bluuebunny/crossref_metadata_2025 huggingface dataset:
Shallow trench isolation stress modification by optimal shallow trench isolation process for sub-65-nm low power complementary metal oxide semiconductor technology
Authors: Hu Chan-Yuan , Chen Jone F. , Chen Shih-Chih , Chang Shoou-Jinn , Wang Shih-Ming , Lee Chih-Ping , Lee Kay-Ming
Published: March 2010

Shallow trench isolation (STI) induced mechanical stress affects the device behavior in the advanced complementary metal oxide semiconductor (CMOS) technology. This article presents how to use an optimal STI process to reduce transistor mismatch and leakage current induced standby current in static random access memory (SRAM). The STI induced mechanical stress affects the device behavior in the advanced CMOS technology. The optimized STI process can reduce junction and bulk leakage that occurs on the STI sidewall due to STI compressive stress enhancing boron diffusion and increasing junction electric field of STI sidewall resulting in band-to-band-tunneling (BTBT) degradation. An obvious decrease in BTBT occurs on STI edge sidewall that is observed by using the optimized STI process. Meanwhile, the optimized STI process has better length of diffusion effect. Moreover, the optimized STI process can improve the parasitic device at STI edge because of smaller divot. Since random fluctuation of channel dopant and process induced device mismatch are major considerations in SRAM cell, we examine STI sidewall boron dopant diffusion effect on SRAM due to BTBT increasing exponentially with increasing doping concentration in the P-well of negative metal oxide semiconductor field effect transistor. The mismatch of passing gate of SRAM and Vcc_min can also be improved by leakage reduction from the optimized STI process due to improved random dopant fluctuation.
Fabrication of two-dimensional polymer photonic crystals by nanoimprinting using anodic porous alumina mold
Authors: Yanagishita Takashi , Nishio Kazuyuki , Masuda Hideki
Published: March 2010

Two-dimensional (2D) photonic crystals composed of polymer pillar arrays were fabricated by a nanoimprinting process using ordered anodic porous alumina molds. The obtained 2D polymer photonic crystals exhibited a clear stop band in the visible wavelength region, which originated from the periodic pillar arrays. The position of the stop band could be controlled by changing the geometrical structure of the anodic porous alumina mold. The process allows the high throughput production of 2D photonic crystals, which are required for the preparation of various types of functional optical devices.
Real-time spectroellipsometric characterization of nucleation, islanding, and coalescence behavior of boron films grown by soft x-ray excited chemical vapor deposition
Authors: Akazawa Housei
Published: March 2010

Real-time spectroscopic ellipsometry was applied to the in situ monitoring of soft x-ray excited chemical vapor deposition of boron films on a Si(001) substrate. While B2H6 molecules cannot reactively stick to a Si clean surface below 400 °C, the decomposition of the precursor molecule through electronic excitation enables boron atoms to secure themselves on the surface. After the incubation period had ended, boron islands began to grow at isolated nucleation centers, exhibiting the Volmer–Weber-type growth. The activation energy for creating the nucleation centers was 2.9 kcal/mol, which presumably corresponded to the clustering of deposited boron atoms. The following growth stage was scaled with an activation energy of 10.3 kcal/mol. The thermally activated process corresponded to the networking of surface-terminating hydrides while releasing H2. As further growth continued, boron islands coalesced, which eventually became two-dimensional boron film. The amorphous boron films could be transformed into a crystallite phase through postannealing at 1000 °C and they were characterized in terms of their optical properties.
Electrostatic quadrupole plasma mass spectrometer measurements during thin film depositions using simultaneous matrix assisted pulsed laser evaporation and magnetron sputtering
Authors: Hunter C. N. , Check M. H. , Muratore C. , Voevodin A. A.
Published: March 2010

A hybrid plasma deposition process, combining matrix assisted pulsed laser evaporation (MAPLE) of carbon nanopearls (CNPs) with magnetron sputtering of gold was investigated for growth of composite films, where 100 nm sized CNPs were encapsulated into a gold matrix. Composition and morphology of such composite films was characterized with x-ray photoelectron spectroscopy, scanning electron microscopy, and transmission electron microscopy (TEM) analysis. Carbon deposits on a gold magnetron sputter target and carbon impurities in the gold matrices of deposited films were observed while codepositing from gold and frozen toluene-CNP MAPLE targets in pure argon. Electrostatic quadrupole plasma analysis was used to determine that a likely mechanism for generation of carbon impurities was a reaction between toluene vapor generated from the MAPLE target and the argon plasma originating from the magnetron sputtering process. Carbon impurities of codeposited films were significantly reduced by introducing argon-oxygen mixtures into the deposition chamber; reactive oxygen species such as O and O+ effectively removed carbon contamination of gold matrix during the codeposition processes. Increasing the oxygen to argon ratio decreased the magnetron target sputter rate, and hence hybrid process optimization to prevent gold matrix contamination and maintain a high sputter yield is needed. High resolution TEM with energy dispersive spectrometry elemental mapping was used to study carbon distribution throughout the gold matrix as well as embedded CNP clusters. This research has demonstrated that a hybrid MAPLE and magnetron sputtering codeposition process is a viable means for synthesis of composite thin films from premanufactured nanoscale constituents, and that cross-process contaminations can be overcome with understanding of hybrid plasma process interaction mechanisms.
Asian Monsoon Transport of Pollution to the Stratosphere
Authors: Randel William J. , Park Mijeong , Emmons Louisa , Kinnison Doug , Bernath Peter , Walker Kaley A. , Boone Chris , Pumphrey Hugh
Published: March 2010

Riding the Monsoon

Most air transport from the troposphere to the stratosphere occurs in the tropics, but additional transport may occur in areas of strong upward convection.

