Patient-specific computational haemodynamics: generation of structured and conformal hexahedral meshes from triangulated surfaces of vascular bifurcations

Measuring the blood flow is still limited by current imaging technologies and is generally overcome using computational fluid dynamics (CFD) which, because of the complex geometry of blood vessels, has widely relied on tetrahedral meshes. Hexahedral meshes offer more accurate results with lower-density meshes and faster computation as compared to tetrahedral meshes, but their use is limited by the far more complex mesh generation. We present a robust methodology for conformal and structured hexahedral mesh generation - applicable to complex arterial geometries as bifurcating vessels - starting from triangulated surfaces. Cutting planes are used to slice the lumen surface and to construct longitudinal Bezier splines. Afterwards, an isoparametric transformation is used to map a parametrically defined quadrilateral surface mesh into the vessel volume, resulting in stacks of sections which can then be used for sweeping. Being robust and open source based, this methodology may improve the current standard in patient-specific mesh generation and enhance the reliability of CFD to patient-specific haemodynamics.     

QTL Analysis of High Thermotolerance with Superior and Downgraded Parental Yeast Strains Reveals New Minor QTLs and Converges on Novel Causative Alleles Involved in RNA Processing

Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor QTLs that are relevant for the phenotypic difference between the original parents.     

Epidemiology of Noise-Induced Tinnitus and the Attitudes and Beliefs towards Noise and Hearing Protection in Adolescents

Background and objectives

Previous research showed an increase of noise-induced symptoms in adolescents. Permanent tinnitus as a consequence of loud music exposure is usually considered as noise-induced damage. The objective was to perform an epidemiological study in order to obtain prevalence data of permanent noise-induced tinnitus as well as temporary tinnitus following noise exposure in a young population. In addition the attitudes and beliefs towards noise and hearing protection were evaluated in order to explain the use/non-use of hearing protection in a young population.

Methods

A questionnaire was completed by 3892 high school students (mean age: 16.64 years old, SD: 1.29 years). The prevalence of temporary and permanent tinnitus was assessed. In addition the ‘Youth Attitudes to Noise Scale’ and the ‘Beliefs About Hearing Protection and Hearing Loss’ were used in order to assess the attitudes and beliefs towards noise and hearing protection respectively.

Results

The prevalence of temporary noise-induced tinnitus and permanent tinnitus in high school students was respectively 74.9% and 18.3%. An increasing prevalence of temporary tinnitus with age was present. Most students had a ‘neutral attitude’ towards loud music and the use of hearing protection was minimal (4.7%). The limited use of hearing protection is explained by a logistic regression analysis showing the relations between certain parameters and the use of hearing protection.

Conclusions

Despite the very high prevalence of tinnitus in such a young population, the rate of hearing protection use and the knowledge about the risks of loud music is extremely low. Future preventive campaigns should focus more on tinnitus as a warning signal for noise-induced damage and emphasize that also temporary symptoms can result in permanent noise-induced damage.     

Anatomical and functional changes in the upper airways of sleep apnea patients due to mandibular repositioning: a large scale study

The obstructive sleep apnea-hypopnea syndrome (OSAHS) is a sleep related breathing disorder. A popular treatment is the use of a mandibular repositioning appliance (MRA) which advances the mandibula during the sleep and decreases the collapsibility of the upper airway. The success rate of such a device is, however, limited and very variable within a population of patients. Previous studies using computational fluid dynamics have shown that there is a decrease in upper airway resistance in patients who improve clinically due to an MRA. In this article, correlations between patient-specific anatomical and functional parameters are studied to examine how MRA induced biomechanical changes will have an impact on the upper airway resistance. Low-dose computed tomography (CT) scans are made from 143 patients suffering from OSAHS. A baseline scan and a scan after mandibular repositioning (MR) are performed in order to study variations in parameters. It is found that MR using a simulation bite is able to induce resistance changes by changing the pharyngeal lumen. The change in minimal cross-sectional area is the best parameter to predict the change in upper airway resistance. Looking at baseline values, the ideal patients for MR induced resistance decrease seem to be women with short airways, high initial resistance and no baseline occlusion.     

