Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names

There is no control over the information provided with sequences when they are deposited in the sequence databases. Consequently mistakes can seed the incorrect annotation of other sequences. Grouping genes into families and applying controlled annotation overcomes the problems of incorrect annotation associated with individual sequences. Two databases (http://www.mendel.ac.uk) were created to apply controlled annotation to plant genes and plant ESTs: Mendel-GFDb is a database of plant protein (gene) families based on gapped-BLAST analysis of all sequences in the SWISS-PROT family of databases. Sequences are aligned (ClustalW) and identical and similar residues shaded. The families are visually curated to ensure that one or more criteria, for example overall relatedness and/or domain similarity relate all sequences within a family. Sequence families are assigned a ‘Gene Family Number’ and a unified description is developed which best describes the family and its members. If authority exists the gene family is assigned a ‘Gene Family Name’. This information is placed in Mendel-GFDb. Mendel-ESTS is primarily a database of plant ESTs, which have been compared to Mendel-GFDb, completely sequenced genomes and domain databases. This approach associated ESTs with individual sequences and the controlled annotation of gene families and protein domains; the information being placed in Mendel-ESTS. The controlled annotation applied to genes and ESTs provides a basis from which a plant transcription database can be developed.

Geographical structuring in the mtDNA of Italians.

Geographical patterns of mtDNA variation were studied in 12 Italian samples (1072 individuals) by two different spatial autocorrelation methods. Separate analyses of the frequencies of 12 restriction morphs show North-South clines, differences between Sardinia and the mainland populations, and the effects of isolation by distance. A recently developed autocorrelation statistic summarizing molecular similarity at all sites (AIDA; autocorrelation index for DNA analysis) confirms the presence of a clinical pattern; differences between random pairs of haplotypes tend to increase with their geographical distance. The partition of gene diversity, however, reveals that most variability occurs within populations, whereas differences between populations are minor (GST = 0.057). When the data from the 12 samples are pooled, two descriptors of genetic variability (number of polymorphic sites and average sequence difference between pairs of individuals) do not behave as expected under neutrality. The presence of clinal patterns, Tajima's tests, and a simulation experiment agree in suggesting that population sizes increased rapidly in Italy and Sicily but not necessarily so in Sardinia. The distribution of pairwise sequence differences in the Italian peninsula (excluding Sardinia) permits a tentative location of the demographic increase between 8000 and 20,500 years ago. These dates are consistent with archaeological estimates of two distinct expansion processes, occurring, respectively, in the Neolithic and after the last glacial maximum in the Paleolithic. Conversely, there is no genetic evidence that such processes have had a major impact on the Sardinian population.

An idea from Donnellan: deferential and non-deferential uses of proper names

When we use a proper name, by virtue of what do we succeed in saying something about an individual? In other words, how are we supposed to explain the seemingly trivial fact that by uttering “Aristotle was wise” we actually predicate something of the famous philosopher? Questions like these have animated a fervent debate among philosophers of language; however, nowadays the standard answer is that by using “Aristotle” we say something about that famous philosopher because the name we have used in our utterance refers to him. Even though no general consensus has been reached on how to characterize the relation of reference – there are still different and competing accounts of the latter on the philosophical market – almost everybody believes, especially after the publication of Saul Kripke’s "Naming and necessity", that reference is the only semantic relation that connects our uses of proper names to individuals in the world. Contrary to this widespread assumption, in this dissertation I shall claim that our uses of proper names are not always referential.

Digitization for Preservation and Access: Restoring the Usefulness of the Nitrate Negative Collections at the American Geographical Society Library

Film-based photographic collections of nitrate negatives pose major challenges to preservation and access because of unstable media and the lack of item-level indexing. Digitization offers an opportunity to capture the content of deteriorating negatives, to extend access to them, and to restore their usefulness as information resources. Digitization as a preservation strategy has been the subject of ongoing debate. This article contributes to the discussion by exploring access to and the preservation of film-based photographic collections and by presenting the digiti- zation project at the American Geographical Society Library as a case study. The project, Saving and Sharing the AGS Library’s Historic Nitrate Negative Images, was undertaken from 2010 to 2012 to preserve and provide access to over 69,000 nitrate negatives from its historic collections.

Una aproximación basada en corpus para la detección del foco geográfico en el texto

El foco geográfico de un documento identifica el lugar o lugares en los que se centra el contenido del texto. En este trabajo se presenta una aproximación basada en corpus para la detección del foco geográfico en el texto. Frente a otras aproximaciones que se centran en el uso de información puramente geográfica para la detección del foco, nuestra propuesta emplea toda la información textual existente en los documentos del corpus de trabajo, partiendo de la hipótesis de que la aparición de determinados personajes, eventos, fechas e incluso términos comunes, pueden resultar fundamentales para esta tarea. Para validar nuestra hipótesis, se ha realizado un estudio sobre un corpus de noticias geolocalizadas que tuvieron lugar entre los años 2008 y 2011. Esta distribución temporal nos ha permitido, además, analizar la evolución del rendimiento del clasificador y de los términos más representativos de diferentes localidades a lo largo del tiempo.