Randel
et al.

(p.
611
, published online 25 March) report satellite measurements of atmospheric hydrogen cyanide over the region where the Asian summer monsoon occurs, which indicate that air is transported from the surface to deep within the stratosphere. This mechanism represents a pathway for pollutants to enter the global stratosphere, where they might affect ozone chemistry, aerosol characteristics, and radiative properties.
Protein Kinase C-θ Mediates Negative Feedback on Regulatory T Cell Function
Authors: Zanin-Zhorov Alexandra , Ding Yi , Kumari Sudha , Attur Mukundan , Hippen Keli L. , Brown Maryanne , Blazar Bruce R. , Abramson Steven B. , Lafaille Juan J. , Dustin Michael L.
Published: March 2010

Yin-Yang T Cell Signaling

Immune responses are kept in check by CD4
+
regulatory T cells (T
reg
) that suppress other immune cells, including CD4
+
effector T cells (T
eff
). T
reg
and T
eff
cells have many signaling components in common, yet triggering through their T cell receptors (TCRs) leads to very different outcomes.

Zanin-Zhorov
et al.

(p.
372
, published online 25 March) compared the recruitment of signaling molecules to the immunological synapse after TCR triggering in T
reg
and T
eff
cells. Although T
reg
cells do form synapses, signaling molecules that promote T
eff
activation, such as protein kinase C-θ (PKC-θ), were not recruited. Inhibition or depletion of PKC-θ in T
reg
cells led to suppressive activity against T
eff
cells, whereas costimulation enhanced PKC-θ recruitment and less suppression. Together, this suggests that PKC-θ is inflammatory in both T
reg
and T
eff
cells; however, by excluding it from the synapse, T
reg
cells are able to maintain suppression in the face of TCR signaling.
KinD Is a Checkpoint Protein Linking Spore Formation to Extracellular-Matrix Production in Bacillus subtilis Biofilms
Authors: Aguilar Claudio , Vlamakis Hera , Guzman Alejandra , Losick Richard , Kolter Roberto
Published: March 2010

Bacillus subtilis
cells form multicellular biofilm communities in which spatiotemporal regulation of gene expression occurs, leading to differentiation of multiple coexisting cell types. These cell types include matrix-producing and sporulating cells. Extracellular matrix production and sporulation are linked in that a mutant unable to produce matrix is delayed for sporulation. Here, we show that the delay in sporulation is not due to a growth advantage of the matrix-deficient mutant under these conditions. Instead, we show that the link between matrix production and sporulation is through the Spo0A signaling pathway. Both processes are regulated by the phosphorylated form of the master transcriptional regulator Spo0A. When cells have low levels of phosphorylated Spo0A (Spo0A~P), matrix genes are expressed; however, at higher levels of Spo0A~P, sporulation commences. We have found that Spo0A~P levels are maintained at low levels in the matrix-deficient mutant, thereby delaying expression of sporulation-specific genes. This is due to the activity of one of the components of the Spo0A phosphotransfer network, KinD. A deletion of
kinD
suppresses the sporulation defect of matrix mutants, while its overproduction delays sporulation. Our data indicate that KinD displays a dual role as a phosphatase or a kinase and that its activity is linked to the presence of extracellular matrix in the biofilms. We propose a novel role for KinD in biofilms as a checkpoint protein that regulates the onset of sporulation by inhibiting the activity of Spo0A until matrix, or a component therein, is sensed.

IMPORTANCE
A question in the field of biofilm development has remained virtually unaddressed: how do the biofilm cells sense the completion of the synthesis of extracellular matrix? The presence of an extracellular matrix that holds the cells together is a defining feature of biofilms. How cells sense that matrix has been assembled and how this signal is transduced have not been investigated.
Bacillus subtilis
provides an excellent system in which to address this question, as the molecular pathways involved in regulation of differentiation are well characterized. We provide the first evidence for a protein that senses the presence of matrix. We identify a membrane sensor histidine kinase, KinD, that alters its activity, depending on the presence or absence of the extracellular matrix. This activity feeds back to the master regulator Spo0A to regulate expression of genes involved in producing matrix and genes necessary for the progression into sporulation.
Hydrogeomorphic effects on bedload scour in bull char (Salvelinus confluentus) spawning habitat, western Washington, USA
Authors: Shellberg Jeffrey G. , Bolton Susan M. , Montgomery David R.
Published: March 2010