Development and Validation of a Real-Time PCR for Chlamydia suis Diagnosis in Swine and Humans

Pigs are the natural host for Chlamydia suis, a pathogen which is phylogenetically highly related to the human pathogen C. trachomatis. Chlamydia suis infections are generally treated with tetracyclines. In 1998, tetracyline resistant C. suis strains emerged on U.S. pig farms and they are currently present in the Belgian, Cypriote, German, Israeli, Italian and Swiss pig industry. Infections with tetracycline resistant C. suis strains are mainly associated with severe reproductive failure leading to marked economical loss. We developed a sensitive and specific TaqMan probe-based C. suis real-time PCR for examining clinical samples of both pigs and humans. The analytical sensitivity of the real-time PCR is 10 rDNA copies/reaction without cross-amplifying DNA of other Chlamydia species. The PCR was successfully validated using conjunctival, pharyngeal and stool samples of slaughterhouse employees, as well as porcine samples from two farms with evidence of reproductive failure and one farm without clinical disease. Chlamydia suis was only detected in diseased pigs and in the eyes of humans. Positive humans had no clinical complaints. PCR results were confirmed by culture in McCoy cells. In addition, Chlamydia suis isolates were also examined by the tet(C) PCR, designed for demonstrating the tetracycline resistance gene tet(C). The tet(C) gene was only present in porcine C. suis isolates.     

Good Quality of Life in Former Buruli Ulcer Patients with Small Lesions: Long-Term Follow-up of the BURULICO Trial

Background

Buruli Ulcer is a tropical skin disease caused by Mycobacterium ulcerans, which, due to scarring and contractures can lead to stigma and functional limitations. However, recent advances in treatment, combined with increased public health efforts have the potential to significantly improve disease outcome.

Objectives

To study the Quality of Life (QoL) of former Buruli Ulcer patients who, in the context of a randomized controlled trial, reported early with small lesions (cross-sectional diameter <10 cm), and received a full course of antibiotic treatment.

Methods

127 Participants of the BURULICO drug trial in Ghana were revisited. All former patients aged 16 or older completed the Dermatology Life Quality Index (DLQI) and the abbreviated World Health Organization Quality of Life scale (WHOQOL-BREF). The WHOQOL-BREF was also administered to 82 matched healthy controls. Those younger than 16 completed the Childrens'' Dermatology Life Quality Index (CDLQI) only.

Results

The median (Inter Quartile Range) score on the DLQI was 0 (0–4), indicating good QoL. 85% of former patients indicated no effect, or only a small effect of the disease on their current life. Former patients also indicated good QoL on the physical and psychological domains of the WHOQOL-BREF, and scored significantly higher than healthy controls on these domains. There was a weak correlation between the DLQI and scar size (ρ = 0.32; p<0.001).

Conclusions

BU patients who report early with small lesions and receive 8 weeks of antimicrobial therapy have a good QoL at long-term follow-up. These findings contrast with the debilitating sequelae often reported in BU, and highlight the importance of early case detection.     

Patients lacking classical poor prognostic markers might also benefit from a step-down glucocorticoid bridging scheme in early rheumatoid arthritis: week 16 results from the randomized multicenter CareRA trial

