bluuebunny/crossref_metadata_2025 huggingface dataset:
Activity of Ceftolozane-Tazobactam against a Broad Spectrum of Recent Clinical Anaerobic Isolates
Authors: Snydman David R. , McDermott Laura A. , Jacobus Nilda V.
Published: November 2013

We evaluated
in vitro
activity of ceftolozane-tazobactam (TOL-TAZ), formerly CXA-201, against recent clinical anaerobic isolates with emphasis on the
Bacteroides fragilis
group. Ceftolozane-tazobactam showed good activity against
B. fragilis
species and intermediate to limited activity against other species of
Bacteroides
. Ceftolozane-tazobactam showed very good activity against
Prevotella
spp.,
Fusobacterium
spp., and
Propionibacterium
spp., varying activities against Gram-positive cocci, and limited activity against
Clostridium
spp.
Liposomal Cholesterol Delivery Activates the Macrophage Innate Immune Arm To Facilitate Intracellular Leishmania donovani Killing
Authors: Ghosh June , Guha Rajan , Das Shantanabha , Roy Syamal
Published: November 2013

Leishmania donovanicauses visceral leishmaniasis (VL) by infecting the monocyte/macrophage lineage and residing inside specialized structures known as parasitophorous vacuoles. The protozoan parasite has adopted several means of escaping the host immune response, with one of the major methods being deactivation of host macrophages. Previous reports highlight dampened macrophage signaling, defective antigen presentation due to increased membrane fluidity, and the downregulation of several genes associated withL. donovaniinfection. We have reported previously that the defective antigen presentation in infected hamsters could be corrected by a single injection of a cholesterol-containing liposome. Here we show that cholesterol in the form of a liposomal formulation can stimulate the innate immune arm and reactivate macrophage function. Augmented levels of reactive oxygen species (ROS) and reactive nitrogen intermediates (RNI), along with proinflammatory cytokines such as tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6), corroborate intracellular parasite killing. Cholesterol incorporation kinetics is favored in infected macrophages more than in normal macrophages. Such an enhanced cholesterol uptake is associated with preferential apoptosis of infected macrophages in an endoplasmic reticulum (ER) stress-dependent manner. All these events are coupled with mitogen-activated protein (MAP) kinase activation, while inhibition of such pathways resulted in increased parasite loads. Hence, liposomal cholesterol is a potential facilitator of the macrophage effector function in favor of the host, independently of the T-cell arm.
Porphyromonas gingivalis Lipid A Phosphatase Activity Is Critical for Colonization and Increasing the Commensal Load in the Rabbit Ligature Model
Authors: Zenobia Camille , Hasturk Hatice , Nguyen Daniel , Van Dyke Thomas E. , Kantarci Alpdogan , Darveau Richard P.
Published: November 2013

Periodontitis is a disease of polymicrobial etiology characterized by inflammation, degradation of host tissue, and bone that irreversibly destroys the supporting apparatus of teeth.
Porphyromonas gingivalis
contains lipid A with structural heterogeneity that has been postulated to contribute to the initiation of dysbiosis in oral communities by modulating the host response, thereby creating a permissive environment for its growth. We examined two
P. gingivalis
lipid A phosphatase mutants which contain different “locked” lipid A structures that induce different host cellular responses for their ability to induce dysbiosis and periodontitis in rabbits. Lipopolysaccharide (LPS) preparations obtained from these strains were also examined. After repeated applications of all strains and their respective LPS preparations,
P. gingivalis
wild type, but not the lipid A mutants, had a significant impact on both the oral commensal microbial load and composition. In contrast, in rabbits exposed to the mutant strains or the LPS preparations, the microbial load did not increase, and yet significant changes in the oral microbial composition were observed. All strains and their respective LPS preparations induced periodontitis. Therefore, the ability to alter the lipid A composition in response to environmental conditions by lipid A phosphatases is required for both colonization of the rabbit and increases in the microbial load. Furthermore, the data demonstrate that multiple dysbiotic oral microbial communities can elicit periodontitis.
Large-Scale Investigation of Leishmania Interaction Networks with Host Extracellular Matrix by Surface Plasmon Resonance Imaging
Authors: Fatoux-Ardore Marie , Peysselon Franck , Weiss Anthony , Bastien Patrick , Pratlong Francine , Ricard-Blum Sylvie
Published: November 2013

We have set up an assay to study the interactions of live pathogens with their hosts by using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have used this assay to characterize the interactions ofLeishmaniapromastigotes with ∼70 mammalian host biomolecules (extracellular proteins, glycosaminoglycans, growth factors, cell surface receptors). We have identified, in total, 27 new partners (23 proteins, 4 glycosaminoglycans) of procyclic promastigotes of sixLeishmaniaspecies and 18 partners (15 proteins, 3 glycosaminoglycans) of three species of stationary-phase promastigotes for all the strains tested. The diversity of the interaction repertoires ofLeishmaniaparasites reflects their dynamic and complex interplay with their mammalian hosts, which depends mostly on the species and strains ofLeishmania. Stationary-phaseLeishmaniaparasites target extracellular matrix proteins and glycosaminoglycans, which are highly connected in the extracellular interaction network. Heparin and heparan sulfate bind to mostLeishmaniastrains tested, and 6-O-sulfate groups play a crucial role in these interactions. NumerousLeishmaniastrains bind to tropoelastin, and some strains are even able to degrade it. Several strains interact with collagen VI, which is expressed by macrophages. MostLeishmaniapromastigotes interact with several regulators of angiogenesis, including antiangiogenic factors (endostatin, anastellin) and proangiogenic factors (ECM-1, VEGF, and TEM8 [also known as anthrax toxin receptor 1]), which are regulated by hypoxia. Since hypoxia modulates the infection of macrophages by the parasites, these interactions might influence the infection of host cells byLeishmania.
Reversible Lipid Accumulation and Associated Division Arrest of Mycobacterium avium in Lipoprotein-Induced Foamy Macrophages May Resemble Key Events during Latency and Reactivation of Tuberculosis
Authors: Caire-Brändli Irène , Papadopoulos Alexia , Malaga Wladimir , Marais David , Canaan Stéphane , Thilo Lutz , de Chastellier Chantal
Published: November 2013

