bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing spatial and environmental drivers of phylogenetic structure in Brazilian Araucaria forests
Authors: Duarte Leandro D. S. , Prieto Pablo V. , Pillar Valério D.
Published: February 2012

Evidence of phylogenetic conservatism in plant ecological traits has accumulated over the past few years, suggesting an interplay between the distribution of phylogenetic clades and major environmental gradients. Nonetheless, determining what environmental factors underlie the distribution of phylogenetic lineages remains a challenge because environmental factors are correlated with spatial gradients where the latter might indicate some degree of dispersal limitation in phylogenetic pools. We analyzed the phylogenetic structure of plant assemblages across the Brazilian Araucaria forests and assessed how phylogenetic structure responds to environmental and spatial gradients. We compiled data on plant occurrence in 45 plots across the Araucaria forest biome. The phylogenetic structure of the plots was characterized using phylogenetic fuzzy‐weighting followed by principal coordinates of phylogenetic structure (PCPS). We used distance‐based redundancy analysis (db‐RDA) to analyze the relationships between phylogenetic clades and environmental and spatial factors. Variation partitioning showed that the phylogenetic structure of Brazilian Araucaria forests was better explained by environment factors (altitude and annual mean temperature) than by space. Yet, spatially‐structured environmental variation explained about one‐third of total variation in the phylogenetic structure. Thus, the influence of spatial filters on the phylogenetic structure was more related to environmental gradients across the Brazilian Araucaria forest biome than to dispersal limitation of phylogenetic lineages. Furthermore, the influence of explanatory factors on the phylogenetic structure was concentrated in few nodes, the one splitting tree ferns from seed plants, and a second splitting malvids from other eurosids. Assessing the functional links between species distribution patterns and environmental gradients is not an easy task when we have to deal with large species pools. Identifying major phylogenetic gradients across an environmental and/or geographical range of interest can represent a first step towards a better understanding of general assembly processes in ecological communities.
Habitat change and the scale of habitat selection: shifting gradients used by coexisting Arctic rodents
Authors: Morris Douglas W. , Dupuch Angélique
Published: February 2012

The conservation and understanding of biodiversity requires development and testing of models that illustrate how climate change and other anthropogenic effects alter habitat and its selection at different spatial scales. Models of fitness along a habitat gradient illustrate the connection between fine‐scale variation in fitness and the selection of habitat as discontinuous patches in the landscape. According to these models, climate change can increase fitness values of static habitats, shift the fitness value of habitat patches along underlying gradients of habitat quality, or alter both fitness and habitat quality. It should be possible to differentiate amongst these scenarios by associating differences in the abundance and distribution of species with metrics of habitat that document the gradient while controlling for changes in density at larger scales of analysis. Comparisons of habitat selection by two species of lemmings, over an interval of 15 years, are consistent with the theory. The pattern of habitat selection at the scale of wet versus dry tundra habitats changed through time. The change in habitat selection was reflected by different, but nevertheless density‐dependent, patterns of association with the structure and composition of habitat. Abundant collared lemmings abandoned stations where altered habitat characteristics caused a shift to new locations along the wet‐to‐dry gradient. The confirmation of scale‐dependent theory provides new insights into how one might begin to forecast future habitat selection under different scenarios of climate and habitat change.
Sic1 as a timer of Clb cyclin waves in the yeast cell cycle – design principle of not just an inhibitor
Authors: Barberis Matteo
Published: February 2012

Cellular systems biology aims to uncover design principles that describe the properties of biological networks through interaction of their components in space and time. The cell cycle is a complex system regulated by molecules that are integrated into functional modules to ensure genome integrity and faithful cell division. In budding yeast, cyclin‐dependent kinases (Cdk1/Clb) drive cell cycle progression, being activated and inactivated in a precise temporal sequence. In this module, which we refer to as the ‘Clb module’, different Cdk1/Clb complexes are regulated to generate waves of Clb activity, a functional property of cell cycle control. The inhibitor Sic1 plays a critical role in the Clb module by binding to and blocking Cdk1/Clb activity, ultimately setting the timing of DNA replication and mitosis. Fifteen years of research subsequent to the identification of Sic1 have lead to the development of an integrative approach that addresses its role in regulating the Clb module. Sic1 is an intrinsically disordered protein and achieves its inhibitory function by cooperative binding, where different structural regions stretch on the Cdk1/Clb surface. Moreover, Sic1 promotes S phase entry, facilitating Cdk1/Clb5 nuclear transport, and therefore revealing a double function of inhibitor/activator that rationalizes a mechanism to prevent precocious DNA replication. Interestingly, the investigation of Clb temporal dynamics by mathematical modelling and experimental validation provides evidence that Sic1 acts as a timer to coordinate oscillations of Clb cyclin waves. Here we review these findings, focusing on the design principle underlying the Clb module, which highlights the role of Sic1 in regulating phase‐specific Cdk1/Clb activities.
The effect of cost surface parameterization on landscape resistance estimates
Authors: KOEN ERIN L. , BOWMAN JEFF , WALPOLE AARON A.
Published: February 2012

