What Darwin Disturbed: The Biology that Might have been.

Uses counterfactual history to argue that Darwin had a unique impact on the development of moern biology.

Roche tomography of cataclysmic variables - V. A high-latitude star-spot on RU Pegasi

We present Roche tomograms of the secondary star in the dwarf nova system RU Pegasi derived from blue and red arm ISIS data taken on the 4.2-m William Herschel Telescope. We have applied the entropy landscape technique to determine the system parameters and obtained component masses of M1 = 1.06 Msun, M2 = 0.96 Msun, an orbital inclination angle of i = 43 degrees, and an optimal systemic velocity of gamma = 7 km/s. These are in good agreement with previously published values. Our Roche tomograms of the secondary star show prominent irradiation of the inner Lagrangian point due to illumination by the disc and/or bright spot, which may have been enhanced as RU Peg was in outburst at the time of our observations.We find that this irradiation pattern is axi-symmetric and confined to regions of the star which have a direct view of the accretion regions. This is in contrast to previous attempts to map RU Peg which suggested that the irradiation pattern was non-symmetric and extended beyond the terminator. We also detect additional inhomogeneities in the surface distribution of stellar atomic absorption that we ascribe to the presence of a large star-spot. This spot is centred at a latitude of about 82 degrees and covers approximately 4 per cent of the total surface area of the secondary. In keeping with the high latitude spots mapped on the cataclysmic variables AE Aqr and BV Cen, the spot on RU Peg also appears slightly shifted towards the trailing hemisphere of the star. Finally, we speculate that early mapping attempts which indicated non-symmetric irradiation patterns which extended beyond the terminator of CV donors could possibly be explained by a superposition of symmetric heating and a large spot.

The solution structure of 1:2 phenol/N-methylpyridinium bis{(trifluoromethyl)sulfonyl}imide liquid mixtures

Neutron diffraction has been used to investigate the liquid structure of a 1:2 solution of phenol in the ionic liquid N-methylpyridinium bis{(trifluoromethyl)sulfonyl}imide at 60 ◦C, using the empirical potential structure refinement (EPSR) process to model the data obtained from the SANDALS diffractometer at ISIS. Addition of phenol results in suppression of the melting point of the pyridinium salt and formation of a room temperature solution with aromatic phenol–cation and phenol-OH to anion hydrogen-bonding interactions.

Haptic Aurality – performing in a digital world

Paper accepted at 2015 ISIS in Utrecht. This presentation will examine the performative body from the viewpoint of the listening body in digital media platforms, and thus investigates the proposed conference issues which are at the intersections of ‘play’, ‘perform’ and ‘participate’.

Interhemispheric inhibition of corticospinal projections to forearm muscles

OBJECTIVE: Interhemispheric inhibition (IHI) is typically examined via responses elicited in intrinsic hand muscles. As the cortical representations of proximal and distal muscles in the upper limb are distinguished in terms of their inter-hemispheric projections, we sought to determine whether the IHI parameters established for the hand apply more generally.

METHODS: We investigated IHI at 5 different conditioning stimulus (CS) intensities and a range of short-latency inter-stimulus intervals (ISIs) in healthy participants. Conditioning and test stimuli were delivered over the M1 representation of the right and left flexor carpi radialis respectively.

RESULTS: IHI increased as a function of CS intensity, and was present for ISIs between 7 and 15ms. Inhibition was most pronounced for the 10ms ISI at all CS intensities.

CONCLUSIONS: The range of parameters for which IHI is elicited in projections to the forearm is similar to that reported for the hand. The specific utility lies in delineation of stimulus parameters that permit both potentiation and attenuation of IHI to be assessed.

SIGNIFICANCE: In light of evidence that there is a greater density of callosal projections between cortical areas that represent proximal muscles than between those corresponding to distal limb muscles, and in view of the assumption that variations in functional connectivity to which such differences give rise may have important implications for motor behavior, it is critical to determine whether processes mediating the expression of IHI depend on the effector that is studied. This issue is of further broad significance given the practical utility of movements generated by muscles proximal to the wrist in the context of upper limb rehabilitation.

