bluuebunny/crossref_metadata_2025 huggingface dataset:
Ketoglutarate Transport Protein KgtP Is Secreted through the Type III Secretion System and Contributes to Virulence in Xanthomonas oryzae pv. oryzae
Authors: Guo Wei , Cai Lu-Lu , Zou Hua-Song , Ma Wen-Xiu , Liu Xi-Ling , Zou Li-Fang , Li Yu-Rong , Chen Xiao-Bin , Chen Gong-You
Published: June 2012

The phytopathogenic prokaryote
Xanthomonas oryzae
pv. oryzae is the causal agent of bacterial leaf blight (BB) of rice and utilizes a type III secretion system (T3SS) to deliver T3SS effectors into rice cells. In this report, we show that the ketoglutarate transport protein (KgtP) is secreted in an HpaB-independent manner through the T3SS of
X. oryzae
pv. oryzae PXO99
A
and localizes to the host cell membrane for α-ketoglutaric acid export.
kgtP
contained an imperfect PIP box (plant-inducible promoter) in the promoter region and was positively regulated by HrpX and HrpG. A
kgtP
deletion mutant was impaired in bacterial virulence and growth
in planta
; furthermore, the mutant showed reduced growth in minimal media containing α-ketoglutaric acid or sodium succinate as the sole carbon source. The reduced virulence and the deficiency in α-ketoglutaric acid utilization by the
kgtP
mutant were restored to wild-type levels by the presence of
kgtP
in
trans
. The expression of
OsIDH
, which is responsible for the synthesis of α-ketoglutaric acid in rice, was enhanced when KgtP was present in the pathogen. To our knowledge, this is the first report demonstrating that KgtP, which is regulated by HrpG and HrpX and secreted by the T3SS in
Xanthomonas oryzae
pv. oryzae, transports α-ketoglutaric acid when the pathogen infects rice.
Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182
Authors: Le Bars Hervé , Bousarghin Latifa , Bonnaure-Mallet Martine , Jolivet-Gougeon Anne , Barloy-Hubler Frédérique
Published: June 2012

In bacteria, normal mutation frequencies are mostly around 10
−10
per base pair. However, there exists natural isolates, called “mutators,” that exhibit permanent mutation occurrences up to 1,000-fold greater than usual. As mutations play essential roles, particularly in the evolution of antibiotic resistance, bacteria showing elevated mutation rates could have an important responsibility in the emergence of antibiotic resistance, especially in the clinical background. In this announcement, we report the first complete genome sequence of the
Salmonella enterica
subsp.
enterica
serotype Heidelberg B182 mutator strain, isolated from bovine feces (France), which consists of a 4,750,465-bp circular chromosome (cB182_4750; GC, 52.2%) and one circular plasmid of 37,581 bp (pB182_37; GC, 42.8%).
Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17, Which Forms Biofilms on Hydrophobic Organic Compounds
Authors: Grimaud Regis , Ghiglione Jean-François , Cagnon Christine , Lauga Béatrice , Vaysse Pierre-Joseph , Rodriguez-Blanco Arturo , Mangenot Sophie , Cruveiller Stephane , Barbe Valérie , Duran Robert , Wu Long-Fei , Talla Emmanuel , Bonin Patricia , Michotey Valerie
Published: June 2012

Marinobacter hydrocarbonoclasticus
SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.
The MscS and MscL Families of Mechanosensitive Channels Act as Microbial Emergency Release Valves
Authors: Booth Ian R. , Blount Paul
Published: June 2012

Single-celled organisms must survive exposure to environmental extremes. Perhaps one of the most variable and potentially life-threatening changes that can occur is that of a rapid and acute decrease in external osmolarity. This easily translates into several atmospheres of additional pressure that can build up within the cell. Without a protective mechanism against such pressures, the cell will lyse. Hence, most microbes appear to possess members of one or both families of bacterial mechanosensitive channels, MscS and MscL, which can act as biological emergency release valves that allow cytoplasmic solutes to be jettisoned rapidly from the cell. While this is undoubtedly a function of these proteins, the discovery of the presence of MscS homologues in plant organelles and MscL in fungus and mycoplasma genomes may complicate this simplistic interpretation of the physiology underlying these proteins. Here we compare and contrast these two mechanosensitive channel families, discuss their potential physiological roles, and review some of the most relevant data that underlie the current models for their structure and function.
Enzymology and Structure of the GH13_31 Glucan 1,6-α-Glucosidase That Confers Isomaltooligosaccharide Utilization in the Probiotic Lactobacillus acidophilus NCFM
Authors: Møller Marie S. , Fredslund Folmer , Majumder Avishek , Nakai Hiroyuki , Poulsen Jens-Christian N. , Lo Leggio Leila , Svensson Birte , Abou Hachem Maher
Published: June 2012