A cost or resistance surface is a representation of a landscape’s permeability to animal movement or gene flow and is a tool for measuring functional connectivity in landscape ecology and genetics studies. Parameterizing cost surfaces by assigning weights to different landscape elements has been challenging however, because true costs are rarely known; thus, expert opinion is often used to derive relative weights. Assigning weights would be made easier if the sensitivity of different landscape resistance estimates to relative costs was known. We carried out a sensitivity analysis of three methods to parameterize a cost surface and two models of landscape permeability: least cost path and effective resistance. We found two qualitatively different responses to varying cost weights: linear and asymptotic changes. The most sensitive models (i.e. those leading to linear change) were accumulated least cost and effective resistance estimates on a surface coded as resistance (i.e. where high‐quality elements were held constant at a low‐value, and low‐quality elements were varied at higher values). All other cost surface scenarios led to asymptotic change. Developing a cost surface that produces a linear response of landscape resistance estimates to cost weight variation will improve the accuracy of functional connectivity estimates, especially when cost weights are selected through statistical model fitting procedures. On the other hand, for studies where cost weights are unknown and model selection is not being used, methods where resistance estimates vary asymptotically with cost weights may be more appropriate, because of their relative insensitivity to parameterization.
Conducting a meta‐analysis: basics and good practices
Authors: Cheung Mike W.‐L. , Ho Roger C. M. , Lim Yonghao , Mak Anselm
Published: February 2012

Meta‐analysis is a statistical method to compare and combine effect sizes from a pool of relevant empirical studies. It is now a standard approach to synthesize research findings in many disciplines, including medical and healthcare research. This paper is the third paper of a mini‐series introducing systematic review and meta‐analysis. First, common effect sizes used in meta‐analysis are presented. Fixed‐, random‐ and mixed‐effects models are then introduced. Next, a real data set from a published meta‐analysis will be used to illustrate the procedures and interpretations. Last, software packages that may be used to conduct meta‐analyses will be highlighted.
Emotional Intelligence Relates to Well‐Being: Evidence from the Situational Judgment Test of Emotional Management
Authors: Burrus Jeremy , Betancourt Anthony , Holtzman Steven , Minsky Jennifer , MacCann Carolyn , Roberts Richard D.
Published: February 2012

Background: This research was conducted to examine whether people high in emotional intelligence (EI) have greater well‐being than people low in EI. Method: The Situational Test of Emotion Management, Scales of Psychological Well‐being, and Day Reconstruction Method were completed by 131 college students. Results: Responses to the Situational Test of Emotion Management were strongly related to eudaimonic well‐being as measured by responses on the Scales of Psychological Well‐being (r = .54). Furthermore, the ability to manage emotions was related to hedonic well‐being, correlating with both the frequency of experienced positive affect and the frequency of experienced negative affect, as measured by the Day Reconstruction Method. Conclusion: Two aspects of these results suggest a relationship between EI and well‐being. First, the observed relationship between ability EI and psychological well‐being is the largest reported in the literature to date. Second, this study is the first use of the Day Reconstruction Method to examine the relationship between well‐being and EI. Results are discussed in terms of the potential for training emotion management to enhance well‐being. Methodological advances for future research are also suggested.
Experimental Investigation on Flow Regime of Steam-Water Two-Phase Flow in a Pseudo-Pebble-Bed
Authors: Wang Xiong , Zhang Zhen , Yan Xiao , Xiao Zejun , Chen Bingde
Published: February 2012

In the concept of BWR-PB with a relatively low power level, the core region is filled with a large number of coated particles, which are directly cooled by boiling light water. It’s significant to understand the two-phase flow characteristics in such a complicated pebble-bed structure. A visualization experiment was carried out to investigate the flow phenomena of steam-water two-phase flow in a pseudo-three-dimensional pebble bed using a high-speed video camera. The pebble bed in the experiment was constructed of hundreds of glass beads and a specially designed stainless heating plate, which was used to simulate the heat-generation of solid particles. Based on our observation, five typical flow regimes were identified to distinguish different phase distribution characteristics: bubbly flow, bubbly-slug flow, slug flow, slug-annular flow and pure annular flow. System pressure, mass flow rate and inlet subcooling were considered as the key influence factors for flow regime transition in the experiment. A flow pattern map for low pressure and low inlet subcooling condition was obtained from the experimental data.
Role of Residual Stresses and Strains Fields Generated by Heat Treatments on the Hydrogen Embrittlement of a Nuclear Reactor Pressure Vessel
Authors: Toribio J. , Vergara D. , Lorenzo M. , Marti´n J. J.
Published: February 2012

The wall of a nuclear reactor pressure vessel can undergo a reduction of its mechanical properties due to the presence of hydrogen, a process known as hydrogen embrittlement (HE). A numerical model of hydrogen diffusion assisted by stress and strain was used in this paper to evaluate the HE process in the wall of a real nuclear reactor pressure vessel, formed by a bimaterial (stainless steel and low carbon steel). In this sense, a quantitative analysis was carried out of the influence of tempering heat treatments conditions applied to these two steels on hydrogen concentration accumulated in the nuclear reactor vessel during its operation time. To this end, the most relevant parameters of these heat treatments were considered: (i) tempering temperature and (ii) tempering time.
Computational Intelligence as a Tool for Small Modular Reactors
Authors: Manic Milos , Sabharwall Piyush
Published: February 2012

