The Azorean Biodiversity Portal: an internet database for regional biodiversity outreach

Copyright © 2010 The Natural History Museum.There is a growing interest in academia to provide biodiversity data to both the scientific community and the public. We present an internet database of the terrestrial lichens, bryophytes, vascular plants, molluscs, arthropods, vertebrates and coastal invertebrates of the Azores archipelago (Portugal, North Atlantic): the Azorean Biodiversity Portal (ABP, http://www.azoresbioportal.angra.uac.pt/). This is a unique resource for fundamental research in systematics, biodiversity, education and conservation management. The ABP was based on a regional species database (ATLANTIS), comprised of grid-based spatial incidence information for c. 5000 species. Most of the data rely on a comprehensive literature survey (dating back to the 19th century) as well as unpublished records from recent field surveys in the Azores. The ABP disseminates the ATLANTIS database to the public, allowing universal, unrestricted access to much of its data. Complementarily, the ABP includes additional information of interest to the general public (e.g. literature on Macaronesian biodiversity) together with images from collections and/or live specimens for many species. In this contribution we explain the implementation of a regional biodiversity database, its architecture, achievements and outcomes, strengths and limitations; we further include a number of suggestions in order to implement similar initiatives

How to ask sensitive questions in conservation: A review of specialized questioning techniques

Tools for social research are critical for developing an understanding of conservation problems and assessing the feasibility of conservation actions. Social surveys are an essential tool frequently applied in conservation to assess both people’s behaviour and to understand its drivers. However, little attention has been given to the weaknesses and strengths of different survey tools. When topics of conservation concern are illegal or otherwise sensitive, data collected using direct questions are likely to be affected by non-response and social desirability biases, reducing their validity. These sources of bias associated with using direct questions on sensitive topics have long been recognised in the social sciences but have been poorly considered in conservation and natural resource management. We reviewed specialized questioning techniques developed in a number of disciplines specifically for investigating sensitive topics. These methods ensure respondent anonymity, increase willingness to answer, and critically, make it impossible to directly link incriminating data to an individual. We describe each method and report their main characteristics, such as data requirements, possible data outputs, availability of evidence that they can be adapted for use in illiterate communities, and summarize their main advantages and disadvantages. Recommendations for their application in conservation are given. We suggest that the conservation toolbox should be expanded by incorporating specialized questioning techniques, developed specifically to increase response accuracy. By considering the limitations of each survey technique, we will ultimately contribute to more effective evaluations of conservation interventions and more robust policy decisions

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Heck Arylation Of Styrenes With Arenediazonium Salts: Short, Efficient, And Stereoselective Synthesis Of Resveratrol, Dmu-212, And Analogues

