Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

A sea urchin (Diadema africanum Rodriguez et al., 2013) and a pipe fish (Syngnathus phlegon Risso, 1827) : two new records for the Azores

Maciel & Costa (2010) reported the presence of 17 species of costal sea urchins (Echinoidea) in the Azores, while Porteiro et al. (2010) reported six species of pipefishes (Syngnathidae) for the area. During SCUBA diving at Santa Maria Island, the first author detected a sea urchin and a pipe fish which are new to the marine fauna of the Azores.

Records of predatory, con-specific and human induced mauls on fish from the Northeast Atlantic and Black Sea

Present study aims to describe records of mauled and con-specific injures in various fish inhabiting different environment and to discuss possible impacts on fish behavior and ontogenesis. The fish specimens were collected from the Black Sea and Azores Islands (NE Atlantic). Individuals of European flounder, Pleuronectes flesus, common stingray, Dasyatis pastinaca and turbot, Scophthalmus maximus with missing dorsal and caudal fins and flesh, were found in the Black Sea. Specimens with severe mauls of the ocean sunfish, Mola mola, almaco jack, Seriola rivoliana and sargo, Diplodus sargus were recorded from the Azores Islands. All of them were caught alive and survived severe mauls caused by predators or by accidents with propellers, fishing nets. The NE Atlantic records, although possibly caused by natural predation, are more probably than not the result of negative interactions with human activity. Numerous records of mauled fish species from both regions show that the problem with adverse effects of fisheries is quite important. Predatory and con-specific injuries obviously are compatible with basic fish vital functions of described cases. The problem with negative anthropogenic interactions seems to be insufficiently investigated and need more attention by responsible managers and decision makers.

New records of mosquito species (Diptera: Culicidae) from Neuquén and La Rioja provinces, Argentina

The presence of Aedes aegypti is reported beyond its current limit of distribution in Argentina, in the city of Neuquén, Neuquén Province. Ovitraps were placed to collect Ae. aegypti eggs between December 2009 and April 2010. The geographical distribution of Culex eduardoi, Psorophora ciliata and Ps. cingulata is extended with new records from two provinces.

New records of Histoplasma capsulatum from wild animals in the Brazilian Amazon

Twenty-eight isolates of Histoplasma capsulation were obtained from eight species of forest mammals from the States of Amazonas, Pará and Rondônia in the Amazon Region of Brazil. Primary isolates were obtained by inoculating triturated liver and spleen tissue intradermally and intraperito-neally in hamsters. Mycological diagnosis in hamsters presenting lesions was confirmed by histopathology and culture on Sabouraud dextrose-agar. Infected hamsters developed signs of disease within two to nine months; all had disseminated visceral lesions and most also had skin lesions at the sites of inoculation. None of the hamsters inoculated with skin macerates of the original hosts developed histoplasmosis, and histopathological examination of the viscera of the wild hosts failed to reveal H. capsulation. Prevalence of infection was considerably higher in females than in males both for the opossum Didelphis marsupialis and for total wild animals (479) examined. It is proposed that canopy-dwelling mammals may acquire the infection from conidia borne on convective currents in hollow trees with openings at ground-level.

Current distribution of Achatina fulica, in the State of São Paulo including records of Aelurostrongylus abstrusus (Nematoda) larvae infestation

The currently known distribution range of Achatina fulica Bowdich, 1822, in the state of São Paulo, Brazil, is presented. The record of A. fulica naturally infested with Aelurostrongylus abstrusus larvae (Railliet, 1898) (Nematoda: Metastrongylidae) can be found in the city of Guaratinguetá. It was found A. fulica with Metastrongylidae larvae without known medical and veterinary importance in the cities of Carapicuíba, Embu-Guaçu, Itapevi, São Caetano do Sul, São Paulo and Taboão da Serra.

Sistema para avaliação das vibrações no braço e ombro de um tenista

Este trabalho propõe o desenvolvimento de um módulo capaz de medir a intensidade das vibrações sofridas por um tenista no braço e ombro durante um jogo. Numa primeira fase foi estudada a biomecânica do braço humano e a biomecânica dos movimentos envolvidos no ténis. Foi realizada uma pesquisa sobre os dispositivos MEMs mais adequados bem como o hardware e software a utilizar, tendo sido analisados os requisitos do sistema a implementar. Foi desenvolvido um protótipo electrónico microcontrolado compacto e de baixo custo baseado na utilização de sensores microeletromecânicos (MEMs) de aceleração, permitindo obter informações biomecânicas do desportista e monitoriza-lo durante o treino de maneira não evasiva, possibilitando que ele esteja no seu ambiente natural de treino. O sistema envia as informações dos sensores para um PC através da porta USB sendo estas processados no mesmo. Foi desenvolvida uma interface gráfica intuitiva, para a apresentação dos dados resultantes das medidas, de fácil leitura pelos treinadores. Esta interface grava e apresenta os dados em tempo real. Os testes de campo foram realizados no campo de ténis que existe na Quinta das Freiras em Rio Tinto. O protótipo é de fácil fixação no atleta e permite a monitorização no local de treino sendo pequeno ((20x15mm) e muito leve (2g), tornando-se uma alternativa versátil para o auxilio de atletas e treinadores, aperfeiçoamento da técnica e como ferramenta de pesquisa na área de educação física.