During the dormant phase of tuberculosis,
Mycobacterium tuberculosis
persists in lung granulomas by residing in foamy macrophages (FM) that contain abundant lipid bodies (LB) in their cytoplasm, allowing bacilli to accumulate lipids as intracytoplasmic lipid inclusions (ILI). An experimental model of FM is presented where bone marrow-derived mouse macrophages are infected with
M. avium
and exposed to very-low-density lipoprotein (VLDL) as a lipid source. Quantitative analysis of detailed electron microscope observations showed the following results. (i) Macrophages became foamy, and mycobacteria formed ILI, for which host triacylglycerides, rather than cholesterol, was essential. (ii) Lipid transfer occurred via mycobacterium-induced fusion between LB and phagosomes. (iii) Mycobacteria showed a thinned cell wall and became elongated but did not divide. (iv) Upon removal of VLDL, LB and ILI declined within hours, and simultaneous resumption of mycobacterial division restored the number of mycobacteria to the same level as that found in untreated control macrophages. This showed that the presence of ILI resulted in a reversible block of division without causing a change in the mycobacterial replication rate. Fluctuation between ILI either partially or fully extending throughout the mycobacterial cytoplasm was suggestive of bacterial cell cycle events. We propose that VLDL-driven FM constitute a well-defined cellular system in which to study changed metabolic states of intracellular mycobacteria that may relate to persistence and reactivation of tuberculosis.
Toxoplasma gondii Inhibits Gamma Interferon (IFN-γ)- and IFN-β-Induced Host Cell STAT1 Transcriptional Activity by Increasing the Association of STAT1 with DNA
Authors: Rosowski Emily E. , Nguyen Quynh P. , Camejo Ana , Spooner Eric , Saeij Jeroen P. J.
Published: November 2013

The gamma interferon (IFN-γ) response, mediated by the STAT1 transcription factor, is crucial for host defense against the intracellular pathogenToxoplasma gondii, but prior infection withToxoplasmacan inhibit this response. Recently, it was reported that theToxoplasmatype II NTE strain prevents the recruitment of chromatin remodeling complexes containing Brahma-related gene 1 (BRG-1) to promoters of IFN-γ-induced secondary response genes such asCiitaand major histocompatibility complex class II genes in murine macrophages, thereby inhibiting their expression. We report here that a type I strain ofToxoplasmainhibits the expression of primary IFN-γ response genes such asIRF1through a distinct mechanism not dependent on the activity of histone deacetylases. Instead, infection with a type I, II, or III strain ofToxoplasmainhibits the dissociation of STAT1 from DNA, preventing its recycling and further rounds of STAT1-mediated transcriptional activation. This leads to increased IFN-γ-induced binding of STAT1 at theIRF1promoter in host cells and increased global IFN-γ-induced association of STAT1 with chromatin.Toxoplasmatype I infection also inhibits IFN-β-induced interferon-stimulated gene factor 3-mediated gene expression, and this inhibition is also linked to increased association of STAT1 with chromatin. The secretion of proteins into the host cell by a type I strain ofToxoplasmawithout complete parasite invasion is not sufficient to block STAT1-mediated expression, suggesting that the effector protein responsible for this inhibition is not derived from the rhoptries.
Changes in blood gas transport of altitude native soccer players near sea-level and sea-level native soccer players at altitude (ISA3600)
Authors: Wachsmuth Nadine , Kley Marlen , Spielvogel Hilde , Aughey Robert J , Gore Christopher J , Bourdon Pitre C , Hammond Kristal , Sargent Charli , Roach Gregory D , Sanchez Rudy Soria , Claros Jesus C Jimenez , Schmidt Walter F , Garvican-Lewis Laura A
Published: November 2013

Objectives

The optimal strategy for soccer teams playing at altitude is not known, that is, ‘fly-in, fly-out’ versus short-term acclimatisation. Here, we document changes in blood gas and vascular volumes of sea-level (Australian, n=20) and altitude (Bolivian, n=19) native soccer players at 3600 m.

Methods

Haemoglobin-oxygen saturation (Hb-sO2), arterial oxygen content (CaO2), haemoglobin mass (Hbmass), blood volume (BV) and blood gas concentrations were measured before descent (Bolivians only), together with aerobic fitness (via Yo-YoIR1), near sea-level, after ascent and during 13 days at 3600 m.

