bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparable Genital Tract Infection, Pathology, and Immunity in Rhesus Macaques Inoculated with Wild-Type or Plasmid-Deficient Chlamydia trachomatis Serovar D
Authors: Qu Yanyan , Frazer Lauren C. , O'Connell Catherine M. , Tarantal Alice F. , Andrews Charles W. , O'Connor Shelby L. , Russell Ali N. , Sullivan Jeanne E. , Poston Taylor B. , Vallejo Abbe N. , Darville Toni
Published: July 2015

Rhesus macaques were studied to directly address the potential for plasmid-deficient
Chlamydia trachomatis
to serve as a live attenuated vaccine in the genital tract. Five repeated cervical inoculations of rhesus macaques with wild-type serovar D strain D/UW-3/Cx or a plasmid-deficient derivative of this strain, CTD153, resulted in infections with similar kinetics and induced comparable levels of protective immunity. After all animals received five challenges with D/UW-3/Cx, levels of inflammation observed grossly and histologically were similar between the groups. Animals in both groups developed evidence of oviduct dilatation; however, reduced oviduct dilatation was observed for “controllers,” i.e., animals without detectable chlamydial DNA in the fimbriae at weeks 5 and 12. Grouping animals into “ascenders” and “controllers” revealed that elevated early T cell responses were associated with protection, whereas higher antibody responses were associated with ascension. Protected animals shared common major histocompatibility complex (MHC) alleles. Overall, genetic differences of individual animals, rather than the presence or absence of the chlamydial plasmid in the primary infecting strain, appeared to play a role in determining the outcome of infection.
Adherent-Invasive Escherichia coli Production of Cellulose Influences Iron-Induced Bacterial Aggregation, Phagocytosis, and Induction of Colitis
Authors: Ellermann Melissa , Huh Eun Young , Liu Bo , Carroll Ian M. , Tamayo Rita , Sartor R. Balfour
Published: July 2015

Adherent-invasive
Escherichia coli
(AIEC), a functionally distinct subset of resident intestinal
E. coli
associated with Crohn's disease, is characterized by enhanced epithelial adhesion and invasion, survival within macrophages, and biofilm formation. Environmental factors, such as iron, modulate
E. coli
production of extracellular structures, which in turn influence the formation of multicellular communities, such as biofilms, and bacterial interactions with host cells. However, the physiological and functional responses of AIEC to variable iron availability have not been thoroughly investigated. We therefore characterized the impact of iron on the physiology of AIEC strain NC101 and subsequent interactions with macrophages. Iron promoted the cellulose-dependent aggregation of NC101. Bacterial cells recovered from the aggregates were more susceptible to phagocytosis than planktonic cells, which corresponded with the decreased macrophage production of the proinflammatory cytokine interleukin-12 (IL-12) p40. Prevention of aggregate formation through the disruption of cellulose production reduced the phagocytosis of iron-exposed NC101. In contrast, under iron-limiting conditions, where NC101 aggregation is not induced, the disruption of cellulose production enhanced NC101 phagocytosis and decreased macrophage secretion of IL-12 p40. Finally, abrogation of cellulose production reduced NC101 induction of colitis when NC101 was monoassociated in inflammation-prone
Il10
−/−
mice. Taken together, our results introduce cellulose as a novel physiological factor that impacts host-microbe-environment interactions and alters the proinflammatory potential of AIEC.
Acetate Exposure Determines the Diauxic Behavior of Escherichia coli during the Glucose-Acetate Transition
Authors: Enjalbert Brice , Cocaign-Bousquet Muriel , Portais Jean-Charles , Letisse Fabien
Published: July 2015

Growth of
Escherichia coli
on glucose in batch culture is accompanied by the excretion of acetate, which is consumed by the cells when glucose is exhausted. This glucose-acetate transition is classically described as a diauxie (two successive growth stages). Here, we investigated the physiological and metabolic properties of cells after glucose exhaustion through the analysis of growth parameters and gene expression. We found that
E. coli
cells grown on glucose in batch culture produce acetate and consume it after glucose exhaustion but do not grow on acetate. Acetate is catabolized, but key anabolic genes—such as the genes encoding enzymes of the glyoxylate shunt—are not upregulated, hence preventing growth. Both the induction of the latter anabolic genes and growth were observed only after prolonged exposure to low concentrations of acetate and could be accelerated by high acetate concentrations. We postulate that such decoupling between acetate catabolism and acetate anabolism might be an advantage for the survival of
E. coli
in the ever-changing environment of the intestine.

