bluuebunny/crossref_metadata_2025 huggingface dataset:
Motor‐cortical oscillations in early stages of Parkinson's disease
Authors: Pollok B. , Krause V. , Martsch W. , Wach C. , Schnitzler A. , Südmeyer M.
Published: May 2012

Key points

Parkinson's disease (PD) is a common movement disorder due to dopaminergic denervation of the basal ganglia. It is characterized by exaggerated oscillatory activity within central motor‐control loops, while cerebro‐muscular coherence is reduced at frequencies below 30 Hz.

So far, studies investigating the neurophysiological alterations of PD have focused on patients with advanced PD. It remains open to what extent changes of oscillatory activity might occur at early disease stages, representing a characteristic feature of the disease.

Using magnetoencephalography we show that cerebro‐muscular coherence is unaffected in early PD while beta band oscillations of bilateral primary sensori‐motor cortices are already increased at the earliest stages of PD and, as the disease progresses, evolve a hemispheric imbalance associated with movement execution.

Abstract  Pathophysiological changes in basal ganglia‐thalamo‐cortical circuits are well established in idiopathic Parkinson's disease (PD). However, it remains open whether such alterations already occur at early stages representing a characteristic neurophysiological marker of PD. Therefore, the present study aims at elucidating changes of synchronised oscillatory activity in early PD patients. In this study, we performed whole‐head magnetoencephalography (MEG) in a resting condition and during steady state contraction of the more severely affected forearm in 10 drug–naive, de novo patients, in 10 early‐stage patients with chronic medication and in 10 age‐matched control subjects. While cortico‐muscular coherence (CMC) did not differ between groups, patients showed increased sensori‐motor cortical power at beta frequency (13–30 Hz) during rest as well as during isometric contraction compared to controls. In healthy control subjects the power of the contralateral hemisphere was significantly suppressed during isometric contraction. By contrast, both hemispheres were activated equally strongly in de novo patients. In medicated patients, the pattern was found to be reversed. Contralateral beta power was significantly correlated with motor impairment during isometric contraction but not during rest. The present results suggest that the reduced ability of the primary motor cortex to disengage from increased beta band oscillations during the execution of movements is an early marker of PD.
Performance improvement of GaN-based ultraviolet metal–semiconductor–metal photodetectors using chlorination surface treatment
Authors: Lee Hsin-Ying , Lu De-En , Lee Ching-Ting
Published: May 2012

Chlorination surface treatment was used to improve the performance of GaN-based ultraviolet metal–semiconductor–metal photodetectors (MSM-PDs). The noise equivalent power of chlorine-treated MSM-PDs measured at 5 V was 1.60 × 10−12 W, which was less than that of untreated ones (6.68 × 10−12 W). The normalized detectivity of chlorine-treated MSM-PDs was 1.90 × 1011 cm Hz0.5 W−1, which was higher than the measured value of 4.72 × 1010 cm Hz0.5 w−1 of untreated ones. The dark current of chlorine-treated and untreated MSM-PDs operating at 10 V was 21.4 and 762.0 pA, respectively. The improvement was attributed to the passivation of the GaN surface and the reduction of surface states as a result of the chlorination surface treatment.
Science Signaling
Podcast: 1 May 2012
Authors: Suga Hiroshi , VanHook Annalisa M.
Published: May 2012

Receptor tyrosine kinases existed in the unicellular ancestors of multicellular animals and underwent diversification in the metazoan lineage.
I Love Leucine
Authors: Wong Wei
Published: May 2012

The leucyl-tRNA synthetase acts as a leucine sensor for mTOR complex 1.
Gut Reaction
Authors: Mueller Kristen
Published: May 2012

An inhibitory receptor is important for gut microflora containment by immunoglobulin A.
In Vitro
Activity of Ertapenem versus Ceftriaxone against Neisseria gonorrhoeae Isolates with Highly Diverse Ceftriaxone MIC Values and Effects of Ceftriaxone Resistance Determinants: Ertapenem for Treatment of Gonorrhea?
Authors: Unemo Magnus , Golparian Daniel , Limnios Athena , Whiley David , Ohnishi Makoto , Lahra Monica M. , Tapsall John W.
Published: May 2012