Computational intelligence techniques (CITs) traditionally consist of artificial neural networks (ANNs), fuzzy systems and genetic algorithms. This article overviews diverse implementations of ANNs, which are the most prominent in nuclear engineering problems, especially for small modular reactors (SMRs). Advanced computational intelligence-based tools will allow data to be transformation into knowledge, thus improving understanding, predictability (can be seen from the two case studies for thermal-hydraulic prediction), sustainability, and performance of SMRs with real time analysis and monitoring.
Development of Aluminum Alloy Coating for Advanced Nuclear Systems Using Lead Alloys
Authors: Kurata Yuji , Yokota Hitoshi , Suzuki Tetsuya
Published: February 2012

Small and medium reactors using lead alloys as coolant are one of the promising reactor concepts with improved safety because of their thermal-physical and chemical properties. This paper focuses on development of Al-alloy coating for nuclear systems using liquid lead-bismuth eutectic (LBE). Since corrosion attack becomes severe against structural steels at high temperatures in liquid LBE, it is necessary to improve corrosion resistance of steels. An Al-alloy coating method using Al, Ti and Fe powders, and laser beam heating has been developed. Main defects formed in an Al-powder-alloy coating process are surface defects and cracks. Conditions required to avoid these defects are employment of the laser beam scanning rate of 20 mm/min and adjustment of the Al concentration in the coating layer. According to results of the corrosion tests at 550°C in liquid LBE, the Al-alloy coating layers on 316SS protect severe corrosion attack such as grain boundary corrosion and LBE penetration observed in 316SS without coating. The good corrosion resistance of the Al-alloy coating is based on the thin Al-oxide film which can be regenerated in liquid LBE. From the viewpoints of the soundness of produced Al-powder-alloy coating layers and preservation of their corrosion resistance, it is estimated that the range of the adequate Al concentration in the coating layer is from 4 to 12 wt%.
Obstacles to Overcome by Small Modular Reactors (SMRs)
Authors: Levy Salomon
Published: February 2012

The development of and support for small modular nuclear power plants (NPPs) is gaining strong momentum in USA. The reasons are that they could require reduced financing and shortened construction schedule. Also, they could address the reduced size need for electricity in some USA locations and, in particular, in developing foreign countries. However, the prevailing enthusiasm needs to be moderated until several potential obstacles are overcome. There are three principal USA obstacles: (1) the successful licensing and certification of the SMRs by the Nuclear Regulatory Commission (NRC) to confirm their safety; (2) SMRs ability to demonstrate that they can compete financially against less costly modular natural gas power plants or the limited purchase of electricity from new large light water reactors (LWRs); and (3) the need to work into the prevailing fuel cycle while not deteriorating spent fuel disposal or increasing proliferation. Clearly, Babcock & Wilcox’s and Nu Scale Power’s SMRs have the earliest chance for success because they would rely upon the present LWR regulatory and fuel cycle experience. Their main obstacle will be demonstrated costs from prototype plants and the willingness to accept fixed turnkey contracts for additional units. The more visionary SMRs such as GE-Hitachi PRISM or the Hyperion Power Generation smaller liquid metal closed fuel cycle reactors will have to overcome more difficult and lengthy regulatory assessments. Also, a complete fuel cycle infrastructure will need to be developed. Penetration of developing foreign countries will be the most difficult because it will demand the development and establishment of a nuclear safety infrastructure in those countries. The International Atomic Energy Agency (IAEA NG-G-31) has detailed the numerous actions and large time schedule and efforts to achieve an adequate safety culture. Also, several export licenses and monetary loans will be required. Furthermore, it will be necessary to overcome the lack of insurance for severe accidents and the anticipated USA refusal to accept domestic disposal of foreign High Level Waste (HLW). This means that government owned suppliers such as Russia have definite advantages over the USA private suppliers because of their willingness to provide loans and handling HLW. This paper first summarizes the power history growth of USA reactors and the recent momentum developed for USA SMRs; it is followed by available brief descriptions of USA LWR SMRs and some of their potential obstacles; more advanced USA SMRs designs and their potential difficulties come next; foreign applications are covered last and they are followed by a Conclusions section.
An Overview of the Westinghouse Small Modular Reactor
Authors: Fetterman Robert J. , Harkness Alexander W. , Smith Matthew C. , Taylor Creed
Published: February 2012