Territories of scarcity and creativity: a critical view of informal settlements and emerging tactics under conditions of scarcity in Nairobi, Kenya and Quito, Ecuador

This thesis explores the processes through which scarcity is constructed in informal settlements and how conditions emerging within its limits gives way to particular socio-spatial phenomena and influence the emergence of self-organisation and creative strategies from a non-expert perspective. At the same time, this thesis deconstructs these emerging tactics (reactive and transformative) in a diagrammatic way to generate a critical study of their potential for socio-spatial change that goes beyond the everyday survival. Most people associate scarcity with “not having enough” of something, most usually of a material nature. In contrast, this paper is based on the premise that scarcity is a constructed condition, therefore exploring it beyond its immediate manifestation and illustrating its discursive, distributive and socio-material components. In this line, the research uses Assemblage Theory as both an approach and a tool for analysis. This approach allows the research to depart from everyday narratives of the residents, and gradually evolve into a multi-scalar, non-linear reading of scarcity, by following leads into different realms and unpacking a series of routine events to uncover their connections to wider processes and particular elements affecting the settlement and the city as a whole. For this purpose, the research is based on a qualitative, flexible and multi-sited methodology, using different case studies as testing grounds. Collected data stems from a 11-months ethnographic fieldwork in informal settlements in Ecuador and Kenya, analysing the socio-spatial practices and strategies deployed by the different actors producing the built environment and arising from everyday and latent experiences of scarcity. The thesis examines the multi-scalar nature of these strategies, including self-building and management tactics, the mobilisation of grassroots organisations, the innovative ways of collaborating deployed by different coalitions and the reformulation of urban development policies. As outcomes of the research, the thesis will show illustrative diagrams that allow a better understanding of, firstly, the construction of scarcity in the built environment beyond its immediate manifestation and secondly, the way that emerging tactics a) improve existing conditions of scarcity, b) reinforce the status quo or c) contribute to the worsening of the original condition. Therefore, this thesis aims to offer lessons with both practical and theoretical considerations, by firstly, giving an insight into the complexity and transcalar nature of the construction of scarcity in informal settlements; secondly, by illustrating how acute conditions related to scarcity gives birth to a plethora of particular phenomena shaping the territory, social relationships and processes; and thirdly, by identifying specific characteristics within the informal that might allow for new readings of the city and possibilities for socio-spatial change under conditions of scarcity.

Criação de um Microtesauro na área da Dança

Dissertação realizada no âmbito do Mestrado em Ciências Documentais, Variante Bibliotecas e Centros de Documentação, da Universidade Lusófona de Humanidades e Tecnologias(ULHT). [O documento original encontra-se depositado no Repositório Científico Lusófona]

Development of metabolic labeling strategies to study changes in protein expression