Short, efficient, and stereoselective synthesis of the trans-stilbenes resveratrol, DMU-212, and analogues of both compounds are described. The synthesis of these important anti-cancer agents feature the palladium catalyzed Heck-Matsuda arylation of styrenes with arenediazonium tetrafluoroborates. © 2008 Elsevier Ltd. All rights reserved.493956685671Renaud, S., De Lorgeril, M., (1992) Lancet, 339, p. 1523Baur, J.A., Pearson, K.J., Price, N.L., Jamieson, H.A., Lerin, C., Kalra, A., Prabhu, V.V., Sinclair, D.A., (2006) Nature, 444, p. 337Kimura, Y., Okuda, H., Arichi, S., (1985) Biochim. Biophys. Acta, 834, p. 275Inamori, Y., Kubo, M., Tsujibo, H., Ogawa, M., Saito, Y., Miki, Y., Takemura, S., (1987) Chem. Pharm. Bull., 35, p. 887Jang, D.S., Kang, B.S., Ryu, S.Y., Chang, I.M., Min, K.E., Kim, Y., (1999) Biochem. Pharmacol., 57, p. 705Chanvitayapongs, S., Draczynaka-Lusiak, B., Sun, A., (1997) Neuroreport, 8, p. 1499Mgbonnyebi, O., Russo, J., Russo, I., (1998) Int. J. Oncol., 12, p. 865Bhat, K.P., Lantvit, D., Christov, K., Mehta, R.G., Moon, R.C., Pezzuto, J.M., (2001) Cancer Res., 61, p. 7456Wang, Y., Lee, K.W., Chan, F.L., Chen, S., Leung, L.K., (2006) Toxicol. Sci., 92, p. 71Gupta, Y.K., Chaudhary, G., Srivastava, A.K., (2002) Pharmacology, 65, p. 170Doeherty, J.J., Fu, M.M.H., Stiffler, B.S., Limperos, R.J., Pokabla, C.M., DeLucia, A.L., (1999) Antiviral Res., 43, p. 145Stivala, L.A., Savio, M., Carafoli, F., Perucca, P., Bianchi, L., Maga, G., Forti, L., Vannini, V., (2001) J. Biol. Chem., 276, p. 22586Torres-Lopez, J.E., Ortiz, M.I., Castaneda-Hernandez, G., Alonso-Lopez, R., Asomoza-Espinosa, R., Grandos-Soto, V., (2002) Life Sci., 70, p. 1669Wang, Z.R., Huang, Y.Z., Zou, J.C., Cao, K.J., Xu, Y.N., Wu, J.M., (2002) Int. J. Mol. Med., 9, p. 77Sale, S., Verschoyle, R.D., Boocock, D., Jones, D.J.L., Wilsher, N., Ruparelia, K.C., Steward, W.P., Gescher, A.J., (2004) Br. J. Cancer, 90, p. 736Potter, G.A., Butler, P.C., Ruparelia, K.C., Ijaz, T., Wilsher, N., Wanogho, E., Tan, H.L., Burke, M.D., (2002) Br. J. Cancer, 86, pp. S117Sale, S., Tunstall, R.G., Ruparelia, K.C., Potter, G.A., Steward, W.P., Gescher, A.J., (2005) Int. J. Cancer, 115, p. 194Ferré-Filmon, K., Delaude, L., Demonceau, A., Noels, A.F., (2004) Coord. Chem. Rev., 248, p. 2323. , For a review on the synthesis of stilbenes, including resveratrol, see:Eddarir, S., Abdelhadi, Z., Rolando, C., (2001) Tetrahedron Lett., 42, p. 9127Yu, J., Gaunt, M.J., Spencer, J.B., (2002) J. Org. Chem., 67, p. 4627Guiso, M., Marra, C., Farina, A., (2002) Tetrahedron Lett., 43, p. 597Farina, A., Ferranti, C., Marra, C., (2006) Nat. Prod. Res., 20, p. 247Jeffery, T., Ferber, B., (2003) Tetrahedron Lett., 44, p. 193Andrus, M.B., Liu, J., Meredith, E.L., Nartey, E., (2003) Tetrahedron Lett., 44, p. 4819Botella, L., Nájera, C., (2004) Tetrahedron, 60, p. 5563Lebel, H., Ladjel, C., Bréthous, L., (2007) J. Am. Chem. Soc., 129, p. 13321Bazin, M.-A., Kihel, L.E., Lancelot, J.-C., Rault, S., (2007) Tetrahedron Lett., 48, p. 4347Ferre-Filmon, K., Delaude, L., Demonceau, A., Noels, A.F., (2005) Eur. J. Org. Chem., p. 3319Velder, J., Ritter, S., Lex, J., Schmalz, H.-G., (2006) Synthesis, p. 273Cross, G.G., Eisnor, C.R., Gossage, R.A., Jenkins, H.A., (2006) Tetrahedron Lett., 47, p. 2245Robinson, J.E., Taylor, R.J.K., (2007) Chem. Commun., p. 1617Roglans, A., Pla-Quintana, A., Moreno-Manas, M., (2006) Chem. Rev., 106, p. 4622. , For an excellent review, consult:Severino, E.A., Costenaro, E.R., Garcia, A.L.L., Correia, C.R.D., (2003) Org. Lett., 5, p. 305Meira, P.R.R., Moro, A.V., Correia, C.R.D., (2007) Synthesis, p. 2279Burtoloso, A.C.B., Garcia, A.L.L., Miranda, K.C., Correia, C.R.D., (2006) Synlett, p. 3145Pastre, J.C., Correia, C.R.D., (2006) Org. Lett., 8, p. 1657da Silva, K.P., Godoi, M.N., Correia, C.R.D., (2007) Org. Lett., 9, p. 2815Farina, A., Ferranti, C., Marra, C., Guiso, M., Norcia, G., (2007) Nat. Prod. Res., 21, p. 564Siegrist, U., Rapold, T., Blaser, H.-U., (2003) Org. Proc. Res. Dev., 7, p. 429. , The 3,4,5-trimethoxybenzenediazonium tetrafluoroborate was washed with a saturated aqueous solution sulfamic acid in order to destroy some residual sodium nitrite. This arenediazonium salt seems to perform at its best only after treatment with sulfamic acid( )Brooks, P.R., Wirtz, M.C., Vetelino, M.G., Rescek, D.M., Woodworth, G.F., Morgan, B.P., Coe, J.W., (1999) J. Org. Chem., 64, p. 971