IMPORTANCE
The glucose-acetate transition is a valuable experimental model for comprehensive investigations of metabolic adaptation and a current paradigm for developing modeling approaches in systems microbiology. Yet, the work reported in our paper demonstrates that the metabolic behavior of
Escherichia coli
during the glucose-acetate transition is much more complex than what has been reported so far. A decoupling between acetate catabolism and acetate anabolism was observed after glucose exhaustion, which has not been reported previously. This phenomenon could represent a strategy for optimal utilization of carbon resources during colonization and persistence of
E. coli
in the gut and is also of significant interest for biotechnological applications.
Acetate Dissimilation and Assimilation in Mycobacterium tuberculosis Depend on Carbon Availability
Authors: Rücker Nadine , Billig Sandra , Bücker René , Jahn Dieter , Wittmann Christoph , Bange Franz-Christoph
Published: July 2015

Mycobacterium tuberculosispersists inside granulomas in the human lung. Analysis of the metabolic composition of granulomas from guinea pigs revealed that one of the organic acids accumulating in the course of infection is acetate (B. S. Somashekar, A. G. Amin, C. D. Rithner, J. Troudt, R. Basaraba, A. Izzo, D. C. Crick, and D. Chatterjee, J Proteome Res 10:4186–4195, 2011, doi:http://dx.doi.org/10.1021/pr2003352), which might result either from metabolism of the pathogen or might be provided by the host itself. Our studies characterize a metabolic pathway by whichM. tuberculosisgenerates acetate in the cause of fatty acid catabolism. The acetate formation depends on the enzymatic activities of Pta and AckA. Using actyl coenzyme A (acetyl-CoA) as a substrate, acetyl-phosphate is generated and finally dephosphorylated to acetate, which is secreted into the medium. Knockout mutants lacking either theptaorackAgene showed significantly reduced acetate production when grown on fatty acids. This effect is even more pronounced when the glyoxylate shunt is blocked, resulting in higher acetate levels released to the medium. The secretion of acetate was followed by an assimilation of the metabolite when other carbon substrates became limiting. Our data indicate that during acetate assimilation, the Pta-AckA pathway acts in concert with another enzymatic reaction, namely, the acetyl-CoA synthetase (Acs) reaction. Thus, acetate metabolism might possess a dual function, mediating an overflow reaction to release excess carbon units and resumption of acetate as a carbon substrate.

IMPORTANCEDuring infection, host-derived lipid components present the major carbon source at the infection site. β-Oxidation of fatty acids results in the formation of acetyl-CoA. In this study, we demonstrate that consumption of fatty acids byMycobacterium tuberculosisactivates an overflow mechanism, causing the pathogen to release excess carbon intermediates as acetate. The Pta-AckA pathway mediating acetate formation proved to be reversible, enablingM. tuberculosisto reutilize the previously secreted acetate as a carbon substrate for metabolism.
The DNA-Binding Protein from Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple Stresses
Authors: Karas Vlad O. , Westerlaken Ilja , Meyer Anne S.
Published: July 2015

Bacteria deficient in the DNA-binding protein from starved cells (Dps) are viable under controlled conditions but show dramatically increased mortality rates when exposed to any of a wide range of stresses, including starvation, oxidative stress, metal toxicity, or thermal stress. It remains unclear whether the protective action of Dps against specific stresses derives from its DNA-binding activity, which may exclude destructive agents from the chromosomal region, or its ferroxidase activity, which neutralizes and sequesters potentially damaging chemical species. To resolve this question, we have identified the critical residues of
Escherichia coli
Dps that bind to DNA and modulate iron oxidation. We uncoupled the biochemical activities of Dps, creating Dps variants and mutant
E. coli
strains that are defective in either DNA-binding or ferroxidase activity. Quantification of the contribution of each activity to the protection of DNA integrity and cellular viability revealed that both activities of Dps are required in order to counteract many differing stresses. These findings demonstrate that Dps plays a multipurpose role in stress protection via its dual activities, explaining how Dps can be of vital importance to bacterial viability over a wide range of stresses.

IMPORTANCE
The DNA-binding protein from starved cells (Dps) protects bacterial cells against many different types of stressors. We find that DNA binding and iron oxidation by Dps are performed completely independently of each other. Both biochemical activities are required to protect
E. coli
against stressors, as well as to protect DNA from oxidative damage
in vitro
. These results suggest that many stressors may cause both oxidative stress and direct DNA damage.
Chikungunya fever presenting with acute optic neuropathy
Authors: Mohite Abhijit Anand , Agius-Fernandez Adriana
Published: July 2015

Chikungunya fever is a vector borne virus that typically causes a self-limiting systemic illness with fever, skin rash and joint aches 2 weeks after infection. We present the case of a 69-year-old woman presenting with an acute unilateral optic neuropathy as a delayed complication of Chikungunya virus (CHIKV) infection contracted during a recent trip to the West Indies. She presented to our ophthalmology department with acute painless visual field loss in the right eye and a recent flu-like illness. She was found to have a right relative afferent pupillary defect (RAPD) with unilateral optic disc swelling. Serology confirmed recent CHIKV infection. Treatment with intravenous methylprednisolone was delayed while awaiting MRI scans and serology results. At 5-month follow-up, there was a persistent right RAPD and marked optic atrophy with a corresponding inferior scotoma in the visual field.
Rare manifestations of infective endocarditis: the long known, never to be forgotten diagnosis
Authors: Medani Samar , O'Callaghan Patrick
Published: July 2015

