The Rose Bengal test in human brucellosis: a neglected test for the diagnosis of a neglected disease

Brucellosis is a highly contagious zoonosis affecting livestock and human beings. The human disease lacks pathognomonic symptoms and laboratory tests are essential for its diagnosis. However, most tests are difficult to implement in the areas and countries were brucellosis is endemic. Here, we compared the simple and cheap Rose Bengal Test (RBT) with serum agglutination, Coombs, competitive ELISA, Brucellacapt, lateral flow immunochromatography for IgM and IgG detection and immunoprecipitation with Brucella proteins. We tested 208 sera from patients with brucellosis proved by bacteriological isolation, 20 contacts with no brucellosis, and 1559 sera of persons with no recent contact or brucellosis symptoms. RBT was highly sensitive in acute and long evolution brucellosis cases and this related to its ability to detect IgM, IgG and IgA, to the absence of prozones, and to the agglutinating activity of blocking IgA at the pH of the test. RBT was also highly specific in the sera of persons with no contact with Brucella. No test in this study outperformed RBT, and none was fully satisfactory in distinguishing contacts from infected patients. When modified to test serum dilutions, a diagnostic titer >4 in RBT resulted in 87.4% sensitivity (infected patients) and 100% specificity (contacts). We discuss the limitations of serological tests in the diagnosis of human brucellosis, particularly in the more chronic forms, and conclude that simplicity and affordability of RBT make it close to the ideal test for small and understaffed hospitals and laboratories.

Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

Background: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

Ancient DNA of the extinct Lava shearwater (Puffinus olsoni) from the Canary Islands reveals incipient differentiation within the P. puffinus complex

The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands.

The whereabouts of an ancient wonderer: Global phylogeography of the solitary ascidian Styela plicata

Genetic tools have greatly aided in tracing the sources and colonization history of introduced species. However, recurrent introductions and repeated shuffling of populations may have blurred some of the genetic signals left by ancient introductions. Styela plicata is a solitary ascidian distributed worldwide. Although its origin remains unclear, this species is believed to have spread worldwide by travelling on ship's hulls. The goals of this study were to infer the genetic structure and global phylogeography of S. plicata and to look for present-day and historical genetic patterns. Two genetic markers were used: a fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and a fragment of the nuclear gene Adenine Nucleotide Transporter/ADP-ATP Translocase (ANT). A total of 368 individuals for COI and 315 for ANT were sequenced from 17 locations worldwide. The levels of gene diversity were moderate for COI to high for ANT. The Mediterranean populations showed the least diversity and allelic richness for both markers, while the Indian, Atlantic and Pacific Oceans had the highest gene and nucleotide diversities. Network and phylogenetic analyses with COI and ANT revealed two groups of alleles separated by 15 and 4 mutational steps, respectively. The existence of different lineages suggested an ancient population split. However, the geographic distributions of these groups did not show any consistent pattern, indicating different phylogeographic histories for each gene. Genetic divergence was significant for many population-pairs irrespective of the geographic distance among them. Stochastic introduction events are reflected in the uneven distribution of COI and ANT allele frequencies and groups among many populations. Our results confirmed that S. plicata has been present in all studied oceans for a long time, and that recurrent colonization events and occasional shuffling among populations have determined the actual genetic structure of this species.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Evolution: the end of an ancient asexual scandal.

Bdelloid rotifers were believed to have persisted and diversified in the absence of sex. Two papers now show they exchange genes with each other, via horizontal gene transfers as known in bacteria and/or via other forms of non-canonical sex.

Urban environments and situated institutions : everyday governance in west Bengal