Isomaltooligosaccharides (IMO) have been suggested as promising prebiotics that stimulate the growth of probiotic bacteria. Genomes of probiotic lactobacilli from the acidophilus group, as represented by
Lactobacillus acidophilus
NCFM, encode α-1,6 glucosidases of the family GH13_31 (glycoside hydrolase family 13 subfamily 31) that confer degradation of IMO. These genes reside frequently within maltooligosaccharide utilization operons, which include an ATP-binding cassette transporter and α-glucan active enzymes, e.g., maltogenic amylases and maltose phosphorylases, and they also occur separated from any carbohydrate transport or catabolism genes on the genomes of some acidophilus complex members, as in
L. acidophilus
NCFM. Besides the isolated locus encoding a GH13_31 enzyme, the ABC transporter and another GH13 in the maltooligosaccharide operon were induced in response to IMO or maltotetraose, as determined by reverse transcription-PCR (RT-PCR) transcriptional analysis, suggesting coregulation of α-1,6- and α-1,4-glucooligosaccharide utilization loci in
L. acidophilus
NCFM. The
L. acidophilus
NCFM GH13_31 (
La
GH13_31) was produced recombinantly and shown to be a glucan 1,6-α-glucosidase active on IMO and dextran and product-inhibited by glucose. The catalytic efficiency of
La
GH13_31 on dextran and the dextran/panose (trisaccharide) efficiency ratio were the highest reported for this class of enzymes, suggesting higher affinity at distal substrate binding sites. The crystal structure of
La
GH13_31 was determined to a resolution of 2.05 Å and revealed additional substrate contacts at the +2 subsite in
La
GH13_31 compared to the GH13_31 from
Streptococcus mutans
(
Sm
GH13_31), providing a possible structural rationale to the relatively high affinity for dextran. A comprehensive phylogenetic and activity motif analysis mapped IMO utilization enzymes from gut microbiota to rationalize preferential utilization of IMO by gut residents.
Type IV Pilus Assembly in Pseudomonas aeruginosa over a Broad Range of Cyclic di-GMP Concentrations
Authors: Jain Ruchi , Behrens Anna-Janina , Kaever Volkhard , Kazmierczak Barbara I.
Published: June 2012

Pseudomonas aeruginosais a Gram-negative, opportunistic pathogen that utilizes polar type IV pili (T4P) for twitching motility and adhesion in the environment and during infection. Pilus assembly requires FimX, a GGDEF/EAL domain protein that binds and hydrolyzes cyclic di-GMP (c-di-GMP). Bacteria lacking FimX are deficient in twitching motility and microcolony formation. We carried out an extragenic suppressor screen in PA103ΔfimXbacteria to identify additional regulators of pilus assembly. Multiple suppressor mutations were mapped to PA0171, PA1121 (yfiR), and PA3703 (wspF), three genes previously associated with small-colony-variant phenotypes. Multiple independent techniques confirmed that suppressors assembled functional surface pili, though at both polar and nonpolar sites. Whole-cell c-di-GMP levels were elevated in suppressor strains, in agreement with previous studies that had shown that the disrupted genes encoded negative regulators of diguanylate cyclases. Overexpression of the regulated diguanylate cyclases was sufficient to suppress the ΔfimXpilus assembly defect, as was overexpression of an unrelated diguanylate cyclase fromCaulobacter crescentus. Furthermore, under natural conditions of high c-di-GMP, PA103ΔfimXformed robust biofilms that showed T4P staining and were structurally distinct from those formed by nonpiliated bacteria. These results are the first demonstration thatP. aeruginosaassembles a surface organelle, type IV pili, over a broad range of c-di-GMP concentrations. Assembly of pili at low c-di-GMP concentrations requires a polarly localized c-di-GMP binding protein and phosphodiesterase, FimX; this requirement for FimX is bypassed at high c-di-GMP concentrations. Thus,P. aeruginosacan assemble the same surface organelle in distinct ways for motility or adhesion under very different environmental conditions.
Synthesis of Long-Chain Chitooligosaccharides by a Hypertransglycosylating Processive Endochitinase of Serratia proteamaculans 568
Authors: Purushotham Pallinti , Podile Appa Rao
Published: June 2012

We describe the heterologous expression and characterization of a 407-residue single-domain glycosyl hydrolase family 18 chitinase (
Sp
ChiD) from Gram-negative
Serratia proteamaculans
568 that has unprecedented catalytic properties.
Sp
ChiD was optimally active at pH 6.0 and 40°C, where it showed a

K
m

of 83 mg ml
−1
, a
k
cat
of 3.9 × 10
2
h
−1
, and a
k
cat
/

K
m

of 4.7 h mg
−1
ml
−1
on colloidal chitin. On chitobiose, the

K
m

,
k
cat
, and
k
cat
/

K
m

were 203 μM, 1.3 × 10
2
h
−1
, and 0.62 h
−1
μM
−1
, respectively. Hydrolytic activity on chitooligosaccharides (CHOS) and colloidal chitin indicated that
Sp
ChiD was an endo-acting processive enzyme, with the unique ability to convert released chitobiose to
N
-acetylglucosamine, the major end product.
Sp
ChiD showed hyper transglycosylation (TG) with trimer-hexamer CHOS substrates, generating considerable amounts of long-chain CHOS. The TG activity of
Sp
ChiD was dependent on both the length and concentration of the oligomeric substrate and also on the enzyme concentration. The length and amount of accumulated TG products increased with increases in the length of the substrate and its concentration and decreased with increases in the enzyme concentration. The
Sp
ChiD bound to insoluble and soluble chitin substrates despite the absence of accessory domains. Sequence alignments and structural modeling indicated that
Sp
ChiD would have a deep substrate-binding groove lined with aromatic residues, which is characteristic of processive enzymes.
Sp
ChiD shows a combination of properties that seems rare among family 18 chitinases and that may resemble the properties of human chitotriosidase.
Cell Biology of Cnidarian-Dinoflagellate Symbiosis
Authors: Davy Simon K. , Allemand Denis , Weis Virginia M.
Published: June 2012

The symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genusSymbiodiniumis of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidarian-dinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between greenHydraand its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future.
A cohort study comparing cardiovascular risk factors in rural Māori, urban Māori and non-Māori communities in New Zealand
Authors: Cameron Vicky A , Faatoese Allamanda F , Gillies Matea W , Robertson Paul J , Huria Tania M , Doughty Rob N , Whalley Gillian A , Richards Mark A , Troughton Richard W , Tikao-Mason Karen N , Wells Elisabeth J , Sheerin Ian G , Pitama Suzanne G
Published: June 2012

Objectives

To understand health disparities in cardiovascular disease (CVD) in the indigenous Māori of New Zealand, diagnosed and undiagnosed CVD risk factors were compared in rural Māori in an area remote from health services with urban Māori and non-Māori in a city well served with health services.

