bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis
Authors: Woolfit Megan , Rozpędowska Elżbieta , Piškur Jure , Wolfe Kenneth H. 
Published: February 2007

ABSTRACTThe hemiascomycete yeastDekkera bruxellensis, also known asBrettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected withD. bruxellensisdevelop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however,D. bruxellensishas been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain ofD. bruxellensisto obtain 0.4× coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to theirSaccharomyces cerevisiaeorthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship betweenD. bruxellensis,S. cerevisiae, andCandida albicansis close to a trichotomy. The estimated rate of chromosomal rearrangement inD. bruxellensisis slower than that calculated forC. albicans, while its rate of amino acid evolution is somewhat higher. The proteome ofD. bruxellensisis enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of theBurkholderia cepaciaspecies complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution ofD. bruxellensisand of the genetic bases of its physiological capabilities.
Drosophila melanogaster Thor
and Response to
Candida albicans
Infection
Authors: Levitin A. , Marcil A. , Tettweiler G. , Laforest M. J. , Oberholzer U. , Alarco A. M. , Thomas D. Y. , Lasko P. , Whiteway M. 
Published: February 2007

ABSTRACT

We used
Drosophila melanogaster
macrophage-like Schneider 2 (S2) cells as a model to study cell-mediated innate immunity against infection by the opportunistic fungal pathogen
Candida albicans
. Transcriptional profiling of S2 cells coincubated with
C. albicans
cells revealed up-regulation of several genes. One of the most highly up-regulated genes during this interaction is the
D. melanogaster
translational regulator 4E-BP encoded by the
Thor
gene. Analysis of
Drosophila 4E
-
BP

null

mutant survival upon infection with
C. albicans
showed that 4E-BP plays an important role in host defense, suggesting a role for translational control in the
D. melanogaster
response to
C. albicans
infection.
Characterization of the Proteasome Accessory Factor (paf) Operon inMycobacterium tuberculosis
Authors: Festa Richard A. , Pearce Michael J. , Darwin K. Heran 
Published: February 2007

ABSTRACTIn a previous screen forMycobacterium tuberculosismutants that are hypersusceptible to reactive nitrogen intermediates (RNI), two genes associated with theM. tuberculosisproteasome were identified. One of these genes,pafA(proteasomeaccessoryfactor A), encodes a protein of unknown function. In this work, we determined thatpafAis in an operon with two additional genes,pafBandpafC. In order to assess the contribution of these genes to RNI resistance, we isolated mutants with transposon insertions inpafBandpafC. In contrast to thepafAmutant, thepafBandpafCmutants were not severely sensitized to RNI, butpafBandpafCwere nonetheless required for full RNI resistance. We also found that PafB and PafC interact with each other and that each is likely required for the stability of the other protein inM. tuberculosis. Finally, we show that the presence of PafA, but not PafB or PafC, regulates the steady-state levels of three proteasome substrates. Taken together, these data demonstrate that PafA, but not PafB or PafC, is critical for maintaining the steady-state levels of known proteasome substrates, whereas all three proteins appear to play a role in RNI resistance.
Changes in bone remodelling and antifracture efficacy of intermittent bisphosphonate therapy: implications from clinical studies with ibandronate
Authors: Papapoulos S E , Schimmer R C 
Published: February 2007

Abstract
Bisphosphonates reduce the rate of bone resorption and bone remodelling. Given daily, they decrease the risk of fractures in postmenopausal osteoporosis. When bisphosphonates were given at extended drug-free intervals this antifracture efficacy was generally not seen. This may be due to the different pattern of bone remodelling changes. Data from randomised clinical studies of ibandronate, given orally or intravenously, at different doses and for variable time intervals to women with osteoporosis were examined to explore the relationship between intermittent bisphosphonate therapy, changes in bone resorption and fracture risk. The magnitude of the reduction of the rate of bone resorption at the end of the drug-free interval rather than its fluctuation pattern after bisphosphonate administration determines antifracture efficacy, provided that these fluctuations occur within the premenopausal range. Prolongation of the drug-free interval beyond 2 weeks should be compensated by a dose higher than the cumulative daily dose.
Setting the Bar in Phase II Trials: The Use of Historical Data for Determining “Go/No Go” Decision for Definitive Phase III Testing
Authors: Vickers Andrew J. , Ballen Vennus , Scher Howard I. 
Published: February 2007

