A multidimensional perspective on microbial interactions

Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.R01 GM121950 - NIGMS NIH HHSPublished versio

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

Metabolic exchange mediates interactions among microbes, helping explain diversity in microbial communities. As these interactions often involve a fitness cost, it is unclear how stable cooperation can emerge. Here we use genome-scale metabolic models to investigate whether the release of “costless” metabolites (i.e. those that cause no fitness cost to the producer), can be a prominent driver of intermicrobial interactions. By performing over 2 million pairwise growth simulations of 24 species in a combinatorial assortment of environments, we identify a large space of metabolites that can be secreted without cost, thus generating ample cross-feeding opportunities. In addition to providing an atlas of putative interactions, we show that anoxic conditions can promote mutualisms by providing more opportunities for exchange of costless metabolites, resulting in an overrepresentation of stable ecological network motifs. These results may help identify interaction patterns in natural communities and inform the design of synthetic microbial consortia.We thank Dr. Niels Klitgord for pioneering ideas that inspired launch of this work. We are also grateful to David Bernstein, Joshua E. Goldford, Meghan Thommes, Demetrius DiMucci, and all members of the Segre Lab for helpful discussions. A.R.P. is supported by a National Academies of Sciences, Engineering, and Medicine Ford Foundation Predoctoral Fellowship and a Howard Hughes Medical Institute Gilliam Fellowship. This work was supported by funding from the Defense Advanced Research Projects Agency (purchase request no. HR0011515303, contract no. HR0011-15-C-0091), the U.S. Department of Energy (grants DE-SC0004962 and DE-SC0012627), the NIH (grants 5R01DE024468, R01GM121950, and Sub_P30DK036836_P&F), the National Science Foundation (grants 1457695 and NSFOCE-BSF 1635070), MURI Grant W911NF-12-1-0390, the Human Frontiers Science Program (grant RGP0020/2016), and the Boston University Inter-disciplinary Biomedical Research Office. (National Academies of Sciences, Engineering, and Medicine Ford Foundation Predoctoral Fellowship; Howard Hughes Medical Institute Gilliam Fellowship; HR0011515303 - Defense Advanced Research Projects Agency; HR0011-15-C-0091 - Defense Advanced Research Projects Agency; DE-SC0004962 - U.S. Department of Energy; DE-SC0012627 - U.S. Department of Energy; 5R01DE024468 - NIH; R01GM121950 - NIH; Sub_P30DK036836_PF - NIH; 1457695 - National Science Foundation; NSFOCE-BSF 1635070 - National Science Foundation; W911NF-12-1-0390 - MURI Grant; RGP0020/2016 - Human Frontiers Science Program; Boston University Inter-disciplinary Biomedical Research Office)Published versio

The Effect of the Number of Lending Banks on the Liquidity Constraints of Firms: Evidence From a Quasi-Experiment

We empirically explore whether firms have a target for the number of banks from which they borrow, and whether having multiple bank relationships has an impact on firms’ liquidity situation. A bank merger in Chile provides a quasi-experiment as it constitutes an exogenous reduction in the number of lenders for firms that were previously borrowing from both merging banks. We find that a significant percentage of firms whose number of bank relationships was reduced by the merger regain their original number of lenders. In particular, firms whose number of bank lending relationships was reduced from two to one as a result of the merger have a 23% higher probability of adding a new bank lending relationship in the five years following the merger than similar firms unaffected by the merger. Overall, we find that a reduction in firms’ number of bank lenders resulting from the merger reduced firms’ access to credit. In particular, a reduction from two to one bank lending relationships generated, on average, a 14.4% decrease in loan size for the affected companies compared to firms unaffected by the merger.

The impact of cheating on IRT equating under the non-equivalent anchor test design

The prevalence of high stakes test scores as a basis for significant decisions necessitates the dissemination of accurate and fair scores. However, the magnitude of these decisions has created an environment prone to examinees resorting to cheating. To reduce the risk of cheating, multiple test forms are commonly administered. When multiple forms are employed, the forms must be equated to account for potential differences in form difficulty. If cheating occurs on one of the forms, the equating procedure may produce inaccurate results. A simulation study was conducted to examine the impact of cheating on IRT true score equating. Recovery of equated scores and scaling constants were assessed for five IRT scaling methods under various conditions. Results indicated that cheating artificially increased the equated scores of the entire examinee group administered the compromised form and no scaling methods adequately mitigated this effect. Future research should focus on the identification and removal of compromised items

Analysis and modelling of the solar energetic particle radiation environment in the inner heliosphere in preparation for Solar Orbiter

