Extreme Diversity Research Articles

A multi-parametric analysis of Trypanosoma cruzi infection: common pathophysiologic patterns beyond extreme heterogeneity of host responses

The extreme genetic diversity of the protozoan Trypanosoma cruzi has been proposed to be associated with the clinical outcomes of the disease it provokes: Chagas disease (CD). To address this question, we analysed the similarities and differences in the CD pathophysiogenesis caused by different parasite strains. Using syngeneic mice infected acutely or chronically with 6 distant parasite strains, we integrated simultaneously 66 parameters: parasite tropism (7 parameters), organ and immune responses (local and systemic; 57 parameters), and clinical presentations of CD (2 parameters). While the parasite genetic background consistently impacts most of these parameters, they remain highly variable, as observed in patients, impeding reliable one-dimensional association with phases, strains, and damage. However, multi-dimensional statistics overcame this extreme intra-group variability for each individual parameter and revealed some pathophysiological patterns that accurately allow defining (i) the infection phase, (ii) the infecting parasite strains, and (iii) organ damage type and intensity. Our results demonstrated a greater variability of clinical outcomes and host responses to T. cruzi infection than previously thought, while our multi-parametric analysis defined common pathophysiological patterns linked to clinical outcome of CD, conserved among the genetically diverse infecting strains.

An integrated information lifecycle management framework for exploiting social network data to identify dynamic large crowd concentration events in smart cities applications

With the current availability of an extreme diversity of data sources and services, emerging from the Internet of Things and Cloud domains, the challenge is shifted towards identifying intelligent, abstracted and adaptive ways of correlating and combining the various levels of information. The purpose of this work is to demonstrate such a combination, on one hand at the service level, through integrating smart cities platforms for user level data, and on the other hand at Complex Event Processing, Storage and Analytics capabilities together with Twitter data. The final goal is to identify events of interest to the user such as Large Crowd Concentration (LCC) in a given area, in order to enrich application level information with related event identification that can enable more sophisticated actions on behalf of that user. The identification is based on observation of Twitter activity peaks compared to historical data on a dynamic time and location of interest. The approach is validated through a two-month experiment in the city of Madrid, identifying LCCs in sporting events around two sports venues and analyzing various approaches with relation to the needed thresholds definition.

Allelopathy prevents competitive exclusion and promotes phytoplankton biodiversity

It has been hypothesized that allelopathy can prevent competitive exclusion and promote phytoplankton diversity in aquatic ecosystems, where numerous species coexist on a limited number of resources. However, experimental proof‐of‐principle is not available to support this hypothesis. Here we present the first experimental evidence to support this hypothesis by demonstrating that allelopathy promotes the coexistence of two phytoplankton species, Ankistrodesmus falcatus and Oscillatoria sp., that compete for a single limiting nutrient. By performing long‐term competition experiments in nitrate‐limited continuous cultures, and by describing the population dynamics using a mechanistic model, we demonstrate that when allelopathy comes into play, one of the following outcomes is possible depending on the relative initial abundances of the species: dominance of the stronger competitor for nitrate (the non‐allelopathic species), oscillatory coexistence, or dominance of the weaker competitor (the allelopathic species). Our model analysis revealed that sustained oscillatory coexistence of the two species would be a common outcome of this experiment. Our study confirms for the first time, based on laboratory experiments combined with mechanistic models, that allelopathy can alter the predicted outcome of inter‐specific competition in a nutrient‐limited environment and increase the potential for the coexistence of more species than resources, thereby contributing to the identification of endogenous mechanisms that explain the extreme diversity of phytoplankton communities.

Overview of methodologies for T-cell receptor repertoire analysis

BackgroundThe T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire.ResultsHere, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis.Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared.ConclusionsSeveral valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods.

On the ill-defined notion of the Milankovitch Theory and its influence on the development of the orbital theory of the paleoclimate

The unique situation around the best-known and universally recognized version of the orbital theory of the paleoclimate (OTP), the Milankovitch theory, is analyzed. The problem lies in the extreme diversity in how the essence of this theory is understood both by various authors and by the same scholars in different periods of their activity. The most impressive fact is that five authors, laureates of the Milutin Milankovitch Medal, are not only at variance in the understanding of its essence but also raise substantial objections relative to a number of its principal theses or even cast doubts on the verity of the paleoclimatic part of the theory, which nevertheless is declared practically universally as the basis of the OTP. This situation hinders the development of a correct, mathematically strict OTP of the Pleistocene, the creation of which will promote a better understanding of the mechanism of the Earth’s “climatic machine” and, consequently, more reliable forecasts of anthropogenic forcing on the natural environment.