Infective endocarditis (IE) is a life-threatening condition often manifesting as a multisystem disease; its heterogeneous features present a diagnostic challenge. We report two cases of IE masquerading as rare extracardiac complications: a splenectomised patient with a periarticular ankle abscess and acute encephalopathy; and a young man with a cutaneous vasculitis following a spontaneous intracerebral haemorrhage. In both cases, the diagnosis was suspected following detection of afebrile bacteraemia and confirmed with echocardiography. Risk factors included a pneumococcal bacteraemia in the asplenic patient and a previously undiagnosed bicuspid aortic valve in the second patient. Both patients recovered well with appropriate antibiotic therapy followed by valve surgery. IE is an important diagnosis to consider in patients with systemic symptoms or organ specific, otherwise unexplained relevant pathology especially in the presence of a cardiac murmur or risk factors for IE including structural heart disease, prosthetic valves or intravascular devices, and in immunosuppressed patients.
Injuries in national Olympic level judo athletes: an epidemiological study
Authors: Kim Keun-Suh , Park Ki Jun , Lee Jaekoo , Kang Byung Yong
Published: July 2015

Purpose

To present an epidemiological study of injuries found among South Korea's National level Judo athletes as a foundation for future injury prevention and skill enhancement in this group.

Methods

This study is a prospective study on a 4-year injury assessment held from January 2010 to December 2013 at the training centre in South Korea for National Level athletes. Athlete's weight class, gender, injury location and injury grade (grade I=1–3 treatment days, grade II=4–7 treatment days, and grade III ≥8 treatment days) were analysed.

Results

There were a total of 782 injuries recorded during this period, equalling to four injuries per athlete annually. Almost half of these injuries (47%) were grade I injuries. Injury occurrence was the highest in the Lower body (44.2%). This was then followed by injuries in the upper body (29.8%), trunk (20.3%) and head and neck (5.6%). Men and women showed similar, non-significantly different trends in the proportion of body parts injured. Women experienced more grade III injuries than males (p=0.0228). Comparison between women in different weight classes also showed that heavyweights incurred more grade III injuries than lightweights (p=0.0087). Lightweights had a higher rate of injury than heavyweights in males and females, although this was statistically significant only among males (p<0.001).

Conclusions

Many body regions are prone to injury in the elite judo population. Women, especially those in the heavyweight classification, were more prone to severe injuries. Lightweights experienced more injuries than heavyweights among male athletes. Specifically, further studies are needed to confirm these findings and to address the impact of rapid weight loss practices on injury risk to implement effective preventive measures.
Outcomes of the Northern Ontario School of Medicine's distributed medical education programmes: protocol for a longitudinal comparative multicohort study
Authors: Hogenbirk John C , French Margaret G , Timony Patrick E , Strasser Roger P , Hunt Dan , Pong Raymond W
Published: July 2015

Introduction

The Northern Ontario School of Medicine (NOSM) has a social accountability mandate to serve the healthcare needs of the people of Northern Ontario, Canada. A multiyear, multimethod tracking study of medical students and postgraduate residents is being conducted by the Centre for Rural and Northern Health Research (CRaNHR) in conjunction with NOSM starting in 2005 when NOSM first enrolled students. The objective is to understand how NOSM's selection criteria and medical education programmes set in rural and northern communities affect early career decision-making by physicians with respect to their choice of medical discipline, practice location, medical services and procedures, inclusion of medically underserved patient populations and practice structure.

Methods and analysis

This prospective comparative longitudinal study follows multiple cohorts from entry into medical education programmes at the undergraduate (UG) level (56–64 students per year at NOSM) or postgraduate (PG) level (40–60 residents per year at NOSM, including UGs from other medical schools and 30–40 NOSM UGs who go to other schools for their residency training) and continues at least 5 years into independent practice. The study compares learners who experience NOSM UG and NOSM PG education with those who experience NOSM UG education alone or NOSM PG education alone. Within these groups, the study also compares learners in family medicine with those in other specialties. Data will be analysed using descriptive statistics, χ2tests, logistic regression, and hierarchical log-linear models.

Ethics and dissemination

Ethical approval was granted by the Research Ethics Boards of Laurentian University (REB #2010-08-03 and #2012-01-09) and Lakehead University (REB #031 11-12 Romeo File #1462056). Results will be published in peer-reviewed scientific journals, presented at one or more scientific conferences, and shared with policymakers and decision-makers and the public through 4-page research summaries and social media such as Twitter (@CRaNHR, @NOSM) or Facebook.
Patient safety incident reporting: a qualitative study of thoughts and perceptions of experts 15 years after ‘To Err is Human’
Authors: Mitchell Imogen , Schuster Anne , Smith Katherine , Pronovost Peter , Wu Albert
Published: July 2015