Results

At baseline, haemoglobin concentration [Hb] and Hbmass were higher in Bolivians (mean±SD; 18.2±1.0 g/dL, 12.8±0.8 g/kg) than Australians (15.0±0.9 g/dL, 11.6±0.7 g/kg; both p≤0.001). Near sea-level, [Hb] of Bolivians decreased to 16.6±0.9 g/dL, but normalised upon return to 3600 m; Hbmass was constant regardless of altitude. In Australians, [Hb] increased after 12 days at 3600 m to 17.3±1.0 g/dL; Hbmass increased by 3.0±2.7% (p≤0.01). BV decreased in both teams at altitude by ∼400 mL. Arterial partial pressure for oxygen (PaO2), Hb-sO2and CaO2of both teams decreased within 2 h of arrival at 3600 m (p≤0.001) but increased over the following days, with CaO2overcompensated in Australians (+1.7±1.2 mL/100 mL; p≤0.001). Yo-YoIR1 was lower on the 3rd versus 10th day at altitude and was significantly related to CaO2.

Conclusions

The marked drop in PaO2and CaO2observed after ascent does not support the ‘fly-in, fly-out’ approach for soccer teams to play immediately after arrival at altitude. Although short-term acclimatisation was sufficient for Australians to stabilise their CaO2(mostly due to loss of plasma volume), 12 days appears insufficient to reach chronic levels of adaption.
Soccer activity profile of altitude versus sea-level natives during acclimatisation to 3600 m (ISA3600)
Authors: Aughey Robert J , Hammond Kristal , Varley Matthew C , Schmidt Walter F , Bourdon Pitre C , Buchheit Martin , Simpson Ben , Garvican-Lewis Laura A , Kley Marlen , Soria Rudy , Sargent Charli , Roach Gregory D , Claros Jesus C Jimenez , Wachsmuth Nadine , Gore Christopher J
Published: November 2013

Objectives

We investigated the effect of high altitude on the match activity profile of elite youth high altitude and sea level residents.

Methods

Twenty Sea Level (Australian) and 19 Altitude-resident (Bolivian) soccer players played five games, two near sea level (430 m) and three in La Paz (3600 m). Match activity profile was quantified via global positioning system with the peak 5 min period for distance ((D5peak)) and high velocity running (>4.17 m/s, HIVR5peak); as well as the 5 min period immediately subsequent to the peak for both distance (D5sub) and high-velocity running (HIVR5sub) identified using a rolling 5 min epoch. The games at 3600 m were compared with the average of the two near sea-level games.

Results

The total distance per minute was reduced by a small magnitude in the first match at altitude in both teams, without any change in low-velocity running. There were variable changes in HiVR, D5peakand HiVR5peakfrom match to match for each team. There were within-team reductions in D5peakin each game at altitude compared with those at near sea level, and this reduction was greater by a small magnitude in Australians than Bolivians in game 4. The effect of altitude on HiVR5peakwas moderately lower in Australians compared with Bolivians in game 3. There was no clear difference in the effect of altitude on maximal accelerations between teams.

Conclusions

High altitude reduces the distance covered by elite youth soccer players during matches. Neither 13 days of acclimatisation nor lifelong residence at high altitude protects against detrimental effects of altitude on match activity profile.
The individual response to training and competition at altitude
Authors: Chapman Robert F
Published: November 2013

Performance in athletic activities that include a significant aerobic component at mild or moderate altitudes shows a large individual variation. Physiologically, a large portion of the negative effect of altitude on exercise performance can be traced to limitations of oxygen diffusion, either at the level of the alveoli or the muscle microvasculature. In the lung, the ability to maintain arterial oxyhaemoglobin saturation (SaO2) appears to be a primary factor, ultimately influencing oxygen delivery to the periphery. SaO2in hypoxia can be defended by increasing ventilatory drive; however, during heavy exercise, many athletes demonstrate limitations to expiratory flow and are unable to increase ventilation in hypoxia. Additionally, increasing ventilatory work in hypoxia may actually be negative for performance, if dyspnoea increases or muscle blood flow is reduced secondary to an increased sympathetic outflow (eg, the muscle metaboreflex response). Taken together, some athletes are clearly more negatively affected during exercise in hypoxia than other athletes. With careful screening, it may be possible to develop a protocol for determining which athletes may be the most negatively affected during competition and/or training at altitude.
Relationship between changes in haemoglobin mass and maximal oxygen uptake after hypoxic exposure
Authors: Saunders Philo U , Garvican-Lewis Laura A , Schmidt Walter F , Gore Christopher J
Published: November 2013

Background

Endurance athletes have been using altitude training for decades to improve near sea-level performance. The predominant mechanism is thought to be accelerated erythropoiesis increasing haemoglobin mass (Hbmass) resulting in a greater maximal oxygen uptake (O2max). Not all studies have shown a proportionate increase inO2maxas a result of increased Hbmass. The aim of this study was to determine the relationship between the two parameters in a large group of endurance athletes after altitude training.

Methods

145 elite endurance athletes (94 male and 51 female) who participated in various altitude studies as altitude or control participants were used for the analysis. Participants performed HbmassandO2maxtesting before and after intervention.

Results

For the pooled data, the correlation between per cent change in Hbmassand per cent change inO2maxwas significant (p<0.0001, r2=0.15), with a slope (95% CI) of 0.48 (0.30 to 0.67) intercept free to vary and 0.62 (0.46 to 0.77) when constrained through the origin. When separated, the correlations were significant for the altitude and control groups, with the correlation being stronger for the altitude group (slope of 0.57 to 0.72).