TWO NEW RECORDS OF Isomyia paurogonita FANG AND FAN, 1986 AND Sumatria latifrons Malloch, 1926 (DIPTERA: CALLIPHORIDAE) FROM NORTHERN THAILAND, WITH REVISED KEY TO THE SPECIES OF Isomyia

During the annual fly survey at Doi Nang Kaew in Doi Saket District, Chiang Mai Province of Thailand in 2011, Isomyia paurogonitaFang & Fan, 1986 (Diptera: Calliphoridae) and Sumatria latifrons Malloch, 1926 (Diptera: Calliphoridae) were collected for the first time in Thailand. They are the rare species of the subfamily Rhiniinae (tribe Cosminini). Prior to this finding, fifteen species of Isomyia and two species of Sumatriawere recorded from Thailand. Therefore, 96 blow fly species have been found in this country. These new locality records of both flies are very important for further research on their biology and ecology in Thailand.

Historical analysis of the records of sylvan yellow fever in the State of Amazonas, Brazil, from 1996 to 2009

IntroductionYellow fever is a non-contagious infectious disease, highly lethal, transmitted by the Aedes, Haemagogus and Sabethes.MethodsDescriptive retrospective study of the yellow fever cases in Amazonas, between 1996 and 2009.ResultsForty two cases of yellow fever were confirmed, with 30 deaths, 10% of which were foreigners.ConclusionsThe presence of Aedes aegypti and Aedes albopictus in both rural Amazonas and its capital demonstrates the dispersion of these vectors and underscores the need for better and continuous epidemiological and entomological control.

The Environmental History of Cetaceans in Portugal: Ten Centuries of Whale and Dolphin Records

The history between cetaceans and humans is documented throughout time not only in reports, descriptions, and tales but also in legal documents, laws and regulations, and tithes. This wealth of information comes from the easy spotting and identification of individuals due to their large size, surface breathing, and conspicuous above water behaviour. This work is based on historical sources and accounts accounting for cetacean presence for the period between the 12th and 17th centuries, as well as scientific articles, newspapers, illustrations, maps, non-published scientific reports, and other grey literature from the 18th century onwards. Information on whale use in Portugal's mainland has been found since as early as the 12th century and has continued to be created throughout time. No certainty can be given for medieval and earlier events, but both scavenging of stranded whales or use of captured ones may have happened. There is an increasing number of accounts of sighted, stranded, used, or captured cetaceans throughout centuries which is clearly associated with a growing effort towards the study of these animals. Scientific Latin species denominations only started to be registered from the 18th century onwards, as a consequence of the evolution of natural sciences in Portugal and increasing interest from zoologists. After the 19th century, a larger number of observations were recorded, and from the 20th century to the present day, regular scientific records have been collected. Research on the environmental history of cetaceans in Portugal shows a several-centuries-old exploitation of whales and dolphins, as resources mainly for human consumption, followed in later centuries by descriptions of natural history documenting strandings and at sea encounters. Most cetaceans species currently thought to be present in Portuguese mainland waters were at some point historically recorded.

A malacological survey in the Manso Power Plant, State of Mato Grosso, Brazil: new records of freshwater snails, including transmitters of schistosomiasis and exotic species

