Showing papers by "University of Johannesburg published in 2017"

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

Abstract: The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

A guide to phylogenetic metrics for conservation, community ecology and macroecology.

Abstract: The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.

Understanding the relationships between tourists' emotional experiences, perceived overall image, satisfaction, and intention to recommend

Abstract: The purpose of this study is to empirically test an integrative model linking tourists’ emotional experiences, perceived overall image, satisfaction, and intention to recommend. The model was tested using data collected from domestic tourists visiting Sardinia, Italy. Results show that tourists’ emotional experiences act as antecedents of perceived overall image and satisfaction evaluations. In addition, overall image has a positive influence on tourist satisfaction and intention to recommend. The study expands current theorizations by examining the merits of emotions in tourist behavior models. From a practical perspective, the study offers important implications for destination marketers.

Performance of the ATLAS trigger system in 2015

Abstract: During 2015 the ATLAS experiment recorded 3.8 fb(-1) of proton-proton collision data at a centre-of-mass energy of 13 TeV. The ATLAS trigger system is a crucial component of the experiment, respons ...

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

Abstract: The reconstruction of the signal from hadrons and jets emerging from the proton–proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

The role of nanomaterials as effective adsorbents and their applications in wastewater treatment

Abstract: Nanomaterials have been extensively studied for heavy metal ions and dye removals from wastewater. This article reviews the role of nanomaterials as effective adsorbents for wastewater purification. In recent years, numerous novel nanomaterial adsorbents have been developed for enhancing the efficiency and adsorption capacities of removing contaminants from wastewater. The innovation, forthcoming development, and challenges of cost-effective and environmentally acceptable nanomaterials for water purification are discussed and reviewed in this article. This review concludes that nanomaterials have many unique morphological and structural properties that qualify them to be used as effective adsorbents to solve several environmental problems.

The Fermi Galactic Center GeV Excess and Implications for Dark Matter

Abstract: The region around the Galactic Center (GC) is now well established to be brighter at energies of a few GeV than what is expected from conventional models of diffuse gamma-ray emission and catalogs of known gamma-ray sources. We study the GeV excess using 6.5 yr of data from the Fermi Large Area Telescope. We characterize the uncertainty of the GC excess spectrum and morphology due to uncertainties in cosmic-ray source distributions and propagation, uncertainties in the distribution of interstellar gas in the Milky Way, and uncertainties due to a potential contribution from the Fermi bubbles. We also evaluate uncertainties in the excess properties due to resolved point sources of gamma rays. The GC is of particular interest, as it would be expected to have the brightest signal from annihilation of weakly interacting massive dark matter (DM) particles. However, control regions along the Galactic plane, where a DM signal is not expected, show excesses of similar amplitude relative to the local background. Based on the magnitude of the systematic uncertainties, we conservatively report upper limits for the annihilation cross-section as a function of particle mass and annihilation channel.

Timing and tempo of the Great Oxidation Event

Abstract: The first significant buildup in atmospheric oxygen, the Great Oxidation Event (GOE), began in the early Paleoproterozoic in association with global glaciations and continued until the end of the Lomagundi carbon isotope excursion ca. 2,060 Ma. The exact timing of and relationships among these events are debated because of poor age constraints and contradictory stratigraphic correlations. Here, we show that the first Paleoproterozoic global glaciation and the onset of the GOE occurred between ca. 2,460 and 2,426 Ma, ∼100 My earlier than previously estimated, based on an age of 2,426 ± 3 Ma for Ongeluk Formation magmatism from the Kaapvaal Craton of southern Africa. This age helps define a key paleomagnetic pole that positions the Kaapvaal Craton at equatorial latitudes of 11° ± 6° at this time. Furthermore, the rise of atmospheric oxygen was not monotonic, but was instead characterized by oscillations, which together with climatic instabilities may have continued over the next ∼200 My until ≤2,250-2,240 Ma. Ongeluk Formation volcanism at ca. 2,426 Ma was part of a large igneous province (LIP) and represents a waning stage in the emplacement of several temporally discrete LIPs across a large low-latitude continental landmass. These LIPs played critical, albeit complex, roles in the rise of oxygen and in both initiating and terminating global glaciations. This series of events invites comparison with the Neoproterozoic oxygen increase and Sturtian Snowball Earth glaciation, which accompanied emplacement of LIPs across supercontinent Rodinia, also positioned at low latitude.