Conclusions

With high statistical power, we conclude that altitude training of endurance athletes will result in an increase inO2maxof more than half the magnitude of the increase in Hbmass, which supports the use of altitude training by athletes. But race performance is not perfectly related to relativeO2max, and other non-haematological factors altered from altitude training, such as running economy and lactate threshold, may also be beneficial to performance.
The sleep of elite athletes at sea level and high altitude: a comparison of sea-level natives and high-altitude natives (ISA3600)
Authors: Roach Gregory D , Schmidt Walter F , Aughey Robert J , Bourdon Pitre C , Soria Rudy , Claros Jesus C Jimenez , Garvican-Lewis Laura A , Buchheit Martin , Simpson Ben M , Hammond Kristal , Kley Marlen , Wachsmuth Nadine , Gore Christopher J , Sargent Charli
Published: November 2013

Background

Altitude exposure causes acute sleep disruption in non-athletes, but little is known about its effects in elite athletes. The aim of this study was to examine the effects of altitude on two groups of elite athletes, that is, sea-level natives and high-altitude natives.

Methods

Sea-level natives were members of the Australian under-17 soccer team (n=14). High-altitude natives were members of a Bolivian under-20 club team (n=12). Teams participated in an 18-day (19 nights) training camp in Bolivia, with 6 nights at near sea level in Santa Cruz (430 m) and 13 nights at high altitude in La Paz (3600 m). Sleep was assessed on every day/night using activity monitors.

Results

The Australians’ sleep was shorter, and of poorer quality, on the first night at altitude compared with sea level. Sleep quality returned to normal by the end of the first week at altitude, but sleep quantity had still not stabilised at its normal level after 2 weeks. The quantity and quality of sleep obtained by the Bolivians was similar, or greater, on all nights at altitude compared with sea level. The Australians tended to obtain more sleep than the Bolivians at sea level and altitude, but the quality of the Bolivians’ sleep tended to be better than that of the Australians at altitude.

Conclusions

Exposure to high altitude causes acute and chronic disruption to the sleep of elite athletes who are sea-level natives, but it does not affect the sleep of elite athletes who are high-altitude natives.
Advance care planning discussions among residents of long term care and designated assisted living: experience from Calgary, Alberta
Authors: Dyason Claire , Simon Jessica , Wityk Martin Tracy Lynn
Published: November 2013

Objectives

Patients, physicians and the healthcare system are faced with the challenge of determining, and respecting, the medical wishes of an aging population. Our study sought to describe who participates in advance care planning (ACP) and decision-making for patients in long-term care and designated assisted living.

Methods

In 2008, Alberta Health Services initiated its ‘Advance Care Planning: Goals of Care Designation’ (Adult) policy in the Calgary zone. This policy encouraged discussions about goals of care and used a tracking form to capture these conversations. A postpolicy implementation chart review was performed at 3 time points: at baseline, at 6 months and at 18 months post implementation in long term care (LTC) and designated assisted living sites.

Results

166 charts were reviewed and 90% had a documented goals of care order. Less than half of residents (47%) were documented as participating in conversations and they were less likely to participate if they had cognitive impairment and were living in LTC. Documented family participation was more prevalent in LTC (51% vs 11%). Nurses participated in 67% of documented conversations with only 34% of discussions documenting physician involvement.

Conclusions

This study identifies the lack of documented resident participation in ACP in LTC. While this finding may be explained by the high prevalence of cognitive impairment in our population, it raises questions about the optimal approach to ACP in LTC. In this setting, ACP appears to be more about relational autonomy than it is about patient autonomy.
A randomised controlled trial of Silirum vaccine for control of paratuberculosis in farmed red deer
Authors: Stringer L. A. , Wilson P. R. , Heuer C. , Mackintosh C. G.
Published: November 2013

A randomised controlled trial to assess the efficacy of Silirum vaccine in control of paratuberculosis in young farmed deer was carried out in 2008–2009 in six New Zealand herds with a history of clinical disease. Vaccination with Silirum was carried out in four‐month‐old deer, and vaccinates (n=1671) and controls (n=1664) were weighed at vaccination and at 8 and 12 months old, when faecal samples were collected from 125 vaccinates and 123 controls on five farms. Deer were slaughtered between 11 and 20 months of age, and the incidence of gross visceral lymph node (VLN) pathology typical of paratuberculosis in deer, that is, enlarged and/or granulomatous VLN, was recorded. Clinical disease was confirmed in 18 controls and seven vaccinates, representing a vaccine efficacy estimate of 60 per cent (95% CI 3 per cent to 83 per cent, P=0.04). Forty‐seven percent (95% CI 38 per cent to 56 per cent) of faecal samples from vaccinates and 55 per cent (95% CI 46 per cent to 64 per cent) from controls were Mycobacterium avium subspecies paratuberculosis positive (P=0.5). Average daily liveweight gain did not differ between the cohorts. At slaughter, 1.4 per cent of vaccinates and 4.5 per cent of controls had VLN pathology, RR=0.32 (95% CI 0.19 to 0.54, P<0.001). These data indicate that vaccination with Silirum may be useful as an aid to control losses associated with clinical paratuberculosis in young deer.
Response of forage yield and quality to thinning and fertilization of young forests: implications for silvopasture management
Authors: Lindgren Pontus M.F. , Sullivan Thomas P.
Published: November 2013