The Westinghouse Small Modular Reactor (SMR) incorporates an integral pressurized water reactor (iPWR) design in which all components associated with the nuclear steam supply system are housed within one pressure vessel. The Westinghouse SMR design also utilizes many of the key features from the AP1000® plant, including passive safety systems. The Westinghouse SMR will be fueled by a derivative of the successful 17×17 Robust Fuel Assembly (RFA) product. An 89 assembly core with an active height of 8 feet will provide a 24 month operating cycle with a power output of 800 MWt. Derived from the AP1000 plant and adapted to operate inside the reactor pressure vessel, 37 control rod drive mechanisms provide reactor shutdown and reactivity control capabilities. Eight seal less pumps provide a nominal reactor coolant flow of 100,000 gallons per minute. An innovative evolution of a straight tube steam generator produces a saturated mixture that is delivered to a steam separating drum located outside of the containment vessel. The steam generator along with the integral pressurizer is attached to the reactor vessel with a single closure flange located near the center of gravity of the reactor assembly and is designed to be removed during refueling operations. Like the AP1000 plant, the Westinghouse SMR relies on the natural forces of gravity and natural circulation to provide core and containment cooling during accident conditions. The passive cooling systems provide sufficient heat removal for seven days without the need for offsite AC power sources. The Westinghouse SMR also includes traditional active components such as diesel generators and pumps; however these components are not required for the safe shutdown of the plant. At a diameter of 32 feet, approximately 25 of the Westinghouse SMR containment vessels can fit within the envelope of the AP1000 containment building. This compact containment will be completely submerged in water during power operation providing a heat sink for postulated accidents. For protection against external threats, the containment vessel and plant safety systems are located below ground level. At approximately one fifth the net electrical output of the AP1000 plant, the Westinghouse SMR is designed to address infrastructure challenges associated with replacing America’s aging fossil fuel plants by providing a safe, clean and reliable energy source. The challenges associated with economies of scale are offset with a compact and simplified plant design, rail shippable components and modular construction.
FCM Fuel Development for SMR Applications
Authors: Terrani Kurt A. , Snead Lance L. , Gehin Jess C.
Published: February 2012

Fully ceramic microencapsulated (FCM) fuels are identified as suitable fuel forms for development and deployment of SMR technologies. High thermal conductivity of the composite fuel coupled with its exceptional radiation and environmental stability enable monolithic compact cores for SMR applications. Meanwhile the built-in redundancy of multiple layers for fission-product retention alleviates the need for structurally demanding pressure vessels and containment buildings. All of the above will enable the reactor designer to achieve a compact and passively safe SMR through utilization of a flexible fuel technology that is currently under active development.
Safety Characteristics of GTHTR and Safety Demonstration Test Program Using HTTR
Authors: Kunitomi Kazuhiko , Yan Xing , Ohashi Hirofumi
Published: February 2012

JAEA has long been designing series of Gas Turbine High Temperature Reactor (GTHTR) based on advanced HTGR technologies developed through the construction and operation of the High Temperature Engineering Test Reactor (HTTR). Inherent safety characteristics of the GTHTR keep the reactor safe and stable condition with no risk of core meltdown even in the worst case accidents such as a primary pipe rupture, station blackout, etc. In addition to design studies of the GTHTR, JAEA conducted or will conduct several safety demonstration tests using the HTTR to examine the reactor transient behavior during the worst case accident and to validate and verify analytical tools of the design for an High Temperature Gas-cooled Reactor (HTGR). These tests are not only valuable to develop design tools, but also are effective to convince safety authority and average people that the GTHTR is a safe and reliable system to be acceptable after the Higashi-Nihon earthquake and to be deployed in 2020s. This paper describes safety design of the GTHTR and a safety demonstration test program of the HTTR. Also, it presents the results of safety evaluation during a primary pipe rupture and the following station blackout. The evaluation results revealed that the maximum fuel temperature is kept under the allowable limit and fission products are safety contained in the fuel due to salient safety characteristics.
Global Structural Response of an SMR Reactor Subjected to an Aircraft Impact
Authors: Lo Frano Rosa , Forasassi Giuseppe
Published: February 2012

Although a 11 September 2001-style vicious attack on a nuclear power plant is considered as ‘beyond design basis’ event, an appropriate design of the nuclear facilities, with features and functional capabilities, is of meaningful importance to demonstrate that the reactor containment could safely withstand the impact of a large commercial aircraft without any radioactive release. This paper deals with the evaluation of the global structural response and of the vulnerability of a reactor building subjected to a deliberate commercial aircraft impact in the assumption of an attack from multiple entry directions. In this framework, separately from penetration and fire, the ‘shock’ loadings due to the progressive aircraft crashing on the power plant buildings were evaluated, taking into account that even if such penetration occurred, together with some concrete crushing and bent steel rebars, it very probably would not reach the reactor vessel. To the purpose a rather refined numerical methodology was employed and three-dimensional models (FEM approach) of a SMR reactor building and possible realistic, even if simplified, aircraft structures were set up and used in the performed analyses, taking also into account a suitable materials behaviour and constitutive laws. The analysis was performed increasing the severity of the crash scenario, assuming that the during the impact the aircraft transfers the full impact energy of the crash to the structure being struck. The obtained results were analysed to check the additional safety margin of the reactor containment and the fuel pool.
Diagnostics and Prognostics for Safe and Secure Operation of Small Modular Reactors
Authors: Ramuhalli Pradeep , Meyer Ryan , Bond Leonard
Published: February 2012

Sustainable nuclear power to promote energy security is a key national energy priority. The development of small modular reactors (SMRs) is expected to provide the United States with an economically viable energy option that supports this priority. Small modular reactors (SMR) are typically defined as nuclear reactors that have electrical output less than about 300 MWe [1]. In recent years, SMRs are seeing renewed interest due to several factors: 1. Economy of scale. Modular or grid-appropriate reactors can be used to expand power plants to meet needs [2], resulting in potential economies of scale that larger reactors cannot easily provide. 2. Ease of fabrication/construction. The forging capabilities for the smaller reactor pressure vessels and piping necessary for SMRs are more readily available. This also enables potentially faster and easier construction of SMRs. 3. Usually grid-following. SMRs can ramp up or down production of electricity as needed as the modular design allows for better control of grid-appropriate reactors. 4. Improved safety characteristics. Most current SMR designs rely on passive rather than active safety systems.
In Vitro
Activity of the New Fluoroketolide Solithromycin (CEM-101) against a Large Collection of Clinical Neisseria gonorrhoeae Isolates and International Reference Strains, Including Those with High-Level Antimicrobial Resistance: Potential Treatment Option for Gonorrhea?
Authors: Golparian Daniel , Fernandes Prabhavathi , Ohnishi Makoto , Jensen Jörgen S. , Unemo Magnus
Published: February 2012

