthal mode plays a dominant role in the transitions.
Russian Theatre Festival at the Soho
Authors: Birksted-Breen Noah
Published: August 2010

As Noah Birksted-Breen, founder of Sputnik Theatre Company (noah@sputniktheatre.co.uk), starts planning the second Russian Theatre Festival in mid-2011, he looks back on why he founded the festival, what to look out for in new Russian drama, why he chose this year's plays, and what comes next. The first festival was held at the Soho Theatre, London, 1–4 February 2010.
The efficiency of three-visit square surveys vs. one-visit line transects in censusing sparsely distributed birds in managed forest landscapes
Authors: SOLONEN TAPIO , JOKIMÄKI JUKKA
Published: August 2010

We conducted three-visit surveys of 1-km2plots and traditional Finnish single-visit line transects (considering only the 50 m wide main belt) to evaluate these methods in censusing of a predetermined set of 23 target species known to prefer old forests in three regions in Finland. The efficiency of the two methods was compared on the basis of the number of territories recorded per hour. An attempt was made to find indicators of the occurrence of suitable habitats for species preferring old forest in general, including the rarest ones, and so also largely indicating total diversity of forest bird fauna of the study area. The total number of pairs observed per hour and the abundance of sedentary bird species were significantly higher in the square surveys than in the main belt of the line transects. There were significant positive relationships between the densities of relatively abundant (density > 1.0 pairs km−2) and less abundant target species. There emerged five common forest bird species that seemed to form a suitable set of indicators of the occurrence of habitats for birds preferring old forest in the northern boreal zone: Great Spotted WoodpeckerDendrocopos major, Mistle ThrushTurdus viscivorus, Willow TitParus montanus, Eurasian TreecreeperCerthia familiaris, and Eurasian BullfinchPyrrhula pyrrhula. We concluded that sedentary species preferring old forest are good candidates for indicators to characterize some threatened aspects of forest bird diversity.
Provision of artificial shelter on beaches is associated with improved shorebird fledging success
Authors: MAGUIRE GRAINNE S. , DUIVENVOORDEN ANDREW K. , WESTON MICHAEL A. , ADAMS ROBYN
Published: August 2010

Artificial chick shelters might improve productivity of beach-nesting birds threatened by anthropogenic disturbance. We investigated the efficacy of three different chick shelter designs against four criteria: accessibility to chicks over time, thermal insulation, conspicuousness to beach-goers, and practicality (cost and ease of transport). One design (‘A-frame’) was selected because it offered the greatest thermal insulation, was the least conspicuous, most cost effective, and performed equally well in terms of accessibility. We deployed these artificial shelters on Hooded PloverThinornis rubricollisterritories where broods were present (n= 11), and compared the behaviour and survival rate of chicks to that at control sites (n= 10). We were unable to discern any difference in the behaviour of broods when artificial shelters were available. However, the survival rate of chicks to fledging was 71.8% higher where an artificial shelter was provided (n= 21 broods). This was validated by analysing data from a larger sample of broods monitored as part of an active volunteer-based management programme; shelters conferred a 42.8% increase in survival to fledging (n= 81 broods). Thus, artificial shelters have the potential to increase survival rates of threatened shorebird chicks, though the mechanisms through which survival is increased require further investigation.
UNFOLDING FINITIST ARITHMETIC
Authors: FEFERMAN SOLOMON , STRAHM THOMAS
Published: August 2010

The concept of the (full) unfolding$\user1{{\cal U}}(S)$of a schematic system$S$is used to answer the following question: Which operations and predicates, and which principles concerning them, ought to be accepted if one has accepted$S$? The program to determine$\user1{{\cal U}}(S)$for various systems$S$of foundational significance was previously carried out for a system of nonfinitist arithmetic,$NFA$; it was shown that$\user1{{\cal U}}(NFA)$is proof-theoretically equivalent to predicative analysis. In the present paper we work out the unfolding notions for a basic schematic system of finitist arithmetic,$FA$, and for an extension of that by a form$BR$of the so-called Bar Rule. It is shown that$\user1{{\cal U}}(FA)$and$\user1{{\cal U}}(FA + BR)$are proof-theoretically equivalent, respectively, to Primitive Recursive Arithmetic,$PRA$, and to Peano Arithmetic,$PA$.
Experimental constraints on the strength of the lithospheric mantle
Authors: Mei S. , Suzuki A. M. , Kohlstedt D. L. , Dixon N. A. , Durham W. B.
Published: August 2010

