Calculating functional diversity metrics using neighbor‐joining trees

The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers. We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles. We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets. Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space

Front Immunol

HIV-2 infection is characterized by low viremia and slow disease progression as compared to HIV-1 infection. Circulating CD14++CD16+ monocytes were found to accumulate and CD11c+ conventional dendritic cells (cDC) to be depleted in a Portuguese cohort of people living with HIV-2 (PLWHIV-2), compared to blood bank healthy donors (HD). We studied more precisely classical monocytes; CD16+ inflammatory (intermediate, non-classical and slan+ monocytes, known to accumulate during viremic HIV-1 infection); cDC1, important for cross-presentation, and cDC2, both depleted during HIV-1 infection. We analyzed by flow cytometry these PBMC subsets from Paris area residents: 29 asymptomatic, untreated PLWHIV-2 from the IMMUNOVIR-2 study, part of the ANRS-CO5 HIV-2 cohort: 19 long-term non-progressors (LTNP; infection ≥8 years, undetectable viral load, stable CD4 counts≥500/μL; 17 of West-African origin -WA), and 10 non-LTNP (P; progressive infection; 9 WA); and 30 age-and sex-matched controls: 16 blood bank HD with unknown geographical origin, and 10 HD of WA origin (GeoHD). We measured plasma bacterial translocation markers by ELISA. Non-classical monocyte counts were higher in GeoHD than in HD (54 vs. 32 cells/μL, p = 0.0002). Slan+ monocyte counts were twice as high in GeoHD than in HD (WA: 28 vs. 13 cells/μL, p = 0.0002). Thus cell counts were compared only between participants of WA origin. They were similar in LTNP, P and GeoHD, indicating that there were no HIV-2 related differences. cDC counts did not show major differences between the groups. Interestingly, inflammatory monocyte counts correlated with plasma sCD14 and LBP only in PLWHIV-2, especially LTNP, and not in GeoHD. In conclusion, in LTNP PLWHIV-2, inflammatory monocyte counts correlated with LBP or sCD14 plasma levels, indicating a potential innate immune response to subclinical bacterial translocation. As GeoHD had higher inflammatory monocyte counts than HD, our data also show that specific controls are important to refine innate immunity studies

Markovian Equilibrium in Infinite Horizon Economies with Incomplete Markets and Public Policy

We develop an isotone recursive approach to the problem of existence, computation, and characterization of nonsymmetric locally Lipschitz continuous (and, therefore, Clarke-differentiable) Markovian equilibrium for a class of infinite horizon multiagent competitive equilibrium models with capital, aggregate risk, public policy, externalities, one sector production, and incomplete markets. The class of models we consider is large, and examples have been studied extensively in the applied literature in public economics, macroeconomics, and financial economics. We provide sufficient conditions that distinguish between economies with isotone Lipschitizian Markov equilibrium decision processes (MEDPs) and those that have only locally Lipschitzian (but not necessarily isotone) MEDPs. As our fixed point operators are based upon order continuous and compact non-linear operators, we are able to provide sufficient conditions under which isotone iterative fixed point constructions converge to extremal MEDPs via successive approximation. We develop a first application of a new method for computing MEDPs in a system of Euler inequalities using isotone fixed point theory even when MEDPs are not necessarily isotone. The method is a special case of a more general mixed monotone recursive approach. We show MEDPs are unique only under very restrictive conditions. Finally, we prove monotone comparison theorems in Veinott's strong set order on the space of public policy parameters and distorted production functions

Case study: Recovery.Com a psychosocial and convalescent facility

This paper is a requirement in Bus 835 - Strategic Management Class. It is a case study of RECOVERY.COM, a custodial psychiatric care facility located in Quezon City. RECOVERY.COM is a young corporation duly registered with the Securities and Exchange Commission. It is a joint venture initiated by a group of psychiatrists who were looking for a nice and decent place to bring their patients, and decided to put up one when they could not find such a place. RECOVERY.COM belongs to the nursing and residential care facilities segment of the health care industry. It specifically caters to individuals who emotionally challenged such as the mentally ill and the drug dependents/abusers. Psychiatric care facilities are relatively new in the Philippines but it is also one of the fast growing sectors of the industry. This paper looks at the competitive environment in which the RECOVERY.COM operates. It examines the external forces that affect the company including macroenvironmental factors as well as forces within industry that impact the behavior of firms in the industry. It also evaluates the company\u27s internal situation and determines its ability to compete with others in its strategic segment. The paper then proposes a strategy through which the company can renew the competitive and positionally advantage it gained in its short existence. Included are some suggestions on how to implement this strategy

Time for a rethink: time sub-sampling methods in disparity-through-time analyses

Disparity‐through‐time analyses can be used to determine how morphological diversity changes in response to mass extinctions, or to investigate the drivers of morphological change. These analyses are routinely applied to palaeobiological datasets, yet, although there is much discussion about how to best calculate disparity, there has been little consideration of how taxa should be sub‐sampled through time. Standard practice is to group taxa into discrete time bins, often based on stratigraphic periods. However, this can introduce biases when bins are of unequal size, and implicitly assumes a punctuated model of evolution. In addition, many time bins may have few or no taxa, meaning that disparity cannot be calculated for the bin and making it harder to complete downstream analyses. Here we describe a different method to complement the disparity‐through‐time tool‐kit: time‐slicing. This method uses a time‐calibrated phylogenetic tree to sample disparity‐through‐time at any fixed point in time rather than binning taxa. It uses all available data (tips, nodes and branches) to increase the power of the analyses, specifies the implied model of evolution (punctuated or gradual), and is implemented in R. We test the time‐slicing method on four example datasets and compare its performance in common disparity‐through‐time analyses. We find that the way we time sub‐sample taxa can change our interpretations of the results of disparity‐through‐time analyses. We advise using multiple methods for time sub‐sampling taxa, rather than just time binning, to gain a better understanding disparity‐through‐time.© The Palaeontological Association, 2018. The attached document is the authors’ final accepted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it

Words from the guest editors [Special issue in honor of the 60th birthday of Michel Théra]

International audienc