One of the key recommendations of the Institute of Medicine's (IOM) report,To Err is Human, 15 years ago was for greater attention to incident reporting in healthcare, analogous to the role it has played in aviation and other high-risk industries. With the passage of time and maturation of the patient safety field, we conducted semistructured interviews with 11 international patient safety experts with knowledge of the US healthcare and meeting at least one of the following criteria: (1) involved in the development of the IOM's recommendations, (2) responsible for the design and/or implementation of national or regional incident reporting systems, (3) conducted research on patient safety/incident reporting at a national level. Five key challenges emerged to explain why incident reporting has not reached its potential: poor processing of incident reports (triaging, analysis, recommendations), inadequate engagement of doctors, insufficient subsequent visible action, inadequate funding and institutional support of incident reporting systems and inadequate usage of evolving health information technology. Leading patient safety experts acknowledge the current challenges of incident reports. The future of incident reporting lies in targeted incident reporting, effective triaging and robust analysis of the incident reports and meaningful engagement of doctors. Incident reporting must be coupled with visible, sustainable action and linkage of incident reports to the electronic health record. If the healthcare industry wants to learn from its mistakes, miss or near miss events, it will need to take incident reporting as seriously as the health budget.
Intralaryngeal thyroarytaenoid lateralisation using the Fast‐Fix 360 system: a canine cadaveric study
Authors: Stegen Ludo , Kitshoff Adriaan M. , Van Goethem Bart , Vandekerckhove Peter , de Rooster Hilde
Published: July 2015

Introduction

Laryngeal paralysis is a condition in which failure of arytaenoid abduction results in a reduced rima glottidis cross‐sectional area. The most commonly performed surgical techniques rely on unilateral abduction of the arytaenoid, requiring a lateral or ventral surgical approach to the larynx.

Aims and objectives

The aim of the study was to investigate a novel minimally invasive intralaryngeal thyroarytaenoid lateralisation technique, using the Fast‐Fix 360 meniscal repair system.

Materials and methods

Larynges were harvested from large breed canine cadavers. With the aid of Kirschner wires placed between the centre of the vocal process and the centre of an imaginary line between the cranial thyroid fissure and the cricothyroid articulation, the mean insertion angle was calculated.

Results

The Fast‐Fix 360 delivery needle inserted intralaryngeally (n=10), according to a simplified insertion angle (70°), resulted in thyroid penetration (>2.5 mm from margin) in all patients. The Fast‐Fix was applied unilaterally at 70° with the first toggle fired on the lateral aspect of the thyroid cartilage and inside the laryngeal cavity on retraction. The suture was tightened. Preprocedural (61.06±9.21 mm2) and postprocedural (138.37±26.12 mm2) rima glottidis cross‐sectional area was significantly different (P<0.0001). The mean percentage increase in rima glottidis cross‐sectional area was 125.96 per cent (±16.54 per cent).

Conclusion

Intralaryngeal thyroarytaenoid laterlisation using the Fast‐Fix 360 meniscal repair system ex vivo increased the rima glottidis cross‐sectional area significantly.
Effect of hysteresis of soil-water characteristic curves on infiltration under different climatic conditions
Authors: Bashir Rashid , Sharma Jitendra , Stefaniak Halina
Published: July 2015

This paper presents results of a numerical modelling exercise that investigates the effects of hysteresis of the soil-water characteristic curve (SWCC) on the infiltration characteristics of soils subjected to four different climatic conditions — from very dry to wet — within the Canadian province of Alberta. Multi-year climate datasets from four different natural regions and subregions of Alberta are compiled, classified, and applied as the soil–atmosphere boundary condition in one-dimensional finite element unsaturated flow models using Hydrus-1D software. Multi-year simulations are carried out with and without consideration of the SWCC hysteresis. Simulation results are analyzed in terms of water balance at the ground surface and temporal distribution and storage of water within the soil domain. It is demonstrated that hysteresis of the SWCC can significantly affect the prediction of flow, redistribution, and storage of water in the unsaturated zone. It is found that for soils that exhibit hysteretic SWCC, consideration of hysteresis in unsaturated flow modelling results in the prediction of lower infiltration and less movement of water through the soil. It is also found that the use of wetting parameters results in the prediction of increased infiltration and movement of water compared with the predictions using drying or hysteretic parameters. It is concluded that, for soils that exhibit a greater degree of SWCC hysteresis, it is important to measure both the drying and wetting branches of the SWCC accurately and that accurate simulation of hysteretic behaviour requires climate datasets at appropriate resolution. The results presented in this paper highlight the importance of considering SWCC hysteresis for a wide range of geotechnical problems, such as soil cover design, prediction of groundwater recharge, contaminant transport through unsaturated soils, soil erosion, slope stability, and swelling–shrinkage of expansive soils.
Inhibitory efficiencies for mechanism-based inactivators of sialidases
Authors: Khazaei Kobra , Yeung Juliana H.F. , Moore Margo M. , Bennet Andrew J.
Published: July 2015

