Computed wall stress may predict the growth of abdominal aortic aneurysm

Growth rate of abdominal aortic aneurysm (AAA) is thought to be an important indicator of the potential risk of rupture. Wall stress is also thought to be a trigger for its rupture. However, stress change during the expansion of an AAA is unclear. Forty-four patients with AAAs were included in this longitudinal follow-up study. They were assessed by serial abdominal ultrasonography and computerized tomography (CT) scans if a critical size was reached or a rapid expansion occurred. Patient-specific 3-dimensional AAA geometries were reconstructed from the follow-up CT images. Structural analysis was performed to calculate the wall stresses of the AAA models at both baseline and final visit. A non-linear large-strain finite element method was used to compute the wall stress distribution. The average growth rate was 0.66cm/year (range 0-1.32 cm/year). A significantly positive correlation between shoulder tress at baseline and growth rate was found (r=0.342; p=0.02). A higher shoulder stress is associated with a rapidly expanding AAA. Therefore, it may be useful for estimating the growth expansion of AAAs and further risk stratification of patients with AAAs.

Prospects for predicting insect mortality in relation to changing phosphine concentrations

Typically, in bag-stack or silo fumigations the concentration of phosphine is not constant, and yet most of what is known about phosphine efficacy against grain insects comes from studies with fixed concentrations. Indeed, where changing concentration experiments have been performed, researchers have been unable to explain observed efficacy on the basis of data from fixed concentrations. The ability to predict insect mortality in relation to changing phosphine concentrations would facilitate the development of effective fumigation protocols. In this paper, we explore the prospects for making such predictions. After reviewing published and new results, we conclude that the commonly used concentration x time (Ct) product is unreliable for this purpose. New results, for a strongly resistant strain of Rhyzopertha dominica from Australia, suggest that the relationship Cnt = k may be useful for predicting mortality of this type of insect in changing concentrations. However, in the case of a strain of Sitophilus oryzae with a type of resistance common in Australian S. oryzae, the relationship Cnt = k proved to be less reliable.

Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

Background: Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. Results: A microsatellite- enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Conclusion. Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.

CBCT image guidance in head and neck irradiation: The impact of daily and weekly imaging protocols

Purpose This study evaluated the impact of a daily and weekly image-guided radiotherapy protocols in reducing setup errors and setting of appropriate margins in head and neck cancer patients. Materials and methods Interfraction and systematic shifts for the hypothetical day 1–3 plus weekly imaging were extrapolated from daily imaging data from 31 patients (964 cone beam computed tomography (CBCT) scans). In addition, residual setup errors were calculated by taking the average shifts in each direction for each patient based on the first three shifts and were presumed to represent systematic setup error. The clinical target volume (CTV) to planning target volume (PTV) margins were calculated using van Herk formula and analysed for each protocol. Results The mean interfraction shifts for daily imaging were 0·8, 0·3 and 0·5 mm in the S-I (superior-inferior), L-R (left-right) and A-P (anterior-posterior) direction, respectively. On the other hand the mean shifts for day 1–3 plus weekly imaging were 0·9, 1·8 and 0·5 mm in the S-I, L-R and A-P direction, respectively. The mean day 1–3 residual shifts were 1·5, 2·1 and 0·7 mm in the S-I, L-R and A-P direction, respectively. No significant difference was found in the mean setup error for the daily and hypothetical day 1–3 plus weekly protocol. However, the calculated CTV to PTV margins for the daily interfraction imaging data were 1·6, 3·8 and 1·4 mm in the S-I, L-R and A-P directions, respectively. Hypothetical day 1–3 plus weekly resulted in CTV–PTV margins of 5, 4·2 and 5 mm in the S-I, L-R and A-P direction. Conclusions The results of this study show that a daily CBCT protocol reduces setup errors and allows setup margin reduction in head and neck radiotherapy compared to a weekly imaging protocol.