We investigated the vulnerability of fall-spawned bull char ( Salvelinus confluentus ) embryos to redd scour during winter rain and rain-on-snow flood discharges in western Washington, USA. It was hypothesized that the magnitude of bedload scour at bull char redds is reduced by the provision and selection of stable refugia habitat controlled by local-, reach-, or subcatchment-scale variables such as hydraulic habitat unit and channel type. Bedload scour and channel change were measured using 96 scour monitors and 34 elevational transects in three catchments over 2 to 4 years. Scour to cited egg burial depths of bull char did not commence until discharge typically exceeded the 2-year recurrence interval. At a local scale, scour varied significantly among side channel, protected main channel, and unprotected main channel redd sites. Unprotected gravel patches in simplified channel types with moderate gradients were most susceptible to deep scour, especially if coupled with the transient supply and storage of sand and gravel from mass wasting. Partially transport-limited reaches had reduced scour due to lower stream power and armored gravel beds. Complex spawning habitat (i.e., with abundant large woody debris and side channels) was important in providing refuge from deep scour and in buffering embryos against inhospitable hydrologic or sediment regimes.
Impact of macroinvertebrate diet on growth and fatty acid profiles of restocked 0+ Atlantic salmon (Salmo salar) parr from a large European river (the Allier)
Authors: Descroix Aurélie , Desvilettes Christian , Bec Alexandre , Martin Patrick , Bourdier Gilles
Published: March 2010

The influence of macroinvertebrate diet on growth and fatty acid profiles of Atlantic salmon ( Salmo salar ) parr released at the fry stage in three different riffles was studied in a large temperate river (Allier, France). Comparisons were made between sites and between restocked parr and hatchery-reared counterparts fed with a traditional fish diet. Significant differences were observed along the longitudinal gradient of the river and between restocked and hatchery-reared parr. Growth performance and nutritional status were higher in the hatchery and in downstream riffles and low in the most upstream site. These differences appeared to be related to different types of diet and consequently to variations in polar and neutral lipid intakes. The most favorable site for optimum growth appeared to be the intermediary riffle, with values close to those achieved in the hatchery. Simuliids and baetids, preferentially consumed in downstream sites, constitute an interesting type of food, showing quite different fatty acid composition from vegetable oils. This could be of interest for composing a new diet formula for young salmon intended for river restocking, imitating these macroinvertebrate fatty acid profiles.
Potential and realized interactions between two aquatic invasive species: Eurasian watermilfoil (Myriophyllum spicatum) and rusty crayfish (Orconectes rusticus)
Authors: Maezo Maria José , Fournier Henri , Beisner Beatrix E.
Published: March 2010

With multiple invasions, the potential arises for interactions between invasives inhibiting or promoting spread. Our goal was to investigate the interaction between two invasives, Eurasian watermilfoil ( Myriophyllum spicatum ) and rusty crayfish ( Orconectes rusticus ), which co-occur in several lakes in western Quebec, Canada, and to determine their overlap with littoral fish communities. Crayfish potentially aid milfoil dispersal by fragmentation or, alternatively, inhibit its proliferation through destruction and direct consumption. With a mesocosm experiment, we quantified milfoil fragment production versus biomass reduction by crayfish. More fragments were produced at medium to high crayfish densities, with a significant reduction of milfoil only at the highest densities, demonstrating the potential for both positive and negative interactions. Second, we determined the habitat preferences of each species by conducting a survey in the same lake. There was little overlap in the species’ distributions, with each preferring different habitat features, indicating either a low probability of interaction or that interaction occurred historically, resulting in a contemporary exclusion pattern. While our experiment showed a potential for significant interaction, the low natural co-occurrence of these species suggests that they do not currently influence each other or that they previously excluded each other.
Incorporating temporal variation in the growth of red abalone (Haliotis rufescens) using hierarchical Bayesian growth models
Authors: Jiao Yan , Rogers-Bennett Laura , Taniguchi Ian , Butler John , Crone Paul
Published: March 2010

Many marine species exhibit temporal variation in individual growth. Yearly variation in growth has been identified for red abalone ( Haliotis rufescens ) in southern California, USA, but has not been previously incorporated into growth models. In this study, Bayesian hierarchical models were developed to describe variability in growth rates for the Johnsons Lee red abalone population. Although the Bayesian hierarchical modeling estimates are close to estimates of the nonhierarchical highly parameterized model that assigns an estimate of parameters to each data period when the sample sizes are high, the hyperparameters in the hierarchical model are more useful in incorporating the temporal variability into the stock assessment. By ignoring temporal variability, confidence intervals of the estimates of growth can be unrealistically narrow, possibly leading to bias when these models are used for developing biological reference points such as F0.1, Fmax, or Fx%. The use of a Bayesian hierarchical approach is generally suggested for future growth modeling and for per-recruitment models that include growth when determining precautionary management decisions.
Comment on “Differences in predicted catch composition between two widely used catch equation formulations”Appears in Can. J. Fish. Aquat. Sci. 66: 126–132.
Authors: Francis R. I.C. Chris
Published: March 2010

Branch (2009. Can. J. Fish. Aquat. Sci. 66: 126–132) described the two most common catch equation formulations in stock assessment models: the continuous (Baranov) one, which represents fishing mortality as an instantaneous rate, F, and the discrete one, in which it is represented as an exploitation rate, u. He claimed that the continuous formulation is preferable at high fishing mortality where a fish could encounter multiple sets of gear within a year. This claim is wrong for two reasons. First, it is based on the false supposition that the discrete catch equations require the assumption that fish encounter at most only one set of fishing gear in a year. Second, it is not possible to determine, for a specific stock assessment, whether one formulation is preferable to another solely on the basis of information about the fishery. The appropriate way to make this decision is to see which fits the data better.
Effects of experimental freezing on soil nitrogen dynamics in soils from a net nitrification gradient in a nitrogen-saturated hardwood forest ecosystem
Authors: Gilliam Frank S. , Cook Adam , Lyter Salina
Published: March 2010