IntroductionConsidering a lack of efficacy data in patients with early rheumatoid arthritis (eRA) presenting without classical markers of poor prognosis, we compared methotrexate (MTX) with or without step-down glucocorticoids in the CareRA trial.MethodsDisease-modifying antirheumatic drug–naïve patients with eRA were stratified into a low-risk group based on prognostic markers that included non-erosiveness, anti–citrullinated protein antibodies and rheumatoid factor negativity and low disease activity (Disease Activity Score in 28 joints based on C-reactive protein (DAS28(CRP)) ≤3.2). Patients were randomized to 15 mg of MTX weekly (MTX with tight step-up (MTX-TSU)) or 15 mg of MTX weekly with prednisone bridging, starting at 30 mg and tapered to 5 mg daily from week 6 (COmbinatie therapie bij Reumatoïde Artritis (COBRA Slim)). A TSU approach was applied. Outcomes assessed were DAS28(CRP)-determined remission, cumulative disease activity, Health Assessment Questionnaire (HAQ) scores and adverse events (AEs) after 16 treatment weeks.ResultsWe analyzed 43 COBRA Slim and 47 MTX-TSU patients and found that 65.1% in the COBRA Slim group and 46.8% in the MTX-TSU group reached remission (P = 0.081). Mean ± standard deviation area under the curve values of DAS28(CRP) were 13.84 ± 4.58 and 11.18 ± 4.25 for the MTX-TSU and COBRA Slim patients, respectively (P = 0.006). More COBRA Slim patients had an HAQ score of 0 (51.2% versus 23.4%, P = 0.006) at week 16. Therapy-related AEs between groups did not differ.ConclusionIn patients with low-risk eRA, MTX with step-down glucocorticoid bridging seems more efficacious than MTX step-up monotherapy, with a comparable number of AEs observed over the first 16 treatment weeks.

Trial registration

EU Clinical Trials Register Identifier: EudraCT number 2008-007225-39. Registered 5 November 2008.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0611-8) contains supplementary material, which is available to authorized users.     

Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification

AimCandida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples.ResultsFor 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample.DiscussionMost of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method compensate for its disadvantages.     

Urbanization drives cross‐taxon declines in abundance and diversity at multiple spatial scales

The increasing urbanization process is hypothesized to drastically alter (semi‐)natural environments with a concomitant major decline in species abundance and diversity. Yet, studies on this effect of urbanization, and the spatial scale at which it acts, are at present inconclusive due to the large heterogeneity in taxonomic groups and spatial scales at which this relationship has been investigated among studies. Comprehensive studies analysing this relationship across multiple animal groups and at multiple spatial scales are rare, hampering the assessment of how biodiversity generally responds to urbanization. We studied aquatic (cladocerans), limno‐terrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground‐ and web spiders, macro‐moths, orthopterans and snails) invertebrate groups using a hierarchical spatial design, wherein three local‐scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape‐scale (3 km × 3 km) urbanization levels. We tested for local and landscape urbanization effects on abundance and species richness of each group, whereby total richness was partitioned into the average richness of local communities and the richness due to variation among local communities. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups with respect to the richness component and the spatial scale at which urbanization impacts richness. Depending on the group, species richness declined due to biotic homogenization and/or local species loss. This resulted in an overall decrease in total richness across groups in urban areas. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanization on biodiversity.     

Comparison of the hemodynamics in 6mm and 4-7 mm hemodialysis grafts by means of CFD

The aim of our study is to investigate with computational fluid dynamics (CFD) whether different arterial anastomotic geometries result in a different hemodynamics at the arterial (AA) and venous anastomosis (VA) of hemodialysis vascular access grafts. We have studied a 6mm graft (CD) and a 4-7 mm graft (TG). A validated three-dimensional CFD model is developed to simulate flow in the two graft types. Only the arterial anastomosis (AA) geometry differs. The boundary conditions applied are a periodic velocity signal at the arterial inlet and a periodic pressure wave at the venous outlet. Flow rate is set to 1,000 ml/min. The time dependent Navier-Stokes equations are solved. Wall shear stress (WSS), wall shear stress gradient (WSSG) and pressure gradient (PG) are calculated. Anastomotic flow is asymmetric although the anastomosis geometry is symmetric. The hemodynamic parameters, WSS, WSSG and PG, values at the suture line of the arterial anastomosis of the TG are at least twice as much as in the CD. Comparing the parameters at the two AA indicate that little flow rate increase introduces the risk of hemolysis in the TG whereas the CD is completely free of hemolysis. The hemodynamic parameter values at the venous anastomosis of the CD are 24 till 35% higher compared to the values of the TG. WSS values (> 3 Pa) in the VA are in the critical range for stenosis development in both graft geometries. The zones where the parameters reach extreme values correspond to the locations where intimal hyperplasia formation is reported in literature. In all anastomoses, the hemodynamic parameter levels are in the range where leucocytes and platelets get activated. Our simulations confirm clinical results where TG did not show a better outcome when compared to the CD.