bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of Tinto River Sediment Microbial Communities: Importance of Sulfate-Reducing Bacteria and Their Role in Attenuating Acid Mine Drainage
Authors: Sánchez-Andrea Irene , Knittel Katrin , Amann Rudolf , Amils Ricardo , Sanz José Luis
Published: April 2012

Tinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed reporter deposition fluorescence
in situ
hybridization with domain-specific probes showed that
Bacteria
(>98%) dominated over
Archaea
(<2%) at both sites, important differences were detected at the class and genus levels, reflecting differences in pH, redox potential, and heavy metal concentrations. At SN, where the pH and redox potential are similar to that of the water column (pH 2.5 and +400 mV), the most abundant organisms were identified as iron-reducing bacteria:
Acidithiobacillus
spp. and
Acidiphilium
spp., probably related to the higher iron solubility at low pH. At the JL dam, characterized by a banded sediment with higher pH (4.2 to 6.2), more reducing redox potential (−210 mV to 50 mV), and a lower solubility of iron, members of sulfate-reducing genera
Syntrophobacter
,
Desulfosporosinus
, and
Desulfurella
were dominant. The latter was quantified with a newly designed CARD-FISH probe. In layers where sulfate-reducing bacteria were abundant, pH was higher and redox potential and levels of dissolved metals and iron were lower. These results suggest that the attenuation of ARD characteristics is biologically driven by sulfate reducers and the consequent precipitation of metals and iron as sulfides.
Recombinogenic Properties of Pyrococcus furiosus Strain COM1 Enable Rapid Selection of Targeted Mutants
Authors: Farkas Joel , Stirrett Karen , Lipscomb Gina L. , Nixon William , Scott Robert A. , Adams Michael W. W. , Westpheling Janet
Published: April 2012

We recently reported the isolation of a mutant of
Pyrococcus furiosus
, COM1, that is naturally and efficiently competent for DNA uptake. While we do not know the exact nature of this mutation, the combined transformation and recombination frequencies of this strain allow marker replacement by direct selection using linear DNA. In testing the limits of its recombination efficiency, we discovered that marker replacement was possible with as few as 40 nucleotides of flanking homology to the target region. We utilized this ability to design a strategy for selection of constructed deletions using PCR products with subsequent excision, or “pop-out,” of the selected marker. We used this method to construct a “markerless” deletion of the
trpAB
locus in the GLW101 (COM1 Δ
pyrF
) background to generate a strain (JFW02) that is a tight tryptophan auxotroph, providing a genetic background with two auxotrophic markers for further strain construction. The utility of
trpAB
as a selectable marker was demonstrated using prototrophic selection of plasmids and genomic DNA containing the wild-type
trpAB
alleles. A deletion of
radB
was also constructed that, surprisingly, had no obvious effect on either recombination or transformation, suggesting that its gene product is not involved in the COM1 phenotype. Attempts to construct a
radA
deletion mutation were unsuccessful, suggesting that this may be an essential gene. The ease and speed of this procedure will facilitate the construction of strains with multiple genetic changes and allow the construction of mutants with deletions of virtually any nonessential gene.
TatAc, the Third TatA Subunit of
Bacillus subtilis
, Can Form Active Twin-Arginine Translocases with the TatCd and TatCy Subunits
Authors: Monteferrante Carmine G. , Baglieri Jacopo , Robinson Colin , van Dijl Jan Maarten
Published: April 2012

Two independent twin-arginine translocases (Tat) for protein secretion were previously identified in the Gram-positive bacterium
Bacillus subtilis
. These consist of the TatAd-TatCd and TatAy-TatCy subunits. The function of a third TatA subunit named TatAc was unknown. Here, we show that TatAc can form active protein translocases with TatCd and TatCy.
Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil
Authors: Nunney Leonard , Yuan Xiaoli , Bromley Robin E. , Stouthamer Richard
Published: April 2012

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in
Xylella fastidiosa
subsp.
pauca
from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (
leuA
,
petC
,
malF
,
cysG
, and
holC
). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another
X. fastidiosa
subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that
X. fastidiosa
subsp.
pauca
became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly
X. fastidiosa
subsp.
multiplex
). This hypothesis predicts that nonrecombinant native
X. fastidiosa
subsp.
pauca
(not yet isolated) does not cause disease in citrus or coffee.
Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH
Authors: Rimaux T. , Rivière A. , Illeghems K. , Weckx S. , De Vuyst L. , Leroy F.
Published: April 2012