To provide a better understanding of rheological properties of mantle rocks under lithospheric conditions, we carried out a series of experiments on the creep behavior of polycrystalline olivine at high pressures (∼4–9 GPa), relatively low temperatures (673 ≤ T ≤ 1273 K), and anhydrous conditions, using a deformation‐DIA. Differential stress and sample displacement were monitored in situ using synchrotron X‐ray diffraction and radiography, respectively. Experimental results were fit to the low‐temperature plasticity flow law, . On the basis of this analysis, the low‐temperature plasticity of olivine deformed under anhydrous conditions is well constrained by our data with a Peierls stress of σP = 5.9 ± 0.2 GPa, a zero‐stress activation energy of Ek(0) = 320 ± 50 kJ mol−1, and AP = 1.4 × 10−7 s−1 MPa−2. Compared with published results for high‐temperature creep of olivine, a transition from low‐temperature plasticity to high‐temperature creep occurs at ∼1300 K for a strain rate of ∼10−5 s−1. For a geological strain rate of 10−14 s−1, extrapolation of our low‐temperature flow law to 873 K, the cutoff temperature for earthquakes in the mantle, yields a strength of ∼600 MPa. The low‐temperature, high‐stress flow law for olivine in this study provides a solid basis for modeling tectonic processes occurring within Earth's lithosphere.
Controls of riverine CO2 over an annual cycle determined using direct, high temporal resolution pCO2 measurements
Authors: Lynch Janet K. , Beatty Cory M. , Seidel Matthew P. , Jungst Laura J. , DeGrandpre Michael D.
Published: August 2010

Autonomous CO2 sensors were deployed in the Clark Fork River, Montana, USA, to characterize the partial pressure of CO2 (pCO2) during an annual cycle. A total of 23,941 measurements were made spanning the period 2002–2006. These data were compiled into a composite data set covering ∼309 days, giving an unprecedented yearlong view of the carbon cycle dynamics of a riverine system. Seasonal pCO2 varied from a winter minimum of ∼100 μatm to a fall maximum of ∼900 μatm. The pCO2 changed by as much as 460 μatm during a diel period, much larger than the range of the seasonal mean, in contrast to most other aquatic ecosystems where seasonal variability dominates. The diel pCO2 amplitude was primarily controlled by the net ecosystem production (NEP) throughout the year, although heating/cooling and air‐water exchange significantly altered the diel pCO2 (and pH) magnitude. Although infrequent, rain events contributed ∼21% to the cumulative short‐term changes in inorganic carbon through CO2‐enriched runoff. The seasonal cycle was controlled by temperature, NEP, and discharge. The Clark Fork River maintained pCO2 levels that were supersaturated with respect to the atmosphere for the majority of the year. River‐to‐atmosphere CO2 gas exchange was estimated to be between 4.7 and 7.1 mol C m−2 yr−1. The loss of CO2 to the atmosphere arises from net heterotrophy that averaged 13.8 mmol m−2 d−1. The time series also captured important episodic events including macrophyte sloughing that led to a pulse of respiration that represented 7% of the annual CO2 gas efflux and cloudy periods that occurred every 7–18 days that dramatically decreased the pCO2 through cooling.
New Surveys of a Branch of the Indonesian Throughflow
Authors: Susanto R. Dwi , Fang Guohong , Soesilo Indroyono , Zheng Quanan , Qiao Fangli , Wei Zexun , Sulistyo Budi
Published: August 2010

Global ocean circulation is a primary mechanism for transporting energy and nutrients around the planet. At its most basic level, this circulation transports water from the Pacific Ocean through the Indonesian archipelago into the Indian Ocean; these waters join the Agulhas Current, which loops around Africa and in turn joins the Gulf Stream in the Atlantic Ocean. Upon reaching the North Atlantic, waters sink, creep south along the ocean floor as deep water, trace around Antarctica as bottom water, and move to the Pacific Ocean where they upwell, only to seep back into the Indian Ocean through the straits and channels surrounding Indonesia.

