Persistence matters: Estimation of the statistical significance of paleoclimatic reconstruction statistics from autocorrelated time series

Proxy data forms natural time series used to lengthen instrumental climatic records, and may contain a significant portion of autocorrelation. Increased serial correlation limits the number of independent observations, not satisfying the assumptions of conventional statistical methods. We estimate the significance of calibration and verification statistics used in dendroclimatic reconstructions by combining Monte-Carlo iterations with frequency (Ebisuzaki) or time (Burg) domain time series modelling. Significance tests are presented for Coefficient of Determination (R²), Coefficient of Correlation (r²), Reduction of Error (RE) and Coefficient of Error (CE) for time series ranging from very low to very high autocorrelation. Increased autocorrelation implies higher occurrences of relatively high but spurious reconstruction statistics. Ebisuzaki time series modelling shows greater robustness and its use is recommended over Burg's method, which penalizes the restriction in the number of autocorrelation coefficients imposed by the Akaike Information Criterion. Positive RE and CE values, traditionally viewed as successful reconstruction statistics, are not necessarily significant and depend on the temporal structure of the time series used. This approach is further implemented successfully to compute confidence intervals based on the temporal structure of the residuals of the transfer function. A Matlab^® package and a Windows executable file for non-Matlab^® users are provided to perform the described analyses.     

CFD analysis of the Ahmed Glaucoma Valve and design of an alternative device

Computational fluid dynamics (CFD) modelling based on a commercial package, FLUENT, has been used in the present study. The primary aim of this study is to develop a novel implant by employing CFD techniques. Firstly, CFD analyses on the best design commercially available, which is the Ahmed Glaucoma Valve (AGV^®), are accomplished. In the light of the results, the new design focus is selected as the valve. The new design is analysed using GAMBIT and FLUENT software. CFD analyses of the new design and the AGV^® are compared and the strengths of the new design are revealed. The results are also compared with the experimental studies AGV^® in the literature. It is deduced that the proposed model shows a nonlinear pressure drop response, which is quite similar to that of AGV^®. The optimum combination would be a flow rate of 2.5 μl/min and a pressure drop of 1054.58 Pa for the proposed model.     

Known Knowns,Known Unknowns,and Unknown Unknowns: Coverage in MS Experiments

A mathematical model from ecology, namely, the capture–recapture model with a closed population and time‐varying and heterogeneous individual probabilities of capture, is implemented to model the number of protein identifications across the various cycles of a mass spectroscopy experiment. Rcapture, a package available in the R computing environment, can easily provide estimates of the cardinality of the proteome from such experiments. Alternatively, model fitting can be undertaken in other software platforms, such as Matlab, that can accommodate general linear models. It has not escaped our notice that capture–recapture models can be more broadly applied to other settings, so as to estimate the number of missing observations in an experiment.     

An automated cell-counting algorithm for fluorescently-stained cells in migration assays

A cell-counting algorithm, developed in Matlab^®, was created to efficiently count migrated fluorescently-stained cells on membranes from migration assays. At each concentration of cells used (10,000, and 100,000 cells), images were acquired at 2.5 ×, 5 ×, and 10 × objective magnifications. Automated cell counts strongly correlated to manual counts (r² = 0.99, P < 0.0001 for a total of 47 images), with no difference in the measurements between methods under all conditions. We conclude that our automated method is accurate, more efficient, and void of variability and potential observer bias normally associated with manual counting.     

Validation du logiciel de semi-quantification DaTQUANT® dans l’aide à l’analyse visuelle en TEMP au 123I-FP-CIT dans l’étude des pathologies neurodégénératives

ObjectiveSemi-quantification is a valuable tool increasing the diagnosis accuracy of the single photon emission computer tomography (SPECT) with FP-CIT-¹²³I (DaTSCAN^®), particularly in cases where visual analysis is unclear and especially on the posterior putamen. The DaTQUANT^® software (GE^® Healthcare), allows a quick and simple uptake assessment on several regions of interest. It also provides deviation values compared to a database of healthy subjects obtained in the ENC-DAT project. However, any threshold value is currently validated routinely.Patients and methodsA retrospective study was conducted in 55 patients (33 men, 22 women) referred for a suspicion of neurological disorders and who underwent SPECT imaging with DaTSCAN^® on camera D670 GE^®. Final diagnosis made by neurologist time after the SPECT was established as a reference, reinforced by clinical evolution. Analysis was initially visual without semi-quantitative results, realized by two experimented nuclear physicians, and then semi-quantitative analysis was made by DaTQUANT^® with calculation of Youden indices and ROC curves so as to define threshold values for six regions of interest (caudate, putamen anterior, posterior putamen, bilaterally).ResultsInterobserver match in the blind visual analysis was excellent with kappa coefficient = 0.91, CI at 95% = [0.87–0.95]. The semi-quantitative and statistical analysis by DaTQUANT^® determined pathological threshold values for each region of interest, setting a standard deviation percentage from a database of healthy subjects, worth −16.3% for the right posterior putamen (sensitivity of 100% and specificity of 88%) and −18.3% for the left posterior putamen (sensitivity of 100% and specificity of 97%).ConclusionThe pathological threshold values defined by our study would improve the data analysis obtained from DaTQUANT^® software and would support the DaTSCAN^® visual analysis. Nevertheless, such statistical values are complementary to visual analysis.     