Gonorrhea may become untreatable, and new treatment options are essential. We investigated the
in vitro
activity of the first fluoroketolide, solithromycin. Clinical
Neisseria gonorrhoeae
isolates and reference strains (
n
= 246), including the two extensively drug-resistant strains H041 and F89 and additional isolates with clinical cephalosporin resistance and multidrug resistance, were examined. The activity of solithromycin was mainly superior to that of other antimicrobials (
n
= 10) currently or previously recommended for gonorrhea treatment. Solithromycin might be an effective treatment option for gonorrhea.
Molecular Characterization of Extended-Spectrum-β-Lactamase-Producing and Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli Isolated from Stray Dogs in South Korea
Authors: Tamang Migma Dorji , Nam Hyang-Mi , Jang Geum-Chan , Kim Su-Ran , Chae Myung Hwa , Jung Suk-Chan , Byun Jae-Won , Park Yong Ho , Lim Suk-Kyung
Published: February 2012

A total of 47 extended-spectrum-cephalosporin-resistant
Escherichia coli
strains isolated from stray dogs in 2006 and 2007 in the Republic of Korea were investigated using molecular methods. Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase phenotypes were identified in 12 and 23
E. coli
isolates, respectively. All 12 ESBL-producing isolates carried
bla
CTX-M
genes. The most common CTX-M types were CTX-M-14 (
n
= 5) and CTX-M-24 (
n
= 3). Isolates producing CTX-M-3, CTX-M-55, CTX-M-27, and CTX-M-65 were also identified. Twenty-one of 23 AmpC β-lactamase-producing isolates were found to carry
bla
CMY-2
genes. TEM-1 was associated with CTX-M and CMY-2 β-lactamases in 4 and 15 isolates, respectively. In addition to
bla
TEM-1
, two isolates carried
bla
DHA-1
, and one of them cocarried
bla
CMY-2
. Both CTX-M and CMY-2 genes were located on large (40 to 170 kb) conjugative plasmids that contained the insertion sequence IS
Ecp1
upstream of the
bla
genes. Only in the case of CTX-M genes was there an IS
903
sequence downstream of the gene. The spread of ESBLs and AmpC β-lactamases occurred via both horizontal gene transfer, accounting for much of the CTX-M gene dissemination, and clonal spread, accounting for CMY-2 gene dissemination. The horizontal dissemination of
bla
CTX-M
and
bla
CMY-2
genes was mediated by IncF and IncI1-Iγ plasmids, respectively. The clonal spread of
bla
CMY-2
was driven mainly by
E. coli
strains of virulent phylogroup D lineage ST648. To our knowledge, this is the first report of
bla
DHA-1
in
E. coli
strains isolated from companion animals. This study also represents the first report of CMY-2 β-lactamase-producing
E. coli
isolates from dogs in the Republic of Korea.
The Staphylococcus aureus Alpha-Toxin Perturbs the Barrier Function in Caco-2 Epithelial Cell Monolayers by Altering Junctional Integrity
Authors: Kwak Young-Keun , Vikström Elena , Magnusson Karl-Eric , Vécsey-Semjén Beatrix , Colque-Navarro Patricia , Möllby Roland
Published: February 2012

Increased microvascular permeability is a hallmark of sepsis and septic shock. Intestinal mucosal dysfunction may allow translocation of bacteria and their products, thereby promoting sepsis and inflammation. Although
Staphylococcus aureus
alpha-toxin significantly contributes to sepsis and perturbs the endothelial barrier function, little is known about possible effects of
S. aureus
alpha-toxin on human epithelial barrier functions. We hypothesize that
S. aureus
alpha-toxin in the blood can impair the intestinal epithelial barrier and thereby facilitate the translocation of luminal bacteria into the blood, which may in turn aggravate a septic condition. Here, we showed that staphylococcal alpha-toxin disrupts the barrier integrity of human intestinal epithelial Caco-2 cells as evidenced by decreased transepithelial electrical resistance (TER) and reduced cellular levels of junctional proteins, such as ZO-1, ZO-3, and E-cadherin. The Caco-2 cells also responded to alpha-toxin with an elevated cytosolic calcium ion concentration ([Ca
2+
]
i
), elicited primarily by calcium influx from the extracellular environment, as well as with a significant reduction in TER, which was modulated by intracellular calcium chelation. Moreover, a significantly larger reduction in TER and amounts of the junctional proteins,
viz
., ZO-3 and occludin, was achieved by basolateral than by apical application of the alpha-toxin. These experimental findings thus support the hypothesis that free staphylococcal alpha-toxin in the bloodstream may cause intestinal epithelial barrier dysfunction and further aggravate the septic condition by promoting the release of intestinal bacteria into the underlying tissues and the blood.
Different Patterns of Toll-Like Receptor 2 Polymorphisms in Populations of Various Ethnic and Geographic Origins
Authors: Ioana M. , Ferwerda B. , Plantinga T. S. , Stappers M. , Oosting M. , McCall M. , Cimpoeru A. , Burada F. , Panduru N. , Sauerwein R. , Doumbo O. , van der Meer J. W. M. , van Crevel R. , Joosten L. A. B. , Netea M. G.
Published: February 2012