The seepage of warm equatorial waters from the western Pacific Ocean into the Indian Ocean is called the Indonesian Throughflow (ITF). Long recognized as a key component of global ocean circulation, the ITF's magnitude and variability play an important role in determining heat and nutrient exchange to other ocean basins. Scientists' ability to estimate ITF behavior is therefore essential for understanding the global climate system.
AGU Strategic Plan
Authors: Anonymous
Published: August 2010

The purpose of the American Geophysical Union (AGU) is to promote discovery in Earth and space science for the benefit of humanity.
Auroral Substorms Paradigm Shifts in Research
Authors: Akasofu Syun‐Ichi
Published: August 2010

The study of scientific advancement is the study of evolving thought. Disciplines progress as old prevailing theoretical ideas are toppled by new ones, one after another. Provided that new ideas can be independently verified, scientists at any level can greatly contribute to their field.

Though space weather is a young field, it has been riddled with such paradigm shifts. As a scientist who has worked on auroral and magnetospheric substorm research during several of these moments, I have witnessed firsthand how diligence, patience, and creativity combine to advance science.
Protein Kinase C Activation Modulates Reversible Increase in Cortical Blood–Brain Barrier Permeability and Tight Junction Protein Expression during Hypoxia and Posthypoxic Reoxygenation
Authors: Willis Colin L , Meske Diana S , Davis Thomas P
Published: August 2010

Hypoxia (Hx) is a component of many disease states including stroke. Ischemic stroke occurs when there is a restriction of cerebral blood flow and oxygen to part of the brain. During the ischemic, and subsequent reperfusion phase of stroke, blood–brain barrier (BBB) integrity is lost with tight junction (TJ) protein disruption. However, the mechanisms of Hx and reoxygenation (HR)-induced loss of BBB integrity are not fully understood. We examined the role of protein kinase C (PKC) isozymes in modifying TJ protein expression in a rat model of global Hx. The Hx (6% O2) induced increased hippocampal and cortical vascular permeability to 4 and 10 kDa dextran fluorescein isothiocyanate (FITC) and endogenous rat-IgG. Cortical microvessels revealed morphologic changes in nPKC-θ distribution, increased nPKC-θ and aPKC-ζ protein expression, and activation by phosphorylation of nPKC-θ (Thr538) and aPKC-ζ (Thr410) residues after Hx treatment. Claudin-5, occludin, and ZO-1 showed disrupted organization at endothelial cell margins, whereas Western blot analysis showed increased TJ protein expression after Hx. The PKC inhibition with chelerythrine chloride (5 mg/kg intraperitoneally) attenuated Hx-induced hippocampal vascular permeability and claudin-5, PKC (θ and ζ) expression, and phosphorylation. This study supports the hypothesis that nPKC-θ and aPKC-ζ signaling mediates TJ protein disruption resulting in increased BBB permeability.
HMBG1 Mediates Ischemia—Reperfusion Injury by TRIF-Adaptor Independent Toll-Like Receptor 4 Signaling
Authors: Yang Qing-Wu , Lu Feng-Lin , Zhou Yu , Wang Lin , Zhong Qi , Lin Sen , Xiang Jing , Li Jing-Cheng , Fang Chuan-Qing , Wang Jing-Zhou
Published: August 2010