Evolution And Synthetic Applications Of The Heck-matsuda Reaction: The Return Of Arenediazonium Salts To Prominence

This review highlights the potential and the versatility of arenediazonium salts as viable alternatives to conventional aryl halides and oxygen-based electrophiles for Pd-catalyzed Heck reactions. It also presents an overview of the field over the last decade, including some historical perspective of the Heck-Matsuda (HM) reaction with general considerations regarding reaction conditions, type of catalysts used, and the application of arenediazonium salts as reagents for the HM arylation of several types of alkenes. Throughout this review, the principal aspects related to reactivity and selectivity are discussed, and when applicable a comparison is made between the HM and the conventional Heck reactions. One-pot procedures that involve generation of the arenediazonium salt in situ from the corresponding aniline have been presented as well as some useful heterogeneous catalytic protocols. Allylic alcohols, conjugated alkenes, unsaturated heterocycles, and unactivated alkenes are capable of being arylated with arenediazonium salts by using simple catalysts such as Pd(OAc)2 or Pd2(dba)3 at room temperature in air and in benign and conventional solvents. In addition to the intramolecular variant of the HM reaction, intermolecular tandem coupling-cyclization processes have also been developed for the construction of a range of oxygen and nitrogen heterocycles. Finally, several applications towards the total synthesis of biologically active natural and nonnatural compounds are highlighted as well as the use of the HM reaction in the synthesis of new chiral, nonracemic ligands. This review highlights the synthetic potential and the versatility of arenediazonium salts as viable electrophiles for Pd-catalyzed Heck reactions. 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Highly Regio- And Stereoselective Heck Reaction Of Allylic Esters With Arenediazonium Salts: Application To The Synthesis Of Kavalactones