Clinical resistance to the currently recommended extended-spectrum cephalosporins (ESCs), the last remaining treatment options for gonorrhea, is being reported. Gonorrhea may become untreatable, and new treatment options are crucial. We investigated the
in vitro
activity of ertapenem, relative to ceftriaxone, against
N. gonorrhoeae
isolates and the effects of ESC resistance determinants on ertapenem. MICs were determined using agar dilution technique or Etest for international reference strains (
n
= 17) and clinical
N. gonorrhoeae
isolates (
n
= 257), which included the two extensively drug-resistant (XDR) strains H041 and F89 and additional isolates with high ESC MICs, clinical ESC resistance, and other types of clinical high-level and multidrug resistance (MDR). Genetic resistance determinants for ESCs (
penA
,
mtrR
, and
penB
) were sequenced. In general, the MICs of ertapenem (MIC
50
= 0.032 μg/ml; MIC
90
= 0.064 μg/ml) paralleled those of ceftriaxone (MIC
50
= 0.032 μg/ml; MIC
90
= 0.125 μg/ml). The ESC resistance determinants mainly increased the ertapenem MIC and ceftriaxone MIC at similar levels. However, the MIC ranges for ertapenem (0.002 to 0.125 μg/ml) and ceftriaxone (<0.002 to 4 μg/ml) differed, and the four (1.5%) ceftriaxone-resistant isolates (MIC = 0.5 to 4 μg/ml) had ertapenem MICs of 0.016 to 0.064 μg/ml. Accordingly, ertapenem had
in vitro
advantages over ceftriaxone for isolates with ceftriaxone resistance. These
in vitro
results suggest that ertapenem might be an effective treatment option for gonorrhea, particularly for the currently identified ESC-resistant cases and possibly in a dual antimicrobial therapy regimen. However, further knowledge regarding the genetic determinants (and their evolution) conferring resistance to both antimicrobials, and clear correlates between genetic and phenotypic laboratory parameters and clinical treatment outcomes, is essential.
In VitroAntiviral Characteristics of HIV-1 Attachment Inhibitor BMS-626529, the Active Component of the Prodrug BMS-663068
Authors: Nowicka-Sans Beata , Gong Yi-Fei , McAuliffe Brian , Dicker Ira , Ho Hsu-Tso , Zhou Nannan , Eggers Betsy , Lin Pin-Fang , Ray Neelanjana , Wind-Rotolo Megan , Zhu Li , Majumdar Antara , Stock David , Lataillade Max , Hanna George J. , Matiskella John D. , Ueda Yasutsugu , Wang Tao , Kadow John F. , Meanwell Nicholas A. , Krystal Mark
Published: May 2012

BMS-663068 is the phosphonooxymethyl prodrug of BMS-626529, a novel small-molecule attachment inhibitor that targets HIV-1 gp120 and prevents its binding to CD4+T cells. The activity of BMS-626529 is virus dependent, due to heterogeneity within gp120. In order to better understand the anti-HIV-1 spectrum of BMS-626529 against HIV-1,in vitroactivities against a wide variety of laboratory strains and clinical isolates were determined. BMS-626529 had half-maximal effective concentration (EC50) values of <10 nM against the vast majority of viral isolates; however, susceptibility varied by >6 log10, with half-maximal effective concentration values in the low pM range against the most susceptible viruses. Thein vitroantiviral activity of BMS-626529 was generally not associated with either tropism or subtype, with few exceptions. Measurement of the binding affinity of BMS-626529 for purified gp120 suggests that a contributory factor to its inhibitory potency may be a relatively long dissociative half-life. Finally, in two-drug combination studies, BMS-626529 demonstrated additive or synergistic interactions with antiretroviral drugs of different mechanistic classes. These results suggest that BMS-626529 should be active against the majority of HIV-1 viruses and support the continued clinical development of the compound.
Rifapentine Is Not More Active than Rifampin against Chronic Tuberculosis in Guinea Pigs
Authors: Dutta Noton K. , Illei Peter B. , Peloquin Charles A. , Pinn Michael L. , Mdluli Khisimuzi E. , Nuermberger Eric L. , Grosset Jacques H. , Karakousis Petros C.
Published: May 2012

Rifamycins are key sterilizing drugs in the current treatment of active tuberculosis (TB). Daily dosing of rifapentine (P), a potent rifamycin with high intracellular accumulation, in place of rifampin (R) in the standard antitubercular regimen significantly shortens the duration of treatment needed to prevent relapse in a murine model of active TB. We undertook the current study to compare directly the activities of human-equivalent doses of P and R in a guinea pig model of chronic TB, in which bacilli are predominantly extracellular within human-like necrotic granulomas. Hartley strain guinea pigs were aerosol infected with ∼200 bacilli of
Mycobacterium tuberculosis
H37Rv, and treatment given 5 days/week was initiated 6 weeks later. R at 100 mg/kg of body weight and P at 100 mg/kg were given orally alone or in combination with isoniazid (H) at 60 mg/kg and pyrazinamide (Z) at 300 mg/kg. Culture-positive relapse was assessed in subgroups of guinea pigs after completion of 1 and 2 months of treatment. Human-equivalent doses of R and P showed equivalent bactericidal activity when used alone and in combination therapy. In guinea pigs treated with rifampin, isoniazid, and pyrazinamide (RHZ) or PHZ, microbiological relapse occurred in the lungs of 8/10 animals treated for 1 month and in 0/10 animals treated for 2 months. Substitution of P for R in the standard antitubercular regimen did not shorten the time to cure in this guinea pig model of chronic TB. Data from ongoing clinical trials comparing the activity of these two drugs are awaited to determine the relevance of the guinea pig TB model in preclinical drug screening.
The Order Bacillales Hosts Functional Homologs of the Worrisome
cfr
Antibiotic Resistance Gene
Authors: Hansen Lykke H. , Planellas Mercè H. , Long Katherine S. , Vester Birte
Published: May 2012