Design

Prospective cohort study.

Setting

Hauora Manawa is a cohort study of diagnosed and previously undiagnosed CVD, diabetes and risk factors, based on random selection from electoral rolls of the rural Wairoa District and Christchurch City, New Zealand.

Participants

Screening clinics were attended by 252 rural Māori, 243 urban Māori and 256 urban non-Māori, aged 20–64 years.

Main outcome measures

The study documented personal and family medical history, blood pressure, anthropometrics, fasting lipids, insulin, glucose, HbA1c and urate to identify risk factors in common and those that differ among the three communities.

Results

Mean age (SD) was 45.7 (11.5) versus 42.6 (11.2) versus 43.6 (11.5) years in rural Māori, urban Māori and non-Māori, respectively. Age-adjusted rates of diagnosed cardiac disease were not significantly different across the cohorts (7.5% vs 5.8% vs 2.8%, p=0.073). However, rural Māori had significantly higher levels of type-2 diabetes (10.7% vs 3.7% vs 2.4%, p<0.001), diagnosed hypertension (25.0% vs 14.9% vs 10.7%, p<0.001), treated dyslipidaemia (15.7% vs 7.1% vs 2.8%, p<0.001), current smoking (42.8% vs 30.5% vs 15.2%, p<0.001) and age-adjusted body mass index (30.7 (7.3) vs 29.1 (6.4) vs 26.1 (4.5) kg/m2, p<0.001). Similarly high rates of previously undocumented elevated blood pressure (22.2% vs 23.5% vs 17.6%, p=0.235) and high cholesterol (42.1% vs 54.3% vs 42.2%, p=0.008) were observed across all cohorts.

Conclusions

Supporting integrated rural healthcare to provide screening and management of CVD risk factors would reduce health disparities in this indigenous population.
Interrogating a clinical database to study treatment of hypotension in the critically ill
Authors: Lee Joon , Kothari Rishi , Ladapo Joseph A , Scott Daniel J , Celi Leo A
Published: June 2012

Objective

In intensive care, it is imperative to resolve hypotensive episodes (HEs) in a timely manner to minimise end-organ damage. Clinical practice guidelines generally recommend initial treatment with fluid resuscitation followed by vasoactive agent administration if patients remain hypotensive. However, the impact of such interventions on patient outcomes has not been clearly established. Hence, the objective of this study was to investigate the relationship between fluid and vasoactive agent interventions and patient outcomes, while highlighting the utility of electronic medical records in clinical research.

Design

Retrospective cohort study.

Setting

Intensive care units (ICUs) at a large, academic, tertiary medical center.

Participants

Patients in Multi-parameter Intelligent Monitoring in Intensive Care II (a large electronic ICU database) who experienced a single HE during their ICU stay. 2332 patients had complete data.

Primary and secondary outcome measures

The primary outcome of interest was inhospital mortality. Secondary outcomes were ICU length of stay (LOS), HE duration, Hypotension Severity Index (defined as the mean arterial pressure curve area below 60 mm Hg during the HE) and rise in serum creatinine.

Results

Fluid resuscitation was associated with significantly shorter ICU LOS among ICU survivors (p=0.007). Vasoactive agent administration significantly decreased HE duration (p<0.001) and Hypotension Severity Index (p=0.002) but was associated with increased inhospital mortality risk (p<0.001), prolonged ICU LOS among ICU survivors (p=0.04) and rise in serum creatinine (p=0.002) after adjustment for confounders. Propensity score analyses as well as sensitivity analyses in treatment-, diagnosis- and ICU service-specific subpopulations corroborated the relationship between vasoactive agents and increased inhospital mortality.

Conclusions

An adverse relationship between vasoactive agents and inhospital mortality was found in patients with hypotension. This study has implications for the care of critically ill patients with hypotension and illustrates the utility of electronic medical records in research when randomised controlled trials are difficult to conduct.
Prostate cancer mortality risk in relation to working underground in the Wismut cohort study of German uranium miners, 1970–2003
Authors: Walsh Linda , Dufey Florian , Tschense Annemarie , Schnelzer Maria , Sogl Marion , Kreuzer Michaela
Published: June 2012

Objective

A recent study and comprehensive literature review has indicated that mining could be protective against prostate cancer. This indication has been explored further here by analysing prostate cancer mortality in the German ‘Wismut’ uranium miner cohort, which has detailed information on the number of days worked underground.

Design

An historical cohort study of 58 987 male mine workers with retrospective follow-up before 1999 and prospective follow-up since 1999.

Setting and participants

Uranium mine workers employed during the period 1970–1990 in the regions of Saxony and Thuringia, Germany, contributing 1.42 million person-years of follow-up ending in 2003.

Outcome measure

Simple standardised mortality ratio (SMR) analyses were applied to assess differences between the national and cohort prostate cancer mortality rates and complemented by refined analyses done entirely within the cohort. The internal comparisons applied Poisson regression excess relative prostate cancer mortality risk model with background stratification by age and calendar year and a whole range of possible explanatory covariables that included days worked underground and years worked at high physical activity with γ radiation treated as a confounder.