Analysis of amino acids using serially coupled columns.

Single conventional columns in reversed-phase liquid chromatography are insufficient for analysing the isoindoles of primary amino acids due to their limited functionality. An interesting possibility for increasing the separation power is the combination of several columns of different nature, where the length is modified by coupling small segments. This approach may require a considerable investment to have multiple lengths for each stationary phase. However, the combination of only two columns of fixed length can be enough to resolve satisfactorily relatively complex mixtures, provided that an optimised gradient program is applied. In this work, a mixture of 19 primary amino acid isoindoles found in proteins was analysed. Four stationary phases were assayed: C18, pentafluorophenyl-C18, C4 and cyano. The mixture of isoindoles was successfully resolved in practical times using a pentafluorophenyl-C18 column coupled to a C4 column, in spite of the extremely poor performance obtained when each column is used isolatedly, independently of the length. The extreme diversity in the polarities of the isoindoles and the need of extrapolating the retention behaviour in certain regions of the solvent content domain makes the modelling of the retention behaviour of the isoindoles particularly difficult. Nevertheless, the predicted optimal separations were very satisfactory.

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths.

The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.

Income distribution, quality differentiation and product line design

The purpose of this paper is to characterize the relationship between quality differentiation, income distribution and product line design. According to the findings, the author can explain the trend of quality differentiation and the phenomenon of extreme product diversity in different conditions of income distribution. When the middle class of consumers reach a certain critical few number, the quality for them will descend. Only the high-end and low-end quality left for this extreme condition; that is, the product quality spectrum will shrink. The product quality for middle and low class will gradually get worse and worse, even lower than original quality. The product line design will be reconsidered to the opposite extremes.

When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations.

For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human‐mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well‐studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution‐adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.

A relevant and robust vacuum-drying model applied to hardwoods

A robust mathematical model was developed to simulate the heat and mass transfer process that evolves during vacuum-drying of four commercially important Australian native hardwood species. The hardwood species investigated were spotted gum (Corymbia citriodora), blackbutt (Eucalyptus pilularis), jarrah (Eucalyptus marginata), and messmate (Eucalyptus obliqua). These species provide a good test for the model based on their extreme diversity between wood properties and drying characteristics. The model uses boundary condition data from a series of vacuum-drying trials, which were also used to validate predictions. By using measured diffusion coefficient values to calibrate empirical formula, the accuracy of the model was greatly improved. Results of a sensitivity analysis showed that the model outputs provide excellent agreement with experimental observation despite the large range of species behaviour and variation in wood properties. This study confirms that the drying rate is significantly improved as a direct result of the enhanced convective and diffusive transfer along the board thickness. Contrary to softwood, it appears that longitudinal migration provides only a secondary effect. Not only is the model able to predict the heat and mass transfer behaviour of a range of hardwood species, it is also flexible enough to predict the behaviour for both conventional and vacuum-drying scenarios. The outcomes of this work provide the hardwood industry with a well-calibrated predictive drying tool that can be used to optimise drying schedules.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.

Clinical genomic profiling to identify actionable alterations for investigational therapies in patients with diverse sarcomas.

BackgroundThere are currently no United States Food and Drug Administration approved molecularly matched therapies for sarcomas except gastrointestinal stromal tumors. Complicating this is the extreme diversity, heterogeneity, and rarity of these neoplasms. Few therapeutic options exist for relapsed and refractory sarcomas. In clinical practice many oncologists refer patients for genomic profiling hoping for guidance on treatment options after standard therapy. However, a systematic analysis of actionable mutations has yet to be completed. We analyzed genomic profiling results in patients referred to MD Anderson Cancer Center with advanced sarcomas to elucidate the frequency of potentially actionable genomic alterations in this population.MethodsWe reviewed charts of patients with advanced sarcoma who were referred to investigational cancer therapeutics department and had CLIA certified comprehensive genomic profiling (CGP) of 236 or 315 cancer genes in at least 50ng of DNA. Actionable alterations were defined as those identifying anti-cancer drugs on the market, in registered clinical trials, or in the Drug-Gene Interaction Database.ResultsAmong the 102 patients analyzed median age was 45.5 years (range 8-76), M: F ratio 48:54. The most common subtypes seen in our study were leiomyosarcoma (18.6%), dedifferentiated liposarcoma (11%), osteosarcoma (11%), well-differentiated liposarcoma (7%), carcinosarcoma (6%), and rhabdomyosarcoma (6%). Ninety-five out of 102 patients (93%) had at least one genomic alteration identified with a mean of six mutations per patient. Of the 95 biopsy samples with identifiable genomic alterations, the most commonly affected genes were TP53 (31.4%), CDK4 (23.5%), MDM2 (21.6%), RB1 (18.6%), and CDKN2A/B (13.7%). Notable co-segregating amplifications included MDM2-CDK4 and FRS2-FGF. Sixteen percent of patients received targeted therapy based on CGP of which 50% had at least stable disease.ConclusionsIncorporating CGP into sarcoma management may allow for more precise diagnosis and sub-classification of this diverse and rare disease, as well as personalized matching of patients to targeted therapies such as those available in basket clinical trials.