The adaptation of
Lactobacillus sakei
to a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. In
L. sakei
CTC 494, the
arc
operon (
arcABCTDR
) shows the same gene order and organization as that in
L. sakei
23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case of
L. sakei
CTC 494 and in the mid-exponential growth phase of
L. sakei
23K. Also, the environmental pH influenced the relative expression level of the
arc
operon, as shown for
L. sakei
CTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of the
arc
operon. Furthermore, a differential relative expression of the individual genes of the
arc
operon was found, with the highest relative gene expression occurring for the first two genes of the
arc
operon (
arcA
and
arcB
). Finally, it was shown that some
L. sakei
strains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putative
arc
operon.
Involvement of a Natural Fusion of a Cytochrome P450 and a Hydrolase in Mycophenolic Acid Biosynthesis
Authors: Hansen Bjarne Gram , Mnich Ewelina , Nielsen Kristian Fog , Nielsen Jakob Blæsbjerg , Nielsen Morten Thrane , Mortensen Uffe Hasbro , Larsen Thomas Ostenfeld , Patil Kiran Raosaheb
Published: April 2012

Mycophenolic acid (MPA) is a fungal secondary metabolite and the active component in several immunosuppressive pharmaceuticals. The gene cluster coding for the MPA biosynthetic pathway has recently been discovered in
Penicillium brevicompactum
, demonstrating that the first step is catalyzed by MpaC, a polyketide synthase producing 5-methylorsellinic acid (5-MOA). However, the biochemical role of the enzymes encoded by the remaining genes in the MPA gene cluster is still unknown. Based on bioinformatic analysis of the MPA gene cluster, we hypothesized that the step following 5-MOA production in the pathway is carried out by a natural fusion enzyme MpaDE, consisting of a cytochrome P450 (MpaD) in the N-terminal region and a hydrolase (MpaE) in the C-terminal region. We verified that the fusion gene is indeed expressed in
P. brevicompactum
by obtaining full-length sequence of the
mpaDE
cDNA prepared from the extracted RNA. Heterologous coexpression of
mpaC
and the fusion gene
mpaDE
in the MPA-nonproducer
Aspergillus nidulans
resulted in the production of 5,7-dihydroxy-4-methylphthalide (DHMP), the second intermediate in MPA biosynthesis. Analysis of the strain coexpressing
mpaC
and the
mpaD
part of
mpaDE
shows that the P450 catalyzes hydroxylation of 5-MOA to 4,6-dihydroxy-2-(hydroxymethyl)-3-methylbenzoic acid (DHMB). DHMB is then converted to DHMP, and our results suggest that the hydrolase domain aids this second step by acting as a lactone synthase that catalyzes the ring closure. Overall, the chimeric enzyme MpaDE provides insight into the genetic organization of the MPA biosynthesis pathway.
Interleukin-10 Induction Is an Important Virulence Function of the Yersinia pseudotuberculosis Type III Effector YopM
Authors: McPhee Joseph B. , Mena Patricio , Zhang Yue , Bliska James B.
Published: May 2012

PathogenicYersiniaspecies modulate host immune responses through the activity of a plasmid-encoded type III secretion system and its associated effector proteins. One effector, YopM, is a leucine-rich-repeat-containing protein that is important for virulence in murine models ofYersiniainfection. Although the mechanism by which YopM promotes virulence is unknown, we previously demonstrated that YopM was required for the induction of high levels of the immunosuppressive cytokine interleukin-10 (IL-10) in sera of C57BL/6J mice infected withYersinia pseudotuberculosis. To determine if IL-10 production is important for the virulence function of YopM, C57BL/6J or congenic IL-10−/−mice were infected intravenously with wild-type oryopMmutantY. pseudotuberculosisstrains. Analysis of cytokine levels in serum and bacterial colonization in the spleen and liver showed that YopM is required for IL-10 induction in C57BL/6J mice infected with either the IP32953 or the 32777 strain ofY. pseudotuberculosis, demonstrating that the phenotype is conserved in the species. In single-strain infections, the ability of the 32777ΔyopMmutant to colonize the liver was significantly increased by the delivery of exogenous IL-10 to C57BL/6J mice. In mixed infections, the competitive advantage of ayopM+32777 strain over an isogenicyopMmutant to colonize spleen and liver, as observed for C57BL/6J mice, was significantly reduced in IL-10−/−animals. Thus, by experimentally controlling IL-10 levels in a mouse infection model, we obtained evidence that the induction of this cytokine is an important mechanism by which YopM contributes toY. pseudotuberculosisvirulence.
Socio-demographic determinants of worsening in frailty among community-dwelling older people in 11 European countries
Authors: Etman Astrid , Burdorf Alex , Van der Cammen Tischa J M , Mackenbach Johan P , Van Lenthe Frank J
Published: April 2012

Background

The rapid increase of frail older people worldwide will have a substantial impact on healthcare systems. The frailty process may be delayed or even reversed, which makes it attractive for early interventions. However, little is known about the determinants of frailty state changes. The aim of this study is to compare socio-demographic determinants of worsening in frailty state in 11 European countries.