Integration of trees with forage and livestock production (silvopastoralism) could increase productivity of forest and range resources in western North America. Pre-commercial thinning (PCT) and fertilization are two silvicultural practices that could enhance silvopasture. We tested two hypotheses (H): that yield and quality of forage would be enhanced by (H1) heavy thinning (PCT) to ≤1000 stems·ha−1 and by (H2) repeated fertilization in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) stands. Study areas were located near Summerland and Kelowna in south-central British Columbia, Canada. Each study area had six treatments: three pairs of stands thinned to densities of ∼500 (low), ∼1000 (medium), and ∼2000 (high) stems·ha−1 with one stand of each pair fertilized five times at 2 year intervals. Forage yield was enhanced by PCT, but only within fertilized stands. Forage quality was generally not affected by PCT, except for crude protein of herbs that was poorer in heavily thinned stands. Fertilization tended to enhance forage yield and quality in the heavily thinned stands. Significantly improved quality of pinegrass (Calamagrostis rubescens Buckley) indicated that repeated fertilization, coupled with heavy thinning, may extend the period when high-quality forage is available, thereby allowing for increased stocking densities of cattle (Bos taurus L.) and perhaps extending the grazing season into the fall.
Lipopolysaccharide glycotyping of clarithromycin-resistant and clarithromycin-susceptible Canadian isolates ofHelicobacter pylori
Authors: Altman Eleonora , Harrison Blair A. , Chandan Vandana , Slinger Robert
Published: November 2013

Lipopolysaccharide (LPS) of Helicobacter pylori exhibits several unique structures, such as Lewis (Le) antigens, α-1,6-glucan, and dd-heptan. To investigate the relationship between LPS structure and resistance to clarithromycin, 41 Canadian isolates of H. pylori were characterized by whole-cell ELISA (enzyme-linked immunosorbent assay), sugar analysis, immunoblotting, and indirect immunofluorescence. The expression of type 2 Lewis X and (or) Lewis Y antigens was detected in 22 of 23 (95.7%) clarithromycin-resistant and in 14 of 18 (77.7%) clarithromycin-susceptible H. pylori strains (P < 0.05), and 8 isolates co-expressed type 1 and type 2 Le antigens (8/41, 19.5%). A significantly higher frequency of α-1,6-glucan (P < 0.01) was detected in clarithromycin-resistant strains than in clarithromycin-susceptible strains (19/23 (82.6%) versus 11/18 (61.1%)). Sugar analysis of selected α-1,6-glucan-positive H. pylori strains confirmed that they frequently contained elevated amounts of dd-heptose. Clarithromycin-resistant isolates were also characterized by low expression levels or absence of CagA (17/23, 73.9%). Indirect immunofluorescence studies carried out on selected H. pylori strains with rabbit immune sera specific for α-1,6-glucan confirmed broad recognition of α-1,6-glucan epitope. The binding was not affected by LPS glycotype of H. pylori isolates examined nor by their CagA status or resistance to clarithromycin. These findings suggest α-1,6-glucan as a potential vaccine target, especially in an era of increasing clarithromycin resistance in H. pylori.
Thickness dependence of electron transport in pure a-Se photoconductive films
Authors: Mortensen Derek , Belev George , Koughia Kirill (Cyril) , Johanson Robert E. , Kasap S.O.
Published: November 2013

Electron transport in vacuum-deposited a-Se films with thicknesses varying from 13 to 501 μm has been investigated by conventional time-of-flight (TOF) and interrupted field TOF experiments. To separate the influences of electric field and the thickness, all TOF experiments were performed at a constant electric field. It has been found that the electron mobility is relatively constant in thick films (L > 50 μm) and increases in thinner films (L < 50 μm) with decreasing thickness. On the other hand, the electron lifetime is relatively thickness independent in films with thickness L > 50 μm, but drops sharply in thin films when L < 50 μm. These observations can be explained based on the density of states model that includes three types of traps forming Gaussian-like distributions within the mobility gap as reported in Koughia et al. (J. Appl. Phys. 97, 033706 (2005)).
Assessment of arterial stiffness using applanation tonometry
Authors: Kim David H. , Braam Branko
Published: November 2013

Augmentation index (AIx) and pulse wave velocity (PWV) assess functional and structural aspects of the vascular wall and are independent markers of cardiovascular morbidity and mortality. Like blood pressure, many factors, genetic, structural, and physiological, affect AIx and PWV. AIx and PWV can be assessed noninvasively using applanation tonometry. The technique is simple, but comes with a number of practical and technical limitations that have not been well documented and (or) explored. This review considers pulse wave analysis in the context of cardiovascular disease, and considers its limitations. Data are presented indicating that the placement of the probe is critical, and that the amplitude of the obtained signal is related to the variability in measurements. On a more theoretical note, issues are discussed regarding the applied transfer functions that are built in the devices to assess central AIx from peripheral waveforms. Altogether, PWV and its analysis are useful additions to the arsenal of parameters that can be used to assess vascular health and to estimate vascular risk. Yet, our analysis underscores the necessity for precise operating procedures, and calls for transparency regarding the applied transfer functions of commercial devices.
Species composition and abundance of ants and other invertebrates in stands of crested wheatgrass (Agropyron cristatum) and native grasslands in the northern Great Plains
Authors: Radtke T.M. , Glasier J.R.N. , Wilson S.D.
Published: November 2013