A Fixed-Precision Sequential Sampling Plan for the Potato Tuberworm Moth, <Emphasis Type="Italic">Phthorimaea operculella</Emphasis> Zeller (Lepidoptera: Gelechidae), on Potato Cultivars

Phthorimaea operculella Zeller is an important pest of potato in Iran. Spatial distribution and fixed-precision sequential sampling for population estimation of the pest on two potato cultivars, Arinda^® and Sante^®, were studied in two separate potato fields during two growing seasons (2013–2014 and 2014–2015). Spatial distribution was investigated by Taylor’s power law and Iwao’s patchiness. Results showed that the spatial distribution of eggs and larvae was random. In contrast to Iwao’s patchiness, Taylor’s power law provided a highly significant relationship between variance and mean density. Therefore, fixed-precision sequential sampling plan was developed by Green’s model at two precision levels of 0.25 and 0.1. The optimum sample size on Arinda^® and Sante^® cultivars at precision level of 0.25 ranged from 151 to 813 and 149 to 802 leaves, respectively. At 0.1 precision level, the sample sizes varied from 5083 to 1054 and 5100 to 1050 leaves for Arinda^® and Sante^® cultivars, respectively. Therefore, the optimum sample sizes for the cultivars, with different resistance levels, were not significantly different. According to the calculated stop lines, the sampling must be continued until cumulative number of eggs + larvae reached to 15–16 or 96–101 individuals at precision levels of 0.25 or 0.1, respectively. The performance of the sampling plan was validated by resampling analysis using resampling for validation of sampling plans software. The sampling plant provided in this study can be used to obtain a rapid estimate of the pest density with minimal effort.     

A generalized numerical approach to steady-state enzyme kinetics: Applications to protein kinase inhibition

A generalized numerical treatment of steady-state enzyme kinetics is presented. This new approach relies on automatic computer derivation of the underlying mathematical model (a system of simultaneous nonlinear algebraic equations) from a symbolic representation of the reaction mechanism (a system of biochemical equations) provided by the researcher. The method allows experimental biochemists to analyze initial-rate enzyme kinetic data, under the steady-state approximation, without having to use any mathematical equations. An illustrative example is based on the inhibition kinetics of p56^lck kinase by an ATP competitive inhibitor. A computer implementation of the new method, in the modified software package DYNAFIT [Kuzmi?, P. (1996) Anal. Biochem. 237, 260–273], is freely available to all academic researchers.     

Influence of the application methods and doses on the susceptibility of black vine weevil larvae Otiorhynchus sulcatus to Metarhizium anisopliae in field-grown strawberries

Entomopathogenic fungi are commercially available for the control of insect pests, including the black vine weevil (BVW) Otiorhynchus sulcatus Fabricius (Coleoptera:Curculionidae). However, Metarhizium anisopliae (Metsch.) Sorokin (Clavicipitaceae) has not been used to control BVW in field-grown strawberries. Field trials were conducted in different locations in the UK during 2009–2010 to evaluate the different formulations (granular vs. drench) and application methods (premixed, drench, bare root treatment) of commercial strain of M. anisopliae Met52^® (=F52), the entomopathogenic nematodes and the organophosphate insecticide Cyren^® against BVW. The highest dose (10¹⁴ cfu ha^?1) tested provided significantly better control than the intermediate (10¹³ cfu ha^?1) or low (10¹² cfu ha^?1) doses. BVW larval control at the high, intermediate and low doses was 71–96, 40–75 and 6–11 %, respectively. Premixing, drench or bare root treatment with Met52^® gave similar levels of BVW control. Irrespective of the application methods or soil types, the high dose rate of Met52^® provided the best control. Significantly high larval control was achieved (78–97 %) when chlorpyrifos was applied at planting than eight weeks post planting (53 %). There were significant differences in BVW control between Met52^® (88 %) and reduced doses of Heterorhabditis bacteriophora Poinar (20–29 %) or Steinernema kraussei Steiner (39–75 %) when applied alone. However, when used together, low dose of S. kraussei and Met52^® provided 100 % control of BVW larvae. This study shows that Met52^® has considerable potential for the control of BVW larvae in commercial field-grown strawberry, thereby offering an environmentally benign alternative to chemical insecticides.     