Methods

Data of 14 424 community-dwelling persons aged ≥55 years, enrolled in 2004 in the Survey of Health, Ageing and Retirement in Europe, were analysed. Three frailty states were identified (non-frail, pre-frail and frail) using Fried's criteria, and frailty state changes over a 2-year period were determined. Multinomial regression analyses adjusted for baseline frailty state were conducted to investigate whether sex, age, marital status and level of education determined a worsening in frailty state in the total and country-specific European population.

Results

Of all individuals, 22.1% worsened, 61.8% showed no change and 16.1% improved in frailty state. Women, those aged ≥65 years, and lower educated persons showed an increased risk of worsening in frailty state. In Southern European countries, there was an earlier and larger increase in risk of worsening in frailty state in life, which was more pronounced in women compared with men.

Conclusions

In Europe, persons aged ≥65 years, women and lower educated persons are at increased risk of worsening in frailty state. Differences between countries indicate that interventions aimed at delaying the frailty process in Southern European countries should start earlier with more attention towards women.
Seven-year hospital and nursing home care use according to age and proximity to death: variations by cause of death and socio-demographic position
Authors: Martikainen Pekka , Murphy Michael , Metsä-Simola Niina , Häkkinen Unto , Moustgaard Heta
Published: April 2012

Background

Provision of hospital and long-term care services for the growing number of older people is a major policy concern. The authors estimate hospital and nursing home care use by age and proximity to death for selected causes and by gender, education and marital status.

Methods

A 40% random sample of the Finnish population aged 65+ years alive at the end of 1997 was followed to death in 1998–2002. Use of hospital and nursing home care was assessed up to 7 years prior to death for those who died and prior to the end of 2002 for survivors.

Results

In the 7-year period, before death total average care days were 294 (95% CI 286 to 301) for men and 430 (95% CI 423 to 438) for women. For surviving men and women, the corresponding figures were 89 (95% CI 86 to 92) and 136 (95% CI 130 to 141) days. Use of hospital and particularly nursing home care increased rapidly with age, while proximity to death was more important for hospital care. The married used less care than the non-married. Care use of those dying from dementia was approximately twice that for all causes combined and was substantial for an extended period before death.

Conclusions

The effects of age are more substantial for nursing home than for hospital care use, and both are larger the older the age at death. Care use will be considerably higher among the non-married. Increasing longevity coupled with a rising trend of dementia is likely to mean a major shift towards higher nursing home care use in the future.
Dose–response relationships between physical activity, walking and health-related quality of life in mid-age and older women
Authors: Heesch Kristiann C , van Uffelen Jannique G Z , van Gellecum Yolanda R , Brown Wendy J
Published: April 2012

Background

Although physical activity is associated with health-related quality of life (HRQL), the nature of the dose–response relationship remains unclear.

Objectives

To examine the concurrent and prospective dose–response relationships between total physical activity (TPA) and (only) walking with HRQL in two age cohorts of women.

Methods

Participants were 10 698 women born in 1946–1951 and 7646 born in 1921–1926, who completed three mailed surveys for the Australian Longitudinal Study on Women's Health. They reported weekly TPA minutes (sum of walking, moderate and vigorous minutes). HRQL was measured with the Medical Outcomes Study Short-Form 36 Health Status Survey (SF-36). Linear mixed models, adjusted for socio-demographic and health-related variables, were used to examine associations between TPA level (none, very low, low, intermediate, sufficient, high and very high) and SF-36 scores. For women who reported walking as their only physical activity, associations between walking and SF-36 scores were also examined.

Results

Curvilinear trends were observed between TPA and walking with SF-36 scores. Concurrently, HRQL scores increased significantly with increasing TPA and walking, in both cohorts, with increases less marked above sufficient activity levels. Prospectively, associations were attenuated although significant and meaningful improvements in physical functioning and vitality were observed across most TPA and walking categories above the low category.

Conclusion

For women in their 50s–80s without clinical depression, greater amounts of TPA are associated with better current and future HRQL, particularly physical functioning and vitality. Even if walking is their only activity, women, particularly those in their 70s–80s, have better HRQL.
The stent anchor technique for distal access through a large or giant aneurysm
Authors: Fargen Kyle M , Velat Gregory J , Lawson Matthew F , Hoh Brian L , Mocco J
Published: April 2012

Large and giant aneurysms pose significant challenges to the endovascular techniques of coil embolization or parent vessel reconstruction. Many large aneurysms are wide-necked with bulbous domes and frequently require stent-assisted coiling or flow diversion to reconstruct and preserve flow through the parent artery. Often the wire must be looped in the dome before catheterization of the exiting portion of the parent vessel is possible. In addition, it can be challenging to obtain stable distal purchase of the microcatheter that will allow the loop to be withdrawn from the aneurysm without the entire microcatheter unwinding, resulting in herniation into the aneurysm or proximal vessels. The stent anchor technique, a novel method of obtaining distal purchase that allows straightening of the catheter loop within a large aneurysm for the purposes of stenting for vessel reconstruction across large or giant aneurysms, is presented. This technique may facilitate the use of new stent technologies in the treatment of large aneurysms that have traditionally been exceedingly difficult to treat via an endovascular approach.
Evaluation of PIMA point-of-care CD4 testing in a large UK HIV service
Authors: Herbert Sophie , Edwards Simon , Carrick Gina , Copas Andrew , Sandford Christopher , Amphlett Marc , Benn Paul
Published: April 2012

Objectives

To evaluate the performance and patient acceptability of the PIMA point-of-care (POCT) CD4 test.