Upon the invasion of the host by microorganisms, innate immunity is triggered through pathogen recognition by pattern recognition receptors (PRRs). Toll-like receptors (TLRs) are the best-studied class of PRRs, and they recognize specific pathogen-associated molecular patterns (PAMPs) from various microorganisms. A large number of studies have shown that genetic variation in TLRs may influence susceptibility to infections. We assessed the genetic variation of
TLR2
, which encodes one of the most important TLRs, in various populations around the globe and correlated it with changes in the function of the molecule. The three best-known nonsynonymous
TLR2
polymorphisms (1892C>A, 2029C>T, and 2258G>A) were assessed in different populations from the main continental masses: Romanians, Vlax-Roma, Dutch (European populations), Han Chinese (East Asia), Dogon, Fulani (Africa), and Trio Indians (America). The 2029C>T polymorphism was absent in both European and non-European populations, with the exception of the Vlax-Roma, suggesting that this polymorphism most likely arose in Indo-Aryan people after migration into South Asia. The 1892C>A polymorphism that was found exclusively in European populations, but not in Asian, African, or American volunteers, probably occurred in proto-Indo-Europeans. Interestingly, 2258G>A was present only in Europeans, including Vlax-Roma, but at a very low frequency. The differential pattern of the
TLR2
polymorphisms in various populations may explain some of the differences in susceptibility to infections between these populations.
Regulation of Subtilase Cytotoxin-Induced Cell Death by an RNA-Dependent Protein Kinase-Like Endoplasmic Reticulum Kinase-Dependent Proteasome Pathway in HeLa Cells
Authors: Yahiro Kinnosuke , Tsutsuki Hiroyasu , Ogura Kohei , Nagasawa Sayaka , Moss Joel , Noda Masatoshi
Published: February 2012

Shiga-toxigenic
Escherichia coli
(STEC) produces subtilase cytotoxin (SubAB), which cleaves the molecular chaperone BiP in the endoplasmic reticulum (ER), leading to an ER stress response and then activation of apoptotic signaling pathways. Here, we show that an early event in SubAB-induced apoptosis in HeLa cells is mediated by RNA-dependent protein kinase (PKR)-like ER kinase (PERK), not activating transcription factor 6 (ATF6) or inositol-requiring enzyme 1(Ire1), two other ER stress sensors. PERK knockdown suppressed SubAB-induced eIF2α phosphorylation, activating transcription factor 4 (ATF4) expression, caspase activation, and cytotoxicity. Knockdown of eIF2α by small interfering RNA (siRNA) or inhibition of eIF2α dephosphorylation by Sal003 enhanced SubAB-induced caspase activation. Treatment with proteasome inhibitors (i.e., MG132 and lactacystin), but not a general caspase inhibitor (Z-VAD) or a lysosome inhibitor (chloroquine), suppressed SubAB-induced caspase activation and poly(ADP-ribose) polymerase (PARP) cleavage, suggesting that the ubiquitin-proteasome system controls events leading to caspase activation, i.e., Bax/Bak conformational changes, followed by cytochrome
c
release from mitochondria. Levels of ubiquitinated proteins in HeLa cells were significantly decreased by SubAB treatment. Further, in an early event, some antiapoptotic proteins, which normally turn over rapidly, have their synthesis inhibited, and show enhanced degradation via the proteasome, resulting in apoptosis. In PERK knockdown cells, SubAB-induced loss of ubiquitinated proteins was inhibited. Thus, SubAB-induced ER stress is caused by BiP cleavage, leading to PERK activation, not by accumulation of ubiquitinated proteins, which undergo PERK-dependent degradation via the ubiquitin-proteasome system.
A Glycosylphosphatidylinositol Anchor Is Required for Membrane Localization but Dispensable for Cell Wall Association of Chitin Deacetylase 2 in Cryptococcus neoformans
Authors: Gilbert Nicole M. , Baker Lorina G. , Specht Charles A. , Lodge Jennifer K.
Published: February 2012

Cell wall proteins (CWPs) mediate important cellular processes in fungi, including adhesion, invasion, biofilm formation, and flocculation. The current model of fungal cell wall organization includes a major class of CWPs covalently bound to β-1,6-glucan via a remnant of a glycosylphosphatidylinositol (GPI) anchor. This model was established by studies of ascomycetes more than a decade ago, and relatively little work has been done with other fungi, although the presumption has been that proteins identified in the cell wall which contain a predicted GPI anchor are covalently linked to cell wall glucans. The pathogenic basidiomycete
Cryptococcus neoformans
encodes >50 putatively GPI-anchored proteins, some of which have been identified in the cell wall. One of these proteins is chitin deacetylase 2 (Cda2), an enzyme responsible for converting chitin to chitosan, a cell wall polymer recently established as a virulence factor for
C. neoformans
infection of mammalian hosts. Using a combination of biochemistry, molecular biology, and genetics, we show that Cda2 is GPI anchored to membranes but noncovalently associated with the cell wall by means independent of both its GPI anchor and β-1,6-glucan. We also show that Cda2 produces chitosan when localized to the plasma membrane, but association with the cell wall is not essential for this process, thereby providing insight into the mechanism of chitosan biosynthesis. These results increase our understanding of the surface of
C. neoformans
and provide models of cell walls likely applicable to other undercharacterized basidiomycete pathogenic fungi.