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species.

LANGUAGE IDEOLOGIES AND THE POLITICS OF LANGUAGE IN POST-COLONIAL AFRICA

Academic and political discourse on language policies and nation-building in post-colonial Africa is highly ideologised. Facing two extreme ideological positions, namely what one might call ‘19th century European nation state-ideology’ vs ‘20th/21st century African Renaissance-ideology’, language planners and decision makers in Africa are caught between a rock and a hard place. The paper begins by sketching out salient differences between the two sets of ideological positions: (1) Ideologies based on European historical-cultural experience which gave rise to a particular ‘Western’ mind-set; this mind-set is built on convictions regarding European exceptionalism and on notions linked to linguistically and culturally homogenous nations. (2) Ideologies informed by anti-colonialist struggle and anti-imperialist philosophy which, further, rest on the recognition of sociolinguistic realities in Africa, the latter being characterised by extreme ethnolinguistic plurality and diversity. While the first set continues to have considerable impact on academic and political discourse in terms of prevailing Eurocentric perspective and attitudes infested by Orientalism, the second is rooted in idealistic positions relating to Universal Human Linguistic Rights and notions of African Identity and Personality. Such strategies have been and still are widely discussed in academic and political circles across Africa. A third position is that of bridging this ideological gap by advocating multilingual policies which would combine indigenous languages of local and regional relevance with imported languages of global reach towards the strategic goal of mother tongue-based multilingualism (MTBML). The ongoing highly controversial debate, however, tends to overlook the fact that MTBML is exactly the ‘language(s)-in-education policy’ that most so-called developed countries, including the former colonial powers of Europe, have long since installed to best serve their own political interests and economic progress.

Evaluation of hydrophobic chitosan-based particulate formulations of porcine reproductive and respiratory syndrome virus vaccine candidate T cell antigens

PRRS control is hampered by the inadequacies of existing vaccines to combat the extreme diversity of circulating viruses. Since immune clearance of PRRSV infection may not be dependent on the development of neutralising antibodies and the identification of broadly-neutralising antibody epitopes have proven elusive, we hypothesised that conserved T cell antigens represent potential candidates for development of a novel PRRS vaccine. Previously we had identified the M and NSP5 proteins as well-conserved targets of polyfunctional CD8 and CD4 T cells. To assess their vaccine potential, peptides representing M and NSP5 were encapsulated in hydrophobically-modified chitosan particles adjuvanted by incorporation of a synthetic multi-TLR2/TLR7 agonist and coated with a model B cell PRRSV antigen. For comparison, empty particles and adjuvanted particles encapsulating inactivated PRRSV-1 were prepared. Vaccination with the particulate formulations induced antigen-specific antibody responses, which were most pronounced following booster immunisation. M and NSP5-specific CD4, but not CD8, T cell IFN-γ reactivity was measurable following the booster immunisation in a proportion of animals vaccinated with peptide-loaded particles. Upon challenge, CD4 and CD8 T cell reactivity was detected in all groups, with the greatest responses being detected in the peptide vaccinated group but with limited evidence of an enhanced control of viraemia. Analysis of the lungs during the resolution of infection showed significant M/NSP5 specific IFN-γ responses from CD8 rather than CD4 T cells. Vaccine primed CD8 T cell responses may therefore be required for protection and future work should focus on enhancing the cross-presentation of M/NSP5 to CD8 T cells.

A phylogenetic study of floral morphology of some members of Asclepiadaceae R.Br

Floral morphological diversity and phylogenetic relationship were studied in the family Asclepiadaceae. This family characterized by unique features that contributes to extreme floral complexity and diversity. In this paper, we used preliminary phylogenetic hypothesis for the family Asclepiadaceae to explore the mode of diversification in pollinarium and coronal structure. The occurance, size, shape, position, orientation of pollinia, mode of pollination and the presence of form of coralline corona and gynostegial corona were studied for similarity indices between two subfamilies Periplocoideae and Asclepiadoideae.