Habitat alteration by exotic plant species can have profound effects on vertebrates, but its effects on invertebrates are less well-known. Crested wheatgrass (Agropyron cristatum (L.) Gaertn.) is a perennial grass that has been planted on >106ha of the Great Plains. We tested the hypothesis that invertebrate communities (especially ants) differed between native grasslands and A. cristatum stands, using pitfall traps in Saskatchewan and Montana. Ant species composition differed significantly between native grasslands and A. cristatum stands, but there were no differences in total ant abundance, the abundance of functional groups, or species richness. Ant species richness was significantly greater in Montana than Saskatchewan. In Saskatchewan, bare ground was positively related to total ant abundance and the abundance of “cold-climate specialist” and “opportunist” functional groups of ants. In Montana, the cover of forbs was positively related to total ant abundance. The abundances of individual ant species were not predicted by any vegetation characteristics, except for Formica obscuripes Forel, 1886, which increased significantly with litter. The total abundance of other invertebrates was greater in native grasslands than in A. cristatum stands, although not significantly so. Within each vegetation type, variation in ant communities may depend either directly on the effects of vegetation species composition, or indirectly via the effect of vegetation on other factors such as temperature. The results suggest that ant community composition was influenced more by variation within grasslands and between locations than by differences between native and exotic grasslands.
A SIMPLE SYNCHRONIZATION SCHEME OF GENESIO–TESI SYSTEM BASED ON THE BACK-STEPPING DESIGN
Authors: WANG ZUOLEI , JIANG YAOLIN
Published: November 2013

Synchronization of the Genesio–Tesi chaotic system is investigated via back-stepping method. Based on the Lyapunov stability theory, a novel scheme is designed. A global asymptotical synchronization can be realized via two simpler controllers, each controller involving only one state variable. Furthermore, the convergence speed can be adjusted by control coefficient. Finally, some numerical simulations are employed to verify the effectiveness of the proposed methods.
Determinants of Internet Financial Reporting Practices: Evidence from the UAE
Authors: Miniaoui Hela , Oyelere Peter
Published: November 2013

The objective of this paper is to undertake an in-depth study of the Internet financial reporting (IFR) practices of UAE-listed companies. The survey is aimed at identifying IFR versus non-IFR companies, and the nature and extent of their IFR practices. Logistic regression analysis was undertaken to establish the determinants of IFR by the companies.

The findings of this study identify the size, the leverage, industry sector, and profitability as the most important predictors of IFR adoption by UAE listed-companies. Larger companies with greater leverage are more likely to set up a website and use it for IFR than smaller less leveraged ones. It was noticed that 62% of IFR companies is from banking, investment & finance sector and from insurance sector as well.

This study is expected to inform monetary authorities on this subject and give more support to these two industries, as they were peers for other sectors in the UAE. Furthermore, the outcome of this paper will provide policy-makers with insight into the factors that motivate IFR among corporate organizations.
A sedimentary archive of tectonic switching from Emeishan Plume to Indosinian orogenic sources in SW China
Authors: Yang Jianghai , Cawood Peter A. , Du Yuansheng , Huang Hu , Hu Lisha
Published: November 2013

Upper Permian to Middle Triassic sedimentary rocks in the Youjiang Basin, SW China, record a change from a within-plate mafic-dominated source to the NW, to a mixed source involving magmatic arc and recycled orogenic detritus that lay to the west and east. Upper Permian and some Lower Triassic sedimentary rocks are characterized by relatively high contents of TiO
2
and Nb, and low ratios of Al
2
O
3
/TiO
2
and Th/Nb. Detrital zircons yield U–Pb ages of
c
. 260 Ma and have geochemical affinities to those crystallized from the within-plate type magmas. These features, combined with extensive basaltic lithic fragments and plagioclase grains in the sandstones, imply a sedimentary source dominated by the Emeishan Large Igneous Province exposed to the NW of the basin. The Early and Middle Triassic marked a significant change in sediment provenance, with rocks displaying geochemical affinity to upper continental crust. U–Pb ages and trace elements of detrital zircons from this material show input from multiple sedimentary sources including the subduction–collision rocks related to the Indosinian Orogeny to the west of the basin and the recycled Precambrian–early Palaeozoic sedimentary and granitic rocks in the South China hinterland to the east of the basin. The Early Triassic change in the nature of the source supplying detritus to the Youjiang Basin, together with regional sedimentary and tectonothermal events, suggests a tectonic transition from the Emeishan Plume to the Indosinian Orogeny in SW China. Regional stratigraphic correlation and provenance data suggest that the Emeishan basalts provided a large sediment influx for the riverine–littoral–marine systems in the Late Permian. This basaltic particulate and dissolved input may have contributed significant unradiogenic Sr to the Late Permian seawater.