Supplementation of 2nd break mushroom compost with isoleucine, leucine, valine, phenylalanine, Fermenten® and SoyPlus®

Three mushroom (Agaricus bisporus) crops (Crops 1, 2, 3) were grown to evaluate the effects of re-supplementing “spent” mushroom compost (MC) with the crystalline amino acids isoleucine (ile), leucine (leu), valine (val) and phenylalanine (phe) singly or in combination with Fermenten^® or SoyPlus^® on mushroom yield. Fermenten^® is a rumen fermentation enhancer while SoyPlus^® is a commercial delayed release mushroom nutrient. The most important single amino acid found for stimulating mushroom yield from 2nd break MC was ile. Crystalline ile added to 2nd break MC at 3.6% (dry wt) increased mushroom yields by 28.3% and 68.7% (average 48.5%) in Crops 1 and 2, respectively, compared to the non-supplemented control. In Crop 3, the addition of 5% or 10% ile to Fermenten^® and SoyPlus^® (3.6% total combined dry wt) did not significantly improve mushroom yield over treatments containing Fermenten^® or SoyPlus^® (3.6% total dry wt) alone. However, mixtures of equal quantities of Fermenten^®, ile and val significantly increased yield over Fermenten^® alone. Use of ile and val as supplements to stimulate mushroom yield from 2nd break MC is not economically viable because these amino acids are not commercially available at feed grade prices.     

Deceased tissue donor serology and molecular testing for HIV,hepatitis B and hepatitis C viruses: a lack of cadaveric validated tests

Vital to patient safety is the accurate assessment and minimization of risk for human immunodeficiency virus (HIV), Hepatitis C (HCV), and Hepatitis B (HBV) virus transmission by deceased donor organ and tissue transplantation. The pathogens are tested by serological kits based on enzyme-linked immunosorbent assay (ELISA), chemiluminescence (CLIA) and eletrochemiluminescence (ECLIA) immunoassays. Organ transplantation is a highly successful life-saving treatment in Brazil, but the Brazilian Health Surveillance Agency currently mandates that all deceased organ donors are screened for HIV, HCV and HBV following living donor policies. In this review, six ELISA (Wama^®, Bio-Rad^®, Biomerieux^®, DiaSorin^®, Acon Biotech^® and Biokit^®), three CLIA (Abbott^®, Siemens^®, Diasorin^®) and one ECLIA (Roche^®) were utilized for evaluating the effectiveness of those serological tests for deceased donors in Brazil according to manufacturer’s guidelines. NAT for HIV, HCV and HBV can assist with detection of pre-seroconversion for those infections, and only Cobas^® TaqScreen MPX^® test, the Tigris System^® Procleix Ultrio Assay^® and the Bio-Manguinhos^® HIV/HCV/HBV NAT are commercially available. Between all the tests, only the manufacturer Abbott^® and Cobas^® TaqScreen MPX^® test are currently validated for cadaver samples.     

Facteurs influençant la détectabilité de l’activité myocardique en caméra à semi-conducteurs

Body weight was already shown to be a major factor for the detectability of myocardial activity with conventional cameras and thus, for the optimization of injected activities and or recording times. This study was aimed to identify the factors affecting this detectability on a new solid-state camera showing a high sensitivity of detection (D.SPECT camera Cyclopharma^®).Patients and methodsThe study population involved 101 patients, who underwent myocardial SPECT with Sestamibi on a one-day stress/rest protocol. Each conventional acquisition (DST-XL General Electric Healthcare^® USA) was immediately followed by a D-SPECT^® one. Myocardial activity was determined on each acquisition in counts per seconds and expressed in fraction of the injected activity for assessing the detectability of myocardial activity.ResultsMyocardial activity was on average 12 ± 3 fold higher when recorded with the D-SPECT^® camera than with the DST-XL^® one. Body weight and especially body mass index (BMI) were the most significant correlates of the detectability of myocardial activity for both cameras. According to these correlations, an increase in the BMI from 25 to 35 kg/m was associated with a 47% decrease in the detectability of myocardial activity at stress with the DST-XL^® and of only 30% with the D-SPECT.ConclusionThe detectability of myocardial activity provided by the D.SPECT camera is dramatically higher than that documented for conventional cameras of the DST-XL^® type and is affected by the increase in body weight and in body mass index but at a lower rate than for the Anger camera.     