Résumé : Les progrès techniques de la spectrométrie de masse (MS) ont contribué au récent développement de la protéomique. Cette technique peut actuellement détecter, identifier et quantifier des milliers de protéines. Toutefois, elle n'est pas encore assez puissante pour fournir une analyse complète des modifications du protéome corrélées à des phénomènes biologiques. Notre objectif était le développement d'une nouvelle stratégie pour la détection spécifique et la quantification des variations du protéome, basée sur la mesure de la synthèse des protéines plutôt que sur celle de la quantité de protéines totale. Pour cela, nous volions associer le marquage pulsé des protéines par des isotopes stables avec une méthode d'acquisition MS basée sur le balayage des ions précurseurs (precursor ion scan, ou PIS), afin de détecter spécifiquement les protéines ayant intégré les isotopes et d'estimer leur abondance par rapport aux protéines non marquées. Une telle approche peut identifier les protéines avec les plus hauts taux de synthèse dans une période de temps donnée, y compris les protéines dont l'expression augmente spécifiquement suite à un événement précis. Nous avons tout d'abord testé différents acides aminés marqués en combinaison avec des méthodes PIS spécifiques. Ces essais ont permis la détection spécifique des protéines marquées. Cependant, en raison des limitations instrumentales du spectromètre de masse utilisé pour les méthodes PIS, la sensibilité de cette approche s'est révélée être inférieure à une analyse non ciblée réalisée sur un instrument plus récent (Chapitre 2.1). Toutefois, pour l'analyse différentielle de deux milieux de culture conditionnés par des cellules cancéreuses humaines, nous avons utilisé le marquage métabolique pour distinguer les protéines d'origine cellulaire des protéines non marquées du sérum présentes dans les milieux de culture (Chapitre 2.2). Parallèlement, nous avons développé une nouvelle méthode de quantification nommée IBIS, qui utilise des paires d'isotopes stables d'acides aminés capables de produire des ions spécifiques qui peuvent être utilisés pour la quantification relative. La méthode IBIS a été appliquée à l'analyse de deux lignées cellulaires cancéreuses complètement marquées, mais de manière différenciée, par des paires d'acides aminés (Chapitre 2.3). Ensuite, conformément à l'objectif initial de cette thèse, nous avons utilisé une variante pulsée de l'IBIS pour détecter des modifications du protéome dans des cellules HeLa infectée par le virus humain Herpes Simplex-1 (Chapitre 2.4). Ce virus réprime la synthèse des protéines des cellules hôtes afin d'exploiter leur mécanisme de traduction pour la production massive de virions. Comme prévu, de hauts taux de synthèse ont été mesurés pour les protéines virales détectées, attestant de leur haut niveau d'expression. Nous avons de plus identifié un certain nombre de protéines humaines dont le rapport de synthèse et de dégradation (S/D) a été modifié par l'infection virale, ce qui peut donner des indications sur les stratégies utilisées par les virus pour détourner la machinerie cellulaire. En conclusion, nous avons montré dans ce travail que le marquage métabolique peut être employé de façon non conventionnelle pour étudier des dimensions peu explorées en protéomique. Summary : In recent years major technical advancements greatly supported the development of mass spectrometry (MS)-based proteomics. Currently, this technique can efficiently detect, identify and quantify thousands of proteins. However, it is not yet sufficiently powerful to provide a comprehensive analysis of the proteome changes correlated with biological phenomena. The aim of our project was the development of ~a new strategy for the specific detection and quantification of proteomé variations based on measurements of protein synthesis rather than total protein amounts. The rationale for this approach was that changes in protein synthesis more closely reflect dynamic cellular responses than changes in total protein concentrations. Our starting idea was to couple "pulsed" stable-isotope labeling of proteins with a specific MS acquisition method based on precursor ion scan (PIS), to specifically detect proteins that incorporated the label and to simultaneously estimate their abundance, relative to the unlabeled protein isoform. Such approach could highlight proteins with the highest synthesis rate in a given time frame, including proteins specifically up-regulated by a given biological stimulus. As a first step, we tested different isotope-labeled amino acids in combination with dedicated PIS methods and showed that this leads to specific detection of labeled proteins. Sensitivity, however, turned out to be lower than an untargeted analysis run on a more recent instrument, due to MS hardware limitations (Chapter 2.1). We next used metabolic labeling to distinguish the proteins of cellular origin from a high background of unlabeled (serum) proteins, for the differential analysis of two serum-containing culture media conditioned by labeled human cancer cells (Chapter 2.2). As a parallel project we developed a new quantification method (named ISIS), which uses pairs of stable-isotope labeled amino acids able to produce specific reporter ions, which can be used for relative quantification. The ISIS method was applied to the analysis of two fully, yet differentially labeled cancer cell lines, as described in Chapter 2.3. Next, in line with the original purpose of this thesis, we used a "pulsed" variant of ISIS to detect proteome changes in HeLa cells after the infection with human Herpes Simplex Virus-1 (Chapter 2.4). This virus is known to repress the synthesis of host cell proteins to exploit the translation machinery for the massive production of virions. As expected, high synthesis rates were measured for the detected viral proteins, confirming their up-regulation. Moreover, we identified a number of human proteins whose synthesis/degradation ratio (S/D) was affected by the viral infection and which could provide clues on the strategies used by the virus to hijack the cellular machinery. Overall, in this work, we showed that metabolic labeling can be employed in alternative ways to investigate poorly explored dimensions in proteomics.

Recueil d'épitaphes, précédé d'un journal des principaux événements arrivés à Paris de 1557 à 1590.