Here we describe the measurement of the inactivation rate constants for the mechanism-based inactivator 2,3-difluorosialic acid acting upon the sialidase from Micromonospora viridifaciens. Using double mixing stopped-flow experiments conducted in a 3-(N-morpholino)propanesulfonic acid buffer (100 mmol/L, pH 7.00) at 25 °C, the derived kinetic parameters are kinact/Ki= (3.9 ± 0.8) × 106(mol/L)–1s–1and Ki= 1.7 ± 0.4 μmol/L. We demonstrate that the inhibitory efficiency of the inactivation event is similar to the catalytic efficiency for this sialidase acting upon a typical substrate, 4-methylumbelliferone α-d-sialoside, kcat/Km= (7.2 ± 2.8) × 106(mol/L)–1s–1. Furthermore, we show that the catalytic efficiencies for inactivation and hydrolysis by the Kdnase from Aspergillus fumigatus are similar for the corresponding Kdn-analogues. We conclude that the deactivating effect of incorporating an axial 3-fluoro substituent onto the sialic acid scaffold is comparable to the enhanced activation that occurs when the 4-methylumbelliferone leaving group is changed to the more nucleofugal fluoride ion.
Systematic dismantling of a carefully designed PCcarbeneP pincer ligand via C–C bond activations at an iridium centre
Authors: Smith Joel D. , Borau-Garcia Javier , Piers Warren E. , Spasyuk Denis
Published: July 2015

An electron-rich PCsp2P ligand, incorporating N,N-dimethylamino groups para to the anchoring carbene donor of the ligand, was prepared and coordinated to iridium, producing the iridium carbene chloride 2. This species undergoes facile reaction with N2O to afford an iridaepoxide complex, 3, in which an oxygen atom has been transferred to the Ir=C bond. The rate of this reaction is significantly faster than that observed for the less electron rich, unsubstituted ligand. However, further reaction of 3 involving cleavage of one of the ligand C–C bonds was observed, producing the bis-phosphine chorido complex 4. This process was accelerated by the presence of H2. Heating 4 under H2 resulted in hydrogenolysis of the ortho-metalated phosphine ligand to give a hydrido complex (5) and decarbonylation of the acyl phosphine ligand to give, finally, Vaska’s complex analog 6. All compounds were fully characterized, and the sequence represents the dismantling of the PCsp2P ligand framework.
Application of a putative alarm cue hastens the arrival of invasive sea lamprey (Petromyzon marinus) at a trapping location
Authors: Hume John B. , Meckley Trevor D. , Johnson Nicholas S. , Luhring Thomas M. , Siefkes Michael J. , Wagner C. Michael
Published: July 2015

The sea lamprey Petromyzon marinus is an invasive pest in the Laurentian Great Lakes basin, threatening the persistence of important commercial and recreational fisheries. There is substantial interest in developing effective trapping practices via the application of behavior-modifying semiochemicals (odors). Here we report on the effectiveness of utilizing repellent and attractant odors in a push–pull configuration, commonly employed to tackle invertebrate pests, to improve trapping efficacy at permanent barriers to sea lamprey migration. When a half-stream channel was activated by a naturally derived repellent odor (a putative alarm cue), we found that sea lamprey located a trap entrance significantly faster than when no odor was present as a result of their redistribution within the stream. The presence of a partial sex pheromone, acting as an attractant within the trap, was not found to further decrease the time to when sea lamprey located a trap entrance relative to when the alarm cue alone was applied. Neither the application of alarm cue singly nor alarm cue and partial sex pheromone in combination was found to improve the numbers of sea lamprey captured in the trap versus when no odor was present — likely because nominal capture rate during control trials was unusually high during the study period. Behavioural guidance using these odors has the potential to both improve control of invasive non-native sea lamprey in the Great Lakes as well as improving the efficiency of fish passage devices used in the restoration of threatened lamprey species elsewhere.
Energy levels of the 5d3/2nf, 6p3/2nd autoionizing series of Hg I
Authors: Zhou Chao , Wang Zhan-Min , He Hua-Yue
Published: July 2015

In this paper, three autoionizing Rydberg series energy levels [Formula: see text] (n = 5–20), [Formula: see text] (n = 6–20), and [Formula: see text] (n = 6–20) for Hg I are calculated using the WBE potential model (WBEPM) theory, considering foreign level perturbation corrections. The theoretically calculated results are in good agreement with present known experimental data, and some energy levels of these three series without experimental values are predicted.
Potential energy curves and dipole moment of NF molecule with inner electron correlation
Authors: Wan Mingjie , Luo Huafeng , Jin Chengguo , Huang Duohui , Wang Fanhou
Published: July 2015

The potential energy curves and dipole moments for the low-lying electronic states of the NF molecule are found by using highly accurate multireference configuration interaction plus the Davidson correction with the AV5Z basis set. All 16 electrons are used in the correlation energy calculations, which are used to characterize the spectroscopic properties of a manifold for singlet and triplet states. X3Σ–, a1Δ, b1Σ+, A3Π, 23Σ–, 23Π, 21Δ, 33Σ–, 13Σ+, and 13Δ electronic states correlate with the two lowest dissociation channels N(4Su) + F(2Pu) and N(2Du) + F(2Pu) are investigated. Note that the b1Σ+ state has two depth wells, but only one depth well was observed in the experiment. The spectroscopic parameters (Re, ωe, ωeχe, De, Be, and Te) are derived, which are in excellent agreement with the available experimental data and the other theoretical values. The molecular parameters and dipole moments for the ground and excited states are also obtained.
Tetrahydroxystilbene glucoside inhibits TNF-α-induced migration of vascular smooth muscle cells via suppression of vimentin
Authors: Yao Wenjuan , Sun Qinju , Huang Lei , Meng Guoliang , Wang Huiming , Jing Xiang , Zhang Wei
Published: July 2015

