bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid membrane protein topology prediction
Authors: Hennerdal Aron , Elofsson Arne 
Published: April 2011

Abstract
Summary: State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ∼6% worse than the best method that is utilizing multiple sequence alignments.
Availability and Implementation: TOPCONS-single is available as a web server from http://single.topcons.net/ and is also included for local installation from the web site. In addition, consensus-based topology predictions for the entire international protein index (IPI) is available from the web server and will be updated at regular intervals.
Contact: arne@bioinfo.se
Supplementary information: Supplementary data are avaliable at Bioinformatics online.
Restaurant staff's knowledge of anaphylaxis and dietary care of people with allergies
Authors: Bailey S. , Albardiaz R. , Frew A. J. , Smith H. 
Published: April 2011

SummaryBackground
Deaths caused by food‐induced anaphylactic reactions are increasing, with most caused by food purchased outside the home. Primary prevention by allergen avoidance is desirable, but is easier in the home than when eating out, where the responsibility is shared with restaurant staff.Objective
To investigate restaurant staff's knowledge about food allergies.Method
A structured telephone questionnaire was administered to a member of staff at 90 table‐service restaurants in Brighton.Results
Fifty‐six percent (90/162) restaurants that were contacted agreed to participate. Responders included seven owners, 48 managers, 20 waiters and 15 chefs. Ninety per cent (81/90) reported food hygiene training; 33% (30/90) reported specific food allergy training. Fifty‐six percent (50/90) could name three or more food allergens. Eighty‐one percent reported confidence (very or somewhat) in providing a safe meal to a food‐allergic customer. Answers to true–false questions indicated some frequent misunderstandings: 38% believed an individual experiencing a reaction should drink water to dilute the allergen; 23% thought consuming a small amount of an allergen is safe; 21% reported allergen removal from a finished meal would render it safe; 16% agreed cooking food prevents it causing allergy and 12% were unaware allergy could cause death. Forty‐eight percent expressed interest in further training on food allergy.Conclusions and Clinical Relevance
Despite a high confidence level, there are obvious gaps in restaurant staff's knowledge of allergy. Food‐allergic patients need to be aware of this and adapt their behaviour accordingly. Our data challenge the impact of current food allergy training practice for restaurant staff, and support the need for more rigorous and accessible training. Cite this as: S. Bailey, R. Albardiaz, A. J. Frew and H. Smith, Clinical & Experimental Allergy, 2011 (41) 713–717.
The utility of contemporary and historical estimates of dispersal in determining response to habitat fragmentation in a tropical forest‐dependent bird community
Authors: BOWIE RAURI C. K. 
Published: April 2011

It is often assumed that species which exhibit a greater propensity for dispersal are less susceptible to the impacts of habitat fragmentation; however, a growing body of literature suggests that such generalizations should be carefully evaluated as not all species appear to be equally sensitive to fragmentation. In this issue of Molecular Ecology, Callens et al. (2011) take an innovative approach to compare contemporary estimates of dispersal from an extensive mark‐recapture and patch occupancy data set with historical estimates derived from multilocus population genetic models for seven sympatric forest‐dependent species in the Taita Hills, Africa. As has been observed for forest‐dependent species from the Amazon, populations of sedentary species were more strongly differentiated and clustered when compared to those of more dispersive taxa. The most intriguing result recovered though, was that the five species with similar historical estimates of gene flow (dispersal) differed substantially in their contemporary dispersal rates, suggesting that for some species the propensity for dispersal has decreased over time. As a consequence, the authors suggest that post‐fragmentation estimates of dispersal on their own may not be the best predictors of how habitat fragmentation could affect forest‐dependent animal communities. This work significantly advances our understanding of the dynamics of habitat fragmentation and makes a strong case for the need to integrate data on historical processes with contemporary data.
The genomic and physiological basis of life history variation in a butterfly metapopulation
Authors: KLEPSATEL PETER , FLATT THOMAS 
Published: April 2011

Unravelling the mechanisms underlying variation in life history traits is of fundamental importance for our understanding of adaptation by natural selection. While progress has been made in mapping fitness‐related phenotypes to genotypes, mainly in a handful of model organisms, functional genomic studies of life history adaptations are still in their infancy. In particular, despite a few notable exceptions, the genomic basis of life history variation in natural populations remains poorly understood. This is especially true for the genetic underpinnings of life history phenotypes subject to diversifying selection driven by ecological dynamics in patchy environments—as opposed to adaptations involving strong directional selection owing to major environmental changes, such as latitudinal gradients, extreme climatic events or transitions from salt to freshwater. In this issue of Molecular Ecology, Wheat et al. (2011) now make a significant leap forward by applying the tools of functional genomics to dispersal‐related life history variation in a butterfly metapopulation. Using a combination of microarrays, quantitative PCR and physiological measurements, the authors uncover several metabolic and endocrine factors that likely contribute to the observed life history phenotypes. By identifying molecular candidate mechanisms of fitness variation maintained by dispersal dynamics in a heterogeneous environment, they also begin to address fascinating interactions between the levels of physiology, ecology and evolution.
Methoprene and protein supplements accelerate reproductive development and improve mating success of male tephritid flies
Authors: Teal P. E. A. , Pereira R. , Segura D. F. , Haq I. , Gómez‐Simuta Y. , Robinson A. S. , Hendrichs J. 
Published: April 2011