The
cfr
gene encodes the Cfr methyltransferase that methylates a single adenine in the peptidyl transferase region of bacterial ribosomes. The methylation provides resistance to several classes of antibiotics that include drugs of clinical and veterinary importance. This paper describes a first step toward elucidating natural residences of the worrisome
cfr
gene and functionally similar genes. Three
cfr
-like genes from the order
Bacillales
were identified from BLAST searches and cloned into plasmids under the control of an inducible promoter. Expression of the genes was induced in
Escherichia coli
, and MICs for selected antibiotics indicate that the
cfr
-like genes confer resistance to PhLOPSa (phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A) antibiotics in the same way as the
cfr
gene. In addition, modification at A2503 on 23S rRNA was confirmed by primer extension. Finally, expression of the Cfr-like proteins was verified by SDS gel electrophoresis of whole-cell extracts. The work shows that
cfr
-like genes exist in the environment and that
Bacillales
are natural residences of
cfr
-like genes.
Impact of Cefepime Therapy on Mortality among Patients with Bloodstream Infections Caused by Extended-Spectrum-β-Lactamase-Producing Klebsiella pneumoniae and Escherichia coli
Authors: Chopra Teena , Marchaim Dror , Veltman Jennifer , Johnson Paul , Zhao Jing J. , Tansek Ryan , Hatahet Dania , Chaudhry Khawar , Pogue Jason M. , Rahbar Hiro , Chen Ting-Yi , Truong Thientu , Rodriguez Victor , Ellsworth Joseph , Bernabela Luigino , Bhargava Ashish , Yousuf Adnan , Alangaden George , Kaye Keith S.
Published: May 2012

Extended-spectrum-β-lactamase (ESBL)-producing pathogens are associated with extensive morbidity and mortality and rising health care costs. Scant data exist on the impact of antimicrobial therapy on clinical outcomes in patients with ESBL bloodstream infections (BSI), and no large studies have examined the impact of cefepime therapy. A retrospective 3-year study was performed at the Detroit Medical Center on adult patients with BSI due to ESBL-producing
Klebsiella pneumoniae
or
Escherichia coli
. Data were collected from the medical records of study patients at five hospitals between January 2005 and December 2007. Multivariate analysis was performed using logistic regression. One hundred forty-five patients with BSI due to ESBL-producing pathogens, including
K. pneumoniae
(83%) and
E. coli
(16.5%), were studied. The mean age of the patients was 66 years. Fifty-one percent of the patients were female, and 79.3% were African-American. Fifty-three patients (37%) died in the hospital, and 92 survived to discharge. In bivariate analysis, the variables associated with mortality (
P
< 0.05) were presence of a rapidly fatal condition at the time of admission, use of gentamicin as a consolidative therapeutic agent, and presence of one or more of the following prior to culture date: mechanical ventilation, stay in the intensive care unit (ICU), and presence of a central venous catheter. In multivariate analysis, the predictors of in-hospital mortality included stay in the intensive care unit (odds ratio [OR], 2.17; 95% confidence interval [CI], 0.98 to 4.78), presence of a central-line catheter prior to positive culture (OR, 2.33; 95% CI, 0.77 to 7.03), presence of a rapidly fatal condition at the time of admission (OR, 5.13; 95% CI, 2.13 to 12.39), and recent prior hospitalization (OR, 1.92; 95% CI, 0.83 to 4.09). When carbapenems were added as empirical therapy to the predictor model, there was a trend between empirical carbapenem therapy and decreased mortality (OR, 0.61; 95% CI, 0.26 to 1.50). When added to the model, receipt of empirical cefepime alone (
n
= 43) was associated with increased mortality, although this association did not reach statistical significance (OR, 1.66; 95% CI, 0.71 to 3.87). The median length of hospital stay was shorter for patients receiving empirical cefepime than for those receiving empirical or consolidated carbapenem therapy. In multivariate analysis, empirical therapy with cefepime for BSI due to an ESBL-producing pathogen was associated with a trend toward an increased mortality risk and empirical carbapenem therapy was associated with a trend toward decreased mortality risk.
Ehrlichia chaffeensis TRP32 Interacts with Host Cell Targets That Influence Intracellular Survival
Authors: Luo Tian , McBride Jere W.
Published: May 2012

Ehrlichia chaffeensis
is an obligately intracellular bacterium that exhibits tropism for mononuclear phagocytes and survives by evading host cell defense mechanisms. Recently, molecular interactions of
E. chaffeensis
tandem repeat proteins 47 and 120 (TRP47 and -120) and the eukaryotic host cell have been described. In this investigation, yeast two-hybrid analysis demonstrated that an
E. chaffeensis
type 1 secretion system substrate, TRP32, interacts with a diverse group of human proteins associated with major biological processes of the host cell, including protein synthesis, trafficking, degradation, immune signaling, cell signaling, iron metabolism, and apoptosis. Eight target proteins, including translation elongation factor 1 alpha 1 (EF1A1), deleted in azoospermia (DAZ)-associated protein 2 (DAZAP2), ferritin light polypeptide (FTL), CD63, CD14, proteasome subunit beta type 1 (PSMB1), ring finger and CCCH-type domain 1 (RC3H1), and tumor protein p53-inducible protein 11 (TP53I11) interacted with TRP32 as determined by coimmunoprecipitation assays, colocalization with TRP32 in HeLa and THP-1 cells, and/or RNA interference. Interactions between TRP32 and host targets localized to the
E. chaffeensis
morulae or in the host cell cytoplasm adjacent to morulae. Common or closely related interacting partners of
E. chaffeensis
TRP32, TRP47, and TRP120 demonstrate a molecular convergence on common cellular processes and molecular cross talk between
Ehrlichia
TRPs and host targets. These findings further support the role of TRPs as effectors that promote intracellular survival.
VirK Is a Periplasmic Protein Required for Efficient Secretion of Plasmid-Encoded Toxin from Enteroaggregative Escherichia coli
Authors: Tapia-Pastrana Gabriela , Chavez-Dueñas Lucia , Lanz-Mendoza Humberto , Teter Ken , Navarro-García Fernando
Published: May 2012