Majorana fermions in the Kitaev quantum spin system α-RuCl 3

Abstract: α-RuCl3 has recently attracted great interest as a possible experimental realization of the Kitaev model. Neutron scattering measurements of a single crystal of this material reveal signatures of Majorana excitations, consistent with Kitaev’s predictions. Geometrical constraints to the electronic degrees of freedom within condensed-matter systems often give rise to topological quantum states of matter such as fractional quantum Hall states, topological insulators, and Weyl semimetals1,2,3. In magnetism, theoretical studies predict an entangled magnetic quantum state with topological ordering and fractionalized spin excitations, the quantum spin liquid4. In particular, the so-called Kitaev spin model5, consisting of a network of spins on a honeycomb lattice, is predicted to host Majorana fermions as its excitations. By means of a combination of specific heat measurements and inelastic neutron scattering experiments, we demonstrate the emergence of Majorana fermions in single crystals of α-RuCl3, an experimental realization of the Kitaev spin lattice. The specific heat data unveils a two-stage release of magnetic entropy that is characteristic of localized and itinerant Majorana fermions. The neutron scattering results corroborate this picture by revealing quasielastic excitations at low energies around the Brillouin zone centre and an hour-glass-like magnetic continuum at high energies. Our results confirm the presence of Majorana fermions in the Kitaev quantum spin liquid and provide an opportunity to build a unified conceptual framework for investigating fractionalized excitations in condensed matter1,6,7,8.

Search for new high-mass phenomena in the dilepton final state using 36 fb−1 of proton-proton collision data at √s=13 TeV with the ATLAS detector

Abstract: A search is conducted for new resonant and non-resonant high-mass phenomena in dielectron and dimuon fi nal states. The search uses 36 : 1 fb(-1) of proton-proton collision data, collected at root ...

Recent advances and challenges of fuel cell based power system architectures and control – A review

Abstract: Renewable energy generation is rapidly growing in the power sector industry and widely used for two categories: grid connected and standalone system. This paper gives the insights about fuel cell operation and application of various power electronics systems. The fuel cell voltage decreases bit by bit with expansion in current because of losses associated with fuel cell. It is difficult in handling large rated fuel cell based power system without regulating mechanism. The issue connected with fuel based structural planning and the arrangements are widely investigated for all sorts of utilization. In order to improve the reliability of fuel cell based power system, the integration of energy storage system and advanced research methods are focused in this paper. The control algorithms of power architecture for the couple of well-known applications are discussed. Additionally, the paper addresses the suitable processor utilized as a part of the energy unit application on the premise of fuel cell characteristics. In this paper, the challenges to improve the dynamics of controller in fuel cell based applications are mentioned.

Analysis and synthesis of networked control systems: A survey of recent advances and challenges.

Abstract: A networked control system (NCS) is a control system which involves a communication network. In NCSs, the continuous-time measurement is usually sampled and quantized before transmission. Then, the measurement is transmitted to the remote controller via the communication channel, during which the signal may be delayed, lost or even sometimes not allowed for transmission due to the communication or energy constraints. In recent years, the modeling, analysis and synthesis of networked control systems (NCSs) have received great attention, which leads to a large number of publications. This paper attempts to present an overview of recent advances and unify them in a framework of network-induced issues such as signal sampling, data quantization, communication delay, packet dropouts, medium access constraints, channel fading and power constraint, and present respective solution approaches to each of these issues. We draw some conclusions and highlight future research directions in end.