Vascular smooth muscle cell (VSMC) migration triggered by TNF-α is an important event that occurs during the development of atherosclerosis. 2,3,5,4′-Tetrahydroxystilbene-2-O-β-d-glucoside (TSG) has been proven to exhibit significant anti-atherosclerotic activity. Herein we investigate the inhibitory effect of TSG on TNF-α-induced VSMC migration and explore the underlying mechanisms. TSG pretreatment markedly inhibited TNF-α-induced cell migration. The inhibition of vimentin redistribution and expression was involved in the inhibitory effect of TSG on VSMC migration. The suppression of vimentin expression by shRNA in VSMCs significantly inhibited TNF-α-induced cell migration. Furthermore, TSG inhibited the TNF-α-induced expression of TGFβ1 and TGFβR1, and phosphorylation of TGFβR1 and Smad2/3. TSG also suppressed the nuclear translocation of Smad4 induced by TNF-α. These results suggest that TSG inhibits VSMC migration induced by TNF-α through inhibiting vimentin rearrangement and expression. The interruption of TGFβ/Smad pathway appears to be responsible for the suppression of TSG on vimentin expression.
Recovery of aquatic and terrestrial populations in the context of European pesticide risk assessment
Authors: Kattwinkel Mira , Liess Matthias , Arena Maria , Bopp Stephanie , Streissl Franz , Römbke Jörg
Published: July 2015

In the present review, we compiled and evaluated the available information supporting the assessment of population and community recovery after pesticide application. This information is crucial for the environmental risk assessment of pesticides. We reviewed more than 3900 manuscripts on those organism groups relevant or likely to become relevant for the risk assessment procedures in Europe, that is, aquatic invertebrates, algae, aquatic plants, fish, aquatic microbes, amphibians, as well as birds and mammals, non-target terrestrial arthropods including honeybees, non-arthropod invertebrates, terrestrial microbes, non-target terrestrial plants, nematodes, and reptiles. Finally, 106 aquatic and 76 terrestrial studies met our selection criteria and were evaluated in detail. We extracted the following general conclusions. (i) Internal recovery depends strongly on reproduction capacity. For aquatic invertebrates, recovery was generally observed within a maximum of five generation times. (ii) In cases where recovery occurred within one generation, migration from uncontaminated areas was identified as the main pathway for aquatic and terrestrial invertebrates, in particular, for insect species with the ability for aerial recolonization. (iii) Community composition in general did not recover within the study duration in the majority of cases. (iv) The ecological context, including factors such as food resources, habitat quality, and recolonization potential, is a crucial factor for recovery from pesticide effects. (v) Indirect effects acting through food chain processes, including predation and competition, are highly relevant for increasing the magnitude of effect and for prolonging recovery time. Based on our findings, we recommend defining realistic scenarios for risk assessment regarding exposure, taxa considered, environmental conditions, and ecological context. In addition to experimental studies, field monitoring was shown to yield valuable information to identify relevant taxa, long-term effects, and the conditions for recovery, and should therefore be considered to validate approaches of risk assessment. Likewise, ecological modelling was found to be a valuable tool for assessing recovery. Finally, both study design and interpretation of results still often suffer from missing ecological information or from neglect of the available knowledge. Hence, a more rigorous utilization of existing knowledge (e.g., from general disturbance ecology) and the generation of systematic ecological knowledge on the various factors influencing recovery are needed.
Thermal duality and thermodynamics of micro black holes
Authors: Jou D. , Sciacca M. , Mongiovì M. S.
Published: July 2015

Starting from a generalized black hole entropy with logarithmic area corrections, in this paper we obtain (for positive value of the coefficient of the correction term) a generalized equation of state for black holes with two dual branches. In one of them (the usual one for macro black holes) T ≃ 1/M, with T temperature and M mass. In the other one, for micro black holes, instead, T ≃ M. We compare the equilibrium and stability between macro black holes and electromagnetic radiation in a finite box with reflecting walls, with the dual situation corresponding to micro black holes and cosmic string loops, also in a finite box. In this model, the dual phenomenon of evaporation of unstable macro black holes into a stable gas of electromagnetic radiation would be the condensation of unstable gas of cosmic string loops into stable micro black holes.
AN ITERATED FUNCTION SYSTEM FOR THE CLOSURE OF THE ADDING MACHINE GROUP
Authors: SALTAN MUSTAFA , DEMİR BÜNYAMİN
Published: July 2015

In this paper, first we equip the automorphism group of the p-ary rooted tree X* with a natural metric and define a family of contractions on Aut(X*). Then, we construct an iterated function system (IFS) whose attractor is the closure of the adding machine group on Aut(X*). Finally, we show that this group is a strong self-similar group in the sense of IFS.
EFFECTS OF POLYNOMIAL TRENDS ON DETRENDING MOVING AVERAGE ANALYSIS
Authors: SHAO YING-HUI , GU GAO-FENG , JIANG ZHI-QIANG , ZHOU WEI-XING
Published: July 2015