High-mobility group protein box-1 (HMGB1) has recently been recognized as a novel candidate in a specific upstream pathway promoting inflammation after brain ischemia. However, its downstream pathway and underlying mechanism have yet to be elucidated. The HMGB1 level in the acute cerebral infarct (ACI) group was significantly increased compared with that of control group, and correlated with the severity of neurologic impairment of ACI patients. Further, recombinant human HMGB1 (rhHMGB1) had no effect on microglia derived from mice lacking the Toll-like receptor 4 (TLR4−/–). Intracerebroventricular injection of rhHMGB1 in TLR4+/+ mice cause significantly more injury after cerebral ischemia–reperfusion than control group. But, TLR4−/– mice administered with rhHMGB1 showed moderate impairment after ischemia–reperfusion than TLR4+/+ mice. To determine the potential downstream signaling of HMGB1/TLR4 in cerebral ischemic injury, we used the ischemic–reperfusion model with Toll/interleukin-1 receptor domain-containing adaptor-inducing interferon-β knockout mice (TRIF−/–) and evaluated the activity and expression of TRIF pathway-related kinases. The results suggest that the TRIF pathway is not likely to be involved in TLR4-mediated ischemia brain injury. Finally, we found that TLR4 expressed by immigrant macrophages was involved in the development of ischemic brain damage. These results suggest that HMBG1 mediates ischemia–reperfusion injury by TRIF-adaptor independent Toll-like receptor 4 signaling. The TLR4 expressed by immigrant macrophages may be involved in the development of ischemic brain damage.
Systematic Studies of Modified Vocalization: Effects of Speech Rate and Instatement Style During Metronome Stimulation
Authors: Davidow Jason H. , Bothe Anne K. , Richardson Jessica D. , Andreatta Richard D.
Published: August 2010

Purpose

This study introduces a series of systematic investigations intended to clarify the parameters of the fluency-inducing conditions (FICs) in stuttering.

Method

Participants included 11 adults, aged 20–63 years, with typical speech-production skills. A repeated measures design was used to examine the relationships between several speech production variables (vowel duration, voice onset time, fundamental frequency, intraoral pressure, pressure rise time, transglottal airflow, and phonated intervals) and speech rate and instatement style during metronome-entrained rhythmic speech.

Results

Measures of duration (vowel duration, voice onset time, and pressure rise time) differed across different metronome conditions. When speech rates were matched between the control condition and metronome condition, voice onset time was the only variable that changed.

Conclusion

Results confirm that speech rate and instatement style can influence speech production variables during the production of fluency-inducing conditions. Future studies of normally fluent speech and of stuttered speech must control both features and should further explore the importance of voice onset time, which may be influenced by rate during metronome stimulation in a way that the other variables are not.
Isotype representing social facts pictorially
Authors: Burke Christopher
Published: August 2010

In developing Isotype, Otto Neurath and his colleagues were the first to systematically explore a consistent visual language as part of an encyclopedic approach to representing all aspects of the physical world. The pictograms used in Isotype have a secure legacy in today’s public information symbols, but Isotype was more than this: it was designed to communicate social facts memorably to less educated groups, including schoolchildren and workers, reflecting its initial testing ground in the socialist municipality of Vienna during the 1920s. The social engagement and methodology of Isotype are examined here in order to draw some lessons for information design today.
Much ado about something remote
Authors: Roziner Ilan , Shlesinger Miriam
Published: August 2010

The article describes the aims, methods, conclusions and recommendations of a large-scale experimental study designed to evaluate the feasibility and implications of the use of remote interpreting (RI) in the European Parliament and other large multilingual settings, where the introduction of a growing number of languages requires the extension of existing arrangements. While the study reveals a relatively small impact on either the quality of the interpreting or interpreters’ health and objective measures of stress, it nevertheless points to considerable psychological effects, including an increase in feelings of isolation and alienation. The study recommends greater use of technological support through the possible introduction of individually computerized workstations and a user-friendly working environment.
Sexual Recombinants Make a Significant Contribution to Epidemics Caused by the Wheat Pathogen Phaeosphaeria nodorum
Authors: Sommerhalder Rubik J. , McDonald Bruce A. , Mascher Fabio , Zhan Jiasui
Published: August 2010