Contient : 1 Journal autographe de JEHAN DE LA FOSSE, où sont notés mois par mois les principaux événements des années 1557 à 1590, arrivés en France et particulièrement à Paris, où vivait l'auteur, curé de St-Leu et de St-Barthélemy ; 2 Recueil d'épitaphes ; « Cavendish,... general Norris,... docter Story,... mylord Treasurer,... Frier Andrew,... Ellis,... earle of Essex, beheaded in the tower », Joannes Rekingale, episcopus Cicestriensis, Gulielmus de Blitz, archidiaconus Nodovicensis ; Thomas Linaerus, regis Henrici VIII medicus, Antonius Riccius Faventiae, « Mr Hofkins », Lucretia Borgia, Honorius P. M., Johannes Riberius ; Galfridus Chaucer, Corythus, filius Oenones et Paridis, Ninus, Assyriae monarcha, Pyramis, lateritia Asychis, Aegypti regis ; Bartholomaeus Platina, Petrus Pomponatius, Pompeius Magnus, Capys, Ennius, Hannibal ; Marcus Antonius Turrianus, Marcus Antonius Coccius, Marcus Antonius Casanova, Sardanapalus, Rufus, Julius Caesar, Augustus Caesar ; Petrus Ciaconius, Nicolaus Macchiavellus, Gulielmus Rondeletus, medicus, Anicia, foemina romana, Callicratea ; Johannes Coletus, Rembertus Dodonaeus, medicus Maximiliani II et Rodolphi imperatorum, Alcaeus poeta, Scipio Africanus ; Paracelsus, Gerardus Noviomagus et Andreas Hyperius, Didacus de Valdes, Albericus de Vere et Gulielmus, primus comes Oxoniensis, Robertus Buc ; Hieronymus Cagnolus Vercellensis, Johannes Stofflerus, mathematicus Tubingae, Remigius Bellaqueus, Pallas, Evandri filius, Zarmanochegas indus, de Bargosa ; Johannes Rivius Attbend, Petrus Bembus, Lucius P. M. Veronae, Gulielmus Norselez, decanus quondam ecclesiae S. Pauli Londini, Mathias Corvinus, rex Pannoniae ; Philippus Callimachus Cracoviae, in aede S. Trinitatis, Ludovicus Bologninus, Bononiae, Rachel, uxor Jacobi Bethleem, Aratus, Plato, Aeschylus ; Joannes Zonaras, Homerus, Menander, Epictetus ; Berengarius, archidiaconus Andegavensis, Andreas Fanzonius, Cyrus, Persarum monarcha, Midas ; Hugo S. Victoris Parisiensis, S. Bernardus, abbas claraevallensis, Petrus de Toledo, Psittacus, Musaeus poeta, Linus, thebanus poeta, Orpheus ; Petrus Lombardus, Petrus Comestor, Pallas, libertus Romae, Megista, Spartanus vates ; Aegidius de Roma, archiepiscopus Bituricensis, Johannes Gerson, Aristocrates, perfidus in Lycaei Jovis luco, Setho, sacerdos Vulcani et Aegypti rex, Rosamunda Cliffordensis, Petrus Aretinus ; Nicolaus de Lyra, Jacobus Pisaurus, Paphi episcopus, Cedwalla, rex Sussexiae ; Alphonsus Tostadus, hispanus, Abulensis episcopus, Albertus Pius de Sabaudia, princeps Carporum, Similis, praefectus praetorianorum, Jupiter, Osyris, Isis ; Aeneas Sylvius, Christophorus Colombus, Hermes, Apollo, Timon, Darius ; Robertus Gaguinus, Johannes de Sacro Busto, Darius, Hystaspis filius, Simandius, Aegypti rex, Idomeneus et Myrio, filii Deucalionis, Semiramis ; Alexander Piccolomineus, Justina, pulchra foemina, quam maritus zelotypus nefarie decollavit, Claudia, nobilis foemina Romae, Carolus Magnus, Carolus V, imperator ; Actius Plautus, Johannes Boccacius, Franciscus Ximenes, cardinalis Hispaniae, Federicus imperator, Sylla, Ricardus I, rex Anglorum ; Johannes Stadius, math. belga, C. Manlia camertina, Johannes de Mandeville, Patricius, Brigida et Columda in Hibernia, la reine d'Angleterre, femme de Jacques Ier ; Johannes Glandorp, Jodocus, medicus Romae, Urandus, sive Durandus, Johannes Jacobus Trivultius, Ludovicus VIII, rex Francorum ; Antonius quidam italus, Fin dal Finale, Battistina Senensis, puella elegantissima ; Chalonerus Dubliniae, Askew Lincolniensis, Christophorus Hatton, Robertus, comes Leicestriae ; Johannes Chidley, Walterus Ralegh, Arturus Gorges, Johannes Parkar, Maria Stafford, Charitas et Carolus Ho., Thomas Wals, Sylvanus Scorus, Johannes Horo et Edwardus Nymark, Edwardus Stanhop, Franciscus Wal ; Philippus Sydney, Franciscus Walsinghan, N. Marsonius, jurisconsultus, Christophorus H, Gulielmus, comes Penbrok, Angliae marescallus, Antonius Deny, frater Lubinus ; Fratislaus, dux Bohemiae, countess of Penbrok, Edward Spenser, Henry Abyngdon, Thomas Nash, N. Dobson ; Dr Hugh a price, Johannes Vitulus, Dr Bently, Hor. Pallavicin, Margaret Ratcliff ; Howlet, Elian, Henry Barron ; James Stuart, Thomas Sackville, Penelope d'Evreux, uxor domini Bar. Rich, pellicis comitis Devonshire, Robert Cecil, Ricardus Bancroft, archiepiscopus Cantuariensis ; Godefridus de Bulion, Balduinus, rex Jerusalem, Allicia, pulchra foemina anglica et forte meretrix, Theobaldus, comes Campaniae, qui vixit tempore regis Angliae Stephani ; Fernandus de Castro, hispanus in Anglia exulans et moriens ob fidem in Dominum Petrum, regem Castellae, Johannes Taylor de Colman street, usurarius, Petrus Miago Vallisoleti, in templo Sancti Stephani, Franciscus Duarte de Mendico, a proveedor de los exercitos y armadas del emperador Carlo V, Henricus, Walliae princeps ; Milo, comes de Anglera, pater Rolandi, a Mauris juxta ripam Ceae occisus, Hecuba, S. Edmundus, rex et martyr, Pindarus, poeta lyricus, Stesichorus, Anacreon, poeta vinosus, Leonidas, dux Lacedemoniorum ad Thermopylas occisus contra Persas, Timotheus, citharedus milesius ; Timocreon Rhodius, Laïs, meretrix Corinthia, sepulta in Thessalia, juxta Peneum fluvium, Acron, antiquissimus medicus Agrigentinus