Editorial: Paradoxical Southeast Asia

Southeast Asia is a space characterized by its extreme diversity. This region for a long time ill-defined and whose name itself was not popularize until World War II, has been distinguished not by its cultural unity like its large neighbors of the Chinese and Indian world, but by its position at the crossroads of the main commercial routes since at least the beginning of the first millennium of the common era. This corner of Asia is culturally perceived as a melting pot, a space open to inten...

Gabor Feature Selection Based on Information Gain

In the field of machine vision object detection has become a popular area over the past several years. It is applied on a large scale in scientific research such as bioinformatics, machine learning and computer vision or in everyday life, like traffic supervision, access control, identification and authentication systems and also in industry, robotics etc.Every application has its own particularities and works only in some well-defined conditions. The main difficulty of general object detection comes from the extreme diversity in which all objects appear. They have a large variety of appearance, aspect, form, dimension, color, position, rotation angle, illumination, shadow or occlusion.In this paper we use numerous Gabor filters for feature extraction, specially tuned for global face and local eye detection. Because the high dimensionality of the data the obtained features are hardly manageable. We propose to apply, in the training and test phases, feature selection. Feature selection is an important step in almost every data mining problem. The selection of the most representative feature-descriptors is done by measuring the pairwise entropy of the filter responses. The final classification result is given by the most informative filter responses obtained from information gain of a weak classifiers computed from the corresponding filter responses on the training set.Besides, this paper compares other learning methods used in our previous works with the currently proposed approach, comparing the role of measuring the information gain and the mutual information between the selected filters.

A comparative look at a centenary. A review of World War I commemorative events in Brussels

The centenary of World War I has marked an abrupt change: historical events will never be commemorated in the same way, especially in Belgium. The federated entities have demonstrated the autonomous role which they intend to play in future events of this type. The Brussels-Capital Region was not outdone. While the political choice to be directly involved in the commemorative events was made later there than in the other main regions and communities, it demonstrated its will and capacity to implement different activities aimed at reaching a very wide public. The systematic study of just over 430 activities identified between January 2014 and June 2017 in the territory of the Brussels-Capital Region thus highlights their extreme diversity as well as the exceptional dynamism of the municipalities which were at the origin of one quarter of them. Overall, the theme of the majority of events studied wavered between two main lines: the daily life of the inhabitants of Brussels and the global history of the conflict in its Belgian dimension. But these approaches were also used to prompt debates and reflection on current issues which make sense in today's society: the defence of freedom, solidarity, democracy, social cohesion, etc. The historical approach was therefore used as a tool for cohesion and as a lever for integration, with a past which concerns everybody: the inhabitants of Brussels from here and elsewhere, history enthusiasts, lovers of historical memory tourism, non-natives, expatriates, tourists for a day, etc.

Molecular phylogeny and population genetic differentiation patterns inBrachionus calyciflorusPallas (Rotifera) complex from two lakes in China

The spatio-temporal patterns of population genetic structures have been attracting increasing attention of late. Few of these efforts, however, have focused on the underlying mechanisms of the seasonal alterations of in rotifer clone groups. To gain insights into the seasonal variation patterns of genetic differentiation in rotifer populations, 158 clones of the Brachionus calyciflorus Pallas species complex, with seasonal sampling from Guangzhou and Wuhu in China, were sequenced and analyzed based on the nuclear internal transcribed spacer (ITS) region and the mitochondrial cytochrome c oxidase subunit I (COI) gene. DNA taxonomy provided estimates of evolving entities ranging from 3 to 21 by combining the mitochondrial and nuclear markers with the different ABGD, PTP, and GMYC models. The most conservative number of the three evolving entities was used for further phylogenetic and population structure analyses. The B. calyciflorus species complex was found to have extreme nucleotide diversity, revealing twice the diversity from the COI dataset than from ITS. The similar patterns of seasonal succession in B. calyciflorus were investigated in the two habitats of Guangzhou and Wuhu, and the clonal groups involved in seasonal succession were actually sibling or cryptic species within the B. calyciflorus complex. We assume that these cryptic species are specialized for their ecological niches, especially in terms of temperature preference. The spatio-temporal patterns of population genetic structure varied with cryptic species, e.g. cryptic species II (-COI/-ITS) had much greater genetic differentiation among sampling sites than among seasonal populations and cryptic species III (-COI/-ITS) displayed a reverse pattern.