131,778 research outputs found
Amphibian diversity, distribution and conservation in the Ethiopian highlands : morphological, molecular and biogeographic investigation on Leptopelis and Ptychadena (Anura)
No full textLittle is known about the diversity, distribution and population status of Ethiopian amphibians in general, and most of the existing knowledge is based on field data recorded about three decades ago or earlier. There are almost no genetic data available for molecular systematics studies. Species of the Tree Frogs (Leptopelis Günther 1859) and Grassland Frogs (Ptychadena Boulenger 1917) are solely distributed in Africa (mainly sub-Saharan), with 52 and 53 known species, respectively. Six species of Leptopelis and thirteen species of Ptychadena were recorded in Ethiopia. Together these two genera comprise 30% of all known species of amphibians in Ethiopia. Many of these species (five Leptopelis and five Ptychadena) are said to be endemic to the Ethiopian Highlands that are part of the Eastern Afromontane Biodiversity Hotspot. Geographically, the Ethiopian Highlands are bisected by the Rift Valley, and further fragmented by valleys and gorges, and comprise the highest concentration of elevated ground in Africa. Earlier taxonomic studies were mainly based on morphological and ecological studies, making it difficult to identify most species in museum collections or during field work. In addition, limited sampling from the geographic areas of each species made it difficult to make good estimates of the ranges of species, and to prioritize them for conservation.
The main objectives of this study are, using Leptopelis and Ptychadena as model taxa, 1) to explore the diversity and phylogeography of some amphibians in the Ethiopian Highlands and parts of the Rift Valley; 2) to preliminarily explain the geo-climatic events that are associated with the evolutionary history of these taxa; and 3) to re-evaluate the conservation status of species and their habitats by associating phylogenetic, biogeographic and ecological information. We tested hypotheses pertaining to correspondence of traditional morphological taxonomy versus molecular phylogeny, biogeographic distinctness of distribution patterns, evolutionary history of diversification, and evaluation of conservation status of species and populations in the highlands.
The field sampling conducted between 2006 and 2010 from several localities across and within the Ethiopian Rift Valley was substantial, but not enough, to fully assess the phylogeography of the above genera. This assessment, conducted for the first time for Ethiopian Leptopelis and Ptychadena, was done using partial mitochondrial DNA sequences of the 12S and 16S genes. Estimation of phylogenetic relationships and divergence times was made using Maximum Likelihood and Maximum Parsimony methods. Morphological observations were made on fresh collections, holotypes and non-type museum materials. Biogeographic patterns were assessed using geographic distribution data. Geographic and spatial data were combined with new phylogenetic groupings to assess geographic ranges and habitat status of populations and species. We followed a new approach of ‘elevation-based’ extent of occurrence (instead of the simple polygons applied in the IUCN Red List maps) to estimate geographic ranges. Results were compared and evaluated with previous reports and online database.
Despite the wide taxonomic variation between the studied genera (Leptopelis and Ptychaena), we found similarities in some of their major taxonomic problems, as well as evolutionary, biogeographic and conservation aspects. The similarities are in: overlaps in many morphological characters (conservatism) among different species; misleading variation in some physical features within a population/species (homoplasy); monophyly of highland endemic species; cryptic phylo-groups embedded within known clades; relatively low genetic distance between species and recent evolutionary divergence times; habitat status and threats for survival of populations.
In both genera, the reconstructed phylogenetic relationships showed that the highland endemic species form well-supported monophyletic groups: the ‘Ethiopian Highland Leptopelis species group’, and the ‘Ptychadena cooperi species group’. Cryptic diversity of highland endemics was revealed, highlighting the possibility of having six candidate species (at least two Leptopelis and four Ptychadena) awaiting description. Two presumed lowland endemic species of Ptychadena (P. filwoha and P. harenna) were genetically found to be conspecific with other widely distributed (non-endemic) lowland species (P. mascareniensis and P. anchietae, respectively).
Wide overlaps in several morphological features made identification of some closely related species populations difficult. New diagnostic features were identified to characterize some of the most difficult groups (e.g., presence of spicules in males of P. neumanni contrasted with absence in P. erlangeri or P. nana).
As compared with some other African species for which molecular data are available, relatively small evolutionary distances were found among the highland species within each genus, explained by a possibly very recent radiation as estimated in the corresponding divergence times. Diversification of the highland endemics was probably associated with formation of the Ethiopian Highlands by volcanic activities and uplifting, and accompanying climatic changes between 30 and 6 Mya.
We observed congruence of phylogenetic groups with clear patterns of geographic distribution, allowing us to identify distinct biogeographic categories that can potentially serve as units for conservation of Ethiopian amphibians. The Rift Valley and major river gorges appear important horizontal barriers delimiting geographic ranges of most species. There is no considerable vertical (altitudinal) segregation of the highland populations in the two genera.