Results

The analysis is based on miner data for 263 prostate cancer deaths. The overall SMR was 0.85 (95% CI 0.75 to 0.95). A linear excess relative risk model with the number of years worked at high physical activity and the number of days worked underground as explanatory covariables provided a statistically significant fit when compared with the background model (p=0.039). Results (with 95% CIs) for the excess relative risk per day worked underground indicated a statistically significant (p=0.0096) small protective effect of −5.59 (−9.81 to −1.36) ×10−5.

Conclusion

Evidence is provided from the German Wismut cohort in support of a protective effect from working underground on prostate cancer mortality risk.
GaPP: a pilot randomised controlled trial of the efficacy of action of gabapentin for the management of chronic pelvic pain in women: study protocol: Figure 1
Authors: Horne Andrew W , Critchley Hilary O D , Doust Ann , Fehr Daniel , Wilson John , Wu Olivia , Jack S , Porter Maureen , Lewis Steff , Bhattacharya Siladitya
Published: June 2012

Introduction

Chronic pelvic pain (CPP) affects >1 million UK women. Annual healthcare costs are estimated at >£150 million. Proven interventions for CPP are limited, and treatment is often unsatisfactory. Gabapentin is increasingly prescribed due to reports of effectiveness in other chronic pain conditions, but there are insufficient data supporting value in CPP specifically. The mechanism by which gabapentin exerts its analgesic action is unknown. Given the prevalence and costs of CPP, the authors believe that a large, multicentre, placebo-controlled, double-blind randomised controlled trial to evaluate the efficacy of gabapentin in management of CPP is required. The focus of this study is a pilot to inform planning of a future randomised controlled trial.

Methods and analysis

The authors plan to perform a two-arm, parallel, randomised controlled pilot trial. The authors aim to recruit 60 women with CPP in NHS Lothian and NHS Grampian (UK) and randomise them to gabapentin or placebo. Response to treatment will be monitored by questionnaire compared at 0, 3 and 6 months. The primary objective is to assess recruitment and retention rates. The secondary objectives are to determine the effectiveness and acceptability to participants of the proposed methods of recruitment, randomisation, drug treatments and assessment tools and to perform a pretrial cost-effectiveness assessment of treatment with gabapentin.

Ethics and dissemination

Ethical approval has been obtained from the Scotland A Research Ethics Committee (LREC 12/SS/0005). Data will be presented at international conferences and published in peer-reviewed journals.

Trial registration number

ISRCTN70960777.
Multicenter study to assess the efficacy and safety of sacroplasty in patients with osteoporotic sacral insufficiency fractures or pathologic sacral lesions
Authors: Kortman Keith , Ortiz Orlando , Miller Todd , Brook Allan , Tutton Sean , Mathis John , Georgy Bassem
Published: June 2012

Objective

To assess the outcomes and safety after CT-guided percutaneous sacroplasty in patients with painful sacral insufficiency fractures or pathologic sacral lesions.

Methods

A retrospective multicenter analysis of consecutive patients undergoing CT-guided sacroplasty for painful sacral insufficiency fractures or sacral lesions was undertaken. The inclusion criteria consisted of severe sacral pain not responding to conservative medical management with imaging evidence of unilateral or bilateral sacral insufficiency fractures or lesions. Outcome measures included hospitalization status (inpatient or outpatient), pre-treatment and post-treatment visual analog scale (VAS) scores, analgesic use and complications. Patients were followed at approximately 1 month and for at least 1 year after their sacroplasty procedure.

Results

Two hundred and forty-three patients were included in the study, 204 with painful sacral insufficiency fractures and 39 with symptomatic sacral lesions. The average pre-treatment VAS score of 9.2±1.1 was significantly improved after sacroplasty to 1.9±1.7 in patients with sacral insufficiency fractures (p<0.001). The average pre-treatment VAS score of 9.0±0.9 in patients with sacral lesions was significantly improved after sacroplasty to 2.6±2.4 (p<0.001). There were no major complications or procedure-related deaths. One patient who was treated for a sacral insufficiency fracture experienced radicular pain due to local extravasation of cement that subsequently required surgical decompression for symptomatic relief.

Conclusions

CT-guided percutaneous sacroplasty is a safe and effective procedure in the treatment of painful sacral insufficiency fractures or lesions. It is associated with prompt and durable pain relief and should be considered as an effective treatment option in this patient population.
HYBRID JAVA COMPILATION OF JUST-IN-TIME AND AHEAD-OF TIME FOR EMBEDDED SYSTEMS
Authors: OH HYEONG-SEOK , MOON SOO-MOOK , JUNG DONG-HEON
Published: June 2012

Many embedded Java software platforms execute two types of Java classes: those installed statically on the client device and those downloaded dynamically from service providers at runtime. For higher performance, it would be desirable to compile static Java classes by ahead-of-time compiler (AOTC) and to handle dynamically downloaded classes by just-in-time compiler (JITC), providing a hybrid compilation environment. This paper proposes a hybrid Java compilation approach and performs an initial case study with a hybrid environment, which is constructed simply by merging an existing AOTC and a JITC for the same Java virtual machine. Both compilers are developed independently for their own performance advantages with a generally accepted approach of compilation, but we merged them as efficiently as possible. Contrary to our expectations, the hybrid environment does not deliver a performance, in-between of full-JITC's and full-AOTC's. In fact, its performance is even lower than full-JITC's for many benchmarks. We analyzed the result and found that a naive merge of JITC and AOTC may result in inefficiencies, especially due to calls between JITC methods and AOTC methods. Based on these observations, we propose some ideas to reduce such a call overhead. We also observed that the distribution of JITC methods and AOTC methods is also important, and experimented with various distributions to understand when a hybrid environment can deliver a desired performance. Finally, we discuss how JITC and AOTC should be designed for efficient hybrid execution.
EFFECTIVENESS OF COMPILER-DIRECTED PREFETCHING ON DATA MINING BENCHMARKS
Authors: NATARAJAN RAGAVENDRA , MEKKAT VINEETH , HSU WEI-CHUNG , ZHAI ANTONIA
Published: June 2012