The detrending moving average (DMA) algorithm is one of the best performing methods to quantify the long-term correlations in nonstationary time series. As many long-term correlated time series in real systems contain various trends, we investigate the effects of polynomial trends on the scaling behaviors and the performances of three widely used DMA methods including backward algorithm (BDMA), centered algorithm (CDMA) and forward algorithm (FDMA). We derive a general framework for polynomial trends and obtain analytical results for constant shifts and linear trends. We find that the behavior of the CDMA method is not influenced by constant shifts. In contrast, linear trends cause a crossover in the CDMA fluctuation functions. We also find that constant shifts and linear trends cause crossovers in the fluctuation functions obtained from the BDMA and FDMA methods. When a crossover exists, the scaling behavior at small scales comes from the intrinsic time series while that at large scales is dominated by the constant shifts or linear trends. We also derive analytically the expressions of crossover scales and show that the crossover scale depends on the strength of the polynomial trends, the Hurst index, and in some cases (linear trends for BDMA and FDMA) the length of the time series. In all cases, the BDMA and the FDMA behave almost the same under the influence of constant shifts or linear trends. Extensive numerical experiments confirm excellently the analytical derivations. We conclude that the CDMA method outperforms the BDMA and FDMA methods in the presence of polynomial trends.
AN ANALYTIC RECURSIVE METHOD FOR OPTIMAL MULTIPLE STOPPING: CANADIZATION AND PHASE-TYPE FITTING
Authors: LEUNG TIM , YAMAZAKI KAZUTOSHI , ZHANG HONGZHONG
Published: July 2015

We study an optimal multiple stopping problem for call-type payoff driven by a spectrally negative Lévy process. The stopping times are separated by constant refraction times, and the discount rate can be positive or negative. The computation involves a distribution of the Lévy process at a constant horizon and hence the solutions in general cannot be attained analytically. Motivated by the maturity randomization (Canadization) technique by Carr (1998), we approximate the refraction times by independent, identically distributed Erlang random variables. In addition, fitting random jumps to phase-type distributions, our method involves repeated integrations with respect to the resolvent measure written in terms of the scale function of the underlying Lévy process. We derive a recursive algorithm to compute the value function in closed form, and sequentially determine the optimal exercise thresholds. A series of numerical examples are provided to compare our analytic formula to results from Monte Carlo simulation.
Comparison of particle swarm and bacterial foraging optimization algorithms for therapy planning in HIV/AIDS patients
Authors: Kamalanand K. , Mannar Jawahar P.
Published: July 2015

In HIV/AIDS patients, antiretroviral therapy (ART) is used for reducing the viral load and helps in increasing the life span of the individual. However, severe side effects are associated with the use of antiretroviral drugs. Hence, a treatment schedule, using minimal amount of drugs, is required for maintaining a low viral load and a healthy immune system. The objective of this work is to compute the optimal dosage of antiretroviral drugs for therapy planning in HIV/AIDS patients, using intelligent optimization techniques. In this work, two computational swarm intelligence techniques known as the particle swarm optimization (PSO) and bacterial foraging optimization (BFO) in conjunction with the three-dimensional mathematical model of HIV/AIDS have been used for estimating the optimal drug dosage for administering therapy by minimization of viral load as well as the total drug concentration. Results demonstrate that, using the proposed method, it is possible to achieve minimal viral load and an improved immune system, with the estimated drug dosage. Further, it was observed that the efficiency of BFO (CD4 cells [Formula: see text][Formula: see text]cells/mm3 at seventh year of infection) for estimation of optimal drug dosage is higher than the PSO method (CD4 cells [Formula: see text][Formula: see text]cells/mm3 at seventh year of infection). This work seems to be of high clinical relevance since, at present, ART is the widely used procedure for treatment of HIV infected patients.
Large-Scale Cross-Language Web Page Classification via Dual Knowledge Transfer Using Fast Nonnegative Matrix Trifactorization
Authors: Wang Hua , Nie Feiping , Huang Heng
Published: July 2015