Supplementary material:

Details of sample preparation, analytical procedure and results, and additional figures are available at
www.geolsoc.org.uk/SUP18698
.
Using titanium-in-quartz geothermometry and geospeedometry to recover temperatures in the aureole of the Ballachulish Igneous Complex, NW Scotland
Authors: Morgan D. J. , Jollands M. C. , Lloyd G. E. , Banks D. A.
Published: November 2013

‘Titanium-in-Quartz’ geothermometry suggests quartzites could yield reliable temperature estimates. We here apply four calibrations of the titanium-in-quartz geothermometer to contact-metamorphosed quartzites surrounding the Ballachulish Igneous Complex, Scotland. Two agree broadly with thermal modelling and pre-existing geothermometry; two give temperatures consistently too low. As reported in earlier studies, the technique suffers from difficulties in analysing low titanium (Ti) levels with high spatial and analytical precision. However, this study finds that the critical problem is one of Ti heterogeneity, which poses difficulties in constraining the chemical activity of Ti during quartz growth under metamorphic conditions. Scanning electron microscope-cathodoluminescence (SEM-CL) textures support an interpretation of extensive Ti disequilibrium despite the presence of rutile, indicating dynamic interplay between grain boundary diffusion, fluid/melt percolation and grain growth. The strong zonation suggests a possible geothermometer based on apparent volume diffusion of Ti-in-quartz to derive grain growth histories. Analysis of rutile–quartz interaction implies peak contact temperatures of 645±12 °C, precise but reliant on external estimates of cooling rate from thermal models. Our conclusions support caution in applying Ti-in-quartz geothermometry in aureole settings. However, rutile–quartz juxtaposition prior to heating to >600 °C defines a Ti diffusion couple, employable as a thermometer if cooling rates are constrained by other means.
Data science and prediction
Authors: Dhar Vasant
Published: November 2013

Big data promises automated actionable knowledge creation and predictive models for use by both humans and computers.
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters
Authors: Piovesan Damiano , Profiti Giuseppe , Martelli Pier Luigi , Fariselli Piero , Casadio Rita
Published: November 2013

Genome annotation is one of the most important issues in the genomic era. The exponential growth rate of newly sequenced genomes and proteomes urges the development of fast and reliable annotation methods, suited to exploit all the information available in curated databases of protein sequences and structures. To this aim we developed BAR+, the Bologna Annotation Resource.
1
The basic notion is that sequences with high identity value to a counterpart can inherit the same function/s and structure, if available. As a case study we describe how the ATP-binding domain of the ABC transporters can be found and modeled in over 30,000 new sequences not annotated before. We also mapped into BAR+ all the ABC transporters listed in the Transporter Classification DataBase
2
and found that within our environment annotation could be extended to another 256,866 sequences.
Design thinking
Authors: Denning Peter J.
Published: November 2013

Design thinking is the newest fashion for finding better solutions to problems. Combining it with computational thinking offers some real possibilities for improving software design.
Efficient context sensitivity for dynamic analyses via calling context uptrees and customized memory management
Authors: Huang Jipeng , Bond Michael D.
Published: November 2013

State-of-the-art dynamic bug detectors such as data race and memory leak detectors report program locations that are likely causes of bugs. However, programmers need more than
static
program locations to understand the behavior of increasingly complex and concurrent software.
Dynamic calling context
provides additional information, but it is expensive to record calling context frequently, e.g., at every read and write. Context-sensitive dynamic analyses can build and maintain a calling context tree (CCT) to track calling context--but in order to reuse existing nodes, CCT-based approaches require an expensive lookup.

This paper introduces a new approach for context sensitivity that avoids this expensive lookup. The approach uses a new data structure called the
calling context uptree
(CCU) that adds low overhead by avoiding the lookup and instead allocating a new node for each context. A key contribution is that the approach can mitigate the costs of allocating many nodes by extending tracing garbage collection (GC): GC collects unused CCU nodes naturally and efficiently, and we extend GC to merge duplicate nodes lazily.

We implement our CCU-based approach in a high-performance Java virtual machine and integrate it with a staleness-based memory leak detector and happens-before data race detector, so they can report context-sensitive program locations that cause bugs. We show that the CCU-based approach, in concert with an extended GC, provides a compelling alternative to CCT-based approaches for adding context sensitivity to dynamic analyses.
Resurrector
Authors: Xu Guoqing
Published: November 2013

Modern object-oriented applications commonly suffer from severe performance problems that need to be optimized away for increased efficiency and user satisfaction. Many existing optimization techniques (such as object pooling and pretenuring) require precise identification of object lifetimes. However, it is particularly challenging to obtain object lifetimes both precisely and efficiently: precise profiling techniques such as Merlin introduce several hundred times slowdown even for small programs while efficient approximation techniques often sacrifice precision and produce less useful lifetime information. This paper presents a tunable profiling technique, called
Resurrector
, that explores the middle ground between high precision and high efficiency to find the precision-efficiency sweetspot for various livenessbased optimization techniques. Our evaluation shows that Resurrector is both more precise and more efficient than the GC-based approximation, and it is orders-of-magnitude faster than Merlin. To demonstrate Resurrector's usefulness, we have developed client analyses to find allocation sites that create large data structures with disjoint lifetimes. By inspecting program source code and reusing data structures created from these allocation sites, we have achieved significant performance gains. We have also improved the precision of an existing optimization technique using the lifetime information collected by Resurrector.
River trail
Authors: Herhut Stephan , Hudson Richard L. , Shpeisman Tatiana , Sreeram Jaswanth
Published: November 2013

JavaScript is the most popular language on the web and is a crucial component of HTML5 applications and services that run on consumer platforms ranging from desktops to phones. However, despite ample amount of hardware parallelism available to web applications on such platforms, JavaScript web applications remain predominantly sequential. Common parallel programming solutions accepted by other programming languages failed to transfer themselves to JavaScript due to differences in programming models, the additional requirements of the web and different developer expectations.