For today's increasingly power-constrained multicore systems, integrating simpler and more energy-efficient in-order cores becomes attractive. However, since in-order processors lack complex hardware support for tolerating long-latency memory accesses, developing compiler technologies to hide such latencies becomes critical. Compiler-directed prefetching has been demonstrated effective on some applications. On the application side, a large class of data centric applications has emerged to explore the underlying properties of the explosively growing data. These applications, in contrast to traditional benchmarks, are characterized by substantial thread-level parallelism, complex and unpredictable control flow, as well as intensive and irregular memory access patterns. These applications are expected to be the dominating workloads on future microprocessors. Thus, in this paper, we investigated the effectiveness of compiler-directed prefetching on data mining applications in in-order multicore systems. Our study reveals that although properly inserted prefetch instructions can often effectively reduce memory access latencies for data mining applications, the compiler is not always able to exploit this potential. Compiler-directed prefetching can become inefficient in the presence of complex control flow and memory access patterns; and architecture dependent behaviors. The integration of multithreaded execution onto a single die makes it even more difficult for the compiler to insert prefetch instructions, since optimizations that are effective for single-threaded execution may or may not be effective in multithreaded execution. Thus, compiler-directed prefetching must be judiciously deployed to avoid creating performance bottlenecks that otherwise do not exist. Our experiences suggest that dynamic performance tuning techniques that adjust to the behaviors of a program can potentially facilitate the deployment of aggressive optimizations in data mining applications.
TWISTING ALL THE WAY: FROM ALGEBRAS TO MORPHISMS AND CONNECTIONS
Authors: ASCHIERI PAOLO
Published: June 2012

Given a Hopf algebra H and an algebra A that is an H-module algebra we consider the category of left H-modules and A-bimodules [Formula: see text], where morphisms are just right A-linear maps (not necessarily H-equivariant). Given a twist [Formula: see text] of H we then quantize (deform) H to [Formula: see text], A to A⋆ and correspondingly the category [Formula: see text] to [Formula: see text]. If we consider a quasitriangular Hopf algebra H, a quasi-commutative algebra A and quasi-commutative A-bimodules, we can further construct and study tensor products over A of modules and of morphisms, and their twist quantization.

This study leads to the definition of arbitrary (i.e., not necessarily H-equivariant) connections on quasi-commutative A-bimodules, to extend these connections to tensor product modules and to quantize them to A⋆-bimodule connections. Their curvatures and those on tensor product modules are also determined.
NONCOMMUTATIVE PERTURBATIONS OF A CLASSICAL SPACETIME
Authors: BURIĆ MAJA , MADORE JOHN
Published: June 2012

A classical spacetime is chosen and the possible noncommutative perturbations of it are constructed.
NONCOMMUTATIVITY AND HUMANITY — JULIUS WESS AND HIS LEGACY
Authors: DJORDJEVIC GORAN S.
Published: June 2012

A personal view on Julius Wess's human and scientific legacy in Serbia and the Balkan region is given. Motivation for using noncommutative and nonarchimedean geometry on very short distances is presented. In addition to some mathematical preliminaries, we present a short introduction in adelic quantum mechanics in a way suitable for its noncommutative generalization. We also review the basic ideas and tools embedded in q-deformed and noncommutative quantum mechanics. A rather fundamental approach, called deformation quantization, is noted. A few relations between noncommutativity and nonarchimedean spaces, as well as similarities between corresponding quantum theories, in particular, quantum cosmology are pointed out. An extended Moyal product in a frame of an adelic noncommutative quantum mechanics is also considered.
SUBTLE INTERPLAY BETWEEN HYDROGEN AND MAGNETISM IN Co DOPED ZnO
Authors: ZHANG Y. B. , ASSADI M. H. N. , LI S.
Published: June 2012

The effects of hydrogen, either interstitial (HI) or substitutional (Ho), on magnetic properties of Co doped ZnO (ZnO:Co) have been systematically investigated using first-principles density functional calculations. The study discovers the correlation between the distribution of Co ions and the hydrogen point defect and magnetism. It is found that Co ions and hydrogen have a strong tendency toward aggregation and hydrogen mainly contributes to the room temperature ferromagnetism observed experimentally in ZnO:Co . Furthermore, in ZnO:Co , the formation of Ho with four-fold hydrogenic bonds is favored over HI by 0.4 eV.
RATE OF CONFINED PHONON EXCITATION IN RECTANGULAR QUANTUM WIRES
Authors: PHUONG LE THI THU , PHONG TRAN CONG
Published: June 2012

We present a theory of phonon generation via the Cerenkov effect in rectangular quantum wires (RQWs) based on the quantum kinetic equation for phonon population operator. Analytical expressions for the rate of change of the phonon population and conditions for phonon generation are obtained. Both electrons and phonons are confined. Numerical results for a specific RQW show that the amplitude of the laser field must satisfy additional conditions that are different in comparison with those of the generation of bulk phonons.
PECULIARITIES OF VIBRATION CHARACTERISTICS OF AMORPHOUS ICES
Authors: GETS KIRILL V. , SUBBOTIN OLEG S. , BELOSLUDOV VLADIMIR R.
Published: June 2012

