De zakelijke overheid: publieke en bedrijfsmatige waarden in publiek-private samenwerking

Bedrijfsmatig werken bij de overheid is steeds meer in opmars. Tal van werkwijzen en technieken uit het bedrijfsleven worden overgenomen en ingevoerd. Volgens Jane Jacobs is er echter sprake van twee fundamenteel onverenigbare ethische stelsels. Het commerciële ethos omvat alle normen en waarden uit het bedrijfsleven. Winst en de superioriteit van het marktmechanisme staan hierin centraal. Het martiale ethos omvat alle normen en waarden die betrekking hebben op de taken van de overheid. Zou de overheid bedrijfsmatig kunnen zijn of worden? Volgens Jacobs zijn beide stelsels moeilijk tot niet te verenigen. Een bedrijfsmatige overheid brengt altijd het risico van een waardeconflict met zich mee. Hoe zakelijk kan de overheid dan wel opereren? Wij onderzochten dat bij een aantal projecten waar overheden en bedrijven samen verantwoordelijk waren voor een bouwproject of infrastructurele voorziening (PPS). Aan de hand van onze omschrijving van de zakelijke overheid zijn aan een aantal experts vragen voorgelegd met betrekking tot enkele concrete samenwerkingsverbanden. Op basis van de bevindingen kunnen we concluderen dat de overheid zich binnen de grenzen van het martiale ethos redelijk zakelijk gedraagt. Er zou wel meer aandacht moeten worden besteed aan de efficiëntie van projecten alsmede aan de selectieprocedures van de marktpartijen

Do universal codon-usage patterns minimize the effects of mutation and translation error?

BACKGROUND: Do species use codons that reduce the impact of errors in translation or replication? The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon. However, the extent to which organisms optimize the genetic messages written in this code has been far less studied. We tested whether codon and amino-acid usages from 457 bacteria, 264 eukaryotes, and 33 archaea minimize errors compared to random usages, and whether changes in genome G+C content influence these error values. RESULTS: We tested the hypotheses that organisms choose their codon usage to minimize errors, and that the large observed variation in G+C content in coding sequences, but the low variation in G+U or G+A content, is due to differences in the effects of variation along these axes on the error value. Surprisingly, the biological distribution of error values has far lower variance than randomized error values, but error values of actual codon and amino-acid usages are actually greater than would be expected by chance. CONCLUSION: These unexpected findings suggest that selection against translation error has not produced codon or amino-acid usages that minimize the effects of errors, and that even messages with very different nucleotide compositions somehow maintain a relatively constant error value. They raise the question: why do all known organisms use highly error-minimizing genetic codes, but fail to minimize the errors in the mRNA messages they encode

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids

Although functional RNA molecules are known to be biased in overall composition, the effects of background composition on the probability of finding a particular active site by chance has received little attention. The probability of finding a particular motif has important implications both for understanding the distribution of functional RNAs in ancient and modern organisms with varying genome compositions and for tuning SELEX pools to optimize the chance of finding specific functions. Here we develop a new method for calculating the probability of finding a modular motif containing base-paired regions, and use a computational grid to fold several hundred million random RNA sequences containing the core elements of the isoleucine aptamer and the hammerhead ribozyme to estimate the probability that a sequence containing these structural elements will fold correctly when isolated from background sequences of different compositions. We find that the two motifs are most likely to be found in distinct regions of compositional space, and that the regions of greatest abundance are influenced by the probability of finding the conserved bases, finding the flanking helices, and folding, in that order of importance. Additionally, we can refine our estimates of the number of random sequences required for a 50% probability of finding an example of each site in unbiased random pools of length 100 to 4.1 × 10(9) for the isoleucine aptamer and 1.6 × 10(10) for the hammerhead ribozyme. These figures are consistent with the facile recovery of these motifs from SELEX experiments