Abstract
Purpose: Phase II trials aim to determine whether a cancer treatment is sufficiently promising to justify phase III study. Whether an agent is declared promising in a phase II trial depends on prespecified “null” and “alternative” rates of an outcome of interest such as tumor response. In some cases, the null must be determined with reference to historical data. We sought to determine the proportion of phase II trials that require historical data to establish the null and to determine how these historical estimates were derived.
Experimental Design: We conducted a systematic review of phase II trials published in the Journal of Clinical Oncology or Cancer in the 3 years to June 2005. Data were extracted following a prespecified protocol.
Results: We retrieved 251 papers, of which 117 were found to be ineligible; 70 of 134 included trials (52%) were defined as requiring historical data for design. Nearly half (32, 46%) of these papers did not cite the source of the historical data used, and just 9 (13%) clearly gave a single historical estimate as the rationale for the null. Trials that failed to cite prior data appropriately were significantly more likely to declare an agent to be active (82% versus 33%; P = 0.005). No study incorporated statistical methods to account for either sampling error or possible differences in case mix between the phase II sample and the historical cohort.
Conclusions: Many phase II trials require historical data to determine null response rates. Simple guidelines may improve design and reporting of such trials.
Site tenacity in European pond turtle (Emys orbicularis) hatchlings in Northwestern Spain
Authors: Ayres César , Cordero Adolfo 
Published: February 2007

AbstractHigh fidelity of European pond turtle (Emys orbicularis) hatchlings to optimal patches of habitat was observed for the first time in the most western population of Spain. To achieve this information we used a permanent marker to identify hatchlings, which allow us to follow the daily activity of the hatchlings without disturbing their behaviour. Hatchlings were observed associated with dense masses of Potamogeton sp., in areas with shallow water, up to 1.5 m, close to the shoreline. Our hypothesis is that hatchlings used these areas because there are no temporary ponds or streams that could be an optimal habitat. These preliminary data could be useful for planning management of protected wetlands.
Pets and invasion risks: is the Slider turtle strictly carnivorous?
Authors: Prévot-Julliard Anne-Caroline , Gousset Emeline , Archinard Chloé , Cadi Antoine , Girondot Marc 
Published: February 2007

Abstract
According to the International Union for Conservation of Nature (IUCN),
invasive species are one of the most important causes of biodiversity
decline at a global scale. The impact of introduced species on local
ecosystems is thus important to evaluate. Pet voluntary introductions are
made by private people and usually concern only one or two individuals per
occasion. However, the number of release occasions is as numerous as the
number of pet owners that don't want to keep their pet anymore and then
decide to "release" it. Hatchling red-eared slider turtles (Trachemys
scripta elegans) have been massively exported from the United States to
European (until 1997) and Asian countries to be sold as pets. Many owners,
ignoring the potential consequences of their act, have released their grown
up turtle in natural freshwater ecosystems. As a consequence, feral adult
turtles have been detected all over France. In this paper, we provide
information that contradicts public opinion that introduced slider turtle is
strictly carnivorous. By analysing the diet of feral adult turtles, we found
that adult slider turtles are omnivorous, as in their natural areas.
Comparing Filippi and Luiselli's (2000) method with a cartographic approach to assess the conservation status of secretive species: the case of the Iberian snake-fauna
Authors: Santos Xavier , Brito José C. , Pleguezuelos Juan M. , Llorente Gustavo A. 
Published: February 2007

Abstract
The conservation status of the snake fauna of a given region or territory is
often hard to estimate due the secretive habits of these animals, as well as
of the lack of long-term demographic studies and generally low population
densities. We examined the conservation status of the snakes from the
Iberian Peninsula by applying two complementary methods. The first method,
created by Filippi and Luiselli for a study of the Italian snakes
conservation status, takes into account the ecological and non-ecological
attributes which make species vulnerable to extinction. The second is a
cartographic analysis which consists of calculating two indexes derived from
the comparison of old and recent citations in UTM 10 × 10 km squares of
Iberian snakes by means of extensive database sets. For each species, we
calculated the percentage of recent citations, and the percentage of squares
with both old and recent citations. Species with low proportion of recent
citations and new squares appeared to be in decline. We found considerable
coincidence between the two methods in the identification of the most
threatened snake species: Vipera latastei, Coronella girondica, and Natrix
natrix. We suspect that the ecological specialisation and the low
reproductive output make C. girondica and V. latastei prone to extinction
when faced with environmental changes (i.e. habitat loss). For N. natrix, we
argue that this semi-aquatic snake experiences suboptimal environmental
conditions in Mediterranean habitats. A combination of both methods proved
adequate to detect vulnerability to extinction of snake species, hence
revealing an effective tool for establishing conservation strategies in
snakes and other secretive faunas.
The temperature-sensitive period (TSP) during incubation of broad-snouted caiman (Caiman latirostris) eggs
Authors: Piña Carlos , Siroski Pablo , Larriera Alejandro , Lance Valentine , Verdade Luciano M. 
Published: February 2007