This study examined effects of soil freezing on N dynamics in soil along an N processing gradient within a mixed hardwood dominated watershed at Fernow Experimental Forest, West Virginia. Sites were designated as LN (low rates of N processing), ML (moderately low), MH (moderately high), and HN (high). Soils underwent three 7-day freezing treatments (0, –20, or –80 °C) in the laboratory. Responses varied between temperature treatments and along the gradient. Initial effects differed among freezing treatments for net N mineralization, but not nitrification, in soils across the gradient, generally maintained at LN < ML ≤ MH < HN for all treatments. Net N mineralization potential was higher following freezing at –20 and –80 °C than control; all were higher than at 0 °C. Net nitrification potential exhibited similar patterns. LN was an exception, with net nitrification low regardless of treatment. Freezing response of N mineralization differed greatly from that of nitrification, suggesting that soil freezing may decouple two processes of the soil N cycle that are otherwise tightly linked at our site. Results also suggest that soil freezing at temperatures commonly experienced at this site can further increase net nitrification in soils already exhibiting high nitrification from N saturation.
Rare forest types in northeastern Ontario: a classification and analysis of representation in protected areas
Authors: Drever Charles R. , Snider James , Drever Mark C.
Published: March 2010

Our objective was to assess the relative rarity and representation within protected areas of Standard Forest Units (SFUs) in northeastern Ontario by applying the concepts of geographic range, habitat specificity, and local population size. SFUs are stand type classifications, routinely employed by forest managers, based on tree composition, disturbance history, and prescribed silvicultural system. We identified several SFUs as rare because of a narrow distribution, association with only one landform type, or lack of at least one stand larger than an ecoregion-specific threshold. In the Boreal forest, rare SFUs comprised stands dominated by eastern hemlock ( Tsuga canadensis (L.) Carrière), red oak ( Quercus rubra L.), yellow birch ( Betula alleghaniensis Britt.), or eastern white-cedar ( Thuja occidentalis L.). Rare SFUs also included eastern white pine ( Pinus strobus L.) and (or) red pine ( Pinus resinosa Ait.) leading stands managed by shelterwood or seed tree silviculture as well as low-lying deciduous stands and selection-managed stands of shade-tolerant species. In the Great Lakes – St. Lawrence forest, rare SFUs were yellow birch stands, stands dominated by conifer species abundant in the Boreal, and shelterwood-managed hardwood stands. Several rare SFUs had <12% of their total area in protection, i.e., stands dominated by eastern white pine, yellow birch, eastern white pine – red oak, or eastern white-cedar. These rare stand types require increased protection in reserves and tailored silvicultural practices to maintain their probability of persistence.
The preferences of saproxylic beetle species for different dead wood types created in forest restoration treatments
Authors: Toivanen Tero , Kotiaho Janne S.
Published: March 2010

Restoration by imitating natural disturbances is widely practised in boreal forests to increase the availability of habitats for specialized species. We studied the abundance and species richness of saproxylic beetles on different types of created dead wood during 2 years after restoration. The study was conducted on areas of a large-scale experiment in which Norway spruce ( Picea abies (L.) Karst.) forests were restored by controlled burning and partial harvesting with down wood retention in southern Finland. More beetle species were attracted to spruces than to birches and more species were attracted to burnt trees than to unburnt trees killed by girdling. Birch-living species consistently benefited from fire, but on spruce, the abundance of cambium consumers and their associates was negatively affected by fire. Trees at harvested sites attracted more beetles in the first year, but the volume of down wood retention had only minor effects. Beetle assemblages were strongly altered by burning and harvesting. We conclude that burning and harvesting are efficient tools to promote species richness within a short time period, but there is a risk that the dead wood resource may be rapidly exhausted. Moreover, many saproxylic species of spruce forests may not be adapted to open habitats formed by stand-replacing disturbances.
Effects of logging debris treatments on five-year development of competing vegetation and planted Douglas-fir
Authors: Harrington Timothy B. , Schoenholtz Stephen H.
Published: March 2010

Although considerable research has focused on the influences of logging debris treatments on soil and forest regeneration responses, few studies have identified whether debris effects are mediated by associated changes in competing vegetation abundance. At sites near Matlock, Washington, and Molalla, Oregon, studies were initiated after timber harvest to quantify the effects of three logging debris treatments (dispersed, piled, or removed) on the development of competing vegetation and planted Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco var. menziesii ). Each debris treatment was replicated with initial and annual vegetation control treatments, resulting in high and low vegetation abundances, respectively. This experimental design enabled debris effects on regeneration to be separated into effects mediated by vegetation abundance and those independent of vegetation abundance. Two to three years after treatment, covers of Scotch broom ( Cytisus scoparius (L.) Link) at Matlock and trailing blackberry ( Rubus ursinus Cham. & Schltdl.) at Molalla were over 20% greater where debris was piled than where it was dispersed. Debris effects on vegetation abundance were associated with 30% reductions in the survival of Douglas-fir at Matlock (r2 = 0.62) and the stem diameter at Molalla (r2 = 0.39). Douglas-fir survival and growth did not differ among debris treatments when effects were evaluated independent of vegetation abundance (i.e., with annual vegetation control), suggesting negligible short-term effects of debris manipulation on soil productivity.
Patterns in whitebark pine regeneration and their relationships to biophysical site characteristics in southwest Montana, central Idaho, and Oregon, USA
Authors: Larson Evan R. , Kipfmueller Kurt F.
Published: March 2010

