Exploratory Space-Time Analyses of Rift Valley Fever in South Africa in 2008-2011

Background: Rift Valley fever (RVF) is a zoonotic arbovirosis for which the primary hosts are domestic livestock (cattle, sheep and goats). RVF was first described in South Africa in 1950-1951. Mechanisms for short and long distance transmission have been hypothesised, but there is little supporting evidence. Here we describe RVF occurrence and spatial distribution in South Africa in 2008-11, and investigate the presence of a contagious process in order to generate hypotheses on the different mechanisms of transmission. Methodology/Principal Findings: A total of 658 cases were extracted from World Animal Health Information Database. Descriptive statistics, epidemic curves and maps were produced. The space-time K-function was used to test for evidence of space-time interaction. Five RVF outbreak waves (one in 2008, two in 2009, one in 2010 and one in 2011) of varying duration, location and size were reported. About 70% of cases (n = 471) occurred in 2010, when the epidemic was almost country-wide. No strong evidence of space-time interaction was found for 2008 or the second wave in 2009. In the first wave of 2009, a significant space-time interaction was detected for up to one month and over 40 km. In 2010 and 2011 a significant intense, short and localised space-time interaction (up to 3 days and 15 km) was detected, followed by one of lower intensity (up to 2 weeks and 35 to 90 km). Conclusions/Significance: The description of the spatiotemporal patterns of RVF in South Africa between 2008 and 2011 supports the hypothesis that during an epidemic, disease spread may be supported by factors other than active vector dispersal. Limitations of under-reporting and space-time K-function properties are discussed. Further spatial analyses and data are required to explain factors and mechanisms driving RVF spread. © 2012 Métras et al.

Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

BACKGROUND:

We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq.

13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN). The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs) underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p<0.03).

Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

Experimental demonstration of particle energy, conversion efficiency and spectral shape required for ion-based fast ignition

Research on fusion fast ignition (FI) initiated by laser-driven ion beams has made substantial progress in the last years. Compared with electrons, FI based on a beam of quasi-monoenergetic ions has the advantage of a more localized energy deposition, and stiffer particle transport, bringing the required total beam energy close to the theoretical minimum. Due to short pulse laser drive, the ion beam can easily deliver the 200 TW power required to ignite the compressed D-T fuel. In integrated calculations we recently simulated ion-based FI targets with high fusion gain targets and a proof of principle experiment [1]. These simulations identify three key requirements for the success of ion-driven fast ignition (IFI): (1) the generation of a sufficiently high-energetic ion beam (approximate to 400-500 MeV for C), with (2) less than 20% energy spread at (3) more than 10% conversion efficiency of laser to beam energy. Here we present for the first time new experimental results, demonstrating all three parameters in separate experiments. Using diamond nanotargets and ultrahigh contrast laser pulses we were able to demonstrate >500 MeV carbon ions, as well as carbon pulses with Delta E/E

A study of velocity fields in the transition region of ε Eri (K2 V)

Analyses of the widths and shifts of optically thin emission lines in the ultraviolet spectrum of the active dwarf e Eri (K2 V) are presented. The spectra were obtained using the Space Telescope Imaging Spectrograph on the Hubble Space Telescope and the Far Ultraviolet Spectroscopic Explorer. The linewidths are used to find the non-thermal energy density and its variation with temperature from the chromosphere to the upper transition region. The energy fluxes that could be carried by Alfvén and acoustic waves are investigated, to test their possible roles in coronal heating. Acoustic waves do not appear to be a viable means of coronal heating. There is, in principle, ample flux in Alfvén waves, but detailed calculations of wave propagation are required before definite conclusions can be drawn concerning their viability. The high sensitivity and spectral resolution of the above instruments have allowed two-component Gaussian fits to be made to the profiles of the stronger transition region lines. The broad and narrow components that result share some similarities with those observed in the Sun, but in e Eri the broad component is redshifted relative to the narrow component and contributes more to the total line flux. The possible origins of the two components and the energy fluxes implied are discussed. On balance our results support the conclusion of Wood, Linsky & Ayres, that the narrow component is related to Alfvén waves reaching to the corona, but the origin of the broad component is not clear.

The developmental character of cardiac autonomic responses to an acute noxious event in 4- and 8-month-old healthy infants

