Mapping plant diversity in cocoa-based agroforestry systems to improve overall productivity

In cocoa-based agroforestry systems (CAFS), the cocoa trees are associated with other cultivated plant species at variable densities. There, the spatial distribution of the cultivated plants can be regular, random or aggregated, and their age may vary even in the same species. Variables of (i) density, (ii) spatial distribution and (iii) age can thus influence the overall productivity of CAFS and its distribution in space. We studied the relationships between these 3 variables and CAFS productivity based on data collected in 34 experimental yield tracking plots placed in agroforestry fields of producers in the Dominican Republic. A mapping of the cultivated plants was carried out on each plot at their installation and harvests of the ripe products of each individual plant were carried out every two weeks over a period of one year. The first results of this study indicate that optimal CAFS productivity can be maintained along a decreasing density gradient of crops, associated with cocoa tree ageing. In addition, regular and random spatial distribution of all plant species may increase overall productivity. The analysis of the variability of cocoa, fruit, tuber and timber yields allows us to provide recommendations on the most suitable species and the optimal distance between plants to improve overall productivity and therefore the producer's income

An 111In-labelled bis-ruthenium(ii) dipyridophenazine theranostic complex: mismatch DNA binding and selective radiotoxicity towards MMR-deficient cancer cells

Theranostic radionuclides that emit Auger electrons (AE) can generate highly localised DNA damage and the accompanying gamma ray emission can be used for single-photon emission computed tomography (SPECT) imaging. Mismatched DNA base pairs (mismatches) are DNA lesions that are abundant in cells deficient in MMR (mismatch mediated repair) proteins. This form of genetic instability is prevalent in the MMR-deficient subset of colorectal cancers and is a potential target for AE radiotherapeutics. Herein we report the synthesis of a mismatch DNA binding bis-ruthenium(II) dipyridophenazine (dppz) complex that can be radiolabelled with the Auger electron emitting radionuclide indium-111 (111In). Greater stabilisation accompanied by enhanced MLCT (metal to ligand charge-transfer) luminescence of both the bis-Ru(dppz) chelator and non-radioactive indium-loaded complex was observed in the presence of a TT mismatch-containing duplex compared to matched DNA. The radioactive construct [111In]In-bisRu(dppz) ([111In][In-2]4+) targets cell nuclei and is radiotoxic towards MMR-deficient human colorectal cancer cells showing substantially less detrimental effects in a paired cell line with restored MMR function. Additional cell line studies revealed that [111In][In-2]4+ is preferentially radiotoxic towards MMR-deficient colorectal cancer cells accompanied by increased DNA damage due to 111In decay. The biodistribution of [111In][In-2]4+ in live mice was demonstrated using SPECT. These results illustrate how a Ru(II) polypyridyl complex can incorporate mismatch DNA binding and radiometal chelation in a single molecule, generating a DNA-targeting AE radiopharmaceutical that displays selective radiotoxicity towards MMR-deficient cancer cells and is compatible with whole organism SPECT imaging

Resilience, apps and reluctant individualism: Technologies of self in the neoliberal academy

This paper is concerned with the deep crisis affecting universities, as large scale institutional and structural transformations produce a psychosocial and somatic catastrophe amongst academics (and other university workers) that manifests in experiences of chronic stress, anxiety, exhaustion, insomnia and spiralling rates of physical and mental illness. Elsewhere these have been discussed as the 'hidden injuries of the neoliberal university' (Gill, 2010), highlighting the ways in which such experiences are simultaneously acknowledged and recognised by university staff, yet silenced and exorcised from formal spaces of the contemporary academy and without 'proper channels' of expression - being the subject of conference coffee breaks but not keynotes, of after seminar drinks but not departmental meetings, committee minutes or Senate or Council documentation. For future historians seeking to understand through such official records something about the texture of experience of current academic life, the archives will offer no insights.However, in the last few years, this paper suggests, such injuries have moved from being almost completely silenced within universities to becoming the subject of a variety of new spaces and services designed with 'academics in crisis' at their heart. These include the rolling out of 'well-being' services within universities of programmes for stress management, mindfulness and resilience, the development of new 'apps' designed for busy or overworked people, and the rapidly expanding blogosphere which has become a key site for 'naming' and sharing such experiences of distress/injury. The paper looks critically at these three sites. It argues that whilst they recognise at least some aspects of the subjective experience of contemporary academic labouring, they remain locked into a profoundly individualist framework that turns away from systemic or collective politics to offer instead a set of individualised tools by which to 'cope' with the strains of the neoliberal academy

Musical Ratios in Sounds from the Human Cochlea

The physiological roots of music perception are a matter of long-lasting debate. Recently light on this problem has been shed by the study of otoacoustic emissions (OAEs), which are weak sounds generated by the inner ear following acoustic stimulation and, sometimes, even spontaneously. In the present study, a high-resolution time–frequency method called matching pursuit was applied to the OAEs recorded from the ears of 45 normal volunteers so that the component frequencies, amplitudes, latencies, and time-spans could be accurately determined. The method allowed us to find that, for each ear, the OAEs consisted of characteristic frequency patterns that we call resonant modes. Here we demonstrate that, on average, the frequency ratios of the resonant modes from all the cochleas studied possessed small integer ratios. The ratios are the same as those found by Pythagoras as being most musically pleasant and which form the basis of the Just tuning system. The statistical significance of the results was verified against a random distribution of ratios. As an explanatory model, there are attractive features in a recent theory that represents the cochlea as a surface acoustic wave resonator; in this situation the spacing between the rows of hearing receptors can create resonant cavities of defined lengths. By adjusting the geometry and the lengths of the resonant cavities, it is possible to generate the preferred frequency ratios we have found here. We conclude that musical perception might be related to specific geometrical and physiological properties of the cochlea

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole genome mutation screening in Candida albicans and aeruginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p