Declines of whitebark pine ( Pinus albicaulis Engelm.) have occurred across much of the species’ range over the last 40 years due to mountain pine beetle outbreaks and white pine blister rust infection. Management efforts to stem these declines are increasing, yet the long-term success of whitebark pine depends on the species itself adapting to the modern environment. Natural regeneration will be a critical part of this process. We examined patterns in natural whitebark pine regeneration as related to the biophysical environment in sixty 0.1 ha plots in Montana, Idaho, and Oregon. Whitebark pine regeneration was present in 97% of our plots and varied widely in density from 0 to 17 000 seedlings/ha and 0 to 2680 saplings/ha. Using nonparametric correlation analysis and ordination techniques, we found whitebark pine regeneration abundance was unrelated to stand age but significantly related to several biophysical site characteristics, including positive relationships with elevation and canopy tree mortality caused by mountain pine beetle and negative relationships with moisture availability, temperature, and subalpine fir importance. Our findings indicate that whitebark pine is regenerating in many areas and that the widespread mortality from recent mountain pine beetle outbreaks may provide suitable settings for whitebark pine regeneration given sufficient seed sources.
Natural regeneration of white spruce in aspen-dominated boreal mixedwoods following harvesting
Authors: Martin-DeMoor Jonathan , Lieffers Victor J. , Macdonald S. Ellen
Published: March 2010

In some boreal forests sites, there are considerable amounts of natural regeneration of white spruce ( Picea glauca (Moench) Voss) after logging, even without silvicultural treatments to encourage establishment. We assessed the factors controlling the amount of this regeneration 8–15 years postharvest on previously aspen-dominated ( Populus tremuloides Michx.) boreal mixedwood sites. We surveyed 162 transects across 81 cutovers, exploring the effects of mast years, season of harvest, distribution of seed trees, weather conditions around the time of harvest, and abundance of grass or woody vegetation on white spruce regeneration. Substantial amounts of naturally regenerated white spruce were found; however, sites with no seed trees had virtually no spruce regeneration. Average stocking was 7% (percentage of 9 m2plots along a transect across a cutover that had at least one seedling), ranging from 0% to 62%. Stocking levels were higher in cutblocks that had been harvested in the summer, prior to seedfall of a mast year, and where there was a seed source within 60 m. Stocking was lower when conditions were cool and wet the year before and 2 years after harvest and when the site contained extensive cover of grass or woody vegetation.
COUPLED CHEMOTAXIS FLUID MODEL
Authors: LORZ ALEXANDER
Published: March 2010

We consider a model system for the collective behavior of oxygen-driven swimming bacteria in an aquatic fluid. In certain parameter regimes, such suspensions of bacteria feature large-scale convection patterns as a result of the hydrodynamic interaction between bacteria. The presented model consist of a parabolic–parabolic chemotaxis system for the oxygen concentration and the bacteria density coupled to an incompressible Stokes equation for the fluid driven by a gravitational force of the heavier bacteria.

We show local existence of weak solutions in a bounded domain in ℝd, d = 2, 3 with no-flux boundary condition and in ℝ2 in the case of inhomogeneous Dirichlet conditions for the oxygen.
OPINION DYNAMICS AND COMMUNICATION NETWORKS
Authors: BANISCH SVEN , ARAÚJO TANYA , LOUÇÃ JORGE
Published: March 2010

This paper examines the interplay of opinion exchange dynamics and communication network formation. An opinion formation procedure is introduced which is based on an abstract representation of opinions as k-dimensional bit-strings. Individuals interact if the difference in the opinion strings is below a defined similarity threshold dI. Depending on dI, different behavior of the population is observed: low values result in a state of highly fragmented opinions and higher values yield consensus. The first contribution of this research is to identify the values of parameters dI and k, such that the transition between fragmented opinions and homogeneity takes place. Then, we look at this transition from two perspectives: first by studying the group size distribution and second by analyzing the communication network that is formed by the interactions that take place during the simulation. The emerging networks are classified by statistical means and we find that nontrivial social structures emerge from simple rules for individual communication. Generating networks allows to compare model outcomes with real-world communication patterns.
EXPLORING AND UNDERSTANDING CITATION-BASED SCIENTIFIC METRICS
Authors: KRAPIVIN MIKALAI , MARCHESE MAURIZIO , CASATI FABIO
Published: March 2010

This paper explores citation-based metrics, how they differ in ranking papers and authors, and why. We initially take as example three main metrics that we believe significant; the standard citation count, the more and more popular h-index, and a variation we propose of PageRank applied to papers (called PaperRank), that is appealing as it mirrors proven and successful algorithms for ranking web pages. As part of analyzing them, we develop generally applicable techniques and metrics for qualitatively and quantitatively analyzing indexes that evaluate content and people, as well as for understanding the causes of their different behaviors. Finally, we extend the analysis to other popular indexes, to show whether the choice of the index has a significant effect in how papers and authors are ranked. We put the techniques at work on a dataset of over 260 K ACM papers, and discovered that the difference in ranking results is indeed very significant (even when restricting to citation-based indexes), with half of the top-ranked papers differing in a typical 20-element long search result page for papers on a given topic, and with the top researcher being ranked differently over half of the times in an average job posting with 100 applicants.
ER stress and the unfolded protein response in intestinal inflammation
Authors: McGuckin Michael A. , Eri Rajaraman D. , Das Indrajit , Lourie Rohan , Florin Timothy H.
Published: March 2010