Dynamic properties of low (LDA), high (HDA) and very high (VHDA) density amorphous ices were investigated within the approach based on Lattice Dynamics simulations. In this approach, we assume that the short-range molecular order mainly determines the dynamic and thermodynamic properties of amorphous ices. Simulation cell of 512 water molecules with periodical boundary conditions and disordering allows us to study dynamical properties and dispersion curves in the Brillouin zone of pseudo-crystal. Existence of collective phenomena in amorphous ices which is usual for crystals but anomalous for disordered phase was confirmed in our simulations. Molecule amplitudes of delocalized (collective) as well as localized vibrations have been considered.
Mitogen-activated protein kinase phosphatase 2, MKP-2, regulates early inflammation in acute lung injury
Authors: Cornell Timothy T. , Fleszar Andrew , McHugh Walker , Blatt Neal B. , Le Vine Ann Marie , Shanley Thomas P.
Published: June 2012

Acute lung injury (ALI) is mediated by an early proinflammatory response resulting from either a direct or indirect insult to the lung mediating neutrophil infiltration and consequent disruption of the alveolar capillary membrane ultimately leading to refractory hypoxemia. The mitogen-activated protein kinase (MAPK) pathways are a key component of the molecular response activated by those insults triggering the proinflammatory response in ALI. The MAPK pathways are counterbalanced by a set of dual-specific phosphatases (DUSP) that deactivate the kinases by removing phosphate groups from tyrosine or threonine residues. We have previously shown that one DUSP, MKP-2, regulates the MAPK pathway in a model of sepsis-induced inflammation; however, the role of MKP-2 in modulating the inflammatory response in ALI has not been previously investigated. We utilized both MKP-2-null (MKP-2−/−) mice and MKP-2 knockdown in a murine macrophage cell line to elucidate the role of MKP-2 in regulating inflammation during ALI. Our data demonstrated attenuated proinflammatory cytokine production as well as decreased neutrophil infiltration in the lungs of MKP-2−/− mice following direct, intratracheal LPS. Importantly, when challenged with a viable pathogen, this decrease in neutrophil infiltration did not impact the ability of MKP-2−/− mice to clear either gram-positive or gram-negative bacteria. Furthermore, MKP-2 knockdown led to an attenuated proinflammatory response and was associated with an increase in phosphorylation of ERK and induction of a related DUSP, MKP-1. These data suggest that altering MKP-2 activity may have therapeutic potential to reduce lung inflammation in ALI without impacting pathogen clearance.
TAS2R activation promotes airway smooth muscle relaxation despite β2-adrenergic receptor tachyphylaxis
Authors: An Steven S. , Wang Wayne C. H. , Koziol-White Cynthia J. , Ahn Kwangmi , Lee Danielle Y. , Kurten Richard C. , Panettieri Reynold A. , Liggett Stephen B.
Published: June 2012

Recently, bitter taste receptors (TAS2Rs) were found in the lung and act to relax airway smooth muscle (ASM) via intracellular Ca2+concentration signaling generated from restricted phospholipase C activation. As potential therapy, TAS2R agonists could be add-on treatment when patients fail to achieve adequate bronchodilation with chronic β-agonists. The β2-adrenergic receptor (β2AR) of ASM undergoes extensive functional desensitization. It remains unknown whether this desensitization affects TAS2R function, by cross talk at the receptors or distal common components in the relaxation machinery. We studied intracellular signaling and cell mechanics using isolated human ASM, mouse tracheal responses, and human bronchial responses to characterize TAS2R relaxation in the context of β2AR desensitization. In isolated human ASM, magnetic twisting cytometry revealed >90% loss of isoproterenol-promoted decrease in cell stiffness after 18-h exposure to albuterol. Under these same conditions of β2AR desensitization, the TAS2R agonist chloroquine relaxation response was unaffected. TAS2R-mediated stimulation of intracellular Ca2+concentration in human ASM was unaltered by albuterol pretreatment, in contrast to cAMP signaling, which was desensitized by >90%. In mouse trachea, β2AR desensitization by β-agonist amounted to 92 ± 6.0% ( P < 0.001), while, under these same conditions, TAS2R desensitization was not significant (11 ± 3.5%). In human lung slices, chronic β-agonist exposure culminated in 64 ± 5.7% ( P < 0.001) desensitization of β2AR-mediated dilation of carbachol-constricted airways that was reversed by chloroquine. We conclude that there is no evidence for physiologically relevant cross-desensitization of TAS2R-mediated ASM relaxation from chronic β-agonist treatment. These findings portend a favorable therapeutic profile for TAS2R agonists for the treatment of bronchospasm in asthma or chronic obstructive lung disease.
Optimal Determination of Respiratory Airflow Patterns Using a Nonlinear Multicompartment Model for a Lung Mechanics System
Authors: Li Hancao , Haddad Wassim M.
Published: June 2012

We develop optimal respiratory airflow patterns using a nonlinear multicompartment model for a lung mechanics system. Specifically, we use classical calculus of variations minimization techniques to derive an optimal airflow pattern for inspiratory and expiratory breathing cycles. The physiological interpretation of the optimality criteria used involves the minimization of work of breathing and lung volume acceleration for the inspiratory phase, and the minimization of the elastic potential energy and rapid airflow rate changes for the expiratory phase. Finally, we numerically integrate the resulting nonlinear two-point boundary value problems to determine the optimal airflow patterns over the inspiratory and expiratory breathing cycles.
On the Solution of a Class of Nonlinear Systems Governed by an M‐Matrix
Authors: Themistoclakis Woula , Vecchio Antonia
Published: June 2012