Despite the autotransporter (AT) moniker, AT secretion appears to involve the function of periplasmic chaperones. We identified four periplasmic proteins that specifically bound to plasmid-encoded toxin (Pet), an AT produced by enteroaggregative
Escherichia coli
(EAEC). These proteins include the 17-kDa Skp chaperone and the 37-kDa VirK protein. We found that the
virK
gene is present in different
Enterobacteriaceae
. VirK bound to misfolded conformations of the Pet passenger domain, but it did not bind to the folded passenger domain or to the β domain of Pet. Assays with an EAECΔ
virK
mutant and its complemented version showed that, in the absence of VirK, Pet was not secreted but was instead retained in the periplasm as proteolytic fragments. In contrast, Pet was secreted from a Δ
skp
mutant. VirK was not required for the insertion of porin proteins into the outer membrane but assisted with insertion of the Pet β domain into the outer membrane. Loss of VirK function blocked the EAEC-mediated cytotoxic effect against HEp-2 cells. Thus, VirK facilitates the secretion of the AT Pet by maintaining the passenger domain in a conformation that both avoids periplasmic proteolysis and facilitates β-domain insertion into the outer membrane.
Effects of bird ingestion on seed germination of Vaccinium cylindraceum (Ericaceae), an endemic species of the Azores archipelago1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Pereira M.J. , Mourato C.
Published: May 2012

In this paper we investigate the effects of bird ingestion on Vaccinium cylindraceum Smith seed germination characteristics and the effect of a lack of bird dispersal on seed germination in the field. To test the effect of bird ingestion on seed germination, we carried out laboratory germination trials using ingested seeds and manually depulped seeds. To test the effect of a lack of bird dispersal on seed germination, we carried out germination trials using intact fruits above or under a cap of dead leaves under field conditions. The number of damaged seeds per fruit differed between species. Nearly 92% and 70% of the seeds ingested by, respectively, Erithacus rubecula and Turdus merula passed intact through the birds’ digestive tracts, and the germination characteristics of these seeds were not significantly affected. Only 16% of the seeds ingested passed intact through the digestive tract of Fringilla coelebs , and the germination ability of these seeds was significantly reduced. Uncovered intact berries in the field cracked, exposing the seeds to light, thus resulting in 18% of germination. Our results suggest that E. rubecula, T. merula, and F. coelebs can act as seed dispersers of V. cylindraceum. Also, V. cylindraceum seeds do not need to be ingested to germinate, but seed germination is enhanced as a consequence of seed exposure to light.
Beyond botany to genetic resource preservation: the S.P. Vander Kloet Vaccinium collections1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Hummer Kim E. , Jamieson Andrew R. , Newell Ruth E.
Published: May 2012

Sam P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a seed bank and living plant collections at the Agriculture and Agri-Food Canada Research Centre, Kentville, Nova Scotia, Canada; the K.C. Irving Environmental Science Centre and Harriet Irving Botanical Gardens, Acadia University, Wolfville, Nova Scotia, Canada; the Canadian Clonal Genebank, Harrow, Ontario, Canada; and the US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon, United States. Sam P. Vander Kloet’s collections include representatives of wild Ericaceae with special emphasis on collections of North American and subtropical endemic Vaccinium species. These reference collections are significant and represent a lifetime of dedicated research. Representatives of his heritage collections have now been deposited not only in American genebanks (in Canada and the United States) but also in the World Genebank in Svalbard, Norway, for long term conservation and future evaluation of Vaccinium for the service of humanity. The bequest of his wild collected germplasm will continue to be available to facilitate utilization of an extended Vaccinium gene pool for development and breeding throughout the world.
Floral volatile composition of four species of Vaccinium1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Forney Charles F. , Javorek Steven K. , Jordan Michael A. , Vander Kloet Sam P.
Published: May 2012

The floral volatile composition of four species of Vaccinium was profiled to asses the diversity of the floral chemistry within this genus. Flowers of Vaccinium angustifolium Aiton, Vaccinium varingiaefolium Miq., Vaccinium arboreum Marsh., and Vaccinium poasanum Donn. Sm. were sampled from three or more plants, and volatiles were collected and analyzed by gas chromatography – mass spectroscopy. A total of 45 volatile compounds were detected in the air (headspace) surrounding flowers including 40 from V. angustifolium, 34 for V. varingiaefolium, 37 for V. arboreum, and 17 for V. poasanum. Of the volatile compounds identified, 34 were terpenoids, 6 were benzoids and phenylpropanoids, 4 were aliphatics, and 1 was a miscellaneous cyclic compound. Terpenoids accounted for 98%, 80%, 76%, and 67% of the total volatiles for V. angustifolium, V. varingiaefolium, V. arboreum, and V. poasanum, respectively. The most abundant volatile compound emitted from the flowers of each species was α-pinene for V. angustifolium (23%) and V. arboreum (63%), methyl benzoate for V. varingiaefolium (18%), and ethyl benzene for V. poasanum (21%). Substantial variation was observed in the floral volatile composition of these four Vaccinium species, which may reflect their diverse ecological origins.
The regeneration ecology of Empetrum nigrum, the black crowberry, on coastal heathland in Nova Scotia1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Hill Nicholas M. , Vander Kloet Sam P. , Garbary David J.
Published: May 2012