Endotoxin and cancer chemo-prevention

Reduced rates of lung cancer have been observed in several occupational groups exposed to high levels of organic dusts contaminated by endotoxin. The underlying anti-neoplastic mechanism of endotoxin may be an increased secretion of endogenous anti-neoplastic mediators and activation of the toll-like receptors (TLR). A detoxified endotoxin derivative, Monophosphoryl Lipid A (MPL^®) is marketed in Europe since 1999 as part of the adjuvant systems in allergy vaccines for treatment of allergic rhino-conjunctivitis and allergic asthma. Over 200,000 patients have used them to date (nearly 70% in Germany). Since detailed exposure (MPL^® dose and timing of administration) and individual data are potentially available, an observational follow-up study could be conducted in Germany to investigate the protective effect of MPL^® against cancer, comparing cancer incidence in two groups of patients with allergic rhinitis: those treated with allergoids plus MPL^® and those treated with a vaccine including the same allergoids but not MPL^®. The protective effect of MPL^® could be quantified in ever and never smokers. If this proposed observational study provides evidence of protective effects, MPL^® could be immediately used as a chemo-preventive agent since it is already in use as adjuvant in human vaccines against cancer.     

Euclidean distance can recognize the Biojas® concentration that produces the ideal physiological status of pineapple in vitro plantlets

Biojas^® is a fermented broth of Lasiodiplodia theobromae, a jasmonic acid–producing fungus characterized as a plant growth regulator and as biological control of phytopathogenic microorganisms and pests. The present work describes the use of Biojas^® in in vitro culture of pineapple. On the other hand, plant scientists usually record multiple indicators in their experiments. The common statistical data evaluations involve univariate analyses such as t test, Mann-Whitney, and analysis of variance (ANOVA) followed by Tukey’s HSD. Such analyses do not evaluate integrally the effects of the experimental treatments because each indicator is analyzed independently. For this reason, we explored in this study the Euclidean distance combined with the data of the Biojas^® treatment (0–2 mg l⁻¹) on pineapple in vitro plantlets as an integrating indicator. Plant height; number of leaves; D leaf length, width, and area; diameter of the plant base; fresh and dry weights of the plant; levels of chlorophylls; transpiration rate; CO₂ assimilation; and water use efficiency were recorded. Several statistically significant differences among Biojas^® treatments were recorded. However, the most significant effects of Biojas^® treatments were only noted in the plant height, length and area of D leaf, and water use efficiency. Variables mentioned above increased until 1.0 mg l⁻¹ Biojas^® and decreased with high levels of Biojas^®. Calculation of the Euclidean distance from each Biojas^® level to the ideal physiological status of the pineapple plantlets revealed that 1.0 mg l⁻¹ Biojas^® produced the pineapple plantlets with the best physiological status.

     

Use of enzymes in extraction of polyhydroxyalkanoates produced by Cupriavidus necator

Poly(3‐hydroxybutyrate) (P(3HB)) and its copolymer poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) (P(3HB‐co‐3HV), are biodegradable thermoplastic polymers. They are members of the polyhydroxyalkanoate (PHA) family, synthesized and accumulated as a carbon and energy reserve by a variety of microorganisms. The aim of this study was to evaluate the use of the proteases Corolase^® L10, Alcalase^® 2.4L, Corolase^® 7089 and Protemax^® FC and glycosidases Celumax^® BC, Rohament^® CL and Rohalase^® Barley for the recovery of P(3HB) and P(3HB‐co‐3HV) synthesized by Cupriavidus necator. The enzyme Celumax^® BC provided better lysis of the bacterial cell membrane and the results for the optimization of the operating conditions showed that this enzyme is most stable in acetate buffer at pH 4.0, bath at 60°C, hydrolysis time of 1 h and concentration of 0.02% (w/w). The optimization of the operating conditions showed that the enzyme Celumax^® BC provided better lysis of the bacterial cell in acetate buffer at pH 4.0, bath at 60°C, hydrolysis time of 1 h and concentration of 0.02% (w/w). These conditions resulted in lysis of the membrane of the bacteria with a recovery of 93.2% P(3HB‐co‐3HV) with 94% purity. The results showed that the use of enzymes for the polymer extraction is an efficient process that assists in the cell disruption of Cupriavidus necator. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Evaluation of lures and traps for male and female monitoring of Mediterranean fruit fly in pome and stone fruit