We consider a weakly nonlinear system of the form (I + φ(x)A)x = p, where φ(x) is a real function of the unknown vector x, and (I + φ(x)A) is an M‐matrix. We propose to solve it by means of a sequence of linear systems defined by the iteration procedure (I + φ(xr)A)xr+1 = p, r = 0, 1, …. The global convergence is proved by considering a related fixed‐point problem.
Band-Notched Ultrawide Band Planar Inverted-F Antenna
Authors: Chattha H. T. , Ishfaq M. K. , Saleem Y. , Huang Y. , Boyes S. J.
Published: June 2012

A novel ultrawide band planar inverted-F antenna with band-notched characteristics is presented in this paper. The planar inverted-F antenna uses two parasitic elements to enhance the bandwidth to cover the ultrawide band. The band-notched feature is added by inserting a W-shaped slot on the top radiating element of the antenna with a band rejection from 5.08 to 6 GHz (measured). Both the measured and simulated results are obtained to draw the conclusions.
Comparative Characterization of Multiscale Carbon Fiber Composite with Long and Short MWCNTs at Higher Weight Fractions
Authors: Zimmer Michael , Cheng Qunfeng , Li Shu , Brooks James , Liang Richard , Wang Ben , Zhang Chuck
Published: June 2012

There are documented advantages to using carbon nanotubes (CNTs) in composites for various property enhancements. However, to date, only limited studies have been conducted on using of longer CNTs over 1 mm in length. This study used long multiwalled carbon nanotubes (LMWCNTs) and their longer extended networks to test multiple properties in thermal conductivity, electrical conductivity, mechanical strength, and modulus and then compared these properties to those of shorter multi‐walled carbon nanotubes (SMWCNTs). For carbon fiber‐reinforced composites, the longer graphite paths from LMWCNTs in the matrix were expected to improve all properties. The longer networks were expected to allow for more undisturbed phonon transportation to improve thermal conductivity. This in turn relates to improved electrical conductivity and better mechanical properties. However, results have shown that the LMWCNTs do not improve or decrease thermal conductivity, whereas the shorter MWCNTs provide mixed results. LMWCNTs did show improvements in electrical, mechanical, and physical properties, but compared to shorter MWCNTs, the results in other certain properties varied. This perplexing outcome resides in the functioning of the networks made by both the LMWCNTs and shorter MWCNTs.
Dilute Magnetic Semiconductor Cu2FeSnS4 Nanocrystals with a Novel Zincblende Structure
Authors: Liang Xiaolu , Wei Xianhua , Pan Daocheng
Published: June 2012

Diluted magnetic semiconductor Cu2FeSnS4 nanocrystals with a novel zincblende structure have been successfully synthesized by a hot‐injection approach. Cu+, Fe2+, and Sn4+ ions occupy the same position in the zincblende unit cell, and their occupancy possibilities are 1/2, 1/4, and 1/4, respectively. The nanocrystals were characterized by means of X‐ray diffraction (XRD), transmission electron microscopy (TEM), selected area electron diffraction (SAED), energy‐dispersive spectroscopy (EDS), and UV‐vis‐NIR absorption spectroscopy. The nanocrystals have an average size of 7.5 nm and a band gap of 1.1 eV and show a weak ferromagnetic behavior at low temperature.
Expression of MicroRNA-1 and MicroRNA-21 in Different Protocols of Ischemic Conditioning in an Isolated Rat Heart Model
Authors: Duan Xin , Ji Bingyang , Wang Xiaohua , Liu Jinping , Zheng Zhe , Long Cun , Tang Yue , Hu Shengshou
Published: June 2012

Background: ‘Conditioning’ [ischemic preconditioning (IPC), ischemic postconditioning (IPO) and remote ischemic preconditioning (RIPC)] the heart to render it more resistant to an episode of acute myocardial ischemia-reperfusion (I/R) injury is an endogenous cardioprotective strategy. There are several mechanisms proposed for ‘conditioning’, such as endogenous mediators or cytoprotective proteins. In recent reports, microRNAs (miRNAs) were involved in controlling the expression of myocardial ischemia-related genes. Some studies have demonstrated that cardiac miRNA-1 and miRNA-21 were significantly increased by late IPC with an increase in their target proteins [endothelial nitric oxide synthase and heat shock protein 70 (HSP70)], but their expression levels in ‘conditioning’ strategies are currently unknown. Methods: In the current study, Langendorff-perfused Sprague-Dawley rat hearts were randomly assigned to one of four groups [control group (CON group, n = 12), IPC group (n = 12), IPO group (n = 12) and RIPC group (n = 12)]. Cardiac function was digitalized and analyzed. The expression of miRNA-1 and miRNA-21 was detected by real-time reverse transcription polymerase chain reaction. The expression of HSP70, programmed cell death protein 4 (PDCD4), B-cell lymphoma/leukemia-2 (Bcl-2) and Bcl-2-associated X protein (Bax) was detected by Western blot. Cardiac infarct size and myocardial apoptosis were determined using the 2,3,5-triphenyltetrazolium chloride assay and terminal deoxynucleotidyl transferase dUTP nick end labeling assay, respectively. Results: The results revealed that miRNA-1 (233 ± 45%) and miRNA-21 (356 ± 33%) expression was up-regulated in the IPC group, but the expression of miRNA-1 was down-regulated in the RIPC (61 ± 16%) group and IPO group (61 ± 13%). The expression of PDCD4 [IPC (74 ± 11%), RIPC (81 ± 16%), IPO (83 ± 12%)], HSP70 [IPC (74 ± 5%), RIPC (81 ± 6%), IPO (67 ± 11%)] and Bax [IPC (27 ± 6%), RIPC (21 ± 3%), IPO (27 ± 4%)] was down-regulated in the conditioning groups compared with the CON group [PDCD4 (130 ± 11%), HSP70 (121 ± 11%) and Bax (63 ± 8%)]. In the conditioning hearts, infarct size [IPC (31.7 ± 4.1%), RIPC (29.6 ± 6.19%) and IPO (32.8 ± 4.71%)] and myocardial apoptosis [IPC (15.2 ± 4.21%), RIPC (17.2 ± 1.92%) and IPO (15.6 ± 4.04%)] were significantly decreased compared with the CON group (infarct size: 51.77 ± 4.3%, myocardial apoptosis: 32.8 ± 3.96%). Conclusion: We concluded that miRNA-1 and miRNA-21 expression differed in IPC, RIPC and IPO groups, and their target proteins were not inversely correlated with the miRNAs in all the conditioning groups, which revealed that the miRNAs were regulated but complicated by the different conditioning protocols.
Validation of Fingernail Fluoride Concentration as a Predictor of Risk for Dental Fluorosis
Authors: Buzalaf M.A.R. , Massaro C.S. , Rodrigues M.H.C. , Fukushima R. , Pessan J.P. , Whitford G.M. , Sampaio F.C.
Published: June 2012