Ethnobotanic importance of plants used in pigeon-breeding in Eastern Spain

Background: The importance that birds of the Columbidae family have had throughout history is visible on the Mediterranean coast. Pigeon fancying is the art of breeding and training carrier pigeons and currently, several breeds exist. The sport of racing pigeons consists in covering a distance at maximum possible speed. However, pigeon breeding has another modality called “sport pigeon”, where several males follow a female. This study focusses on ethnobotanical knowledge of native and exotic plant species that are used for diet, breeding, stimulation, healing illnesses and staining the plumage of pigeons bred in captivity. Methods: Using semi-structured interviews, we gathered information about the different plant species traditionally used for pigeon-breeding in the region of Valencia. Background material on remedies for bird illnesses was gathered from folk botanical references, local books and journals. The plant species were collected in the study area, then identified in the laboratory using dichotomous keys and vouchered in the ABH (Herbarium of Alicante University). We used Excel ® 2003 to perform a simple statistical analysis of the data collected. Results: We collected 56 species of plants (and one variety) that included 29 botanical families. The total number of species was made up of 35 cultivated and 21 wild plants. The most common were Gramineae (14 species), Leguminosae (6 species), and Compositae (4 species). Conclusions: Pigeon breeding is an immensely popular activity in Eastern Spain, and ethnobiological knowledge about breeding pigeons and caring for them is considerable. The names and traditional uses of plants depend on their geographical location, vernacular names serve as an intangible heritage. Feeding, environmental features, and genetic makeup of individuals are relevant aspects in the maintenance of avian health.

Application of Text Summarization techniques to the Geographical Information Retrieval task

Automatic Text Summarization has been shown to be useful for Natural Language Processing tasks such as Question Answering or Text Classification and other related fields of computer science such as Information Retrieval. Since Geographical Information Retrieval can be considered as an extension of the Information Retrieval field, the generation of summaries could be integrated into these systems by acting as an intermediate stage, with the purpose of reducing the document length. In this manner, the access time for information searching will be improved, while at the same time relevant documents will be also retrieved. Therefore, in this paper we propose the generation of two types of summaries (generic and geographical) applying several compression rates in order to evaluate their effectiveness in the Geographical Information Retrieval task. The evaluation has been carried out using GeoCLEF as evaluation framework and following an Information Retrieval perspective without considering the geo-reranking phase commonly used in these systems. Although single-document summarization has not performed well in general, the slight improvements obtained for some types of the proposed summaries, particularly for those based on geographical information, made us believe that the integration of Text Summarization with Geographical Information Retrieval may be beneficial, and consequently, the experimental set-up developed in this research work serves as a basis for further investigations in this field.

Más allá de las “indiciones”. Reflexión sobre la comunicación a partir de una vivencia

El propósito de este trabajo es describir una reflexión originada a partir de una vivencia. En ella, la interpretación del mensaje fue indispensable. El primer paso de la asistencia sanitaria es la entrevista con el paciente. Tras ello, podemos detectar sus necesidades y empezar a actuar adecuadamente. La interpretación inadecuada de los datos obtenidos mediante la entrevista puede conducir a resultados diferentes de los esperados. Con cierta frecuencia, los pacientes reinterpretan o incluso reinventan los nombres de los fármacos, de las enfermedades, etc. En ocasiones puede suceder también con la descripción de la patología subyacente. Estos hechos suelen estar influenciados por diversos factores (culturales, geográficos, etc.). Descifrar su verdadero significado puede llegar a suponer un verdadero reto en algunas ocasiones. Una conversación reciente con mi abuela me condujo a la reflexión sobre la relación profesional sanitario-paciente presentada en este trabajo.

Delineating zones to increase geographical detail in individual response data files: An application to the Spanish 2011 Census of population

Due to confidentiality considerations, the microdata available from the 2011 Spanish Census have been codified at a provincial (NUTS 3) level except when the municipal (LAU 2) population exceeds 20,000 inhabitants (a requirement that is met by less than 5% of all municipalities). For the remainder of the municipalities within a given province, information is only provided for their classification in wide population intervals. These limitations, hampering territorially-focused socio-economic analyses, and more specifically, those related to the labour market, are observed in many other countries. This article proposes and demonstrates an automatic procedure aimed at delineating a set of areas that meet such population requirements and that may be used to re-codify the geographic reference in these cases, thereby increasing the territorial detail at which individual information is available. The method aggregates municipalities into clusters based on the optimisation of a relevant objective function subject to a number of statistical constraints, and is implemented using evolutionary computation techniques. Clusters are defined to fit outer boundaries at the level of labour market areas.

Records of the Geographical Society, ca. 1796

This small blue-covered paper notebook contains four leaves with the handwritten records of the Geographical Society, an undergraduate organization at Harvard in the late 1790s. The records consist of ten handwritten "Laws of the Geographical Society" and a short list of fines dispensed on October 7th. A list of six student surnames is written on a scrap of paper and attached with pins to the notebook's inside front cover. The surnames likely correspond to six members of the Harvard Class of 1798: John Abbot (1777-1854), Isaac Adams (d. 1807), Francis Brigham (d. November 14, 1796), Humphrey Devereux (1779-1867), Joseph Emerson (1777-1833), and Artemas Sawyer (d. 1826). The notebook is undated but was presumably kept in 1795 or 1796 around the time of Brigham's death on November 14, 1796. While Brigham's surname appears in the list of fines, it is crossed out on the inside front cover.

A catechism geographical, historicall and chronologicall

Notebook of unlined pages holding a handwritten copy of Tutor Flynt's "Catechism" copied by Harvard student Hull Abbot (1702-1774, Harvard AB 1720). The volume lists questions and accompanying answers on various academic subjects.