IMPORTANCE
The surface of a pathogenic microbe is a major interface with its host. In fungi, the outer surface consists of a complex matrix known as the cell wall, which includes polysaccharides, proteins, and other molecules. The mammalian host recognizes many of these surface molecules and mounts appropriate responses to combat the microbial infection.
Cryptococcus neoformans
is a serious fungal pathogen that kills over 600,000 people annually. It converts most of its chitin, a cell wall polysaccharide, to chitosan, which is necessary for virulence. Chitin deacetylase enzymes have been identified in the cell wall, and our studies were undertaken to understand how the deacetylase is linked to the wall and where it has activity. Our results have implications for the current model of chitosan biosynthesis and further challenge the paradigm of covalent linkages between cell wall proteins and polysaccharides through a lipid modification of the protein.
A DIRECT EVALUATION OF MONO-COMPONENTS BY INSTANTANEOUS FREQUENCY
Authors: NIU KAIFU , PENG LIZHONG , PENG SILONG
Published: February 2012

We present a new criterion based on instantaneous frequency (IF) to distinguish mono-components (MCs). We first notice that the "offset of local extremum" caused by low-frequency envelope is often significant on envelope extraction, which determines the calculation of IF for MCs. We estimate the upper and lower bounds of the offset for a general family of signals. Conducted by the offset estimation, we propose a direct and effective algorithm to calculate IF. Our algorithm, which is based on an empirical pursuit of knots and natural splines, provides an accurate estimation of the envelope and derives a well-behaved IF. A theoretical explanation for the good approximation of proposed envelope is also stated. Experiment results show the fast convergence of our algorithm, which leads to a reliable IF and local mean to provide a flexible criterion for MC classification. We emphasize that it is important to pursue a certain balance among different requirements to define MC depending on specific applications.
Hydrogeological insights from groundwater level hydrographs in SE Ireland
Authors: Tedd K. M. , Misstear B. D. R. , Coxon C. , Daly D. , Hunter Williams N. H.
Published: February 2012

Analysis of groundwater level records from Ireland’s South Eastern River Basin District (SERBD) allowed fundamental information about the nature of bedrock and gravel aquifers to be investigated. The hydrogeological setting of a monitoring point (with respect to, for example, recharge area, discharge area or proximity to a river) is the dominant factor influencing hydrograph character in bedrock aquifers, with aquifer type and subsoil properties producing secondary effects. Analysis of seasonal groundwater levels showed that the fractured bedrock aquifers recharge more quickly and typically have a longer recession period than gravel aquifers. The calculated recession periods for bedrock aquifers are longer than previous estimates for similar aquifers. Hydrograph analysis identified a number of notable phenomena including a gravel aquifer’s interaction with surface water and evidence of rejected recharge. Short-term groundwater level fluctuations caused by global seismic events, recorded via chart recorders, are discussed. Specific yield values were calculated, for a number of settings, from annual average groundwater level variations. The values supported estimates from previous research on similar aquifers. An analysis to investigate if any impacts of climate change were evident showed no consistent change in the timing of groundwater level minima or maxima.
Assessing the potential for future first-time slope failures to impact the oil and gas pipeline corridor through the Makarov Mountains, Sakhalin Island, Russia
Authors: Hearn G. , Wise D. , Hart A. , Morgan C. , O’Donnell N.
Published: February 2012

The Sakhalin Energy Investment Company Ltd (SEIC) Sakhalin II Phase 2 oil and gas pipeline corridor is 782 km in length, and extends from landfall sites in the north of the island to a liquefied natural gas plant and oil export terminal in the south. For
c
. 120 km this alignment crosses the Makarov Mountains, an approximately north–south-orientated grouping of ridges and valleys formed in Cretaceous mudstones, Tertiary siltstones, sandstones, coal measures, lavas and tuffs. Situated on the NW Pacific rim, the island is prone to seismic activity, and the design and construction of the pipelines’ alignment has had to take into consideration a number of existing landslides (more than 400 in total). Additionally, the continuing seismic hazard, combined with slope toe erosion by rivers and high groundwater tables brought about by spring snow melt and summer rains, creates a potential for first-time landslides to occur during the 50 year operational period of the pipelines. To assess where such failures might take place a study was undertaken that combined back-analysis and sensitivity analysis, landslide susceptibility analysis (including factor analysis) and qualitative evaluation. The qualitative evaluation allowed a judgement-based assessment to be included in the identification and prioritization of potential future first-time failure areas. Ground truthing was then undertaken in the areas of highest susceptibility, and generally supported the findings of the analysis. In
c
. 50% of these cases the potential for landslide initiation was considered to be sufficiently high to warrant intervention, in terms of ground investigation, slope movement and groundwater monitoring, or engineering mitigation. The study highlights the uncertainties that exist when undertaking exercises such as these where geotechnical information is insufficient to carry out rigorous modelling and where broad geological and geographical assessments have to be made in order to yield the required outputs.
Active learning with semi-automatic annotation for extractive speech summarization
Authors: Zhang Justin Jian , Fung Pascale
Published: February 2012