Endoplasmic reticulum (ER) stress is a phenomenon that occurs when excessive protein misfolding occurs during biosynthesis. ER stress triggers a series of signaling and transcriptional events known as the unfolded protein response (UPR). The UPR attempts to restore homeostasis in the ER but if unsuccessful can trigger apoptosis in the stressed cells and local inflammation. Intestinal secretory cells are susceptible to ER stress because they produce large amounts of complex proteins for secretion, most of which are involved in mucosal defense. This review focuses on ER stress in intestinal secretory cells and describes how increased protein misfolding could occur in these cells, the process of degradation of misfolded proteins, the major molecular elements of the UPR pathway, and links between the UPR and inflammation. Evidence is reviewed from mouse models and human inflammatory bowel diseases that ties ER stress and activation of the UPR with intestinal inflammation, and possible therapeutic approaches to ameliorate ER stress are discussed.
Neuronal nitric oxide inhibits intestinal smooth muscle growth
Authors: Pelletier Anne-Marie , Venkataramana Shriram , Miller Kurtis G. , Bennett Brian M. , Nair Dileep G. , Lourenssen Sandra , Blennerhassett Michael G.
Published: March 2010

Hyperplasia of smooth muscle contributes to the thickening of the intestinal wall that is characteristic of inflammation, but the mechanisms of growth control are unknown. Nitric oxide (NO) from enteric neurons expressing neuronal NO synthase (nNOS) might normally inhibit intestinal smooth muscle cell (ISMC) growth, and this was tested in vitro. In ISMC from the circular smooth muscle of the adult rat colon, chemical NO donors inhibited [3H]thymidine uptake in response to FCS, reducing this to baseline without toxicity. This effect was inhibited by the guanylyl cyclase inhibitor ODQ and potentiated by the phosphodiesterase-5 inhibitor zaprinast. Inhibition was mimicked by 8-bromo (8-Br)-cGMP, and ELISA measurements showed increased levels of cGMP but not cAMP in response to sodium nitroprusside. However, 8-Br-cAMP and cilostamide also showed inhibitory actions, suggesting an additional role for cAMP. Via a coculture model of ISMC and myenteric neurons, immunocytochemistry and image analysis showed that innervation reduced bromodeoxyuridine uptake by ISMC. Specific blockers of nNOS (7-NI, NAAN) significantly increased [3H]thymidine uptake in response to a standard stimulus, showing that nNOS activity normally inhibits ISMC growth. In vivo, nNOS axon number was reduced threefold by day 1 of trinitrobenzene sulfonic acid-induced rat colitis, preceding the hyperplasia of ISMC described earlier in this model. We conclude that NO can inhibit ISMC growth primarily via a cGMP-dependent mechanism. Functional evidence that NO derived from nNOS causes inhibition of ISMC growth in vitro predicts that the loss of nNOS expression in colitis contributes to ISMC hyperplasia in vivo.
The role of the complement and contact systems in the dextran sulfate sodium-induced colitis model: the effect of C1 inhibitor in inflammatory bowel disease
Authors: Lu Fengxin , Fernandes Stacey M. , Davis Alvin E.
Published: March 2010

The complement and contact systems may be involved in the pathophysiological process of inflammatory bowel disease (IBD). C1 inhibitor (C1INH) is the most important inhibitor of both the complement and contact systems. We evaluated the role of these systems and the effect of both active and inactive forms of C1INH (iC1INH) in dextran sulfate sodium (DSS)-induced colitis mouse model. Three percent DSS was used in drinking water to induce colitis in complement C3-deficient (C3−/−) mice, bradykinin type 2 receptor deficient (Bk2R−/−) mice, and C57BL/6 mice. After ten days DSS exposure, C3−/−mice exhibited markedly less weight loss than wild-type (WT) mice (12 ± 3.3% vs. 30 ± 1.2%, P < 0.05) and developed a milder disease-activity index (DAI), histological score, colon shortening, and myeloperoxidase (MPO) elevation ( P < 0.05, respectively). The Bk2R−/−mice were not protected from the disease. Seven-day treatment with either native C1INH or iC1INH reduced the severity of the disease in WT mice, as indicated by decreased weight loss (15 ± 1.8%, 14 ± 2.1% vs. 30 ± 1.2%, P < 0.05, respectively), DAI, intestinal tissue damage, and MPO elevation compared with untreated WT DSS control mice ( P < 0.05, respectively). These findings suggest that complement plays a role in the development of DSS-induced colitis and that blockade of the complement system might be useful for the acute phase of IBD treatment. C1INH, however, leads to an amelioration of DSS-induced colitis via a mechanism that does not involve the inhibition of complement or contact system activation but does result in significant suppression of leukocyte infiltration.
Cyclin D1 regulates hepatic estrogen and androgen metabolism
Authors: Mullany Lisa K. , Hanse Eric A. , Romano Andrea , Blomquist Charles H. , Mason J. Ian , Delvoux Bert , Anttila Chelsea , Albrecht Jeffrey H.
Published: March 2010