Commercial traps and lures have recently become available for monitoring male and female Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) in Australia, with possible applications in monitoring and mass trapping. This study investigated the attractiveness of commercially available male [Capilure^® (CPL), Trimedlure (TML) cone, plugs, and wafers] and female‐targeted synthetic lures (three‐component BioLure^®, BioLure^® Unipak, Ceratitis^® Unipak, TMA Plus^® Unipak and Biotrap^® gel), and five female‐targeted traps [Maxi^® trap, Sorygar Tephri‐trap, Probodelt^® cone trap, and BioTrap Globe^® traps (two versions)]. Results showed that TML and CPL lures were equivalent up to 8 weeks, but TML‐baited traps captured 1.2–4.6 times more male medflies than CPL‐baited traps with lures aged 9–16 weeks. For female‐targeted trapping, all tested lures were female selective. Ceratitis^® Unipak was equivalent to three‐component (3‐C) BioLure^®, whilst BioLure^® Unipak captured 1.1–1.5 times more medflies than 3‐C BioLure^®. The least efficient lures were TMA Plus^® Unipak and Biotrap Fruit Fly Attractant Gel. Tephri‐traps were the least efficient trap, with Maxi traps catching 1.9–6.7 times more medflies than the Tephri‐trap. The appropriate selection of lures and traps for applications in monitoring and mass trapping are discussed.     

The effect of denture adhesives on Candida albicans growth in vitro

doi: 10.1111/j.1741‐2358.2011.00478.x
The effect of denture adhesives on Candida albicans growth in vitro Objective: Denture‐wearing favours the growth of Candida. In view of the fact that many denture wearers regularly use adhesives to enhance denture retention, stability and function, the aim of this work was to study the effect of denture adhesives on Candida albicans growth in vitro. Materials and methods: The denture adhesives tested were Corega^® cream, Kukident^® cream, Novafix^® cream, Polident^® cream, Protefix^® cream, Steradent^® cream, Aderyn^® powder, Corega^® ultra powder, Protefix^® powder and Corega^® strip. C. albicans growth curves were obtained in the presence or absence of a 1% solution of the denture adhesive diluted in Sabouraud broth. Macro‐ and microscopic morphological changes in C. albicans were analysed, as was microbial contamination of the denture adhesive. Results: Most of the denture adhesives studied induced morphological changes in C. albicans cells and colonies, but only two had any significant inhibitory effect on yeast growth. Kukident^® cream markedly inhibited C. albicans growth in a concentration‐dependent way, reducing the growth rate by 95%, whereas Corega^® cream also inhibited C. albicans growth but in a non‐concentration‐dependent way, reducing the growth rate by 37%. In addition, denture adhesives available as powders had detectable microbial contamination. Conclusion: Some commercially available denture adhesives showed microbial contamination and some had significant inhibitory effect on C. albicans growth.     

Modeling small-scale cassava starch extraction. Simulation of the reduction of water consumption through a recycling process

The purpose of this study was to model the extraction unit operation of the cassava starch manufacturing process and to propose a realistic recycling simulation in order to reduce the volumes of effluents. The model was developed from reactors which are commonly used for cassava starch extraction at a household scale in Vietnam. The reactors were tested using inflow starch as a marker at the beginning of the batch process. The experimental residence time distribution (RTD_exp) was calculated by the outflow of the starch concentration. Using Matlab^®, the RTD_exp was compared to the theoretical residence time distribution (RTD_th). The dynamic model obtained was built up on Simulink^® and tested with four different strategies of recycling methods. Sedimented starch was collected from the different types of processes; the pH value and the titratable acidity of starch were then measured. The results showed a good correlation between RTD_exp and RTD_th. The reactors were described by a model of two mixed tanks in series. The simulation of the recycling process revealed a reduction in quantity of water used up to 43%; however, the recycling process increased significantly the titratable acidity of starch up to 6.48 ± 0.11 mequiv. H⁺/100 g dry matter.     