Abstract
All crocodiles studied to date exhibit temperature-dependent sex
determination. During the many weeks from egg laying to hatch there is a
period of 10 to 15 d in the middle third of incubation (in the American
alligator) during which the sex of the embryo is irreversibly fixed,
referred to as the temperature-sensitive period or TSP. In this work we
investigated the TSP in Caiman latirostris eggs incubated at female-inducing
and male-inducing temperatures (29° C and 33° C respectively) by switching
eggs from 29° C to 33° C and vice versa at timed interval throughout
incubation. Compared to Alligator mississippiensis the duration of TSP was
longer, and the onset of TSP was at an earlier stage of incubation.
Habitat selection in the Pampa de Achala toad, Bufo achalensis
Authors: Jofré Gabriela , Reading Christopher , di Tada Ismael 
Published: February 2007

AbstractHabitat selection in adult and juvenile Bufo achalensis was studied at La Ciénaga Stream, Pampa de Achala, Central Argentina from December 1998 to October 2001. Habitat preference was evaluated by comparing the observed use of each habitat type with its availability. Juveniles were surveyed on 32 occasions between January 1999 and March 2001 using 13 permanent transects. The effect of cattle on larval survivorship was also evaluated. Most adult and juvenile B. achalensis occurred within 300 m of each side of the breeding site stream. No correlation was found between body size and distances moved. Juveniles and adults selected granite outcrops after the breeding season and avoided the heavily grazed areas. Adults also selected the stream and used tall tussock grassland in proportion to its availability. Juveniles used loose, flat, relatively small stones as shelters whilst adults used larger rocks. The presence of cattle at the breeding sites directly reduced larval survivorship by trampling, and indirectly through sediment deposition at the breeding sites resulting from increased stream bank erosion. The habitat preferences of B. achalensis suggest that long term cattle grazing also affects them adversely through deterioration of their transition habitat from tall tussock grassland to short sward. Future conservation management plans for B. achalensis must include the protection of the breeding sites and the surrounding terrestrial area if they are to be effective.
Genetic variation within African spiny-tailed lizards (Agamidae: Uromastyx) estimated using mitochondrial DNA sequences
Authors: Harris D. James , Vaconcelos Raquel , Brito José C. 
Published: February 2007

Abstract
African spiny-tailed lizards (Uromastyx) are large, herbivorous lizards
extensively traded locally for food and internationally as pets. Several
species have recently been described, although some remain controversial. To
determine relationships within North African forms, twenty individuals were
analysed for over 1000 bases of mitochondrial DNA sequences. Phylogenetic
analyses indicate four deeply divergent lineages that correspond to sampling
areas, but not to current species designations. These results indicate that
present taxonomy does not reflect the evolutionary history of these
species.
Specialised in-patient treatment for severe, chronic, resistant obsessive–compulsive disorder
Authors: Drummond Lynne M. , Pillay Anusha , Kolb Peter , Rani Shashi 
Published: February 2007

Aims and MethodA naturalistic study was conducted to examine the outcome on self-report and observer-rated measures in patients with severe, chronic, resistant obsessive–compulsive disorder (OCD) admitted to a specialised in-patient unit.ResultsTwenty-six patients were admitted over the study period. The mean age of all patients was 37 years (s.d.=13.8, range 18–61 years) and they had a mean duration of OCD of 18.4 years (s.d.=10.9, range 4–40 years). Instruments measuring severity demonstrated a 37–67% reduction in obsessive–compulsive symptoms and a 64% reduction in depressive symptoms after an average of almost 15 weeks in hospital.Clinical ImplicationsThis study demonstrates that specialised in-patient care can benefit a small group of severely ill patients with OCD who fail to respond to treatment in primary and secondary care.
MRCPsych examinations: cumulative results 1997–2002
Authors: Oyebode Femi , Furlong Elizabeth 
Published: February 2007

Aims and MethodThe aim of this study was to investigate the pattern of performance of candidates in the MRCPsych examinations in the period 1997–2002 inclusive. During this period 6306 candidates sat the MRCPsych part I and 4536 sat the MRCPsych part II.ResultsThe overall pass rates for MRCPsych part I was 44.7% and 48.9% for MRCPsych part II. The majority of those who passed either part of the examinations did so on their first attempt; females performed better than males and graduates of UK and Republic of Ireland medical schools performed better than foreign graduates in all component parts of the examinations.Clinical ImplicationsThe pattern of results suggests that clinical tutors and course organisers need to pay special care to the training needs of trainees who are foreign medical graduates.
Piezoresistive Behavior Study on Finger‐Sensing Silicone Rubber/Graphite Nanosheet Nanocomposites
Authors: Chen L. , Chen G. H. , Lu L. 
Published: January 2007