We propose using active learning for extractive speech summarization in order to reduce human effort in generating reference summaries. Active learning chooses a selective set of samples to be labeled. We propose a combination of informativeness and representativeness criteria for selection. We further propose a semi-automatic method to generate reference summaries for presentation speech by using Relaxed Dynamic Time Warping (RDTW) alignment between presentation speech and its accompanied slides. Our summarization results show that the amount of labeled data needed for a given summarization accuracy can be reduced by more than 23% compared to random sampling.
MobiCon
Authors: Lee Youngki , Iyengar S. S. , Min Chulhong , Ju Younghyun , Kang Seungwoo , Park Taiwoo , Lee Jinwon , Rhee Yunseok , Song Junehwa
Published: February 2012

User context is defined by data generated through everyday physical activity in sensor-rich, resource-limited mobile environments.
A comparative study of cyberattacks
Authors: Kim Seung Hyun , Wang Qiu-Hong , Ullrich Johannes B.
Published: February 2012

Attackers base themselves in countries of convenience, virtually.
A taste of Capsicum
Authors: Watson Robert N. M. , Anderson Jonathan , Laurie Ben , Kennaway Kris
Published: February 2012

Capsicum is a lightweight operating system (OS) capability and sandbox framework planned for inclusion in FreeBSD 9. Capsicum extends, rather than replaces, UNIX APIs, providing new kernel primitives (sandboxed
capability mode
and
capabilities
) and a userspace sandbox API. These tools support decomposition of monolithic UNIX applications into compartmentalized logical applications, an increasingly common goal that is supported poorly by existing OS access control primitives. We demonstrate our approach by adapting core FreeBSD utilities and Google's Chromium Web browser to use Capsicum primitives, and compare the complexity and robustness of Capsicum with other sandboxing techniques.
A cell-autonomous role for the glucocorticoid receptor in skeletal muscle atrophy induced by systemic glucocorticoid exposure
Authors: Watson Monica L. , Baehr Leslie M. , Reichardt Holger M. , Tuckermann Jan P. , Bodine Sue C. , Furlow J. David
Published: February 2012

Glucocorticoids (GCs) are important regulators of skeletal muscle mass, and prolonged exposure will induce significant muscle atrophy. To better understand the mechanism of skeletal muscle atrophy induced by elevated GC levels, we examined three different models: exogenous synthetic GC treatment [dexamethasone (DEX)], nutritional deprivation, and denervation. Specifically, we tested the direct contribution of the glucocorticoid receptor (GR) in skeletal muscle atrophy by creating a muscle-specific GR-knockout mouse line (MGRe3KO) using Cre-lox technology. In MGRe3KO mice, we found that the GR is essential for muscle atrophy in response to high-dose DEX treatment. In addition, DEX regulation of multiple genes, including two important atrophy markers, MuRF1 and MAFbx, is eliminated completely in the MGRe3KO mice. In a condition where endogenous GCs are elevated, such as nutritional deprivation, induction of MuRF1 and MAFbx was inhibited, but not completely blocked, in MGRe3KO mice. In response to sciatic nerve lesion and hindlimb muscle denervation, muscle atrophy and upregulation of MuRF1 and MAFbx occurred to the same extent in both wild-type and MGRe3KO mice, indicating that a functional GR is not required to induce atrophy under these conditions. Therefore, we demonstrate conclusively that the GR is an important mediator of skeletal muscle atrophy and associated gene expression in response to exogenous synthetic GCs in vivo and that the MGRe3KO mouse is a useful model for studying the role of the GR and its target genes in multiple skeletal muscle atrophy models.
cAMP signaling in skeletal muscle adaptation: hypertrophy, metabolism, and regeneration
Authors: Berdeaux Rebecca , Stewart Randi
Published: February 2012

Among organ systems, skeletal muscle is perhaps the most structurally specialized. The remarkable subcellular architecture of this tissue allows it to empower movement with instructions from motor neurons. Despite this high degree of specialization, skeletal muscle also has intrinsic signaling mechanisms that allow adaptation to long-term changes in demand and regeneration after acute damage. The second messenger adenosine 3′,5′-monophosphate (cAMP) not only elicits acute changes within myofibers during exercise but also contributes to myofiber size and metabolic phenotype in the long term. Strikingly, sustained activation of cAMP signaling leads to pronounced hypertrophic responses in skeletal myofibers through largely elusive molecular mechanisms. These pathways can promote hypertrophy and combat atrophy in animal models of disorders including muscular dystrophy, age-related atrophy, denervation injury, disuse atrophy, cancer cachexia, and sepsis. cAMP also participates in muscle development and regeneration mediated by muscle precursor cells; thus, downstream signaling pathways may potentially be harnessed to promote muscle regeneration in patients with acute damage or muscular dystrophy. In this review, we summarize studies implicating cAMP signaling in skeletal muscle adaptation. We also highlight ligands that induce cAMP signaling and downstream effectors that are promising pharmacological targets.