Image Presented A highly efficient palladium-catalyzed Heck reaction of allylic esters with arenediazonium salts is described. The reaction proceeds under mild conditions, with excellent to total regio- and stereochemical control and with retention of the traditional leaving group. Furthermore, the generality of the present methodology is illustrated by the short total synthesis of the natural kavalactones, yangonine, (±)-methysticin, and (±)-dihydromethysticin. © 2009 American Chemical Society.111636423645Beletskaya, I.P., Cheprakov, A.V., (2000) Chem. Rev, 100, p. 3009Alonso, F., Beletskaya, I.P., Yus, M., (2005) Tetrahedron, 61, p. 11771(2002) Handbook of Organopalladium Chemistry for Organic Synthesis, , Negishi, E.-I. Ed, Wiley-Interscience: New YorkTsuji, J., (2004) Palladium Reagents and Catalyst, , Wiley: Chichester, U.KCalò, V., Nacci, A., Monopoli, A., Ferola, V., (2007) J. Org. Chem, 72, p. 2596Bouquillon, S., Ganchegui, B., Estrine, B., Hénin, F., Muzart, J., (2001) J. Organomet. Chem, 634, p. 153Ambrogio, I., Cacchi, S., Fabrizi, G., Goggiamani, A., Sgalla, S., (2009) Synlett, p. 620Zawisza, A.M., Ganchegui, B., González, I., Bouquillon, S., Roglans, A., Hénin, F., Muzart, J., (2008) J. Mol. Catal. A: Chem, 283, p. 140Liu, S., Thomson, N., Pettman, A., Hyder, Z., Mo, J., Xiao, J., (2008) J. Mol. Catal. A: Chem, 279, p. 210Batt, F., Gozzi, C., Fache, F., (2008) Chem. Commun, p. 5830Scrivanti, A., Bertoldini, M., Beghetto, V., Matteoli, U., (2008) Tetrahedron, 64, p. 543Alacid, E., Nájera, C., (2007) Adv. Synth. Catal, 349, p. 2572Berthiol, F., Doucet, H., Santelli, M., (2005) Eur. J. Org. Chem, p. 1367Kang, S., Lee, H., Jang, S., Kim, T., Pyun, S., (1996) J. Org. Chem, 61, p. 2604Bernocchi, E., Cacchi, S., Ciattini, P.G., Morera, E., Ortar, G., (1992) Tetrahedron Lett, 33, p. 3073Ono, K., Fugami, K., Tanaka, S., Tamaru, Y., (1994) Tetrahedron Lett, 35, p. 4133Jeffery, T., (1991) Tetrahedron Lett, 32, p. 2121Masllorens, J., Bouquillon, S., Roglans, A., Hénin, F., Muzart, J., (2005) J. Organomet. Chem, 690, p. 3822Barbero, M., Cadamuro, S., Dughera, S., (2006) Synthesis, p. 3443Cacchi, S., Fabrizi, G., Goggiamani, A., Sferrazza, A., (2009) Synlett, p. 973Perez, R., Veronese, D., Coelho, F., Antunes, O.A.C., (2006) Tetrahedron Lett, 47, p. 1325Sengupta, S., Sadhukhan, S.K., (1998) Tetrahedron Lett, 39, p. 1237Trost, B.M., Van Vranken, D.L., (1996) Chem. Rev, 106, p. 395Pan, D., Chen, A., Su, Zhou, W., Li, S., Jia, W., Xiao, J., Jiao, N., (2008) Angew. Chem., Int. Ed, 47, p. 4729Mariampillai, B., Herse, C., Lautens, M., (2005) Org. Lett, 7, p. 4745. , For Heck arylations followed by -acetoxy elimination, see: aLautens, M., Tayama, E., Herse, C., (2005) J. Am. Chem. Soc, 127, p. 72Delcamp, J.H., White, M.C., (2006) J. Am. Chem. Soc, 128, p. 15076Su, Y., Jiao, N., (2009) Org. Lett, 11, p. 2980Aydin, J., Larsson, J.M., Selander, N., Szabó, K.J., (2009) Org. Lett, 11, p. 2852Bilia, A.R., Scalise, L., Bergonzi, M.C., Vincieri, F.F., (2004) J. Chromatogr. B, 812, p. 203Côté, C.S., Kor, C., Cohen, J., Auclair, K., (2004) Biochem. Biophys. Res. Commun, 322, p. 147Roglans, A., Pla-Quitana, A., Moreno-Manas, M., (2006) Chem. Rev, 106, p. 4622Severino, E.A., Costenaro, E.R., Garcia, A.L.L., Correia, C.R.D., (2003) Org. Lett, 5, p. 305Meira, P.R.R., Moro, A.V., Correia, C.R.D., (2007) Synthesis, p. 2279Burtoloso, A.C.B., Garcia, A.L.L., Miranda, K.C., Correia, C.R.D., (2006) Synlett, p. 3145Pastre, J.C., Correia, C.R.D., (2006) Org. Lett, 8, p. 1657da Silva, K.P., Godoi, M.N., Correia, C.R.D., (2007) Org. Lett, 9, p. 2815Gruber, A.S., Pozebon, D., Monteiro, A.L., Dupont, J., (2001) Tetrahedron Lett, 42, p. 7345. , For other Pd pre-catalysts operating under ligand-free conditions, seeMoro, A.V., Cardoso, F.S.P., Correia, C.R.D., (2008) Tetrahedron Lett, 49, p. 5668Amaral, P.A., Gouault, N., Le Roch, M., Eifler-Lima, V., David, M., (2008) Tetrahedron Lett, 49, p. 6607Hashimoto, T., Suganuma, M., Fujiki, H., Yamada, M., Kohno, T., Asakawa, Y., (2003) Phytomedicine, 10, p. 309Lygo, B., (1995) Tetrahedron, 51, p. 12859Scherer, J., (1998) Adv. Nat. Ther, 15, p. 261Bilia, A.R., Gallori, S., Vincieri, F.F., (2002) Life Sci, 70, p. 258

Stereoselective Synthesis Of Aza Analogues Of Isoaltholactone And Goniothalesdiol - New Applications Of The Heck-matsuda Reaction

The stereoselective synthesis of nitrogen analogues of biologically active isoaltholactone and goniothalesdiol are described. The successful strategy employed a Heck-Matsuda reaction between a chiral endocyclic enecarbamate bearing an ester functionality and arenediazonium tetrafluoroborates in a divergent approach at an early stage of the synthesis. Several aspects related to this critical arylation reaction are discussed to highlight structural features that affect the outcome of the arylation process. The synthesis of (-)-aza-isoaltholactone 6 was successfully accomplished in nine steps from the starting enecarbamate. We also performed the synthesis of the new fully substituted pyrrolidine (-)-(2R,3R,4S,5S)-1-(tert-butoxycarbonyl)-3,4-dihydroxy- 5-phenylpyrrolidin-2-ylacrylic acid 28, which is a potential advanced intermediate in the route to aza-altholactone. 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