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

<p>Abstract</p> <p>Background</p> <p>Identifying coevolving positions in protein sequences has myriad applications, ranging from understanding and predicting the structure of single molecules to generating proteome-wide predictions of interactions. Algorithms for detecting coevolving positions can be classified into two categories: tree-aware, which incorporate knowledge of phylogeny, and tree-ignorant, which do not. Tree-ignorant methods are frequently orders of magnitude faster, but are widely held to be insufficiently accurate because of a confounding of shared ancestry with coevolution. We conjectured that by using a null distribution that appropriately controls for the shared-ancestry signal, tree-ignorant methods would exhibit equivalent statistical power to tree-aware methods. Using a novel t-test transformation of coevolution metrics, we systematically compared four tree-aware and five tree-ignorant coevolution algorithms, applying them to myoglobin and myosin. We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance.</p> <p>Results</p> <p>Consistent with our conjecture, the transformed tree-ignorant metrics (particularly Mutual Information) often outperformed the tree-aware metrics. Our examination of the effect of recoding suggested that charge-based alphabets were generally superior for identifying the stabilizing interactions in alpha helices. Performance was not always improved by recoding however, indicating that the choice of alphabet is critical.</p> <p>Conclusion</p> <p>The results suggest that t-test transformation of tree-ignorant metrics can be sufficient to control for patterns arising from shared ancestry.</p

Force transmissibility and vibration power flow behaviour of inerter-based vibration isolators

This paper investigates the dynamics and performance of inerter-based vibration isolators. Force / displacement transmissibility and vibration power flow are obtained to evaluate the isolation performance. Both force and motion excitations are considered. It is demonstrated that the use of inerters can enhance vibration isolation performance by enlarging the frequency band of effective vibration isolation. It is found that adding inerters can introduce anti-resonances in the frequency-response curves and in the curves of the force and displacement transmissibility such that vibration transmission can be suppressed at interested excitation frequencies. It is found that the introduction of inerters enhances inertial coupling and thus have a large influence on the dynamic behaviour at high frequencies. It is shown that force and displacement transmissibility increases with the excitation frequency and tends to an asymptotic value as the excitation frequency increases. In the high-frequency range, it was shown that adding inerters can result in a lower level of input power. These findings provide a better understanding of the effects of introducing inerters to vibration isolation and demonstrate the performance benefits of inerter-based vibration isolators

Rainfall, geology and landscape position generate large-scale spatiotemporal fire pattern heterogeneity in an African savanna

Fire is considered a critical management tool in fire prone landscapes. Often studies and policies relating to fire focus on why and how the fire regime should be managed, often neglecting to subsequently evaluate management’s ability to achieve these objectives over long temporal and large spatial scales. This study explores to what extent the long-term spatio-temporal fire patterns recorded in the Kruger National Park, South Africa has been influenced by management policies and to what extent it was dictated by underlying variability in the abiotic template. This was done using a spatially explicit fire-scar database from 1941 to 2006 across the 2 million hectare Park. Fire extent (hectares burnt per annum) (i) is correlated with rainfall cycles (ii) exhibits no long-term trend and (iii) is largely non-responsive to prevailing fire management policies. Rainfall, geology and distance from the closest perennial river and the interactions between these variables influence large-scale fire pattern heterogeneity: areas with higher rainfall, on basaltic substrates and far from rivers are more fire prone and have less heterogeneous fire regimes than areas with lower rainfall, on granitic substrates and closer to rivers. This study is the first to illustrate that under a range of rainfall and geological conditions, perennial rivers influence long-term, landscape-scale fire patterns well beyond the riparian zone (typically up to 15 km from the river). It was concluded that despite fire management policies which historically aimed for largely homogeneous fire return regimes, spatially and temporally heterogeneous patterns have emerged. This is primarily because of differences in rainfall, geology and distance from perennial rivers. We postulate that large-scale spatio-temporal fire pattern heterogeneity is implicit to heterogeneous savannas, even under largely homogenizing fire policies. Management should be informed by these patterns, embracing the natural heterogeneity-producing template. We therefore suggest that management actions will be better directed when operating at appropriate scales, nested within the broader implicit landscape patterns, and when focusing on fire regime parameters over which they have more influence (e.g. fire season).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1600-0587hb201