The reproductive cycle of the black crowberry ( Empetrum nigrum L., Ericaceae) was investigated on exposed headlands on the Atlantic coast of Nova Scotia. At the main study site, Gaff Point, aerial photographs revealed a shoreline retreat rate from 1976 to 2011 (ca. 0.3 m·y–1), with a threefold increase in the rate of heath area loss in the last 10 years relative to the previous 25 years (1976–2001). Empetrum nigrum produces a large crop of berries and sets up seedlings via three main dispersers (gulls, passerines, and mink) at the sea edge and woodland margin. Laboratory study demonstrated that seed germination was scant and slow in the season of berry production but that it was rapid and substantial (mean 33%–50% from berry or scat) for seeds that incubated overwinter in berry or in scat. The largest seed bank coincides with the site of greatest berry production in the heath, but seedlings were not observed in its mat. Most of the scat rain (77%) is deposited at the shore edge and seedlings here are lost to coastal erosion over-winter. Spruce tree understories are the only safe sites for seedling establishment, and if these juveniles become adults of heathland formed after the death of edge trees, the crowberry has an ontogenetic niche shift adapted to climate change. A preliminary checklist is provided for conservation managers of coastal heaths.
Antiglycation activity of Vaccinium spp. (Ericaceae) from the Sam Vander Kloet collection for the treatment of type II diabetes1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Ferrier Jonathan , Djeffal Sabrina , Morgan Holly Porter , Vander Kloet Sam P. , Redžić Sulejman , Cuerrier Alain , Balick Michael J. , Arnason John T.
Published: May 2012

In this report, the inhibition of advanced glycation endproducts (AGEs) by extracts of leaves from a collection of six, mainly tropical, Vaccinium L. spp. (Ericaceae) was examined. Indigenous Peoples have used Vaccinium species to treat symptoms of type I and II diabetes. Sustained hyperglycaemia, often associated with diabetes, facilitates crosslinking of sugars with proteins, producing AGEs. AGEs are a therapeutic target since they are responsible for many diabetes symptoms and contribute to ageing and the development of atherosclerosis, kidney, vascular, and neurological diseases. Vaccinium barandanum S. Vidal, Vaccinium consanguineum Klotzsch, Vaccinium gaultheriifolium (Griff.) Hook. f. ex C.B. Clarke, Vaccinium poasanum Donn. Sm., Vaccinium tonkinense Dop, and Disterigma rimbachii (A.C. Sm.) Luteyn (outgroup) were collected from Sam Vander Kloet’s common garden collection. Ethanolic extracts of leaves of these Vaccinium spp. were potent inhibitors of AGEs. Vaccinium and outgroup species extracts tested in an AGE inhibition assay demonstrated concentration dependent inhibition, with a half maximal inhibitory concentration (IC50) ranging from 4.2 to 16.2 µg·mL–1. Phenolic content ranged from 258 to 626 (µg quercetin equivalents·mg extract–1). Activity and phenolic content show that these tropical accessions have a higher phenolic content (p < 0.001, t test) and AGE inhibition (p < 0.03, t test) than six temperate species from our collections in eastern North America. Significant relationships were found between IC50 and latitude of geographic origin.
Correlation between
C
α/
Cc
ratio and index parameters of soils
Authors: Jesmani Mehrab , Vaezi Ramin , Kamalzare Mehrad
Published: May 2012

There is a general acceptance of constant
C
α/
Cc
ratio (secondary compression index/ compression index) after many investigations made with different soil specimens. Therefore it should be possible to find useful correlations between soil properties and a soil’s unique
C
α/
Cc
ratio. In this paper the secondary compression behaviour of Iranian soils was investigated through the performance of a series of conventional and long duration 1D consolidation tests conducted on undisturbed samples from 11 sites in different parts of Iran. The characteristics of the secondary compression index were examined and the relationship between the coefficient of secondary compression,
C
α, and compression index,
Cc
, was established for each site. Single and multiple regression models to estimate the ratio of
C
α/
Cc
were investigated based on soil properties (liquid limit (
LL
), plasticity limit (
PL
), plasticity index (
PI
) and natural water content (ω
0
)), and various equations are presented to predict the value of the
C
α/
Cc
ratio of soils.
Comparison of surface wave techniques to estimate shear wave velocity in a sand and gravel sequence: Holme Pierrepont, Nottingham, UK
Authors: Gunn D. A. , Williams G. , Raines M. G. , Busby J. P. , Williams J. D. O. , Pearson S. G.
Published: May 2012