3FHL: The Third Catalog of Hard Fermi-LAT Sources

Abstract: We present a catalog of sources detected above 10 GeV by the Fermi Large Area Telescope (LAT) in the first 7 years of data using the Pass 8 event-level analysis. This is the Third Catalog of Hard Fermi-LAT Sources (3FHL), containing 1556 objects characterized in the 10 GeV–2 TeV energy range. The sensitivity and angular resolution are improved by factors of 3 and 2 relative to the previous LAT catalog at the same energies (1FHL). The vast majority of detected sources (79%) are associated with extragalactic counterparts at other wavelengths, including 16 sources located at very high redshift (z > 2). Eight percent of the sources have Galactic counterparts and 13% are unassociated (or associated with a source of unknown nature). The high-latitude sky and the Galactic plane are observed with a flux sensitivity of 4.4 to 9.5 ×10 −11 ph cm −2 s −1 , respectively (this is approximately 0.5 % and 1 % of the Crab Nebula flux above 10 GeV). The catalog includes 214 new γ-ray sources. The substantial increase in the number of photons (more than 4 times relative to 1FHL and 10 times to 2FHL) also allows us to measure significant spectral curvature for 32 sources and find flux variability for 163 of them. Furthermore, we estimate that for the same flux limit of 10 −12 erg cm −2 s −1 , the energy range above 10 GeV has twice as many sources as above 50 GeV, highlighting the importance, for future Cherenkov telescopes, of lowering the energy threshold as much as possible.

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.

Abstract: Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens . We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

Search for new phenomena in dijet events using 37 fb-1 of pp collision data collected at √s=13 TeV with the ATLAS detector

Abstract: Dijet events are studied in the proton-proton collision dataset recorded at root s = 13 TeV with the ATLAS detector at the Large Hadron Collider in 2015 and 2016, corresponding to integrated lumino ...

The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa

Abstract: Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa. After the discovery was reported, a number of questions still remained. Not least among these questions was: how old were the fossils? The material was undated, and predictions ranged from anywhere between 2 million years old and 100,000 years old. H. naledi shared several traits with the most primitive of our ancient relatives, including its small brain. As a result, many scientists guessed that H. naledi was an old species in our family tree, and possibly one of the earliest species to evolve in the genus Homo. Now, Dirks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that the fossils are most likely between 236,000 and 335,000 years old. These dates are based on measuring the concentration of radioactive elements, and the damage caused by these elements (which accumulates over time), in three fossilized teeth, plus surrounding rock and sediments from the cave chamber. Importantly, the most crucial tests were carried out at independent laboratories around the world, and the scientists conducted the tests without knowing the results of the other laboratories. Dirks et al. took these extra steps to make sure that the results obtained were reproducible and unbiased. The estimated dates are much more recent than many had predicted, and mean that H. naledi was alive at the same time as the earliest members of our own species – which most likely evolved between 300,000 and 200,000 years ago. These new findings demonstrate why it can be unwise to try to predict the age of a fossil based only on its appearance, and emphasize the importance of dating specimens via independent tests. Finally in two related reports, Berger et al. suggest how a primitive-looking species like H. naledi survived more recently than many would have predicted, while Hawks et al. describe the discovery of more H. naledi fossils from a separate chamber in the same cave system.

Parasite responses to pollution: what we know and where we go in ‘Environmental Parasitology’

Abstract: Environmental parasitology deals with the interactions between parasites and pollutants in the environment. Their sensitivity to pollutants and environmental disturbances makes many parasite taxa useful indicators of environmental health and anthropogenic impact. Over the last 20 years, three main research directions have been shown to be highly promising and relevant, namely parasites as accumulation indicators for selected pollutants, parasites as effect indicators, and the role of parasites interacting with established bioindicators. The current paper focuses on the potential use of parasites as indicators of environmental pollution and the interactions with their hosts. By reviewing some of the most recent findings in the field of environmental parasitology, we summarize the current state of the art and try to identify promising ideas for future research directions. In detail, we address the suitability of parasites as accumulation indicators and their possible application to demonstrate biological availability of pollutants; the role of parasites as pollutant sinks; the interaction between parasites and biomarkers focusing on combined effects of parasitism and pollution on the health of their hosts; and the use of parasites as indicators of contaminants and ecosystem health. Therefore, this review highlights the application of parasites as indicators at different biological scales, from the organismal to the ecosystem.