Introduction Schistosomiasis is a parasitic disease of public health concern in Brazil, and the construction of hydroelectric dams, in addition to increasing permanent human settlement and tourism, has created conditions suitable for the establishment of mollusks that can transmit schistosomiasis. Such areas require a number of actions to prevent the establishment of schistosomiasis. This paper reports on a freshwater malacological survey carried out in the geographical area of the Manso Power Plant. Methods Mollusks were collected in 18 municipalities in the State of Mato Grosso between February 2002 and February 2004 (qualitative study) and from April 2009 to February 2011 (quantitative study). Results Thirty-one species of mollusks were collected, including newly recorded species (Antillorbis nordestensis and Burnupia ingae). In addition, the geographic distributions of known species, including Biomphalaria straminea, a snail vector of Schistosoma mansoni, were expanded. A total of 4,507 specimens were collected in the APM Manso reservoir (Usina Hidrelétrica de Aproveitamento Múltiplo de Manso) during the quantitative study, and Biomphalaria amazonica was found in six of the 10 localities analyzed. The Afroasiatic species Melanoides tuberculata, introduced after February 2009, was the dominant species (relative abundance 94.96%). Conclusions The study area is epidemiologically important due to the occurrence of B. straminea and B. amazonica, which are vectors of schistosomiasis, and M. tuberculata, a snail host of Centrocestus formosanus, which is responsible for centrocestiasis transmission. Observations of M. tuberculata and the exotic freshwater clams Corbicula fluminea and Corbicula largillierti raise concerns about biodiversity.

New pteridophyte records for the territory of Amapá, Brazil.

Eighteen Pteridophyte taxa in 15 genera are reported as new for the Territory of Amapá, Brazil. The collections area a result of a recent Projeto Flora Amazônica/Programa Flora expedition to that region, and update previous lists of taxa for Amapá.In 1975, Tryon and Conant publised a checklist of the ferns of the Brazilian Amazônia reporting 84 taxa for the Territory of Amapá. The paucity of records for Amapá reflects, at least in part, the amount of botanical exploration. The most complete list of taxa occurring in the Territory is an unpublished list of collection compiled by J. M. Pires. This compilation reports 118 taxas for the Territory of Amapá. The following list is intended to update both the Pires compilation an the Tryon and Conant checklist for the Territor. These records are the result of a Projeto Flora Amazônica/Programa Flora expedition to the region in the latter part of 1979. Species were included in this list is not reportes in the compilation of colections for Amapá, or listed as specifically occurrin in Amapá in the monographs and revisions consulted for listed as specifically occurring in Amapá in the monograohs and revisions consulted for identification (Evans, 1969; Kramer, 1957, 1978; de la Sota, 1960; Lellinger, 1972; Maxon & Morton, 1938; Scamman, 1960, Smith, 1971; Tryon, 1941, 1964).This list reports 18 taxa in 15 genera, increasing the number of taxa in Amapá from the 118 listed by Pires to 136. Most of the taxa reported here might have been predicted to occur in Amapá on the basis of their distribution records for surrounding regions.Each species is followed by a collection number. The collection number is that of D. F. Austin, C. E. Nauman, R. S. Secco, C. Rosario, and M. R. Santos except for four collections in which R. S. Secco was absent and B. V. Rabelo was present, and these are indicated after the collection number. Specimens are deposited in the herbaria of the Museu Paraense Emílio Goeldi, Belém, Brazil and the United States. The family system is essentially that used by Tyron and Conant.

New species and records of Psocoptera (Insecta) from Roraima State, Brazil.

Psocoptera. from Ilha de Marcica and Pacaraima, Roraima State, Brazil, representing 103 species are recorded. Sixty-two are new to science. and are described and figured, representing genera Echmepteryx(2), Tapinella(3), Musapsocus, (1), Seopsocus(3),Isth-mopsocis(3), Dolabellopsocus(6), Epipsocus(5), Neurostigma.(1), Nctiopscus(1), Cae-cilius (6) , Enderluinella (1), Xanthocarcilius(1) , Polypsocus(3) , Scytopsocus(1), ar-chipsocus(1), Lachesilla(4), Notolachesilla(1) , Perispsocus(4), Dactylopsocus (1) , Metylophorus(3), Blaste.(4), Lichenomiae(3), Myopsocus (3). Genus Notarchispsu. gen. is erected for Archipsocus macrurusNew and a new species. Genus MonocladellusEu-derlein in placed in synonymy of, PolypsocusHagen. South American species assigned to genus LophopterygllaEnderlein by New (1979) are. reassigned to Myopscus and represent a parallel development in the latter genus.

New records of Fredius denticulatus (H. Milne-Edwards, 1853) and F. reflexifrons (Ortmann, 1897), and the eastern limits of the distribution of pseudothelphusid crabs (Crustacea: Decapoda) in Brazil

The occurence of Fredius reflexifrons (Ortmann, 1897), a pseudothelphusid crab widely distributed in the Amazon region and the Atlantic Guianas, is recorded from the state of Ceará, northeastern Brazil. Other records of this species and Fredius denticulatus (H. Milne-Edwards, 1853) from the Amazon region are also presented. A discussion is made on the eastern limits of the distribution of the family Pseudothelphusidae in Brazil.