Absolute quantitation of Marek's disease virus and Herpesvirus of turkeys in chicken lymphocyte, feather tip and dust samples using real-time PCR

The further development of Taqman quantitative real-time PCR (qPCR) assays for the absolute quantitation of Marek's disease virus serotype 1 (MDV1) and Herpesvirus of turkeys (HVT) viruses is described and the sensitivity and reproducibility of each assay reported. Using plasmid DNA copies, the lower limit of detection was determined to be 5 copies for the MDV1 assay and 75 copies for the HVT assay. Both assays were found to be highly reproducible for Ct values and calculated copy numbers with mean intra- and inter-assay coefficients of variation being less than 5% for Ct and 20% for calculated copy number. The genome copy number of MDV1 and HVT viruses was quantified in PBL and feather tips from experimentally infected chickens, and field poultry dust samples. Parallelism was demonstrated between the plasmid-based standard curves, and standard curves derived from infected spleen material containing both viral and host DNA, allowing the latter to be used for absolute quantification. These methods should prove useful for the reliable differentiation and absolute quantitation of MDV1 and HVT viruses in a wide range of samples.

No-tillage and nitrogen application affects the decomposition of 15N-labelled wheat straw and the levels of mineral nitrogen and organic carbon in a Vertisol

No-tillage (NT) practice, where straw is retained on the soil surface, is increasingly being used in cereal cropping systems in Australia and elsewhere. Compared to conventional tillage (CT), where straw is mixed with the ploughed soil, NT practice may reduce straw decomposition, increase nitrogen immobilisation and increase organic carbon in the soil. This study examined 15N-labelled wheat straw (stubble) decomposition in four treatments (NT v. CT, with N rates of 0 and 75 kg/ha.year) and assessed the tillage and fertiliser N effects on mineral N and organic C and N levels over a 10-year period in a field experiment. NT practice decreased the rate of straw decomposition while fertiliser N application increased it. However, there was no tillage practice x N interaction. The mean residence time of the straw N in soil was more than twice as long under the NT (1.2 years) as compared to the CT practice (0.5 years). In comparison, differences in mean residence time due to N fertiliser treatment were small. However, tillage had generally very little effect on either the amounts of mineral N at sowing or soil organic C (and N) over the study period. While application of N fertiliser increased mineral N, it had very little effect on organic C over a 10-year period. Relatively rapid decomposition of straw and short mean residence time of straw N in a Vertisol is likely to have very little long-term effect on N immobilisation and organic C level in an annual cereal cropping system in a subtropical, semiarid environment. Thus, changing the tillage practice from CT to NT may not necessitate additional N requirement unless use is made of additional stored water in the soil or mineral N loss due to increased leaching is compensated for in N supply to crops.

Delineating environmental envelopes to improve mapping of species distributions, via a hurdle model with CART &/or MaxEnT