Cyclin D1 is a cell cycle control protein that plays an important role in regenerating liver and many types of cancer. Previous reports have shown that cyclin D1 can directly enhance estrogen receptor activity and inhibit androgen receptor activity in a ligand-independent manner and thus may play an important role in hormone-responsive malignancies. In this study, we examine a distinct mechanism by which cyclin D1 regulates sex steroid signaling, via altered metabolism of these hormones at the tissue and cellular level. In male mouse liver, ectopic expression of cyclin D1 regulated genes involved in the synthesis and degradation of sex steroid hormones in a pattern that would predict increased estrogen and decreased androgen levels. Indeed, hepatic expression of cyclin D1 led to increased serum estradiol levels, increased estrogen-responsive gene expression, and decreased androgen-responsive gene expression. Cyclin D1 also regulated the activity of several key enzymatic reactions in the liver, including increased oxidation of testosterone to androstenedione and decreased conversion of estradiol to estrone. Similar findings were seen in the setting of physiological cyclin D1 expression in regenerating liver. Knockdown of cyclin D1 in HuH7 cells produced reciprocal changes in steroid metabolism genes compared with cyclin D1 overexpression in mouse liver. In conclusion, these studies establish a novel link between the cell cycle machinery and sex steroid metabolism and provide a distinct mechanism by which cyclin D1 may regulate hormone signaling. Furthermore, these results suggest that increased cyclin D1 expression, which occurs in liver regeneration and liver diseases, may contribute to the feminization seen in these settings.
Ephrin B2/EphB4 pathway in hepatic stellate cells stimulates Erk-dependent VEGF production and sinusoidal endothelial cell recruitment
Authors: Das Amitava , Shergill Uday , Thakur Lokendra , Sinha Sutapa , Urrutia Raul , Mukhopadhyay Debabrata , Shah Vijay H.
Published: March 2010

Chemotaxis signals between hepatic stellate cells (HSC) and sinusoidal endothelial cells (SEC) maintain hepatic vascular homeostasis and integrity and also regulate changes in sinusoidal structure in response to liver injury. Our prior studies have demonstrated that the bidirectional chemotactic signaling molecules EphrinB2 and EphB4 are expressed in HSC. The aim of our present study was to explore whether and how the EphrinB2/EphB4 system in HSC could promote SEC recruitment, which is essential for sinusoidal structure and remodeling. Stimulation of human HSC (hHSC) with chimeric agonists (2 μg/ml) of either EphrinB2 or EphB4 (EphrinB2 Fc or EphB4 Fc, respectively) significantly increased VEGF mRNA levels in hHSC as assessed by quantitative PCR, with respective small interfering RNAs for EphrinB2 and EphB4 inhibiting this increase ( P < 0.05, n = 3). EphrinB2 agonist-induced increase in VEGF mRNA levels in hHSC was associated with increased phosphorylation of Erk and was significantly blocked by U0126 (20 μM), an inhibitor of MEK, which is a kinase upstream from Erk ( P < 0.05, n = 3). The EphB4 agonist also significantly increased human VEGF promoter activity ( P < 0.05, n = 3) as assessed by promoter reporter luciferase assay in transfected LX2-HSC. This was associated with upregulation of the vasculoprotective transcription factor, Kruppel-like factor 2 (KLF2). In Boyden chamber assays, conditioned media from hHSC stimulated with agonists of EphrinB2 or EphB4 increased SEC chemotaxis in a VEGF-dependent manner, compared with control groups that included basal media with agonists of EphrinB2, EphB4, or HSC-conditioned media from HSC in absence of agonist stimulation ( P < 0.05, n = 3). EphB4 expression was detected in situ within liver sinusoidal vessels of rats after carbon tetrachloride-induced liver injury. In summary, activation of the EphrinB2/EphB4 signaling pathway in HSC promotes chemotaxis of SEC through a pathway that involves Erk, KLF2, and VEGF. These studies identify EphrinB2 or EphB4 as a key intermediary that links HSC signal transduction pathways with angiogenesis and sinusoidal remodeling.
Phase-rectified signal averaging as a sensitive index of autonomic changes with aging
Authors: Campana L. M. , Owens R. L. , Clifford G. D. , Pittman S. D. , Malhotra A.
Published: March 2010

Standard heart rate variability (HRV) techniques have been questioned in the sleep and autonomic fields as imprecise measures of sympathetic and parasympathetic activity. A new technique has emerged, known as phase-rectified signal averaging (PRSA). PRSA is used to quantify the quasi-periodic accelerations and decelerations in short-term heart rate, an effect that is normally masked by artifacts and noise. When applied to a signal of peak-to-peak (RR) time intervals, these quasiperiodicities can be used to estimate overall vagal activity, quantified as deceleration capacity (DC) and acceleration capacity (AC). We applied the PRSA analysis to a healthy cohort (ages 21–60 yr) enrolled in a clinical sleep trial, in which ECG data during wakefulness and sleep were available. We found that DC and AC were significantly attenuated with increasing age: a 0.27 ms/yr decrease in DC and a 0.29 ms/yr increase in AC ( P < 0.001). However, even in the older subjects, DC values were higher then previously found in people post-myocardial infarction. We also found a drop in percentage of normal-to-normal intervals where the current interval deviated >50 ms from the previous interval with age, with a decrease of 0.84%/yr. We did not find any differences between younger and older subjects with traditional HRV techniques, such as low-frequency or high-frequency power. Overall, the study provides normative PRSA data and suggests that PRSA is more sensitive than other HRV measurements. We propose that the decrease in DC and AC may be a sensitive marker for autonomic changes with aging. Further work will be required to determine whether the observed changes predict poorer cardiac health prognosis.
Pulmonary O2 uptake and leg blood flow kinetics during moderate exercise are slowed by hyperventilation-induced hypocapnic alkalosis
Authors: Chin Lisa M. K. , Heigenhauser George J. F. , Paterson Donald H. , Kowalchuk John M.
Published: March 2010