Enhancing faba bean (Vicia faba L.) genome resources

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13Gb) genome. In order to address this challenge, RNA-seq analysis was performed on faba bean (cv Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16,300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10 % could be aligned to known repetitive genetic elements. Over 26,000 of the reference transcriptome unigenes could be aligned to DNA-seq reads with high confidence. Moreover, this comparison identified 56,668 potential splice points in all identified unigenes. Sequence length data was extended at 461 putative loci through alignment of DNA-seq contigs to full length, publically available linkage marker sequences. Reads also yielded coverages of 3466x and 650x for the chloroplast and mitochondrial genomes respectively. Inter- and intra-species organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes

Evaluating the electronic tuberculosis register surveillance system in Eden District, Western Cape, South Africa, 2015

BACKGROUND : Tuberculosis (TB) surveillance data are crucial to the effectiveness of National TB Control Programs. In South Africa, few surveillance system evaluations have been undertaken to provide a rigorous assessment of the platform from which the national and district health systems draws data to inform programs and policies. OBJEVTICE : Evaluate the attributes of Eden District’s TB surveillance system, Western Cape Province, South Africa. METHODS : Data quality, sensitivity and positive predictive value were assessed using secondary data from 40,033 TB cases entered in Eden District’s ETR.Net from 2007 to 2013, and 79 purposively selected TB Blue Cards (TBCs), a medical patient file and source document for data entered into ETR.Net. Simplicity, flexibility, acceptability, stability and usefulness of the ETR.Net were assessed qualitatively through interviews with TB nurses, information health officers, sub-district and district coordinators involved in the TB surveillance. RESULTS : TB surveillance system stakeholders report that Eden District’s ETR.Net system was simple, acceptable, flexible and stable, and achieves its objective of informing TB control program, policies and activities. Data were less complete in the ETR.Net (66–100%) than in the TBCs (76–100%), and concordant for most variables except pre-treatment smear results, antiretroviral therapy (ART) and treatment outcome. The sensitivity of recorded variables in ETR.Net was 98% for gender, 97% for patient category, 93% for ART, 92% for treatment outcome and 90% for pre-treatment smear grading. CONCLUSIONS : Our results reveal that the system provides useful information to guide TB control program activities in Eden District. However, urgent attention is needed to address gaps in clinical recording on the TBC and data capturing into the ETR.Net system. We recommend continuous training and support of TB personnel involved with TB care, management and surveillance on TB data recording into the TBCs and ETR.Net as well as the implementation of a well-structured quality control and assurance system.PEPFAR award and Foundation for Professional Development.http://www.tandfonline.com/loi/zgha20am2017School of Health Systems and Public Health (SHSPH

Genome sequence of Madurella mycetomatis mm55, isolated from a human mycetoma case in Sudan

We present the first genome sequence for a strain of the main mycetoma causative agent, Madurella mycetomatis. This 36.7-Mb genome sequence will offer new insights into the pathogenesis of mycetoma, and it will contribute to the development of better therapies for this neglected tropical disease

The challenges of transdisciplinary knowledge production: from unilocal to comparative research

This reflective paper surveys the lessons learnt and challenges faced by the Mistra Urban Futures (MUF) research centre and its research platforms in Sweden, the UK, South Africa and Kenya in developing and deploying different forms of transdisciplinary co-production of knowledge. Considerable experience with a distinctive portfolio of such methods has been gained and reflective evaluation is now under way. While it is important to understand the local context within which each method has evolved, we seek to explain the potential for adaptation in diverse contexts so that such knowledge co-production methods can be more widely utilized. Furthermore, the current phase of MUF’s work is undertaking innovative comparative transdisciplinary co-production research across its research platforms. Since the specific local projects differ, systematic thematic comparison requires great care and methodological rigour. Transdisciplinary co-production is inherently complex, time consuming and often unpredictable in terms of outcomes, and these challenges are intensified when it is undertaken comparatively