Species distribution modelling (SDM) typically analyses species’ presence together with some form of absence information. Ideally absences comprise observations or are inferred from comprehensive sampling. When such information is not available, then pseudo-absences are often generated from the background locations within the study region of interest containing the presences, or else absence is implied through the comparison of presences to the whole study region, e.g. as is the case in Maximum Entropy (MaxEnt) or Poisson point process modelling. However, the choice of which absence information to include can be both challenging and highly influential on SDM predictions (e.g. Oksanen and Minchin, 2002). In practice, the use of pseudo- or implied absences often leads to an imbalance where absences far outnumber presences. This leaves analysis highly susceptible to ‘naughty-noughts’: absences that occur beyond the envelope of the species, which can exert strong influence on the model and its predictions (Austin and Meyers, 1996). Also known as ‘excess zeros’, naughty noughts can be estimated via an overall proportion in simple hurdle or mixture models (Martin et al., 2005). However, absences, especially those that occur beyond the species envelope, can often be more diverse than presences. Here we consider an extension to excess zero models. The two-staged approach first exploits the compartmentalisation provided by classification trees (CTs) (as in O’Leary, 2008) to identify multiple sources of naughty noughts and simultaneously delineate several species envelopes. Then SDMs can be fit separately within each envelope, and for this stage, we examine both CTs (as in Falk et al., 2014) and the popular MaxEnt (Elith et al., 2006). We introduce a wider range of model performance measures to improve treatment of naughty noughts in SDM. We retain an overall measure of model performance, the area under the curve (AUC) of the Receiver-Operating Curve (ROC), but focus on its constituent measures of false negative rate (FNR) and false positive rate (FPR), and how these relate to the threshold in the predicted probability of presence that delimits predicted presence from absence. We also propose error rates more relevant to users of predictions: false omission rate (FOR), the chance that a predicted absence corresponds to (and hence wastes) an observed presence, and the false discovery rate (FDR), reflecting those predicted (or potential) presences that correspond to absence. A high FDR may be desirable since it could help target future search efforts, whereas zero or low FOR is desirable since it indicates none of the (often valuable) presences have been ignored in the SDM. For illustration, we chose Bradypus variegatus, a species that has previously been published as an exemplar species for MaxEnt, proposed by Phillips et al. (2006). We used CTs to increasingly refine the species envelope, starting with the whole study region (E0), eliminating more and more potential naughty noughts (E1–E3). When combined with an SDM fit within the species envelope, the best CT SDM had similar AUC and FPR to the best MaxEnt SDM, but otherwise performed better. The FNR and FOR were greatly reduced, suggesting that CTs handle absences better. Interestingly, MaxEnt predictions showed low discriminatory performance, with the most common predicted probability of presence being in the same range (0.00-0.20) for both true absences and presences. In summary, this example shows that SDMs can be improved by introducing an initial hurdle to identify naughty noughts and partition the envelope before applying SDMs. This improvement was barely detectable via AUC and FPR yet visible in FOR, FNR, and the comparison of predicted probability of presence distribution for pres/absence.

Australian Bat Lyssavirus

In Chapter 1, the literature relating to rabies virus and the rabies like lyssaviruses is reviewed. In Chapter 2, data are presented from 1170 diagnostic submissions for ABLV testing by fluorescent antibody test (Centocor FAT). All 27 non-bat submissions were ABLV-negative. Of 1143 bat accessions 74 (16%) were ABLV-positive, including 69 of 974 (7.1%) flying foxes (Pteropus spp.), 5 of 7 (71.4%) Saccolaimus flaviventris (Yellow-bellied sheathtail bats), none of 151 other microchiropteran bats, and none of 11 unidentified bats. Statistical analysis of data from 868 wild Black, Grey-headed, Little Red and Spectacled flying foxes (Pteropus alecto, P. poliocephalus, P. scapulatus, and P. conspicillatus) indicated that three factors; species, health status and age were associated with significant (p< 0.001) differences in the proportion of ABLV-positive bats. Other factors including sex, whether the bat bit a person or animal, region, year, and season submitted, were not associated with ABLV. Case data for 74 ABLV-positive bats, including the circumstances in which they were found and clinical signs, is presented. In Chapter 3, the aetiological diagnosis was investigated for 100 consecutive flying fox submissions with neurological signs. ABLV (32%), spinal and head injuries (29%), and neuro-angiostrongylosis (18%) accounted for most neurological syndromes in flying foxes. No evidence of lead poisoning was found in unwell (n=16) or healthy flying foxes (n=50). No diagnosis was reached for 16 cases, all of which were negative for ABLV by TaqMan PCR. The molecular diversity of ABLV was examined in Chapter 4 by sequencing 36 bases of the leader sequence, the entire N gene, and start of the P gene of 28 isolates from pteropid bats and 3 isolates from Yellow-bellied sheathtail (YBST) bats. Phylogenetic analysis indicated all ABLV isolates clustered together as a discrete group within the Lyssavirus genera closely related to rabies virus and European bat lyssavirus-2 isolates. The ABLV lineage consisted of two variants; one (ybst-ABLV) consisted of isolates only from YBST bats, the other (pteropid-ABLV) was common to Black, Grey-headed and Little Red flying foxes. No associations were found between the sequences and either the geographical location or year found, or individual flying fox species. In Chapter 5, 15 inocula prepared from the brains or salivary glands of naturally-infected bats were evaluated by intracerebral (IC) and footpad (FP) inoculation of Quackenbush mice in order to select and characterize a highly virulent inoculum for further use in bats (Inoculum 5). In Chapter 6, nine Grey-headed flying foxes were inoculated with 105.2 to 105.5 MICED50 of Inoculum 5 divided into four sites, left footpad, pectoral muscle, temporal muscle and muzzle. Another bat was inoculated with half this dose divided into the footpad and pectoral muscle only. Seven of 10 bats developed clinical disease of 1 to 4 days duration between PI-days 10 and 19 and were shown to be ABL-positive by FAT, HAM immunoperoxidase staining, virus isolation in mice, and TaqMan PCR. Five of the seven bats displayed overt aggression, one died during a seizure, and one showed intractable agitation, pacing, tremors, and ataxia. Viral antigen was demonstrated throughout the central and peripheral nervous systems and in the epithelial cells of the submandibular salivary glands (n=4). All affected bats had mild to moderate non-suppurative meningoencephalitis and severe ganglioneuritis. No ABLV was detected in three bats that remained well until the end of the experiment on day 82. One survivor developed a strong but transient antibody response. In Chapter 7, the relative virulence of inocula prepared from the brains and salivary glands of experimentally infected flying foxes was evaluated in mice by IC and FP inoculation and TaqMan assay. The effects in mice were correlated to the TaqMan CT value and indicated a crude association between virulence and CT value that has potential application in the selection of inocula. In Chapter 8, 36 Black and Grey-headed flying foxes were vaccinated with one (day 0) or two (+ day 28) doses of Nobivac rabies vaccine and co-vaccinated with keyhole limpet haemocyanin (KLH). All bats responded to the Nobivac vaccine with a rabies-RFFIT titer > 0.5 IU/mL that is nominally indicative of protective immunity. Plasma from bats with rabies titres >2 IU/mL had cross-neutralising ABLV titres >1:154. A specifically developed ELISA detected a strong but transient response to KLH.