This study evaluated the application of surface wave methods to aggregate variability and thickness determinations. We compared the results of field assessments of sand and gravel sequences using three surface wave survey approaches. The first was a seismic refraction approach, the second, a continuous surface wave (CSW) survey approach, and the third adopted a multi-channel analysis of surface waves (MASW) technique to the original refraction field set-up and records. The sand and gravel sequences were highly heterogeneous and the shear wave profiles were not normally dispersive (i.e. did not exhibit a monotonic increase in velocity with depth), which had a significant effect upon the performance of the three field approaches. Both CSW and MASW approaches provided information over a broad spectrum from which velocity–depth profiles were produced, but the upper frequency of operation was limited in both methods because of poorer signal quality at higher frequencies. Shear wave velocity profiles obtained using vertically vibrating sources during CSW surveys were different from profiles obtained using a horizontally polarized source in the refraction survey. This was attributed to different propagation paths and modes of propagation, which were illustrated via additional tomographic inversion of the refraction travel times but could also be attributed to data inversion methods. Probing using an ultra-lightweight cone penetrometer, continuous reflection profiling using ground-penetrating radar, and also an active extraction programme at the field site provided the opportunity to directly observe the subsurface geology and verify field results. Within the sand and gravel sequence, high-velocity layers were associated with matrix-supported coarse gravel lenses, some of which were weakly cemented. Localized high- and low-velocity zones within the underlying bedrock were interpreted as being related to lithostratigraphic heterogeneity and the development of an upper, weathered zone.
Field strength development of repaired pavement using the recycling technique
Authors: Chinkulkijniwat Avirut , Horpibulsuk Suksun
Published: May 2012

The pavement recycling technique is a way to effectively repair damaged pavements. In this study, statistical analysis shows that the field strength is significantly lower than the laboratory strength. The mixing process used in the pavement recycling technique does not significantly affect the field strength reduction, as indicated by the small variation of the field hand-compacted strength (
q
ufh
) and the laboratory strength (
q
u1
). The curing conditions do significantly control the field strength development. A factor of safety of 2.0 is recommended for design. The strength development mainly depends on the soil-water/cement ratio (
w
/
C
) and curing time regardless of the level of compaction energy. A general strength development model as a function of
w
/
C
and curing time is introduced. Only two laboratory strength data from the specimens cured at two different curing times are required in the proposed model. A high accuracy of the strength prediction is reported. This proposed model is a very powerful tool that determines the strength development of cement-stabilized coarse-grained soil after 7 days of curing. It can also be used to determine the correct quantity of cement to be stabilized for different field mixing water contents, compaction energies and curing times.
Bilinear spatiotemporal basis models
Authors: Akhter Ijaz , Simon Tomas , Khan Sohaib , Matthews Iain , Sheikh Yaser
Published: May 2012

A variety of dynamic objects, such as faces, bodies, and cloth, are represented in computer graphics as a collection of moving spatial landmarks. Spatiotemporal data is inherent in a number of graphics applications including animation, simulation, and object and camera tracking. The principal modes of variation in the spatial geometry of objects are typically modeled using dimensionality reduction techniques, while concurrently, trajectory representations like splines and autoregressive models are widely used to exploit the temporal regularity of deformation. In this article, we present the bilinear spatiotemporal basis as a model that simultaneously exploits spatial and temporal regularity while maintaining the ability to generalize well to new sequences. This factorization allows the use of analytical, predefined functions to represent temporal variation (e.g., B-Splines or the Discrete Cosine Transform) resulting in efficient model representation and estimation. The model can be interpreted as representing the data as a linear combination of spatiotemporal sequences consisting of shape modes oscillating over time at key frequencies. We apply the bilinear model to natural spatiotemporal phenomena, including face, body, and cloth motion data, and compare it in terms of compaction, generalization ability, predictive precision, and efficiency to existing models. We demonstrate the application of the model to a number of graphics tasks including labeling, gap-filling, denoising, and motion touch-up.
Continuous sampling from distributed streams
Authors: Cormode Graham , Muthukrishnan S. , Yi Ke , Zhang Qin
Published: May 2012

A fundamental problem in data management is to draw and maintain a sample of a large data set, for approximate query answering, selectivity estimation, and query planning. With large, streaming data sets, this problem becomes particularly difficult when the data is shared across multiple distributed sites. The main challenge is to ensure that a sample is drawn uniformly across the union of the data while minimizing the communication needed to run the protocol on the evolving data. At the same time, it is also necessary to make the protocol lightweight, by keeping the space and time costs low for each participant. In this article, we present communication-efficient protocols for continuously maintaining a sample (both with and without replacement) from
k
distributed streams. These apply to the case when we want a sample from the full streams, and to the sliding window cases of only the
W
most recent elements, or arrivals within the last
w
time units. We show that our protocols are optimal (up to logarithmic factors), not just in terms of the communication used, but also the time and space costs for each participant.
Computational historiography
Authors: Mimno David
Published: May 2012

More than a century of modern Classical scholarship has created a vast archive of journal publications that is now becoming available online. Most of this work currently receives little, if any, attention. The collection is too large to be read by any single person and mostly not of sufficient interest to warrant traditional close reading. This article presents computational methods for identifying patterns and testing hypotheses about Classics as a field. Such tools can help organize large collections, introduce younger scholars to the history of the field, and act as a “survey,” identifying anomalies that can be explored using more traditional methods.
Measuring and coding language change
Authors: Hirschmann Hagen , Lüdeling Anke , Zeldes Amir
Published: May 2012