Methods

Parallel POCT and laboratory CD4 testing were performed in newly diagnosed HIV patients and those with chronic infection attending routine or emergency clinics. Demographics, clinical status and time taken for CD4 results to be available were recorded. Patient acceptability was assessed using a five-point Likert scale. POCT and laboratory results were compared.

Results

283 patients underwent POCT and laboratory CD4 testing. Paired laboratory and POCT results were available in 269 patients. After excluding 15 patients tested during the lead-in period, the test comparison was based on 254 results. Most patients were asymptomatic, male and white British reflecting this patient cohort. 236 patients were chronically infected and 47 were newly diagnosed HIV positive. The POCT result was available within 30 min (86%). The laboratory and POCT results were strongly correlated, r=0.93 (p<0.001), but were generally lower for the POCT (201/254 (79%): p<0.001). As a percentage of the laboratory count, the median (95% range) POCT was 87% (57%–126%). The difference between the POCT and laboratory result was greater for those patients attending the emergency clinic. The sensitivity and specificity of the POCT, to identify patients with laboratory CD4 below 350, were 95% (95% CI 88% to 98%) and 88% (95% CI 82% to 93%), respectively. 235 (83%) patients completed the questionnaire and the POCT was highly acceptable.

Conclusions

POCT CD4 was highly correlated with laboratory CD4 testing in this cohort, provided immediate results and was highly acceptable to patients.
Comparison of berry composition of selectedVacciniumspecies (Ericaceae) withGaylussacia dumosa1This 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. , Kalt Wilhelmina , Vander Kloet Sam P.
Published: May 2012

The genus Vaccinium contains a wide array of plants distributed throughout the world including several commercial species as well as epiphytic shrubs and lianas in the tropics. Vaccinium dumosum Andrews was reclassified as Gaylussacia dumosa (Andrews) Torr. & A. Gray in 1843 owing to its single seeded 10-locular ovary. Since then, evidence suggests G. dumosa be returned to Vaccinium. In this study, fruit composition of G. dumosa was compared with that of Vaccinium corymbosum L., Vaccinium angustifolium Aiton, Vaccinium gaulteriifolium (Griff.) Hook. f., Vaccinium acrobracteatum K. Sch., and Vaccinium hirsutum Buckley. Ripe fruit from each species were collected and analyzed. In each of the species, primary sugars were glucose and fructose, and acids were quinic, malic, and citric. Total phenolic content correlated with antioxidant capacity. Anthocyanin profiles showed that fruit from each of the species studied contained no pelargonidin glucosides, which are common in fruit of other genera. A total of 27 volatile compounds, dominated by terpenes and several esters, were detected. These volatiles were all found in four of the species including G. dumosa. No volatile compounds were detected in G. dumosa that were not found in the Vaccinium species. Gaylussacia dumosa showed no chemical composition that was significantly different than that of the Vaccinium species surveyed, suggesting that G. dumosa is aligned with Vaccinium.
Gold grain morphology and composition as an exploration tool: application to gold exploration in covered areas
Authors: Townley Brian K. , Hérail Gerard , Maksaev Victor , Palacios Carlos , Parseval Philippe de , Sepulveda Fabían , Orellana Rodrigo , Rivas Pablo , Ulloa Cesar
Published: May 2012

The results of research in the use of Au grain morphological and compositional properties applied in primary Au ore exploration are presented here. Two different and independent topics are discussed: (1) morphological characteristics of Au grains from active stream sediments for use as a distance-to-source indicator; (2) compositional signature of Au grains from various deposit types for use as a discrimination tool for source type and present deposit erosion level determination. The purpose of this study is to improve and integrate these two approaches as an exploration tool for Andean covered areas.

Au grain morphology for over 1500 nuggets recovered from 60 active stream sediment samples in the Coastal Cordillera of Central Chile shows morphological variations (general shape, outline, surface, primary crystal imprints, associated minerals, flatness index) characteristic of three distance ranges (0–50 m; 50–300 m; >300 m) from source. Comparison with results from other similar studies of Au morphology characteristics in different climatic and/or sedimentological environments (arid, semi-arid, wet, lateritic, fluvial, fluvio-glacial and glacial) resulted in the determination of the recommended parameters (outline, surface, associated minerals, flatness index) to be used as distance-to-source indicator, independent of the climatic and/or sedimentological environment.