The highland Leptopelis and Ptychadena comprise more diverse endemic species (16) than known before (10), contributing substantially to the biodiversity value of the Ethiopian Highlands. While range extension is revealed for some species in the current study, there is unfortunately a substantial reduction for others from what has been proposed previously. Land cover data and our field observation of many parts of the country for about two decades indicate that large parts of the suitable highland habitats for most species of Leptopelis and Ptychadena are severely degraded and fragmented by human activities. Lakes are drying, levels of rivers are decreasing, and the wooded and grassland vegetation of the highlands and the Rift Valley is being lost. Our revised assessment of populations showed that nine of the 16 studied species appear to be threatened at different levels. This implies an urgent need for revision of existing conservation status of these taxa to protect them in rapidly changing environments. Further work is needed in the areas of phylogeography, taxonomy, and natural history of populations and species in areas that are not covered in this study
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Learning Optimal Dynamic Treatment Regime from Observational Clinical Data through Reinforcement Learning
No full textIn medicine, dynamic treatment regimes (DTRs) have emerged to guide personalized treatment decisions for patients, accounting for their unique characteristics. However, existing methods for determining optimal DTRs face limitations, often due to reliance on linear models unsuitable for complex disease analysis and a focus on outcome prediction over treatment effect estimation. To overcome these challenges, decision tree-based reinforcement learning approaches have been proposed. Our study aims to evaluate the performance and feasibility of such algorithms: tree-based reinforcement learning (T-RL), DTR-Causal Tree (DTR-CT), DTR-Causal Forest (DTR-CF), stochastic tree-based reinforcement learning (SL-RL), and Q-learning with Random Forest. Using real-world clinical data, we conducted experiments to compare algorithm performances. Evaluation metrics included the proportion of correctly assigned patients to recommended treatments and the empirical mean with standard deviation of expected counterfactual outcomes based on estimated optimal treatment strategies. This research not only highlights the potential of decision tree-based reinforcement learning for dynamic treatment regimes but also contributes to advancing personalized medicine by offering nuanced and effective treatment recommendations
Quaternary faulting and volcanism in the main Ethiopian Rift
No full textThe Main Ethiopian Rift (MER) is associated with bimodal Quaternary magmatism. Field, remote sensing, and geochronology data are used to examine the relationships between axial acidic volcanoes and basaltic eruptions. Two main Quaternary magmatic episodes are recognizeable in MER: a) basaltic flows followed by ignimbrites and silicic centers in the rift floor (2-1 Ma) and b) axial silicic volcanoes and basalts since ~650 Ka. The first episode consists mainly of basaltic flows related to the Afar Stratoid and outcrops in the central and northern MER. Scattered silicic centers developed subsequently along the rift floor. In the second episode, spatial and temporal correlation between rift localization and silicic centers becomes more evident. The silicic centers are located at the intersection of the WFB with earlier structures, especially E-W faults. With ageing, these centers become faulted and allow basalts to erupt right through the volcanic edifice, suggesting a decrease in the amount of differentiation in the magma chambers, possibly due to their cooling. This style of evolution appears to be characteristic of continental rifts prior to the onset of drifting
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Scholarly Communication and Publishing Lunch and Learn Talk #11: The ULS Open Access Author Fee Fund
No full textAt the May 2014 talk, you will learn about the ULS Open Access Author Fee Fund--what it is, why we do it, how it works, and how the program is going so far
A Study of Treatment-by-Site Interaction in Multisite Clinical Trials
No full textCurrently, there is little discussion about methods to explain treatment-by-site interaction in multisite clinical trials, so investigators are left to explain these differences post-hoc with no formal statistical tests in the literature. Using mediated moderation techniques, three significance tests used to detect mediation are extended to the multisite setting. Explicit power functions are derived and compared. In the two-site case, the mediated moderation framework is utilized to test two difference-in-coefficients and one product-of-coefficients type tests. The test in the latter group is based on the product of two independent standard normal variables, which is a modified Bessel function of the second kind. Because the alternative distribution does not have a closed form expression, power is approximated using Gauss-Hermite quadrature. This test suffers from an inflated type I error, so two modifications are proposed: a combination of intersection-union and union-intersection tests; and one based on a variance stabilizing transformation. In addition, a modification of one of the difference-in-coefficients tests is proposed. The tests are also extended to deal with multiple sites in the ANOVA and logistic regres- sion models, and the groundwork has been laid to account for multiple mediators as well. The contribution of this is a group of formal significance tests for explaining treatment- by-site interaction in the multisite clinical trial setting. This will serve to inform the design of future clinical trials by accounting for this site-level variability. The proposed methodol- ogy is illustrated in the analysis of the Treatment of SSRI-Resistant Depression in Adolescents study conducted across six sites coordinated at the University of Pittsburgh
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