Stability Analysis of Discrete-Time Neural Networks With Time-Varying Delay via an Extended Reciprocally Convex Matrix Inequality

Abstract: This paper is concerned with the stability analysis of discrete-time neural networks with a time-varying delay. Assessment of the effect of time delays on system stability requires suitable delay-dependent stability criteria. This paper aims to develop new stability criteria for reduction of conservatism without much increase of computational burden. An extended reciprocally convex matrix inequality is developed to replace the popular reciprocally convex combination lemma (RCCL). It has potential to reduce the conservatism of the RCCL-based criteria without introducing any extra decision variable due to its advantage of reduced estimation gap using the same decision variables. Moreover, a delay-product-type term is introduced for the first time into the Lyapunov function candidate such that a delay-variation-dependent stability criterion with the bounds of delay change rate is established. Finally, the advantages of the proposed criteria are demonstrated through two numerical examples.

Crystalline Electric-Field Randomness in the Triangular Lattice Spin-Liquid YbMgGaO4

Abstract: We apply moderate-high-energy inelastic neutron scattering (INS) measurements to investigate ${\mathrm{Yb}}^{3+}$ crystalline electric field (CEF) levels in the triangular spin-liquid candidate ${\mathrm{YbMgGaO}}_{4}$. Three CEF excitations from the ground-state Kramers doublet are centered at the energies $\ensuremath{\hbar}\ensuremath{\omega}=39$, 61, and 97 meV in agreement with the effective spin-$1/2$ $g$ factors and experimental heat capacity, but reveal sizable broadening. We argue that this broadening originates from the site mixing between ${\mathrm{Mg}}^{2+}$ and ${\mathrm{Ga}}^{3+}$ giving rise to a distribution of Yb-O distances and orientations and, thus, of CEF parameters that account for the peculiar energy profile of the CEF excitations. The CEF randomness gives rise to a distribution of the effective spin-$1/2$ $g$ factors and explains the unprecedented broadening of low-energy magnetic excitations in the fully polarized ferromagnetic phase of ${\mathrm{YbMgGaO}}_{4}$, although a distribution of magnetic couplings due to the $\mathrm{Mg}/\mathrm{Ga}$ disorder may be important as well.

The Interplay between Intuition and Rationality in Strategic Decision Making: A Paradox Perspective

Abstract: Both intuition and rationality can play important roles in strategic decision making. However, a framework that specifically accounts for the interplay between intuition and rationality is still missing. This study addresses this gap by using a paradox lens and conceptualizes the intuition–rationality duality as a paradoxical tension. We draw on seven case studies of innovation projects to empirically derive a three-step process for managing this intuition–rationality tension through paradoxical thinking. Our empirical data suggest that management of the tension starts with preparing the ground for paradoxical thinking by creating managerial acceptance for the contradictory elements of rational and intuitive approaches to decision making. The process then continues by developing decision-making outcomes through the integration of intuitive and rational practices. Finally, the outcomes of paradoxical thinking are embedded into the organizational context. For each step of the model, we indicate a set of practices that, by leveraging intuitive or rational characteristics of decision making, practitioners can use to deal with this cognitive tension in the different steps of our model.

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Abstract: In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous (‘weak’ or ‘noisy’) density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state—even from inaccurate maps—by subtracting a proportion of the confounding ‘ground state’; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches. Building a ligand into a weak region of an electron density map of a protein is a subjective process. Here, the authors present a new method to obtain a clear electron density for a bound ligand based on multi-crystal experiments and 3D background correction.

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

Abstract: MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses towards environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic - or abiotic origin.