AbstractA novel finger‐sensing nanocomposite with remarkable and reversible piezoresistivity is successfully fabricated by dispersing homogeneously conductive graphite nanosheets (GNs) in a silicone rubber (SR) matrix. Because of the high aspect ratio of the graphite nanosheets, the nanocomposite displays a very low percolation threshold. The SR/GN nanocomposite with a volume fraction of conductive nanosheets closest to that for the percolation threshold presents a sharp positive‐pressure coefficient effect of the resistivity under very low pressure, namely, in the finger‐pressure range (0.3–0.7 MPa), whereby the abrupt transition could be attributed to compressive‐stress‐induced deformation of the conducting network. The super‐sensitive piezoresistive behavior of the nanocomposite is accounted for by an extension of the tunneling conduction theory which provides a good approximation to the piezoresistive effect.
Cover Picture: Synthesis of Polyaniline Nanotubes with a Reactive Template of Manganese Oxide (Adv. Mater. 3/2007)
Authors: Pan L. J. , Pu L. , Shi Y. , Song S. Y. , Xu Z. , Zhang R. , Zheng Y. D. 
Published: January 2007

AbstractPolyaniline nanotubes can be synthesized through a chemical template method. The shape and major parameters of the tubes are precisely controlled by the reactive templates of MnO2 nanowires, which also act as the oxidative initiator for polymerization. The cover image shows an example where the rectangular tubes are cloned from the cryptomelane‐phase MnO2, as reported on p. 461 by Shi and co‐workers.
High surface area titania photocatalytic microfluidic reactors
Authors: Lindstrom Henrik , Wootton Robert , Iles Alexander 
Published: February 2007

AbstractIn this work a simple method is described for depositing a robust yet highly porous film of anatase titania nanoparticles with a very high surface area onto the inside walls of microfluidic devices. A very high loading of 66 g of titania per liter of reactant solution was achieved. The effectiveness is demonstrated of this deposition method by producing functionalized microfluidic reactor devices and using them to photocatalytically degrade air‐saturated methylene blue solutions. Experiments were performed with and without the addition of gaseous oxygen to the microreactors. The addition of oxygen dramatically enhanced the degradation rate. This highlights the necessity for supplying additional oxygen to microsystems during photocatalysis since dissolved oxygen can be rapidly depleted within the small confined space inside microreactors. With additional gaseous oxygen, the conversion rate for the photodegradation reaction of 0.1mM methylene blue at a flow rate of 12 μl min−1 was 10.6 % s−1. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Modeling l‐dopa purification by chiral ligand‐exchange chromatography
Authors: Sanaie Nooshafarin , Haynes Charles A. 
Published: February 2007

AbstractA model describing elution‐band profiles that combines multiple chemical equilibria theory with the nonideal equilibrium–dispersion equation for solute transport is used to predict and characterize the separation of l,d‐dopa by chiral ligand‐exchange chromatography (CLEC). Formation constants and stoichiometries for all equilibrium complexes formed in the interstitial volume and pore liquid are taken from standard thermodynamic databases and independent potentiometric titration experiments. Formation constants for complexes formed with the stationary phase ligand (N‐octyl‐3‐octylthio‐d‐valine) are determined from potentiometric titration data for a water‐soluble analogue of the ligand. This set of pure thermodynamic parameters is used to calculate the spatially discretized composition of each column volume element as a function of time. The model includes a temperature‐dependent pure‐component parameter, determined by regression to a single elution band for the pure component, that corrects for subtle effects associated with immobilizing the N‐octyl‐3‐octylthio‐d‐valine ligand onto the stationary phase. The model is shown to accurately predict elution chromatograms and separation performance as a function of key column operating variables. The model is then used to better understand the connection between chemical equilibria within the system and changes in band profiles and band separation resulting from changes in column operating conditions. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Marine research, resources and conservation in the Azores
Authors: Santos Ricardo Serrão , Hawkins Stephen , Monteiro Luis Rocha , Alves Mário , Isidro Eduardo José 
Published: February 2007

AbstractA history of marine research on the Azores is outlined. Until two decades ago most oceanic and littoral marine studies had been carried out by foreign scientists. Studies by Azorean scientists started to increase in the early 1980s when the University of the Azores was created.Ocean circulation in this part of the Atlantic is described as a background for biogeography and diversity. The picture emerges that Azores is a ‚meeting point’︁ for shallow water marine fauna and flora of different origins.The species composition of one of the best studied groups of organisms, the fish, is compared between locations in the northeastern Atlantic. The work on fish is also compared with other well studied groups (algae and hydroids) to highlight the interest of the Azores as a natural biogeographical experiment.Studies of marine resources began less than two decades ago. The development of demersal fisheries is described focusing on the switch from small‐scale artisanal fishing to more commercial fisheries.Conservation of species and legislation in force for molluscs, crustaceans, fishes, marine turtles, seabirds and marine mammals are summarized.Protected marine areas already designated are defined, as well as new areas recommended.The paper concludes with a discussion of current threats and future management strategies.