Development of an Ultra-Rapid Diagnostic Method Based on Heart-Type Fatty Acid Binding Protein Levels in the CSF of CJD Patients

Creutzfeldt-Jakob disease (CJD) is a transmissible, fatal, neurodegenerative disease in humans. Recently, various drugs have been reported to be useful in the treatment of CJD; however, for such treatments to be useful it is essential to rapidly and accurately diagnose CJD. 124 CJD patients and 87 with other diseases causing rapid progressive dementia were examined. Cerebral spinal fluid (CSF) from CJD patients was analyzed by 2D-PAGE and the protein expression pattern was compared with that from healthy subjects. One of three CJD-specific spots was found to be fatty acid binding protein (FABP), and heart-type FABP (H-FABP) was analyzed as a new biochemical marker for CJD. H-FABP ELISA results were compared between CJD patients and patients with other diseases (n = 211). Visual readout accuracy of the Rapicheck^® H-FABP test panel for CSF was analyzed using an independent measure of CSF H-FABP concentration. The distribution of H-FABP in the brains of CJD patients was examined by immunohistochemistry. ELISA sensitivity and specificity were 90.3% and 92.9%, respectively, and Rapicheck^® H-FABP sensitivity and specificity were 87.9% and 96.0%, respectively. ELISA and Rapicheck^® H-FABP assays provided comparable results for 14-3-3 protein and total tau protein. Elevated H-FABP levels were associated with an accumulation of abnormal prion protein, astrocytic gliosis, and neuronal loss in the cerebral cortices of CJD patients. In conclusion, Rapicheck^® H-FABP of CSF specimens enabled quick and frequent diagnosis of CJD. H-FABP represents a new biomarker for CJD distinct from 14-3-3 protein and total tau protein.     

Detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method

To culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. Micro-IDent^® and micro-IDent^® Plus (HAIN Lifescience GmbH, Nehren, Germany) tests are two commercially available rapid PCR-based methods for the identification and quantification of putative periodontopathogen bacteria. In this study, we compared these commercial PCR-based hybridization methods with conventional anaerobic culture technique. A total of 36 subgingival plaque samples were collected from periodontal pockets of pregnant women with chronic localized periodontitis. Aliquots of these samples were evaluated with species-specific probes provided by micro-IDent^® and micro-IDent^® Plus tests simultaneously, and from the same samples anaerobic and capnophylic bacteria were cultured on selective media. The overall agreement between both methods was excellent for Eubacterium nodatum, Tannerella forsythia and Porphyromonas gingivalis (97–92%), fair for Capnocytophaga sp, Eikenella corrodens, Actinobacillus actinomycetemcomitans, and Prevotella intermedia (91–89%) and poor for Fusobacterium nucleatum, Parvimonas micra (Micromonas micros), and Campylobacter rectus (86–78%). Discrepancies in the results may be explained by inability of culture method to distinguish between closely related taxa (e.i P. intermedia/Prevotella. nigrescens), and problems of keeping periodontopathogen bacteria viable, which is required for successful detection by standard culture method. Nucleic acid-based methods may replace cultivation method as frequently used methods in microbiological diagnosis of progressive periodontitis, thus micro-IDent^® andmicro-IDent^® Plus tests can be recommended where culture of periodontopathogenic bacteria is not performed in routine microbiology laboratories to analyze subgingival plaque samples.     

Accelerating multiple replica molecular dynamics simulations using the Intel® Xeon Phi™ coprocessor

We investigate the performance increase provided by the Intel^® Xeon Phi? coprocessor in multiple replica molecular dynamics applications using a novel parallelisation scheme. The benefits of the proposed parallelisation scheme are demonstrated by glycine in water, a system of significant interest in the crystallisation simulation community. The molecular dynamics (MD) engine consists of initially serial LAMMPS and NAMD subroutines, and is subsequently modified and parallelised using a heterogeneous programming model, where each MPI rank is paired with a unique Intel^® Xeon Phi? coprocessor and CPU socket. The MD engine is parallelised using an OpenMP atom domain decomposition algorithm on the Intel^® Xeon Phi? coprocessor and OpenMP task parallelism on the host CPU socket. Using nodes with two Intel^® Xeon Phi? coprocessors, one per socket, we demonstrate that a factor of five reduction in the required computational resources is achieved per replica with the coprocessor, when compared against employing the standard spatial domain decomposition algorithm with no accelerator. Furthermore, the proposed parallelisation scheme achieves ideal weak scaling with respect to the number of employed MPI ranks (replicas). The Intel^® Xeon Phi? coprocessor not only allows us to the increase performance output per socket by a factor of five, when compared against no accelerators, but also significantly reduces the parallelisation complexity necessary to achieve this performance, as the Intel^® Xeon Phi? coprocessor operates using the simple OpenMP programming language.