The control of climbing asparagus (Asparagus africanus Lam.) in remnant Brigalow scrub in south-east Queensland

A replicated trial was conducted at Tallegalla in south-east Queensland to assess the effectiveness of a range of control methods for climbing asparagus Asparagus africanus Lam. A total of 18 treatments using mechanical, cut stump, basal bark, foliar spray and splatter gun techniques were trialled with a range of herbicides and application rates. Removing the plant and placing it above the ground surface was most effective in killing climbing asparagus. Basal bark spraying of 24 g triclopyr ester (40 mL Garlon® 600) or 10 g fluroxypyr ester (50 mL Starane® 200) L-1 diesel and the cut stump application of neat diesel or 225 g glyphosate (500 mL Glyphosate CT®) L-1 water offered the best chemical control of climbing asparagus.

Automatic ICD-10 classification of cancers from free-text death certificates

Objective Death certificates provide an invaluable source for cancer mortality statistics; however, this value can only be realised if accurate, quantitative data can be extracted from certificates – an aim hampered by both the volume and variable nature of certificates written in natural language. This paper proposes an automatic classification system for identifying cancer related causes of death from death certificates. Methods Detailed features, including terms, n-grams and SNOMED CT concepts were extracted from a collection of 447,336 death certificates. These features were used to train Support Vector Machine classifiers (one classifier for each cancer type). The classifiers were deployed in a cascaded architecture: the first level identified the presence of cancer (i.e., binary cancer/nocancer) and the second level identified the type of cancer (according to the ICD-10 classification system). A held-out test set was used to evaluate the effectiveness of the classifiers according to precision, recall and F-measure. In addition, detailed feature analysis was performed to reveal the characteristics of a successful cancer classification model. Results The system was highly effective at identifying cancer as the underlying cause of death (F-measure 0.94). The system was also effective at determining the type of cancer for common cancers (F-measure 0.7). Rare cancers, for which there was little training data, were difficult to classify accurately (F-measure 0.12). Factors influencing performance were the amount of training data and certain ambiguous cancers (e.g., those in the stomach region). The feature analysis revealed a combination of features were important for cancer type classification, with SNOMED CT concept and oncology specific morphology features proving the most valuable. Conclusion The system proposed in this study provides automatic identification and characterisation of cancers from large collections of free-text death certificates. This allows organisations such as Cancer Registries to monitor and report on cancer mortality in a timely and accurate manner. In addition, the methods and findings are generally applicable beyond cancer classification and to other sources of medical text besides death certificates.