Livre des Morts de Djéhoutyirydès. Egyptien 133

Colonne 1 : trois vignettes sur trois registres. Sur la vignette supérieure, on voit le défunt en adoration devant Khépri, forme du dieu solaire, qui se trouve sur la barque solaire. La vignette du milieu montre le défunt en adoration devant Osiris assis sur son trône et assisté de Isis. La dernière vignette montre le défunt en adoration devant deux divinités assises, qui symbolisent l'Ennéade.Col. 2, x+1-11 et vignette : chapitre 111 (=108) avec titre en lacune ("Formule pour connaître les âmes de l'Occident"). La vignette montre le défunt en adoration devant deux divinité à tête de faucon.Col. 2, x+12-20 : chapitre 114 avec titre rubrique : "Formule pour connaître les âmes d'Hermopolis". La vignette montre le défunt devant Thot et une table d'offrandes.Col. 3, 1-10 et vignette : chapitre 117 avec titre rubriqué : "Formule (pour s'engager dans les chemins de Rosetchaou)". La vignette montre le défunt s'inclinant, le dos tourné vers une butte. Col. 3, 11-19 et vignette : chapitre 118 avec titre rubriqué : "Formule pour atteindre Rosetchaou". La vignette montre le défunt s'inclinant.Col. 4, 1-12 et vignette : chapitre 119 avec titre rubriqué : "Formule pour sortir de (Rosetchaou)". La vignette montre le défunt debout tourné vers la droite.Col. 4, 13-21 et vignette : chapitre 120 (=12) avec titre rubriqué : "Formule pour entrer et sortir de Rosetchaou". La vignette montre le défunt face à lui-même.Col. 5, 1-30 : début du chapitre 125, déclaration d'innocence.

(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides

(A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene, RNA interference, and aptamers. Although synthesis of RNA sequences faces many challenges, most notably the choice of the 2' -hydroxy protecting group, modified 2' -O-Cpep protected ribonucleotides were synthesized as alternitive building blocks. Altering phosphitylation procedures to incorporate 3' -N,N-diethyl phosphoramidites enhanced the overall reactivity, thus, increased the coupling efficiency without loss of integrety. Furthermore, technical optimizations of solid phase synthesis cycles were carried out to allow for successful synthesis of a homo UIO sequences with a stepwise coupling efficiency reaching 99% and a final yield of 91 %. (B) Over the past few decades, dipyrrometheneboron difluoride (BODIPY) has gained recognition as one of the most versatile fluorophores. Currently, BODIPY labeling of oligonucleotides are carried out post-synthetically and to date, there lacks a method that allows for direct incorporation of BODIPY into oligonucleotides during solid phase synthesis. Therefore, synthesis of BODIPY derived phosphoramidites will provide an alternative method in obtaining fluorescently labelled oligonucleotides. A method for the synthesis and incorporation of the BODIPY analogues into oligonucleotides by phosphoramidite chemistry-based solid phase DNA synthesis is reported here. Using this approach, BODIPY-labeled TlO homopolymer and ISIS 5132 were successfully synthesized.