With the rapid growth of modern technologies, Internet has reached almost every corner of the world. As a result, it becomes more and more important to manage and mine information contained in Web pages in different languages. Traditional supervised learning methods usually require a large amount of training data to obtain accurate and robust classification models. However, labeled Web pages did not increase as fast as the growth of Internet. The lack of sufficient training Web pages in many languages, especially for those in uncommonly used languages, makes it a challenge for traditional classification algorithms to achieve satisfactory performance. To address this, we observe that Web pages for a same topic from different languages usually share some common semantic patterns, though in different representation forms. In addition, we also observe that the associations between word clusters and Web page classes are another type of reliable carriers to transfer knowledge across languages. With these recognitions, in this article we propose a novel joint nonnegative matrix trifactorization (NMTF) based Dual Knowledge Transfer (DKT) approach for cross-language Web page classification. Our approach transfers knowledge from the auxiliary language, in which abundant labeled Web pages are available, to the target languages, in which we want to classify Web pages, through two different paths: word cluster approximation and the associations between word clusters and Web page classes. With the reinforcement between these two different knowledge transfer paths, our approach can achieve better classification accuracy. In order to deal with the large-scale real world data, we further develop the proposed DKT approach by constraining the factor matrices of NMTF to be cluster indicator matrices. Due to the nature of cluster indicator matrices, we can decouple the proposed optimization objective and the resulted subproblems are of much smaller sizes involving much less matrix multiplications, which make our new approach much more computationally efficient. We evaluate the proposed approach in extensive experiments using a real world cross-language Web page data set. Promising results have demonstrated the effectiveness of our approach that are consistent with our theoretical analyses.
Shading-based refinement on volumetric signed distance functions
Authors: Zollhöfer Michael , Dai Angela , Innmann Matthias , Wu Chenglei , Stamminger Marc , Theobalt Christian , Nießner Matthias
Published: July 2015

We present a novel method to obtain fine-scale detail in 3D reconstructions generated with low-budget RGB-D cameras or other commodity scanning devices. As the depth data of these sensors is noisy, truncated signed distance fields are typically used to regularize out the noise, which unfortunately leads to over-smoothed results. In our approach, we leverage RGB data to refine these reconstructions through shading cues, as color input is typically of much higher resolution than the depth data. As a result, we obtain reconstructions with high geometric detail, far beyond the depth resolution of the camera itself. Our core contribution is shading-based refinement directly on the implicit surface representation, which is generated from globally-aligned RGB-D images. We formulate the inverse shading problem on the volumetric distance field, and present a novel objective function which jointly optimizes for fine-scale surface geometry and spatially-varying surface reflectance. In order to enable the efficient reconstruction of sub-millimeter detail, we store and process our surface using a sparse voxel hashing scheme which we augment by introducing a grid hierarchy. A tailored GPU-based Gauss-Newton solver enables us to refine large shape models to previously unseen resolution within only a few seconds.
Parametric self-supporting surfaces via direct computation of airy stress functions
Authors: Miki Masaaki , Igarashi Takeo , Block Philippe
Published: July 2015

This paper presents a method that employs parametric surfaces as surface geometry representations at any stage of a computational process to compute self-supporting surfaces. This approach can be differentiated from existing relevant methods because such methods represent surfaces by a triangulated mesh surface or a network consisting of lines. The proposed method is based on the theory of Airy stress functions. Although some existing methods are also based on this theory, they apply its discrete version to discrete geometries. The proposed method simultaneously applies the theory to parametric surfaces directly and the discrete theory to the edges of parametric patches. The discontinuous boundary between continuous patches naturally corresponds to ribs seen in traditional vault masonry buildings. We use nonuniform rational B-spline surfaces in this study; however, the basic idea can be applied to other parametric surfaces. A variety of self-supporting surfaces obtained by the proposed computational scheme is presented.
Space-time sketching of character animation
Authors: Guay Martin , Ronfard Rémi , Gleicher Michael , Cani Marie-Paule
Published: July 2015

We present a space-time abstraction for the sketch-based design of character animation. It allows animators to draft a full coordinated motion using a single stroke called the
space-time curve
(STC). From the STC we compute a dynamic line of action (DLOA) that drives the motion of a 3D character through projective constraints. Our dynamic models for the line's motion are entirely geometric, require no pre-existing data, and allow full artistic control. The resulting DLOA can be refined by over-sketching strokes along the space-time curve, or by composing another DLOA on top leading to control over complex motions with few strokes. Additionally, the resulting dynamic line of action can be applied to arbitrary body parts or characters. To match a 3D character to the 2D line over time, we introduce a robust matching algorithm based on closed-form solutions, yielding a tight match while allowing squash and stretch of the character's skeleton. Our experiments show that space-time sketching has the potential of bringing animation design within the reach of beginners while saving time for skilled artists.
Controlling procedural modeling programs with stochastically-ordered sequential Monte Carlo
Authors: Ritchie Daniel , Mildenhall Ben , Goodman Noah D. , Hanrahan Pat
Published: July 2015

We present a method for controlling the output of procedural modeling programs using Sequential Monte Carlo (SMC). Previous probabilistic methods for controlling procedural models use Markov Chain Monte Carlo (MCMC), which receives control feedback only for completely-generated models. In contrast, SMC receives feedback incrementally on incomplete models, allowing it to reallocate computational resources and converge quickly. To handle the many possible sequentializations of a structured, recursive procedural modeling program, we develop and prove the correctness of a new SMC variant, Stochastically-Ordered Sequential Monte Carlo (SOSMC). We implement SOSMC for general-purpose programs using a new programming primitive: the stochastic future. Finally, we show that SOSMC reliably generates high-quality outputs for a variety of programs and control scoring functions. For small computational budgets, SOSMC's outputs often score nearly twice as high as those of MCMC or normal SMC.
High-resolution brittle fracture simulation with boundary elements
Authors: Hahn David , Wojtan Chris
Published: July 2015

We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.

Our system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.

Separating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.