We conducted a 2-year mark-release-recapture field experiment to quantify the relative contributions of immigration and sexual and asexual reproduction to epidemics of Stagonospora nodorum blotch caused by Phaeosphaeria nodorum. The epidemic was initiated using nine genetically distinct P. nodorum isolates. Infected plants were sampled four times across two growing seasons. In total, 1,286 isolates were recovered and assayed with 10 microsatellite markers and 1 minisatellite marker. The proportion of isolates having multilocus haplotypes (MLHTs) identical to the inoculated isolates decreased steadily from 86% in the first collection to 25% in the fourth collection. The novel isolates that had different MLHTs compared with the marked inoculants originated through immigration and sexual recombination. By the end of the experiment, nearly three-quarters of the novel isolates originated from sexual recombination. Our results indicate that recombinant offspring and airborne immigrant ascospores can make significant contributions to epidemics of Stagonospora nodorum blotch during a growing season.
Multiple Infection of Apple Trees by Distinct Strains of ‘Candidatus Phytoplasma mali’ and Its Pathological Relevance
Authors: Seemüller Erich , Kiss Emese , Sule Sandor , Schneider Bernd
Published: August 2010

Forty-eight apple trees infected by ‘Candidatus Phytoplasma mali’ were examined using single-strand conformation polymorphism (SSCP) and sequence analysis of a variable hflB gene fragment and the immunodominant membrane protein-encoding imp gene. SSCP analysis of polymerase chain reaction-amplified hflB gene fragments revealed diverse profiles, differing in number and position of the bands. The ‘Ca. P. mali’ content of a single infected apple tree was termed an accession. Cloning of fragments from accessions that yielded fewer bands resulted in clone populations showing uniform or moderately polymorphic SSCP patterns and largely homogenous nucleotide sequences. In contrast, inserts from accessions yielding more bands were heterogeneous and formed two to four distinct groups of profiles. DNA fragments from such accessions were diverse and clustered distantly when subjected to phylogenetic analysis, mostly as two homogenous groups plus one or a few other sequences. Similar results were obtained upon imp gene examination. The collective data indicate that accessions exhibiting more complex patterns were composed of two or three distinct ‘Ca. P. mali’ strains. There is evidence that multiple infections are of pathological relevance due to strain interactions leading to shifts in the populations. In triply infected trees of one accession, no specific symptoms were induced by the presence of two of the strains. The rare appearance of pronounced symptoms was associated with a separate strain that possessed a unique SSCP profile and a unique hflB sequence. The two mild strains from this apple accession also induced only mild symptoms on periwinkle and tobacco and occurred specifically in one of these plants.
Response of Soybean Pathogens to Glyceollin
Authors: Lygin Anatoly V. , Hill Curtis B. , Zernova Olga V. , Crull Laura , Widholm Jack M. , Hartman Glen L. , Lozovaya Vera V.
Published: August 2010

Plants recognize invading pathogens and respond biochemically to prevent invasion or inhibit colonization in plant cells. Enhancing this response in crop plants could improve sustainable methods to manage plant diseases. To enhance disease resistance in soybean, the soybean phytoalexin glyceollin was assessed in soybean hairy roots of two soybean genotypes, Spencer and PI 567374, transformed with either soybean isoflavone synthase (IFS2) or chalcone synthase (CHS6) genes that were inoculated with the soybean pathogens Diaporthe phaseolorum var. meridionales, Macrophomina phaseolina, Sclerotinia sclerotiorum, and Phytophthora sojae. The hairy-root-transformed lines had several-fold decreased levels of isoflavone daidzein, the precursor of glyceollin, and considerably lower concentrations of glyceollin induced by pathogens measured 5 days after fungal inoculation compared with the nontransformed controls without phenolic transgenes. M. phaseolina, P. sojae, and S. sclerotiorum grew much more on IFS2- and CHS6-transformed roots than on control roots, although there was no significant difference in growth of D. phaseolorum var. meridionales on the transformed hairy-root lines. In addition, glyceollin concentration was lower in D. phaseolorum var. meridionales-inoculated transformed and control roots than roots inoculated with the other pathogens. Glyceollin inhibited the growth of D. phaseolorum var. meridionales, M. phaseolina, P. sojae, S. sclerotiorum, and three additional soybean pathogens: Cercospora sojina, Phialophora gregata, and Rhizoctonia solani. The most common product of glyceollin conversion or degradation by the pathogens, with the exception of P. sojae, which had no glyceollin degradation products found in the culture medium, was 7-hydroxyglyceollin.
Quantitative Models for Germination and Infection of Pseudoperonospora cubensis in Response to Temperature and Duration of Leaf Wetness
Authors: Arauz L. F. , Neufeld K. N. , Lloyd A. L. , Ojiambo P. S.
Published: August 2010