Heart rate (HR) has been widely studied as a measure of an individual's response to painful stimuli. It remains unclear whether changes in mean HR or the variability of HR are specifically related to the noxious stimulus (i.e. pain). Neither is it well understood how such changes reflect underlying neurologic control mechanisms that produce these responses, or how these mechanisms change during the first year of life. To study the changes in cardiac autonomic modulation that occur with acute pain and with age during early infancy, the relationship between respiratory activity and short-term variations of HR (i.e. respiratory sinus arrhythmia) was quantified in a longitudinal study of term born healthy infants who underwent a finger lance blood collection at 4 months of age (n = 24) and again at 8 months of age (n = 20). Quantitative respiratory activity and HR were obtained during baseline, lance, and recovery periods. Time and frequency domain analyses from 2.2-min epochs of data yielded mean values, spectral measures of low (0.04-0.15 Hz) and high (0.15-0.80 Hz) frequency power (LF and HF), and the LF/HF ratio. To determine sympathetic and parasympathetic cardiac activity, the transfer relation between respiration and HR was used. At both 4 and 8 months, mean HR increased significantly with the noxious event (p > 0.01). There were age-related differences in the pattern of LF, HF, and LF/HF ratio changes. Although these parameters all decreased (p > 0.01) at 4 months, LF and LF/HF increased at 8 months and at 8 months HF remained stable in response to the noxious stimulus. Transfer gain changes with the lance demonstrated a change from predominant vagal baseline to a sympathetic condition at both ages. The primary finding of this study is that a response to an acute noxious stimulus appears to produce an increase in respiratory-related sympathetic HR control and a significant decrease in respiratory-related parasympathetic control at both 4 and 8 months. Furthermore, with increasing age, the sympathetic and parasympathetic changes appear to be less intense, but more sustained.

Resource utilization and cost analyses of home-based palliative care service provision:The Niagara West End-of-Life Shared-Care Project

Background: Increasing emphasis is being placed on the economics of health care service delivery - including home-based palliative care. Aim: This paper analyzes resource utilization and costs of a shared-care demonstration project in rural Ontario (Canada) from the public health care system's perspective. Design: To provide enhanced end-of-life care, the shared-care approach ensured exchange of expertise and knowledge and coordination of services in line with the understood goals of care. Resource utilization and costs were tracked over the 15 month study period from January 2005 to March 2006. Results: Of the 95 study participants (average age 71 years), 83 had a cancer diagnosis (87%); the non-cancer diagnoses (12 patients, 13%) included mainly advanced heart diseases and COPD. Community Care Access Centre and Enhanced Palliative Care Team-based homemaking and specialized nursing services were the most frequented offerings, followed by equipment/transportation services and palliative care consults for pain and symptom management. Total costs for all patient-related services (in 2007 CAN) were 1,625,658.07 - or 17,112.19 per patient/117.95 per patient day. Conclusion: While higher than expenditures previously reported for a cancer-only population in an urban Ontario setting, the costs were still within the parameters of the US Medicare Hospice Benefits, on a par with the per diem funding assigned for long-term care homes and lower than both average alternate level of care and hospital costs within the Province of Ontario. The study results may assist service planners in the appropriate allocation of resources and service packaging to meet the complex needs of palliative care populations. © 2012 The Author(s).

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Serial chimerism analyses indicate that mixed haemopoietic chimerism influences the probability of graft rejection and disease recurrence following allogeneic stem cell transplantation (SCT) for severe aplastic anaemia (SAA): indication for routine assessment of chimerism post SCT for SAA

Ninety-one patients were studied serially for chimeric status following allogeneic stem cell transplantation (SCT) for severe aplastic anaemia (SAA) or Fanconi Anaemia (FA). Short tandem repeat polymerase chain reaction (STR-PCR) was used to stratify patients into five groups: (A) complete donor chimeras (n = 39), (B) transient mixed chimeras (n = 15) (C) stable mixed chimeras (n = 18), (D) progressive mixed chimeras (n = 14) (E) recipient chimeras with early graft rejection (n = 5). As serial sampling was not possible in Group E, serial chimerism results for 86 patients were available for analysis. The following factors were analysed for association with chimeric status: age, sex match, donor type, aetiology of aplasia, source of stem cells, number of cells engrafted, conditioning regimen, graft-versus-host disease (GvHD) prophylaxis, occurrence of acute and chronic GvHD and survival. Progressive mixed chimeras (PMCs) were at high risk of late graft rejection (n = 10, P <0.0001). Seven of these patients lost their graft during withdrawal of immunosuppressive therapy. STR-PCR indicated an inverse correlation between detection of recipient cells post-SCT and occurrence of acute GvHD (P = 0.008). PMC was a bad prognostic indicator of survival (P = 0.003). Monitoring of chimeric status during cyclosporin withdrawal may facilitate therapeutic intervention to prevent late graft rejection in patients transplanted for SAA.

Genetic and genomic analyses of musculoskeletal differences between BEH and BEL strains

Berlin high (BEH) and Berlin low (BEL) strains selected for divergent growth differ 3-fold in body weight. We aimed at examining muscle mass, which is a major contributor to body weight, by exploring anatomical characteristics of the soleus muscle, its fiber numbers and their cross sectional area (CSA), by analysing transcriptome of the gastrocnemius and by initiating quantitative trait locus (QTL) mapping. BEH muscles were 4-to-8 times larger compared to BEL strain. In sub-strain BEH+/+, mutant myostatin was replaced with a wild type allele, however, BEH+/+muscles still were 2-to-4 times larger compared to the BEL strain. BEH soleus contained 2-times more (P<0.0001) and 2-times larger in CSA (P<0.0001) fibers compared to BEL strain. In addition, soleus femoral attachment anomaly (SFAA) was observed in all BEL mice. One significant (chromosome 1) and four suggestive (chromosomes 3, 4, 6 and 9) muscle weight QTLs were mapped in 21-day old F2 intercross (n=296) between BEH and BEL strains. The frequency of SFAA incidence in the F2 and in the backcross to BEL strain (BCL) suggested the presence of more than one causative gene. Two suggestive SFAA QTLs were mapped in BCL, however, their peak markers were not associated with the phenotype in F2. RNA-Seq analysis revealed 2,148 differentially expressed (P<0.1) genes and 45,673 SNPs and >2,000 indels between BEH+/+ and BEL males. In conclusion, contrasting muscle traits, genomic and gene expression differences between BEH and BEL strains provide a promising model for the search of genes involved in muscle growth and musculoskeletal morphogenesis.