The aim of this study was to validate the use of fingernail fluoride concentrations at ages 2–7 years as predictors of the risk for developing dental fluorosis in the permanent dentition. Fifty-six children of both genders (10–15 years of age) had their incisors and premolars examined for dental fluorosis using the Thylstrup-Fejerskov index. Fingernail fluoride concentrations were obtained from previous studies when children were 2–7 years of age. Data were analyzed by unpaired t test, ANOVA, and Fisher’s exact test when the fingernail fluoride concentrations were dichotomized (≤2 or >2 µg/g). Children with dental fluorosis had significantly higher fingernail fluoride concentrations than those without the condition, and the concentrations tended to increase with the severity of fluorosis (r2 = 0.47, p < 0.0001). Using a fingernail fluoride concentration of 2 µg/g at ages 2–7 years as a threshold, this biomarker had high sensitivity (0.84) and moderate specificity (0.53) as a predictor for dental fluorosis. The high positive predictive value indicates that fingernail fluoride concentrations should be useful in public health research, since it has the potential to identify around 80% of children at risk of developing dental fluorosis.
Some Effects of Digoxin upon the Heart and Circulation in Man
Authors: FERRER M. IRENÉ , HARVEY RÉJANE M. , CATHCART RICHARD T. , WEBSTER CHARLES A. , RICHARDS DICKINSON W. , COURNAND ANDRÉ
Published: June 2012

The effects of acute digitalization upon the dynamics of the circulation were observed in patients with chronic cor pulmonale, using the technic of cardiac catheterization. The state of the circulation was further investigated in the same patients following recovery from failure. The mode of action of intravenous digoxin is discussed, and a tentative concept of the pathogenesis of chronic cor pulmonale is presented.
Gangrene of the Extremities of Venous Origin
Authors: HAIMOVICI HENRY
Published: June 2012

Gangrene of the extremities of venous origin is reviewed; it is a rare but distinct clinicopathologic entity hitherto not widely known. A classification of the cases of thrombophlebitis complicated with gangrene is presented, based on the presence of the peripheral pulses: (1) cases with palpable arteries; (2) cases with nonpalpable but patent arteries. Patency of the entire arterial system of the involved extremity, as verified by anatomic findings, is necessary for correct diagnosis. Complete blockage of the venous system appears to be the initiating and main cause, angiospasm playing a secondary role. The gangrene usually remains superficial and limited. Hence, a conservative surgical attitude is emphasized.
Studies of Congenital Heart Disease
Authors: DOW J. W. , LEVINE H. D. , ELKIN M. , HAYNES F. W. , HELLEMS H. K. , WHITTENBERGER J. W. , FERRIS B. G. , GOODALE W. T. , HARVEY W. P. , EPPINGER E. C. , DEXTER L.
Published: June 2012

Congenital pulmonic stenosis is indicated by cardiac catheterization by the finding of a higher systolic pressure in the right ventricle than in the pulmonary artery. Eight cases of uncomplicated pulmonic stenosis are studied. The findings on history, physical examination, x-ray and fluoroscopy, and electrocardiogram have been analyzed and the variations in circulatory dynamics encountered in these individuals are described in detail.
The Question of the Function of the Right Ventricular Myocardium: An Experimental Study
Authors: BAKOS AUGUSTUS C. P.
Published: June 2012

A laboratory study designed to investigate the independent pump-like function of the right ventricle of the dog heart is presented. Systolic and diastolic pulmonary arterial pressure fluctuations were used as the definitive criterion for pumping efficiency. Control pressure levels are compared with those recorded after complete damage, by electrosurgical coagulation, of the free right ventricular myocardium. The degree of damage so produced was ascertained from an analysis of electrocardiographic, physiologic and histologic observations. The results are discussed and explained in terms of a postulated mechanism based upon the architecture of the individual ventricular muscle bands.
Primary Tumor of the Pericardium Involving the Myocardium: Surgical Removal
Authors: HOCHBERG LEW A. , ROBINSON ALEXANDER I.
Published: June 2012

A case is presented in which a primary tumor of the pericardium, with myocardial involvement, was discovered at the time of surgical exploration. The tumor was removed and the patient has remained well and active at the time of this report, eighteen months after the operation.