Our article explores the possibilities of using deeply annotated, incrementally evolving comparable corpora for the study of language change, in this case for different stages from Old High German to New High German. Using the example of the evolution of German past tenses, we show how a variety of categories ranging from low to high complexity interact with the choice between competing linguistic variants. To adequately explore the influence of these categories, we use a multilayer corpus architecture that develops together with our study. We show that a combination of quantitative and qualitative analyses can recognize relevant contextual factors, which feed into the addition of new annotation layers applying to the same data. By making our categorizations explicit as corpus annotations and our data available to other researchers, we promote an open, extensible, and transparent mode of research, where both raw data and the inferential process are exposed to other researchers.
Parameterized loop tiling
Authors: Renganarayanan Lakshminarayanan , Kim Daegon , Strout Michelle Mills , Rajopadhye Sanjay
Published: May 2012

Loop tiling is a widely used program optimization that improves data locality and enables coarse-grained parallelism. Parameterized tiled loops, where the tile sizes remain symbolic parameters until runtime, are quite useful for iterative compilers and autotuners that produce highly optimized libraries and codes. Although it is easy to generate such loops for (hyper-) rectangular iteration spaces tiled with (hyper-) rectangular tiles, many important computations do not fall into this restricted domain. In the past, parameterized tiled code generation for the general case of convex iteration spaces being tiled by (hyper-) rectangular tiles has been solved with bounding box approaches or with sophisticated and expensive machinery.

We present a novel formulation of the parameterized tiled loop generation problem using a polyhedral set called the
outset
. By reducing the problem of parameterized tiled code generation to that of generating standard loops and simple postprocessing of these loops, the outset method achieves a code generation efficiency that is comparable to existing code generation techniques, including those for fixed tile sizes. We compare the performance of our technique with several other tiled loop generation methods on kernels from BLAS3 and scientific computations. The simplicity of our solution makes it well suited for use in production compilers—in particular, the IBM XL compiler uses the inset-based technique introduced in this article for register tiling. We also provide a complete coverage of parameterized tiling of perfect loop nests by describing three related techniques: (i) a scheme for separating full and partial tiles; (ii) a scheme for generating tiled loops directly from the abstract syntax tree representation of loops; (iii) a formal characterization of parameterized loop tiling using bilinear forms and a Symbolic Fourier-Motzkin Elimination (SFME)-based parameterized tiled loop generation method.
Fairness via Source Throttling
Authors: Ebrahimi Eiman , Lee Chang Joo , Mutlu Onur , Patt Yale N.
Published: May 2012

Cores in chip-multiprocessors (CMPs) share multiple memory subsystem resources. If resource sharing is unfair, some applications can be delayed significantly while others are unfairly prioritized. Previous research proposed separate fairness mechanisms for each resource. Such resource-based fairness mechanisms implemented independently in each resource can make contradictory decisions, leading to low fairness and performance loss. Therefore, a coordinated mechanism that provides fairness in the entire shared memory system is desirable.

This article proposes a new approach that provides fairness in the entire shared memory system, thereby eliminating the need for and complexity of developing fairness mechanisms for each resource. Our technique, Fairness via Source Throttling (FST), estimates unfairness in the
entire memory system
. If unfairness is above a system-software-set threshold, FST throttles down cores causing unfairness by limiting the number of requests they create and the frequency at which they do. As such, our
source-based
fairness control ensures fairness decisions are made in tandem in the entire memory system. FST enforces thread priorities/weights, and enables system-software to enforce different fairness objectives in the memory system.

Our evaluations show that FST provides the best system fairness and performance compared to three systems with state-of-the-art fairness mechanisms implemented in both shared caches and memory controllers.
Decentralized approaches for self-adaptation in agent organizations
Authors: Kota Ramachandra , Gibbins Nicholas , Jennings Nicholas R.
Published: May 2012

Self-organizing multi-agent systems provide a suitable paradigm for developing autonomic computing systems that manage themselves. Towards this goal, we demonstrate a robust, decentralized approach for structural adaptation in explicitly modeled problem solving agent organizations. Based on self-organization principles, our method enables the autonomous agents to modify their structural relations to achieve a better allocation of tasks in a simulated task-solving environment. Specifically, the agents reason about when and how to adapt using only their history of interactions as guidance. We empirically show that, in a wide range of closed, open, static, and dynamic scenarios, the performance of organizations using our method is close (70–90%) to that of an idealized centralized allocation method and is considerably better (10–60%) than the current state-of-the-art decentralized approaches.
Host selection through collective decision
Authors: Saffre Fabrice , Simaitis Aistis
Published: May 2012

In this article, we present a collective decision-making framework inspired by biological swarms and capable of supporting the emergence of a consensus within a population of agents in the absence of environment-mediated communication (stigmergy). Instead, amplification is the result of the variation of a confidence index, stored in individual memory and providing each agent with a statistical estimate of the current popularity of its preferred choice within the whole population. We explore the fundamental properties of our framework using a combination of analytical and numerical methods. We then use Monte Carlo simulation to investigate its applicability to host selection in the presence of multiple alternatives, a problem found in application migration scenarios. The advantages of self-organization and the use of statistically predictive methods in this context are also discussed.
A formalized, taxonomy-driven approach to cross-layer application adaptation
Authors: Popescu Razvan , Staikopoulos Athanasios , Brogi Antonio , Liu Peng , Clarke Siobhán
Published: May 2012