Thermomechanical analyses of ultrasonic welding process using thermal and acoustic softening effects

Ultrasonic welding process is a rapid manufacturing process used to weld thin layers of metal at low temperatures and low energy consumption. Experimental results have shown that ultrasonic welding is a combination of both surface (friction) and volume (plasticity) softening effects. In the presented work, a very first attempt has been made to simulate the ultrasonic welding of metals by taking into account both of these effects (surface and volume). A phenomenological material model has been proposed which incorporates these two effects (i.e. surface and volume). The thermal softening due to friction and ultrasonic (acoustic) softening has been included in the proposed material model. For surface effects a friction law with variable coefficient of friction dependent upon contact pressure, slip, temperature and number of cycles has been derived from experimental friction tests. Thermomechanical analyses of ultrasonic welding of aluminium alloy have been performed. The effects of ultrasonic welding process parameters, such as applied load, amplitude of ultrasonic vibration, and velocity of welding sonotrode on the friction work at the weld interface are being analyzed. The change in the friction work at the weld interface has been explained on the basis of softening (thermal and acoustic) of the specimen during the ultrasonic welding process. In the end, a comparison between experimental and simulated results has been presented showing a good agreement. © 2008 Elsevier Ltd. All rights reserved.

Fibre embedding in aluminium alloy 3003 using ultrasonic consolidation process-thermo-mechanical analyses

This work presents a computational framework based on finite element methods to simulate the fibre-embedding process using ultrasonic consolidation process. The computational approach comprises of a material model which takes into account thermal and acoustic softening effects and a friction model which indicates the realistic friction behaviour at the interfaces. The derived material model and developed friction model have been incorporated in finite element model. Using the implemented material and friction model, thermo-mechanical analyses of embedding of fibre in aluminium alloy 3003 has been performed. Effect of different process parameters, such as velocity of sonotrode, displacement amplitude of ultrasonic vibration and applied loads, is studied and compared with the experimental results. The presented work has specially focused on the quality of the developed weld which could be evaluated by the friction work and the coverage of the fibre which is estimated by the plastic flow around the fibre. The computed friction work obtained from the thermomechanial analyses performed in this study show a similar trend as that of the experimentally found fracture energies. © Springer-Verlag London Limited 2010.

The effect of sub-optimal control and the spectral wave climate on the performance of wave energy converter arrays

A linear hydrodynamic model is used to assess the sensitivity of the performance of a wave energy converter (WEC) array to control parameters. It is found that WEC arrays have a much smaller tolerance to imprecision of the control parameters than isolated WECs and that the increase in power capture of WEC arrays is only achieved with larger amplitudes of motion of the individual WECs. The WEC array radiation pattern is found to provide useful insight into the array hydrodynamics. The linear hydrodynamic model is used, together with the wave climate at the European Marine Energy Centre (EMEC), to assess the maximum annual average power capture of a WEC array. It is found that the maximum annual average power capture is significantly reduced compared to the maximum power capture for regular waves and that the optimum array configuration is also significantly modified. It is concluded that the optimum configuration of a WEC array will be as much influenced by factors such as mooring layout, device access and power smoothing as it is by the theoretical optimum hydrodynamic configuration. © 2009 Elsevier Ltd.

Molecular comparison of Scytalidium thermophilum isolates using RAPD and ITS nucleotide sequence analyses

Scytalidium thermophilum plays an important role in determining selectivity of compost produced for growing Agaricus bisporus. The objective of this study was to characterise S. thermophilum isolates by random amplified polymorphic DNA (RAPD) analysis and sequence analysis of internally transcribed spacer (ITS) regions of the rDNA, to assess the genetic variation exhibited by this species complex and to compare this with existing morphological and thermogravimetric data. RAPD analysis of 34 isolates from various parts of the world revealed two distinct groups, which could be separated on the basis of the differences in the banding patterns produced with five random primers. Nucleotide sequence analysis of the ITS region, which was ca 536 bp in length, revealed only very minor variation among S. thermophilum isolates examined. Several nucleotide base changes within this region demonstrated variation. Genetic distance values among type 1 and 2 S. thermophilum isolates, as determined by ITS sequence analysis, varied by a value of 0.005 %. Molecular analyses carried out in the present study would suggest that isolates within this species complex exhibit genetic differences which correlate well with morphological variation and thermogravimetric data previously determined.