How do processes of power shape the urban environment in small Indian cities? On a day-to-day basis, who actually controls access to and the use of environmental resources? How is this done? Answering these questions contributes to our ability to develop a nuanced understanding the urban condition. In order to investigate these questions an actor-oriented approach is developed, drawing on the anthropological literatures on everyday governance and the everyday state. This conceptual framework informs an urban political ecology approach oriented towards everyday practices and the micro-politics of the (re)production of urban socio-natures. This thesis employs a mixed methods approach to qualitative research. Three cases are presented to explore: para (neighbourhood) clubs as governance actors, the governance of the urban pondscape, and the urban political ecology of solid waste management. These case studies serve to highlight how power shapes the (re)production of urban socio-natures through the everyday environmental governance practices of a complex network of governance actors. This work further demonstrates how multiple intersectionalities, including class, caste and access to political and social authority, shape these practices and their outcomes. Finally, the manner in which balances of power, place making and the formation of subject positions may both result from and shape everyday environmental governance practices and their outcomes is explored. This empirical investigation makes a number of contributions to the literature. It has explores the hereto-understudied topics of environmental governance in small cities in India, the urban political ecologies of non-piped water and of solid waste, and the role of clubs as governance actors. It further contributes to conversations within the literature on how to deepen and broaden Urban Political Ecology by engaging with everyday practices, and cases of ordinary, not-openly contested socio-natures. -- Comment les processus de pouvoir influencent-ils l'environnement urbain dans les petites villes indiennes ? Au quotidien, qui contrôle l'accès et l'utilisation des ressources environnementales ? Comment ce contrôle s'exerce-t-il ? Répondre à ces questions contribue au développement d'une compréhension nuancée de la condition urbaine. Afin d'explorer ces questions une approche actor-oriented de la gouvernance quotidienne est développée, faisant appel aux littératures anthropologiques de la gouvernance quotidienne et de l'everyday state. Ce cadre conceptuel établit ainsi une approche d'Urban Political Ecology orientée vers les pratiques quotidiennes et la micro- politique de la (re) production des socio-natures urbaines. Cette thèse emploie des méthodes qualitatives mixtes. Trois cas sont présentés afin d'étudier : les clubs para (quartier) comme acteurs de la gouvernance; la gouvernance de la pondscape urbaine; et l'urban political ecology de la gestion des déchets solides. Ces études de cas permettent de mettre en lumière la façon dont le pouvoir influence la (re)production des socio-natures urbaines par le biais des pratiques quotidiennes de gouvernance environnementale d'un réseau complexe d'acteurs. Ce travail démontre également comment plusieurs intersectionnalités, y compris la classe, la caste et l'accès au pouvoir politique et social, façonnent ces pratiques de gouvernance et leurs produits. Finalement, cette recherche explore la manière dont les équilibres de pouvoir, la fabrication de lieux et la formation de la position du sujet peuvent à la fois résulter de et contribuer à façonner les pratiques quotidiennes de gouvernance environnementale et leurs produits. Cette investigation empirique fait ainsi plusieurs contributions à la littérature. Elle explore les questions jusque-là sous-étudiées de la gouvernance environnementale dans les petites villes en Inde, de l'urban political ecology de l'eau non courante et des déchets solides, ainsi que du rôle des clubs comme acteurs de la gouvernance. Celle-ci contribue également à des débats sur la façon d'approfondir et d'élargir l'urban political ecology en travaillant sur les pratiques quotidiennes, et sur des cas de socio-natures ordinaires, pas ouvertement contestées.

Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

Truths ancient and modern

The paper presents a comparison of the theories of truth, and the solutions of the liar paradox, proposed by Thomas Bradwardine (c. 1290-1349), Jean Buridan (c. 1295-1358), and Alfred Tarski (1901-1983).

Defining the art of grammar: Ancient perceptions of γραμματική and grammatical

The subject of this dissertation, which belongs to the field of Classical Philology, are the definitions of the art of grammar found in Greek and Latin sources from the Classical era to the second century CE. Definitions survive from grammarians, philosophers, and general scholars. I have examined these definitions from two main points of view: how they are formed, and how they reflect the development of the art itself. Defining formed part of dialectic, in practice also of rhetoric, and was perceived as important from the Classical era onwards. Definitions of grammar seem to have become established as part of preliminary discussions, located at the beginning of grammatical manuals (tékhnai, artes). These discussions included certain principal notions of the art; in addition to the definition, a list of the parts of the art was also typically included. These lists were formed by two different methods: division (diaíresis, divisio) and partition (merismós, partitio). Many of the grammarians may actually have been unfamiliar with these methods, unlike the two most important scholars of the Late Republic, Varro and Cicero. Significant attention was devoted to the question whether the art of grammar is based on lógos or empeiría. This epistemological question had its roots in medical theories, which were prominent in Alexandria. In the history of the concept of grammatiké or grammatica, three stages become evident. In the Classical era, the Greek term is used to refer to a very concrete art of letters (grámmata); from the Hellenistic era onwards it refers to the art developed by the Alexandrian scholars, a matter of textual and literary criticism. Towards the end of the Hellenistic era, the grammarian also becomes involved with the question of correct language, which gradually begins to appear in the definitions as well.

Competitiveness of alexandergrass or Bengal dayflower with soybean

Weeds compete with field crops mainly for water, light and nutrients, and the degree of competition is affected by the weed density and the intrinsic competitive ability of each plant species in coexistence. The objective of this research was to compare the competitiveness of alexandergrass (Brachiaria plantaginea) or Bengal dayflower (Commelina benghalensis) in coexistence with soybean, cv. M-Soy 8045. A factorial experiment (2 x 5) with two weed species and five competition proportions was carried out in a completely randomized design with four replicates. Proportions were based on a replacement series competition design, always maintaining the total density of four plants per 10 L plastic pots, which corresponded to 60 plants m ². The weed-crop proportions were: 0:4; 1:3; 2:2; 3:1; 4:0; that corresponded to the proportion of 100, 75, 50, 25 and 0% of soybean plants and the opposite for weeds, B. plantaginea or C. benghalensis plants. Leaf area, shoot dry mass of the weeds and soybean and number of soybean trifoliate leaves were evaluated when the soybean reached the phenologic stage of full flowering. B. plantaginea was a better competitor than soybean plants. Otherwise, C. benghalensis revealed a similar competitive ability that of the soybean. In both cases, there were evidences that intraspecific competition was more important.