Advances in pervasive technology have made it possible to consider large-scale application types that potentially span heterogeneous organizations, technologies, and device types. This class of application will have a multilayer architecture, where each layer is likely to use languages and technologies appropriate to its own concerns. An example application is a geographically large-scale crisis management system. Typically, such applications are required to dynamically adapt their behavior based on current circumstances, with adaptations potentially affecting all layers of the application. The complexities involved in dynamically adapting multilayer applications will significantly benefit from formal approaches to its specification.

This article presents a new methodology for flexible, multilayer application adaptation, with layer-specific adaptation solution templates bound to application mismatches that are organized into hierarchical taxonomies. Templates can be linked either through direct invocations or through adaptation events, supporting flexible cross-layer adaptation. The methodology illustrates the use of different formalisms for different elements of its specification. In particular, we combine semiformal metamodeling techniques for the system model specification with formal Petri nets, which are used to capture template matchmaking using reachability analysis. This work demonstrates how existing formalisms can be used for the specification of a generic adaptation model for pervasive applications.
FORMS
Authors: Weyns Danny , Malek Sam , Andersson Jesper
Published: May 2012

The challenges of pervasive and mobile computing environments, which are highly dynamic and unpredictable, have motivated the development of self-adaptive software systems. Although noteworthy successes have been achieved on many fronts, the construction of such systems remains significantly more challenging than traditional systems. We argue this is partially because researchers and practitioners have been struggling with the lack of a precise vocabulary for describing and reasoning about the key architectural characteristics of self-adaptive systems. Further exacerbating the situation is the fact that existing frameworks and guidelines do not provide an encompassing perspective of the different types of concerns in this setting. In this article, we present a comprehensive reference model, entitled FOrmal Reference Model for Self-adaptation (FORMS), that targets both issues. FORMS provides rigor in the manner such systems can be described and reasoned about. It consists of a small number of formally specified modeling elements that correspond to the key concerns in the design of self-adaptive software systems, and a set of relationships that guide their composition. We demonstrate FORMS's ability to precisely describe and reason about the architectural characteristics of distributed self-adaptive software systems through its application to several existing systems. FORMS's expressive power gives it a potential for documenting reusable architectural solutions (e.g., architectural patterns) to commonly encountered problems in this area.
Autonomic multi-policy optimization in pervasive systems
Authors: Dusparic Ivana , Cahill Vinny
Published: May 2012

This article describes Distributed W-Learning (DWL), a reinforcement learning-based algorithm for collaborative agent-based optimization of pervasive systems. DWL supports optimization towards multiple heterogeneous policies and addresses the challenges arising from the heterogeneity of the agents that are charged with implementing them. DWL learns and exploits the dependencies between agents and between policies to improve overall system performance. Instead of always executing the locally-best action, agents learn how their actions affect their immediate neighbors and execute actions suggested by neighboring agents if their importance exceeds the local action's importance when scaled using a predefined or learned collaboration coefficient. We have evaluated DWL in a simulation of an Urban Traffic Control (UTC) system, a canonical example of the large-scale pervasive systems that we are addressing. We show that DWL outperforms widely deployed fixed-time and simple adaptive UTC controllers under a variety of traffic loads and patterns. Our results also confirm that enabling collaboration between agents is beneficial as is the ability for agents to learn the degree to which it is appropriate for them to collaborate. These results suggest that DWL is a suitable basis for optimization in other large-scale systems with similar characteristics.
A morphogenetic framework for self-organized multirobot pattern formation and boundary coverage
Authors: Guo Hongliang , Jin Yaochu , Meng Yan
Published: May 2012

Embryonic development of multicellular organisms, also known as morphogenesis, is regarded as a robust self-organization process for pattern generation. Inspired by the recent findings in biology indicating that morphogen gradients, together with a Gene Regulatory Network (GRN), play a key role in biological patterning, we propose a framework for self-organized multirobot pattern formation and boundary coverage based on an artificial GRN model. The proposed framework does not need a global coordinate system, which makes it more practical to be implemented in a physical robotic system. Moreover, an adaptation mechanism is included in the framework so that the self-organization algorithm is robust to changes in the number of robots. Various case studies of multirobot pattern formation and boundary coverage show the effectiveness of the framework.
What can Steve Jobs and Jonathan Ive teach us about designing?
Authors: Dubberly Hugh
Published: May 2012

Models help bridge the gap between observing and making---especially when systems are involved (as in designing for interaction, service, and evolution). This forum introduces new models, links them to existing models, and describes their histories and why they matter.

Hugh Dubberly, Editor
The ACM Multimedia Grand Challenge 2011 in a nutshell
Authors: Friedland Gerald , Jin Yohan
Published: May 2012

The 2011 ACM Multimedia Grand Challenge proved to be the most competitive so far. This article provides a quick summary of the competition. More comprehensive coverage can be found in an IEEE Multimedia Magazine report.