Au grain morphological characteristics may assist in location of target but are not indicators of source type. Study of Au composition via electron microprobe analysis of Au grain cores from epithermal, Au-rich porphyry and Au-rich porphyry Cu systems indicated Au–Ag–Cu contents to be the best discrimination tool for these different types of Au-bearing deposits. In addition, such analysis of grains recovered at different vertical levels from the Cerro Casale Au-rich porphyry provides evidence that the Au compositional signature for a single type of deposit can also aid in the determination of vertical position. This may provide an estimate of the current level of erosion and remaining potential of the source. Some limitations of the proposed techniques are: (1) Au liberated from rock fragments already distant from source would be common in cordilleran and glacial environments, although this would be a detectable feature; (2) these techniques are applicable only for coarse-Au sources; (3) estimate of erosion level of liberated Au is limited to the case here presented.
Enhancing effectiveness and success rates in modern exploration
Authors: Taufen Paul , Baker Phil , Kelley David , Schodde Richard
Published: May 2012

This short paper discusses how to enhance success in minerals exploration by applying the discipline of geochemistry. Modern explorationists are working in an especially challenging time. Our industry is shrinking while technology expands more quickly than ever. Shareholder interest in mining companies is low when sustained investment is needed for exploration success. Exploration, associated research spending, and staffing are down. In the face of these trends, we need to work more efficiently. The minerals exploration industry is working today in more varied, complex, remote, and infrastructure-poor locations around the world. The increased variety of exploration terrains the industry now works in requires more shared knowledge of appropriate geochemical exploration applications. Discovery success has decreased in recent years. Five prominent reasons for this decreased success are stressed information integrity, poor application of known technology, fewer survey designs appropriately matched to the target deposit type and exploration setting, reduced research, innovation and applied technology, and less well-designed survey work. Professionally applied geochemistry can address a number of these factors, and thereby improve the discovery success rate. This paper provides some examples of how this can work.
Sand pumping and well design in consolidated and semi-consolidated sandstone aquifers
Authors: Charalambous A. N. , Packman M. , Burnet B. R.
Published: May 2012

Ingress of sand usually occurs in wells abstracting from sandstone aquifers that are poorly cemented. Impacts can be serious and may add significantly to production costs. They include loss of yield and continuity of supply, a reduction in the efficiency and operational life of wells and pumps, more frequent maintenance of wells and ultimately well replacement. The design of high-capacity sand-free wells in sandstone aquifers is often problematical. This is partly because a substantial proportion of the flow is through fractures, which means that well design criteria of screen slot size and artificial pack grain size and grading that have been developed for unconsolidated granular aquifers are not generally applicable. Also, many sandstone aquifers are multi-layered. Interbedded fine-grained and friable sandstone layers or loose sands are often responsible for sand entering a well. Excluding them is often difficult in practice without blocking productive fracture zones, and, therefore, risking a reduction of well yield. Well design alone is not always capable of controlling sand pumping. Pumping at a lower discharge rate, regulating flow at start-up, and the use of sand traps at the ground surface or inside wells are other measures that can assist in alleviating the problem.
Fast high-resolution appearance editing using superimposed projections
Authors: Aliaga Daniel G. , Yeung Yu Hong , Law Alvin , Sajadi Behzad , Majumder Aditi
Published: May 2012

We present a system that superimposes multiple projections onto an object of arbitrary shape and color to produce high-resolution appearance changes. Our system produces appearances at an improved resolution compared to prior works and can change appearances at near interactive rates. Three main components are central to our system. First, the problem of computing compensation images is formulated as a constrained optimization which yields high-resolution appearances. Second, decomposition of the target appearance into base and scale images enables fast swapping of appearances on the object by requiring the constrained optimization to be computed only once per object. Finally, to make high-quality appearance edits practical, an elliptical Gaussian is used to model projector pixels and their interaction between projectors. To the best of our knowledge, we build the first system that achieves high-resolution and high-quality appearance edits using multiple superimposed projectors on complex nonplanar colored objects. We demonstrate several appearance edits including specular lighting, subsurface scattering, inter-reflections, and color, texture, and geometry changes on objects with different shapes and colors.
Spacetime expression cloning for blendshapes
Authors: Seol Yeongho , Lewis J.P. , Seo Jaewoo , Choi Byungkuk , Anjyo Ken , Noh Junyong
Published: May 2012