The influence of temperature and leaf wetness duration on germination of sporangia and infection of cantaloupe leaves by Pseudoperonospora cubensis was examined in three independent controlled-environment experiments by inoculating plants with a spore suspension and exposing them to a range of leaf wetness durations (2 to 24 h) at six fixed temperatures (5 to 30°C). Germination of sporangia was assessed at the end of each wetness period and infection was evaluated from assessments of disease severity 5 days after inoculation. Three response surface models based on modified forms of the Weibull function were evaluated for their ability to describe germination of sporangia and infection in response to temperature and leaf wetness duration. The models estimated 15.7 to 17.3 and 19.5 to 21.7°C as the optimum temperature (t) range for germination and infection, respectively, with little germination or infection at 5 or 30°C. For wetness periods of 4 to 8 h, a distinct optimum for infection was observed at t = 20°C but broader optimum curves resulted from wetness periods >8 h. Model 1 of the form f(w,t) = f(t) × (1 – exp{–[B × w]D}) resulted in smaller asymptotic standard errors and yielded higher correlations between observed and predicted germination and infection data than either model 2 of the form f(w,t) = A(1 – exp{– [f(t) × (w – C)]D}) or model 3 of the form f(w,t) = [1 – exp{–(B × w)2}]/cosh[(t – F)G/2]. Models 1 and 2 had nonsignificant lack-of-fit test statistics for both germination and infection data, whereas a lack-of-fit test was significant for model 3. The models accounted for ≈87% (model 3) to 98% (model 1) of the total variation in the germination and infection data. In the validation of the models using data generated with a different isolate of P. cubensis, slopes of the regression line between observed and predicted germination and infection data were not significantly different (P > 0.2487) and correlation coefficients between observed and predicted values were high (r2 > 0.81). Models 1 and 2 were used to construct risk threshold charts that can be used to estimate the potential risk for infection based on observed or forecasted temperature and leaf wetness duration.
Information processing by biochemical networks: a dynamic approach
Authors: Bowsher Clive G.
Published: August 2010

Understanding how information is encoded and transferred by biochemical networks is of fundamental importance in cellular and systems biology. This requires analysis of the relationships between the stochastic trajectories of the constituent molecular (or submolecular) species that comprise the network. We describe how to identify conditional independences between the trajectories or time courses of groups of species. These are robust network properties that provide important insight into how information is processed. An entire network can then be decomposed exactly into modules on informational grounds. In the context of signalling networks with multiple inputs, the approach identifies the routes and species involved in sequential information processing between input and output modules. An algorithm is developed which allows automated identification of decompositions for large networks and visualization using a tree that encodes the conditional independences. Only stoichiometric information is used and neither simulations nor knowledge of rate parameters are required. A bespoke version of the algorithm for signalling networks identifies the routes of sequential encoding between inputs and outputs, visualized as paths in the tree. Application to the toll-like receptor signalling network reveals that inputs can be informative in ways unanticipated by steady-state analyses, that the information processing structure is not well described as a bow tie, and that encoding for the interferon response is unusually sparse compared with other outputs of this innate immune system.