In this paper we present River Trail - a parallel programming model and API for JavaScript that provides
safe, portable, programmer-friendly, deterministic
parallelism to JavaScript applications. River Trail allows web applications to effectively utilize multiple cores, vector instructions, and GPUs on client platforms while allowing the web developer to remain within the environment of JavaScript. We describe the implementation of the River Trail compiler and runtime and present experimental results that show the impact of River Trail on performance and scalability for a variety of realistic HTML5 applications. Our experiments show that River Trail has a dramatic positive impact on overall performance and responsiveness of computationally intense JavaScript based applications achieving up to 33.6 times speedup for kernels and up to 11.8 times speedup for realistic web applications compared to sequential JavaScript. Moreover, River Trail enables new interactive web usages that are simply
not even possible
with standard sequential JavaScript.
OCTET
Authors: Bond Michael D. , Kulkarni Milind , Cao Man , Zhang Minjia , Fathi Salmi Meisam , Biswas Swarnendu , Sengupta Aritra , Huang Jipeng
Published: November 2013

Parallel programming is essential for reaping the benefits of parallel hardware, but it is notoriously difficult to develop and debug reliable, scalable software systems. One key challenge is that modern languages and systems provide poor support for ensuring concurrency correctness properties - atomicity, sequential consistency, and multithreaded determinism - because all existing approaches are impractical. Dynamic, software-based approaches slow programs by up to an order of magnitude because capturing and controlling cross-thread dependences (i.e., conflicting accesses to shared memory) requires synchronization at virtually every access to potentially shared memory.

This paper introduces a new software-based concurrency control mechanism called OCTET that soundly captures cross-thread dependences and can be used to build dynamic analyses for concurrency correctness. OCTET achieves low overheads by tracking the locality state of each potentially shared object. Non-conflicting accesses conform to the locality state and require no synchronization; only conflicting accesses require a state change and heavyweight synchronization. This optimistic tradeoff leads to significant efficiency gains in capturing cross-thread dependences: a prototype implementation of OCTET in a high-performance Java virtual machine slows real-world concurrent programs by only 26% on average. A dependence recorder, suitable for record & replay, built on top of OCTET adds an additional 5% overhead on average. These results suggest that OCTET can provide a foundation for developing low-overhead analyses that check and enforce concurrency correctness.
Bottle graphs
Authors: Du Bois Kristof , Sartor Jennifer B. , Eyerman Stijn , Eeckhout Lieven
Published: November 2013

Understanding and analyzing multi-threaded program performance and scalability is far from trivial, which severely complicates parallel software development and optimization. In this paper, we present bottle graphs, a powerful analysis tool that visualizes multi-threaded program performance, in regards to both per-thread parallelism and execution time. Each thread is represented as a box, with its height equal to the share of that thread in the total program execution time, its width equal to its parallelism, and its area equal to its total running time. The boxes of all threads are stacked upon each other, leading to a stack with height equal to the total program execution time. Bottle graphs show exactly how scalable each thread is, and thus guide optimization towards those threads that have a smaller parallel component (narrower), and a larger share of the total execution time (taller), i.e. to the 'neck' of the bottle.

Using light-weight OS modules, we calculate bottle graphs for unmodified multi-threaded programs running on real processors with an average overhead of 0.68%. To demonstrate their utility, we do an extensive analysis of 12 Java benchmarks running on top of the Jikes JVM, which introduces many JVM service threads. We not only reveal and explain scalability limitations of several well-known Java benchmarks; we also analyze the reasons why the garbage collector itself does not scale, and in fact performs optimally with two collector threads for all benchmarks, regardless of the number of application threads. Finally, we compare the scalability of Jikes versus the OpenJDK JVM. We demonstrate how useful and intuitive bottle graphs are as a tool to analyze scalability and help optimize multi-threaded applications.
Miniboxing
Authors: Ureche Vlad , Talau Cristian , Odersky Martin
Published: November 2013

Parametric polymorphism enables code reuse and type safety. Underneath the uniform interface exposed to programmers, however, its low level implementation has to cope with inherently non-uniform data: value types of different sizes and semantics (bytes, integers, floating point numbers) and reference types (pointers to heap objects). On the Java Virtual Machine, parametric polymorphism is currently translated to bytecode using two competing approaches: homogeneous and heterogeneous. Homogeneous translation requires boxing, and thus introduces indirect access delays. Heterogeneous translation duplicates and adapts code for each value type individually, producing more bytecode. Therefore bytecode speed and size are at odds with each other. This paper proposes a novel translation that significantly reduces the bytecode size without affecting the execution speed. The key insight is that larger value types (such as integers) can hold smaller ones (such as bytes) thus reducing the duplication necessary in heterogeneous translations. In our implementation, on the Scala compiler, we encode all primitive value types in long integers. The resulting bytecode approaches the performance of monomorphic code, matches the performance of the heterogeneous translation and obtains speedups of up to 22x over the homogeneous translation, all with modest increases in size.