Open minded and open access: introducing NeoBiota, a new peer-reviewed journal of biological invasions

The Editorial presents the focus, scope, policies, and the inaugural issue of NeoBiota, a new open access peer-reviewed journal of biological invasions. The new journal NeoBiota is a continuation of the former NEOBIOTA publication series. The journal will deal with all aspects of invasion biology and impose no restrictions on manuscript size neither on use of color. NeoBiota implies an XML-based editorial workflow and several cutting-edge innovations in publishing and dissemination, such as semantic markup of and enhancements to published texts, data publication, and extensive cross-linking within the journal and to external sources

Projecte de cultiu ecològic de plantes medicinals i aromàtiques, en una finca a Arenys de Mar (comarca del Maresme)

El cultiu de plantes medicinals i aromàtiques (PAM) a Catalunya és un cultiu minoritari, però podria ser una alternativa a cultius que cada vegada més són menys rendibles. La finca estudiada, situada al terme municipal d’Arenys de Mar, al Maresme, s'ha emprat per al cultiu de plantes hortícoles. Ara ja fa anys que la finca està inactiva, i el nou propietari s’ha interessat en el cultiu de PAM com a possibilitat de tornar a activar la finca, escollint com a sistema de producció, el cultiu ecològic . El projecte presenta el cultiu de quatre espècies de PAM ((Thymus vulgaris, Timó, Lavandula angustifolia, Lavanda, Mentha x piperita, Menta pebrera i Sàlvia comuna, Sàlvia), tenint en compte les seves necessitats i les característiques edafoclimàtiques de la zona, així com el mercat de les PAM, la normativa de producció ecològica i procurant utilitzar tot els mitjans existents a la finca per tal de minimitzar la inversió

Faire connaître la poésie suisse romande outre-Atlantique: Lausanne - New York aller-retour. Récit d'une verticalité entre identité et altérité

Cet article présente la synthèse du travail de traduction à quatre mains par My. Moraz et Tim Keane un collègue new-yorkais des poètes romands Pierre-Alain Tâche et Pierre Chappuis. Nous avons essayé de revenir sur notre manière de travailler et de mettre en relief les choix opérés dans le passage du français à l'anglais dans ce que ces deux langues ont de spécifique.

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: We present the results of EGASP, a community experiment to assess the state-ofthe-art in genome annotation within the ENCODE regions, which span 1% of the human genomesequence. The experiment had two major goals: the assessment of the accuracy of computationalmethods to predict protein coding genes; and the overall assessment of the completeness of thecurrent human genome annotations as represented in the ENCODE regions. For thecomputational prediction assessment, eighteen groups contributed gene predictions. Weevaluated these submissions against each other based on a ‘reference set’ of annotationsgenerated as part of the GENCODE project. These annotations were not available to theprediction groups prior to the submission deadline, so that their predictions were blind and anexternal advisory committee could perform a fair assessment.Results: The best methods had at least one gene transcript correctly predicted for close to 70%of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into accountalternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotidelevel, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programsrelying on mRNA and protein sequences were the most accurate in reproducing the manuallycurated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could beverified.Conclusions: This is the first such experiment in human DNA, and we have followed thestandards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe theresults presented here contribute to the value of ongoing large-scale annotation projects and shouldguide further experimental methods when being scaled up to the entire human genome sequence.

AḤVĀL-i MAWT-i ḤUSAYN-‛ALĪ HĀN VA AḤVĀL-i MAWT-i PISAR

Poème masnavī compose de deux parties, l’histoire (qiṣṣa) de la chute, puis de la mort, du vizir Sayyid ‛Alī Hān (f. 7v- 59), assassiné le 9 octobre 1720 et remplacé par Muḥ. Amīn Hān I‛timād al-Dawla. Cette partie compte 919 bayt. La seconde (f. 61- 102v) en compte 763 et raconte les circonstances de la mort de Lāla Laliyān Mal, fils de l’auteur (f. 62), survenue dix mois après, alors qu’il avait 30 ans, et les campagnes militaires de cette période. Cette qiṣṣ̣a aurait été rédigée vers 1723 (f. 102).Une préface en prose (dībāča), rédigée (f. 5v) par Zōrāvar Singh [comparer à Supplément persan 247] occupe les f. 1v à 6v. Celui-ci indique qu’il édita, après sa mort l’œuvre du poète Rāy Kirpārām (f. 3v), et dédie cette édition (f. 2v) au moghol Abū l-Fatḥ Nāṣir al-Dīn Muḥ. Šāh (m. en 1161H./1748). Ce serait Rāy Kirpārām l’auteur des deux qiṣṣa.

Executive Order Number Thirty Three, August 21, 1987

Continue the TIM Council.

Executive Order Number Forty Six, January 5, 1993

Establish the TIM Council (Telecommunication and Informational Management)

Spinning welfare: The gains from process innovation in cotton and car production

Economists and economic historians want to know how much better life is today than in the past.Fifty years ago economic historians found surprisingly small gains from 19th century US railroads,while more recently economists have found relatively large gains from electricity, computers and cellphones. In each case the implicit or explicit assumption is that researchers were measuring the valueof a new good to society. In this paper we use the same techniques to find the value to society ofmaking existing goods cheaper. Henry Ford did not invent the car, and the inventors of mechanisedcotton spinning in the industrial revolution invented no new product. But both made existing productsdramatically cheaper, bringing them into the reach of many more consumers. That in turn haspotentially large welfare effects. We find that the consumer surplus of Henry Ford s production linewas around 2% by 1923, 15 years after Ford began to implement the moving assembly line, while themechanisation of cotton spinning was worth around 6% by 1820, 34 years after its initial invention.Both are large: of the same order of magnitude as consumer expenditure on these items, and as largeor larger than the value of the internet to consumers. On the social savings measure traditionally usedby economic historians, these process innovations were worth 15% and 18% respectively, makingthem more important than railroads. Our results remind us that process innovations can be at least asimportant for welfare and productivity as the invention of new products.

Concurs de la Ciutat Judicial

Concurs de la Ciutat Judicial

A dynamic model for stem cell homeostasis and patterning in Arabidopsis meristems.

Plants maintain stem cells in their meristems as a source for new undifferentiated cells throughout their life. Meristems are small groups of cells that provide the microenvironment that allows stem cells to prosper. Homeostasis of a stem cell domain within a growing meristem is achieved by signalling between stem cells and surrounding cells. We have here simulated the origin and maintenance of a defined stem cell domain at the tip of Arabidopsis shoot meristems, based on the assumption that meristems are self-organizing systems. The model comprises two coupled feedback regulated genetic systems that control stem cell behaviour. Using a minimal set of spatial parameters, the mathematical model allows to predict the generation, shape and size of the stem cell domain, and the underlying organizing centre. We use the model to explore the parameter space that allows stem cell maintenance, and to simulate the consequences of mutations, gene misexpression and cell ablations.