The goal of a practical facial animation retargeting system is to reproduce the character of a source animation on a target face while providing room for additional creative control by the animator. This article presents a novel spacetime facial animation retargeting method for blendshape face models. Our approach starts from the basic principle that the source and target movements should be similar. By interpreting
movement
as the derivative of position with time, and adding suitable boundary conditions, we formulate the retargeting problem as a Poisson equation. Specified (e.g., neutral) expressions at the beginning and end of the animation as well as any user-specified constraints in the middle of the animation serve as boundary conditions. In addition, a model-specific prior is constructed to represent the plausible expression space of the target face during retargeting. A Bayesian formulation is then employed to produce target animation that is consistent with the source movements while satisfying the prior constraints. Since the preservation of temporal derivatives is the primary goal of the optimization, the retargeted motion preserves the rhythm and character of the source movement and is free of temporal jitter. More importantly, our approach provides spacetime editing for the popular blendshape representation of facial models, exhibiting smooth and controlled propagation of user edits across surrounding frames.
On the (im)possibility of obfuscating programs
Authors: Barak Boaz , Goldreich Oded , Impagliazzo Russell , Rudich Steven , Sahai Amit , Vadhan Salil , Yang Ke
Published: May 2012

Informally, an
obfuscator
O
is an (efficient, probabilistic) “compiler” that takes as input a program (or circuit)
P
and produces a new program
O
(
P
) that has the same functionality as
P
yet is “unintelligible” in some sense. Obfuscators, if they exist, would have a wide variety of cryptographic and complexity-theoretic applications, ranging from software protection to homomorphic encryption to complexity-theoretic analogues of Rice's theorem. Most of these applications are based on an interpretation of the “unintelligibility” condition in obfuscation as meaning that
O
(
P
) is a “virtual black box,” in the sense that anything one can efficiently compute given
O
(
P
), one could also efficiently compute given oracle access to
P
.

In this work, we initiate a theoretical investigation of obfuscation. Our main result is that, even under very weak formalizations of the above intuition, obfuscation is impossible. We prove this by constructing a family of efficient programs
P
that are
unobfuscatable
in the sense that (a) given
any
efficient program
P
' that computes the same function as a program
P
∈
p
, the “source code”
P
can be efficiently reconstructed, yet (b) given
oracle access
to a (randomly selected) program
P
∈
p
, no efficient algorithm can reconstruct
P
(or even distinguish a certain bit in the code from random) except with negligible probability.

We extend our impossibility result in a number of ways, including even obfuscators that (a) are not necessarily computable in polynomial time, (b) only approximately preserve the functionality, and (c) only need to work for very restricted models of computation (

TC
0

). We also rule out several potential applications of obfuscators, by constructing “unobfuscatable” signature schemes, encryption schemes, and pseudorandom function families.
Introduction to the special issue on corpus and computational linguistics, philology, and the linguistic heritage of humanity
Authors: Crane Gregory , Lüdeling Anke
Published: May 2012

The articles in this issue make two complementary assertions: first, language and linguistic sources are a key element of human cultural heritage and, second, we need to integrate the ancient goals of philology with rapidly emerging methods from fields such as Corpus and Computational Linguistics. The first 15,000,000 volumes digitized by Google contained data from more than 400 languages covering more than four thousand years of the human record. We need to develop methods to explore linguistic changes and the ideas that languages encode as these evolve and circulate over millennia and on a global scale.
A data-centric approach to synchronization
Authors: Dolby Julian , Hammer Christian , Marino Daniel , Tip Frank , Vaziri Mandana , Vitek Jan
Published: May 2012

Concurrency-related errors, such as data races, are frustratingly difficult to track down and eliminate in large object-oriented programs. Traditional approaches to preventing data races rely on protecting instruction sequences with synchronization operations. Such control-centric approaches are inherently brittle, as the burden is on the programmer to ensure that all concurrently accessed memory locations are consistently protected. Data-centric synchronization is an alternative approach that offloads some of the work on the language implementation. Data-centric synchronization groups fields of objects into
atomic sets
to indicate that these fields must always be updated atomically. Each atomic set has associated
units of work
, that is, code fragments that preserve the consistency of that atomic set. Synchronization operations are added automatically by the compiler. We present an extension to the Java programming language that integrates annotations for data-centric concurrency control. The resulting language, called AJ, relies on a type system that enables separate compilation and supports atomic sets that span multiple objects and that also supports full encapsulation for more efficient code generation. We evaluate our proposal by refactoring classes from standard libraries, as well as a number of multithreaded benchmarks, to use atomic sets. Our results suggest that data-centric synchronization is easy to use and enjoys low annotation overhead, while successfully preventing data races. Moreover, experiments on the SPECjbb benchmark suggest that acceptable performance can be achieved with a modest amount of tuning.
Algorithmic verification of asynchronous programs
Authors: Ganty Pierre , Majumdar Rupak
Published: May 2012

Asynchronous programming is a ubiquitous systems programming idiom for managing concurrent interactions with the environment. In this style, instead of waiting for time-consuming operations to complete, the programmer makes a non-blocking call to the operation and posts a callback task to a task buffer that is executed later when the time-consuming operation completes. A cooperative scheduler mediates the interaction by picking and executing callback tasks from the task buffer to completion (and these callbacks can post further callbacks to be executed later). Writing correct asynchronous programs is hard because the use of callbacks, while efficient, obscures program control flow.