The performance of broilers offered sorghum - compared to wheat-based diets: a large sacle experiment.

Sufficient evidence tended to indicate that at least four factors can negatively influence broiler performance when offered sorghum-based diets; in particular energy utilisation of sorghum in young birds. It was proposed that mainly CT would further influence sorghum grain AME values when consumed by young chicks (0-7 and 7-14 d old). Overall, birds consuming sorghum-based diets during the starter phase (0-21 d), did not match the performance of birds offered wheat-based diets. The use of phytase enzymes in sorghum-based diets tended to improve bird performance. However, reducing the obtained AME of sorghum grains by -0.8 MJ during the 0-21 d period appears to be a practical solution.

Controlled pollination methods for creating Corymbia hybrids.

Inter-specific Corymbia hybrids are of increasing interest to plantation forestry, yet there is little knowledge of the most suitable controlled pollination methods for this genus. Inter-specific crosses were made between C. torelliana [CT(maternal parent)] and C. citriodora subsp. variegata (CCV), C. henryi (CH) and C. citriodora subsp. citriodora (CCC) using conventional pollination, one-stop pollination (OSP) and artificially-induced protogyny on yellow buds (AIP Y) pollination methods. Additional treatments included AIP on green buds (AIP G) and the use of exclusion bags for the OSP and AIP methods. Inter-specific hybrids (CT x CCV, CT x CH and CT x CCC) were successfully created using all three pollination methods. The AIP Y treatment provided the highest seed yields and achieved time savings of >41% over the conventional and OSP methods, resulting in up to five-fold increases in operator productivity. However, the AIP Y treatment also had the highest C. torelliana contamination levels (9.3–13.2%). The use of exclusion bags with the AIP method had minimal effect on contamination rates, indicating a high proportion of selfpollen contamination. Contamination rates varied between maternal parents, suggesting variation in selfcompatibility for C. torelliana individuals. AIP using semi-ripe green buds was not effective at reducing selfing and had low operator productivity. The AIP method is suitable for use in a large-scale hybrid breeding program for C. torelliana. When self-pollination effects are managed, it could greatly reduce the costs associated with the production of seed of elite family crosses for commercial forestry deployment.

A novel investigation of vapor-phase charge-transfer complexes of halogens with n-donors by electron energy loss spectroscopy

Complexes of I2 with diethyl ether and triethylamine and of Br, with diethyl ether have been investigated in the vapor phase for the first time by employing electron energy loss spectroscopy. Besides the CT bands, blue-shifted vacuum-UV bands of the halogens have been assigned; the amine-I, system appears to exhibit two CT bands,associated with two different excited states of the complex.

ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water

Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, T-g = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called "no man's land" (the range 150-235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at approximate to 225 K. The reorientation of the probe molecules decouples from the viscosity below approximate to 225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes-Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974-12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360: 324-328] and the fragile-to-strong dynamic cross-over at approximate to 228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-tostrong liquid transition in water. Nature 398: 492-494].

Solutions for archiving data in long-term studies: A reply to Whitlock et al.

In our recent paper [1], we discussed some potential undesirable consequences of public data archiving (PDA) with specific reference to long-term studies and proposed solutions to manage these issues. We reaffirm our commitment to data sharing and collaboration, both of which have been common and fruitful practices supported for many decades by researchers involved in long-term studies. We acknowledge the potential benefits of PDA (e.g., [2]), but believe that several potential negative consequences for science have been underestimated [1] (see also 3 and 4). The objective of our recent paper [1] was to define practices to simultaneously maximize the benefits and minimize the potential unwanted consequences of PDA.