The effect of hyperventilation-induced hypocapnic alkalosis (Hypo) on the adjustment of pulmonary O2 uptake (V̇o2p) and leg femoral conduit artery (“bulk”) blood flow (LBF) during moderate-intensity exercise (Mod) was examined in eight young male adults. Subjects completed four to six repetitions of alternate-leg knee-extension exercise during normal breathing [Con; end-tidal partial pressure of CO2 (PetCO2) ∼40 mmHg] and sustained hyperventilation (Hypo; PetCO2 ∼20 mmHg). Increases in work rate were made instantaneously from baseline (3 W) to Mod (80% estimated lactate threshold). V̇o2p was measured breath by breath by mass spectrometry and volume turbine, and LBF (calculated from mean femoral artery blood velocity and femoral artery diameter) was measured simultaneously by Doppler ultrasound. Concentration changes of deoxy (Δ[HHb])-, oxy (Δ[O2Hb])-, and total hemoglobin-myoglobin (Δ[HbTot]) of the vastus lateralis muscle were measured continuously by near-infrared spectroscopy (NIRS). The kinetics of V̇o2p, LBF, and Δ[HHb] were modeled using a monoexponential equation by nonlinear regression. The time constants for the phase 2 V̇o2p (Hypo, 49 ± 26 s; Con, 28 ± 8 s) and LBF (Hypo, 46 ± 16 s; Con, 23 ± 6 s) were greater ( P < 0.05) in Hypo compared with Con. However, the mean response time for the overall Δ[HHb] response was not different between conditions (Hypo, 23 ± 5 s; Con, 24 ± 3 s), whereas the Δ[HHb] amplitude was greater ( P < 0.05) in Hypo (8.05 ± 7.47 a.u.) compared with Con (6.69 ± 6.31 a.u.). Combined, these results suggest that hyperventilation-induced hypocapnic alkalosis is associated with slower convective (i.e., slowed femoral artery and microvascular blood flow) and diffusive (i.e., greater fractional O2 extraction for a given ΔV̇o2p) O2 delivery, which may contribute to the hyperventilation-induced slowing of V̇o2p (and muscle O2 utilization) kinetics.
Perfluorocarbon Improves Post-Transplant Survival and Early Kidney Function following Prolonged Cold Ischemia
Authors: Marada T. , Zacharovova K. , Saudek F.
Published: March 2010

Background: The two-layer organ preservation method (TLM) based on oxygenated perfluorocarbon overlaid with University of Wisconsin (UW) solution has been successfully used in clinical islet and experimental heart and intestine transplantation. We tested whether this technique would prevent tissue damage and improve kidney function in a model of syngeneic kidney transplantation with prolonged ischemia time. Methods: Kidneys were stored for 24 h either in UW solution (n = 16), with TLM (n = 16) or transplanted immediately (control group, n = 12). In half of the animals, survival was observed and in the other animals grafts were procured for semiquantitative histological scoring and TUNEL apoptosis assessment 24 h after transplantation. Results: One-month survival rates in the UW, TLM and control groups were 12.5, 62.5 and 100%, respectively (UW vs. TLM, p < 0.01). Median creatinine levels 24 h after transplantation were 381, 299 and 121 µM, respectively (UW vs. TLM, p < 0.02). Histological scoring showed more severe tissue damage in the UW group than in the TLM group (p < 0.05). Apoptosis was more frequent in the UW group than in the TLM group (p < 0.05). Conclusion: We demonstrated for the first time that conservation with TLM significantly improves the outcome of kidney transplantation in a rat model and should therefore be further studied in larger animals.
Papuloerythroderma 2009: Two New Cases and Systematic Review of the Worldwide Literature 25 Years after Its Identification by Ofuji et al.
Authors: Torchia Daniele , Miteva Maria , Hu Shasa , Cohen Carlos , Romanelli Paolo
Published: March 2010

Background: Even after the description of papuloerythroderma of Ofuji (PEO) in 1984, little is known about this clinical entity. Objective:To report on 2 new cases of PEO and review of the worldwide literature on this topic. Methods: Article citations were searched on several biomedical search engines (PubMed, EMBASE, SCOPUS, Google Scholar). Papers were retrieved either online or in print. Results: A grand total of 170 PEO cases were identified. Most patients were older than 55 years and of Asian or white descent, with an overall male/female ratio of 4.0. Itch and the deck-chair sign were observed in all patients. Peripheral eosinophilia, lymphocytopenia and increased serum IgE were common findings. Histopathology mostly showed aspecific inflammation, while 17 showed histological features of cutaneous T-cell lymphoma (CTCL). Atopy, malignancies, infections and drugs were rarely linked to PEO. Conclusion: PEO represents a rather monomorphous entity both clinically and, with the remarkable exception of CTCL, also histologically. Nonetheless, no causative factor could be identified in the vast majority of cases. An etiological classification and diagnostic criteria are proposed in the attempt to contribute framing this puzzling clinical entity.