We provide a formal model underlying asynchronous programs and study verification problems for this model. We show that the safety verification problem for finite-data asynchronous programs is expspace-complete. We show that liveness verification for finite-data asynchronous programs is decidable and polynomial-time equivalent to Petri net reachability. Decidability is not obvious, since even if the data is finite-state, asynchronous programs constitute infinite-state transition systems: both the program stack for an executing task and the task buffer of pending calls to tasks can be potentially unbounded.

Our main technical constructions are polynomial-time, semantics-preserving reductions from asynchronous programs to Petri nets and back. The first reduction allows the use of algorithmic techniques on Petri nets for the verification of asynchronous programs, and the second allows lower bounds on Petri nets to apply also to asynchronous programs.

We also study several extensions to the basic models of asynchronous programs that are inspired by additional capabilities provided by implementations of asynchronous libraries and classify the decidability and undecidability of verification questions on these extensions.
A Hierarchical Thread Scheduler and Register File for Energy-Efficient Throughput Processors
Authors: Gebhart Mark , Johnson Daniel R. , Tarjan David , Keckler Stephen W. , Dally William J. , Lindholm Erik , Skadron Kevin
Published: May 2012

Modern graphics processing units (GPUs) employ a large number of hardware threads to hide both function unit and memory access latency. Extreme multithreading requires a complex thread scheduler as well as a large register file, which is expensive to access both in terms of energy and latency. We present two complementary techniques for reducing energy on massively-threaded processors such as GPUs. First, we investigate a two-level thread scheduler that maintains a small set of active threads to hide ALU and local memory access latency and a larger set of pending threads to hide main memory latency. Reducing the number of threads that the scheduler must consider each cycle improves the scheduler’s energy efficiency. Second, we propose replacing the monolithic register file found on modern designs with a hierarchical register file. We explore various trade-offs for the hierarchy including the number of levels in the hierarchy and the number of entries at each level. We consider both a hardware-managed caching scheme and a software-managed scheme, where the compiler is responsible for orchestrating all data movement within the register file hierarchy. Combined with a hierarchical register file, our two-level thread scheduler provides a further reduction in energy by only allocating entries in the upper levels of the register file hierarchy for active threads. Averaging across a variety of real world graphics and compute workloads, the active thread count can be reduced by a factor of 4 with minimal impact on performance and our most efficient three-level software-managed register file hierarchy reduces register file energy by 54%.
Efficient load balancing in partitioned queries under random perturbations
Authors: Gounaris Anastasios , Yfoulis Christos A. , Paton Norman W.
Published: May 2012

This work investigates a particular instance of the problem of designing efficient adaptive systems, under the condition that each adaptation decision incurs some nonnegligible cost when enacted. More specifically, we deal with the problem of dynamic, intraquery load balancing in parallel database queries across heterogeneous nodes in a way that takes into account the inherent cost of adaptations and thus avoids both overreacting and deciding when to adapt in a completely heuristic manner. The latter may lead to serious performance degradation in several cases, such as periodic and random imbalances. We follow a control theoretical approach to this problem; more specifically, we propose a multiple-input multiple-output feedback linear quadratic regulation (LQR) controller, which captures the tradeoff between reaching a balanced state and the cost inherent in such adaptations. Our approach, apart from benefitting from and being characterized by a solid theoretical foundation, exhibits better performance than state-of-the-art heuristics in realistic situations, as verified by thorough evaluation.
Introduction to special section on formal methods in pervasive computing
Authors: Bakhouya Mohamed , Campbell Roy , Coronato Antonio , Pietro Giuseppe de , Ranganathan Anand
Published: May 2012

Ubiquitous and pervasive applications may present critical requirements from the point of view of functional correctness, reliability, availability, security, and safety. Unlike traditional safety-critical applications, the behavior of ubiquitous and pervasive applications is affected by the movements and location of users and resources. In this article, we first present emerging formal methods for the description of both entities and their behavior in pervasive computing environments; then, we introduce this special issue. Despite many previous works that have focused on modeling the entities, relatively few have concentrated on modeling or verifying behaviors; and almost none has dealt with combining techniques proposed in these two aspects. The articles accepted in this special issue cover some of the topics aforementioned and constitute a representative sample of the latest development of formal methods in pervasive computing environments.
The living heritage of historic crises
Authors: Liu Sophia B.
Published: May 2012

On Heritage aims to offer and promote a rich discussion at the intersection of art, performance, and culture that expands the boundaries of HCI while broadening our understanding of how things of the past come to matter in the present.