[eng] The Sun is the main source of all kind of solar energetic particles in the Solar System, electrons, protons and ions with energies from few keV to several GeV. These particles are released from the solar corona and spread through the interplanetary space, the heliosphere, influenced by the interplanetary magnetic field and arriving to the Earth and interacting with the terrestrial magnetosphere. The effects of SEP interactions with space-based devices, manned missions and the Earth atmosphere are encompassed by what is known as space weather. This thesis describes the work we performed on this field, that can be divided in three parts: i) observational studies of solar energetic particles carried out using data coming from space-based missions such as STEREO and Helios, as well as tools like SEPEM server; ii) the development of tools and particle instrument modelling in order to use of them with pre-existing models to be used in the simulation of solar events; iii) solar energetic particle event simulations making use of transport models, either adapting tools previously developed by our group, as SEPInversion, or creating new software capable of carrying out full inversions of events, that is, taking into account the angular response and the energetic response of the particle instrument. These tools developed during this work have allow us to study and characterise the radiation conditions in the inner heliosphere applying modelling techniques never used done before. We also explore some of the applications of these tools. We developed a study about the radial dependence of electron peak intensities and anisotropy, we simulate observations of EPD/EPT instrument on board Solar Orbiter using Helios data and finally we studied the expected cumulated fluence and the fluence spectra computed using SEPEM for Solar Orbiter mission. In conclusion, the obtained results as well as the developed tools will be very useful for the study and interpretation of the future scientific data coming from Parker Solar Probe, Solar Orbiter and BepiColombo.[cat] El Sol és la principal font de partícules que podem trobar al medi interplanetari del sistema solar, i els esdeveniments solars de partícules energètiques són la principal font de radiació dins de l'heliosfera. L'estudi i predicció d'aquest tipus d'esdeveniments i les seves causes i conseqüències ha esdevingut una àrea d'especial interès per la seva importància enfront dels perills que suposa aquesta radiació per a les telecomunicacions i la salut durant missions espacials tripulades. En aquesta tesi exposem el treball que hem desenvolupat en aquest camp, dividit en 3 àmbits diferents: i) estudi observacional d'esdeveniments de partícules fent servir dades observacionals de missions espacials com STEREO i Helios, i eines com SEPEM; ii) desenvolupament d'eines i modalització d'instruments de partícules per fer-los servir conjuntament amb els models preexistents per la simulació d'esdeveniments; iii) simulació d'esdeveniments de partícules mitjançant models de transport, tant adaptant eines prèviament desenvolupades pel nostre grup, com SEPInversion, com nou programari capaç de realitzar inversions totals, es a dir, tenint en compte la resposta angular i energètica dels instruments. Les eines desenvolupades ens han permès estudiar les condicions de radiació a l'heliosfera interior com no s'havia fet fins ara. Els resultats obtinguts així com aquestes eines seran molt útils per a l'estudi i interpretació de les dades científiques provinents de les futures missions espacials com Parker Solar Probe o Solar Orbiter. A més a més, les eines desenvolupades ens permetran fer un ús efectiu d'aquestes dades tan aviat com estiguin disponibles

Comparison of Chronic Depression Inventory Scores of Children Diagnosed with Chronic Renal Disease at Two Points in duration of their illness

Hypothesis: Children with a diagnosis of chronic renal disease (CRD) for longer than 2.5 years will have higher T-scores of the Childrens Depression Inventory (CDI) as compared to children with CRD who have been diagnosed with less than 2.5 years ago. Background: Current estimates are that 7.4 million Americans suffer from chronic renal disease. The annual incidence of pediatric kidney disease is 15 per million, ages 0-19. CRD is a serious and progressive disease affecting many different aspects of a childs life. Studies to date have examined the correlation between depression and chronic kidney disease in adults. One study noted 40% of adults with kidney disease also suffered some type of depressive disorder. Research involving children has been very minimal. There is not much research to see if a child has depressive symptoms or if they get better or worse over the duration of their illness. Pervious studies have shown children with chronic medical problems tend to be at higher risk of suffering from depression. Methods: This project will use pediatric patients who are receiving treatment at the University of New Mexico pediatric nephrology clinic. These patients are part of a larger study involving children with CRD and comparing them to the general pediatric population. Thirty-two children between the ages of seven and seventeen, who are currently being treated for a chronic renal disease, will be identified using certain established eligibility requirements. Each patient will be given a CDI, which is standardized survey that assesses depression in children aged seven to seventeen. Each survey will generate a T-score. A T-score above 65 indicates the child may be experiencing some depressive symptoms. The results will then be categorized into two groups. Those that have had a diagnosis of CRD less than 2.5 years in one and those greater than 2.5 years in another. The mean score for these two groups will then be analyzed using a Two-sample t-test. Expected results: It is expected that children who have had a diagnosis of CRD greater than 2.5 years will show more depressive symptoms, based on CDI survey results. Conclusion: This study provides some more information on children and CRD. The results show that children diagnosed with CRD less than 2.5 years did have higher overall T-scores. Being a small study it is difficult to make any major conclusions, however it did appear to show a trend that children in the earlier stages of kidney disease maybe at risk for depressive symptoms.\u2

Production of vanillin from lignin present in the kraft black liquor of the pulp and paper industry

Tese de doutoramento. Engenharia Química. Faculdade de Engenharia. Universidade do Porto. 200