Elisa Giaccardi, Editor
HCI public policy activities in 2012
Authors: Lazar Jonathan , Abascal Julio , Davis Janet , Evers Vanessa , Gulliksen Jan , Jorge Joaquim , McEwan Tom , Paternò Fabio , Persson Hans , Prates Raquel , von Axelson Hans , Winckler Marco , Wulf Volker
Published: May 2012

Public policy increasingly plays a role in influencing the work that we do as HCI researchers, interaction designers, and practitioners. "Public policy" is a broad term that includes both government policy and policy within non-governmental organizations, such as standards bodies. The Interacting with Public Policy forum focuses on topics at the intersection of human-computer interaction and public policy.

Jonathan Lazar, Editor
Parametric analysis and modeling of video signals
Authors: Omidyeganeh Mona
Published: May 2012

Video modeling and analysis have been of great interest in the video research community, due to their essential contribution to systematic improvements concerned in a wide range of video processing techniques. Parametric modeling and analysis of video provides appropriate means for processing the signal and the necessary mining of information for efficient representation of the signal. Video comparison, human action recognition, video retrieval, video abstraction, video transmission, and video clustering are some applications that can benefit from video modeling and analysis.
Query languages for graph databases
Authors: Wood Peter T.
Published: May 2012

Query languages for graph databases started to be investigated some 25 years ago. With much current data, such as linked data on the Web and social network data, being graph-structured, there has been a recent resurgence in interest in graph query languages. We provide a brief survey of many of the graph query languages that have been proposed, focussing on the core functionality provided in these languages. We also consider issues such as expressive power and the computational complexity of query evaluation.
What.s new in SQL:2011
Authors: Zemke Fred
Published: May 2012

SQL:2011 was published in December 2011, replacing the former version (SQL:2008) as the most recent update to the SQL standard for relational databases. This paper surveys the new non-temporal features of SQL:2011.
The curriculum forecast for Portland
Authors: Grossniklaus Michael , Maier David
Published: May 2012

With the advent of cloud computing, new data management technologies and systems have emerged that differ from existing databases in important ways. As a consequence, universities are currently facing the challenge of integrating these topics into their curriculum in order to prepare students for the changed IT landscape. In this report, we describe the approach we have taken at Portland State University to teach data management in the cloud. We also present our experiences with this effort and give an outlook on how it could be adapted to suit the requirements of other universities.
Effects of a Caloric Restriction Weight Loss Diet and Exercise on Inflammatory Biomarkers in Overweight/Obese Postmenopausal Women: A Randomized Controlled Trial
Authors: Imayama Ikuyo , Ulrich Cornelia M. , Alfano Catherine M. , Wang Chiachi , Xiao Liren , Wener Mark H. , Campbell Kristin L. , Duggan Catherine , Foster-Schubert Karen E. , Kong Angela , Mason Caitlin E. , Wang Ching-Yun , Blackburn George L. , Bain Carolyn E. , Thompson Henry J. , McTiernan Anne
Published: May 2012

Obese and sedentary persons have increased risk for cancer; inflammation is a hypothesized mechanism. We examined the effects of a caloric restriction weight loss diet and exercise on inflammatory biomarkers in 439 women. Overweight and obese postmenopausal women were randomized to 1-year: caloric restriction diet (goal of 10% weight loss, N = 118), aerobic exercise (225 min/wk of moderate-to-vigorous activity, N = 117), combined diet + exercise (N = 117), or control (N = 87). Baseline and 1-year high-sensitivity C-reactive protein (hs-CRP), serum amyloid A (SAA), interleukin-6 (IL-6), leukocyte, and neutrophil levels were measured by investigators blind to group. Inflammatory biomarker changes were compared using generalized estimating equations. Models were adjusted for baseline body mass index (BMI), race/ethnicity, and age. Four hundred and thirty-eight (N = 1 in diet + exercise group was excluded) were analyzed. Relative to controls, hs-CRP decreased by geometric mean (95% confidence interval, P value): 0.92 mg/L (0.53–1.31, P < 0.001) in the diet and 0.87 mg/L (0.51–1.23, P < 0.0001) in the diet + exercise groups. IL-6 decreased by 0.34 pg/mL (0.13–0.55, P = 0.001) in the diet and 0.32 pg/mL (0.15–0.49, P < 0.001) in the diet + exercise groups. Neutrophil counts decreased by 0.31 × 109/L (0.09–0.54, P = 0.006) in the diet and 0.30 × 109/L (0.09–0.50, P = 0.005) in the diet + exercise groups. Diet and diet + exercise participants with 5% or more weight loss reduced inflammatory biomarkers (hs-CRP, SAA, and IL-6) compared with controls. The diet and diet + exercise groups reduced hs-CRP in all subgroups of baseline BMI, waist circumference, CRP level, and fasting glucose. Our findings indicate that a caloric restriction weight loss diet with or without exercise reduces biomarkers of inflammation in postmenopausal women, with potential clinical significance for cancer risk reduction. Cancer Res; 72(9); 2314–26. ©2012 AACR.