AbstractWe have been studying the behavioural and physiological mechanisms associated with coordination of reproductive maturity and sex pheromone communication in male tephritid flies in order to develop methods for acceleration of reproductive maturity among sterilized males. Our studies revealed that exposure to the juvenile hormone analogue methoprene can accelerate the rate of sexual maturity in some but not all tephritid species tested. Additionally, we have determined that incorporation of protein hydrolysate into the adult diet improves sexual performance of sterile males. Coupling a diet enriched with protein hydrolysate for adult food and application of methoprene to adult males or pupae was found to advance significantly the age at which males of a number of species of flies from the genus Anastrepha and Bactrocera cucurbitae (Coquillet) become sexually mature and improve reproductive success of the males. These results have led to the development of a novel strategy to accelerate the reproductive development and increased competitiveness of mass‐reared fruit flies for use in the sterile insect technique by incorporating methoprene treatment and protein hydrolysate diets into protocols for fruit fly emergence and release facilities. The following reviews research conducted to develop the system and our suggestions for use in improving efficacy of mating by sterile males destined for release in programmes to control some species of tephritid flies using the sterile insect technique.
Role of pH response in Candida albicans virulence
Authors: Fonzi W. A. 
Published: April 2011

Summary. Over 25 years ago it was noted that the pH of the culture medium influenced germ tube formation of Candida albicans, an opportunistic fungal pathogen. This simple observation has been the stimulus for a number of investigations to discern the mechanisms controlling this response and the significance of this response to the biology of C. albicans. Recent studies have demonstrated that a signaling pathway conserved in several fungal species regulates this morphological response to ambient pH and controls the pH‐conditional expression of multiple genes. Significantly, C. albicans responds to the pH of the host niche and this response is critical for virulence.Zusammenfassung. Bereits vor über 25 Jahren wurde beobachtet, dass der pH‐Wert des Kulturmediums die Keimschlauchbildung des opportunistischen Pilzes Candida albicans beeinflusst. Dies war der Anlass zu Studien über Kontrollmechanismen und Bedeutung dieser pH‐Abhängigkeit in der Biologie von C. albicans. Inzwischen wurde deutlich, dass in mehreren Pilzarten ein Signalweg existiert, der die morphologischen Auswirkungen des Umgebungs‐pH auf den Pilz reguliert und die pH‐abhängige Expression multipler Gene kontrolliert. Candida albicans reagiert in bedeutsamer Weise auf den pH‐Wert in der Wirtsnische, und diese Reaktion beeinflusst maßgeblich die Virulenz.
Histologische Untersuchungen bei Otomykosen*
Authors: Vennewald Irina , Schönlebe J. , Klemm E. 
Published: April 2011

Zusammenfassung. Pilzerkrankungen des Ohres werden am häufigsten als Gehörgangsmykose beschrieben. Ziel unserer Untersuchungen war die Frage nach der Art der Besiedlung im Ohr bei immunkompetenten Patienten. Von 1993 bis 2000 wurden 128 Patienten mit Verdacht auf Otomykose untersucht. 115 Patienten litten an chronischer Otitis media bei persistierender Trommelfellperforation und Ohrsekretion. 13 weitere Patienten hatten klinische Zeichen einer Otitis externa. Bei 59 Patienten wurde eine Gehörgangsmykose diagnostiziert, bei fünf auch eine Pilzinfektion des Mittelohres. Von 139 Proben wurden im Gehörgang 54‐mal, am Trommelfell fünfmal und im Mittelohr fünfmal Pilze nachgewiesen. Zu 2/3 wurden Schimmelpilze und zu 1/3 Hefen isoliert. Dabei dominierten Aspergillus niger und Candida parapsilosis. Bei Mastoiditis oder Cholesteatomverdacht wurden Proben von 15 Patienten entnommen und histologisch nach Pilzfärbung untersucht. Bei vier Patienten wurden Pilzelemente neben der Kultur auch in histologischen Präparaten vom Mittelohr nachgewiesen. Die Pilzhyphen fanden sich in den Hohlräumen des Mittelohres oder zwischen den Hornlamellen des Cholesteatoms. Im Mittelohr immunkompetenter Patienten fand sich eine chronisch‐hyperplastische (polypöse) Entzündung mit starker Sekretion, was wahrscheinlich Ansiedlung und saprophytäres Wachstum der Pilze sowohl im Mittelohr als auch im Gehörgang fördert. Invasives Pilzwachstum in das subepitheliale Bindegewebe hinein wurde nicht beobachtet.Summary. Fungal infections of the ear are mostly described as mycoses of the auditory canal. The aim of our investigations was to find out how fungi colonize the ear in immunocompetent patients. In the years from 1993 to 2000, 128 patients suspected of having otomycosis were examined. Of these 115 patients suffered from chronic otitis media with persisting tympanum perforation and otorrhea. A further 13 patients had clinical signs of otitis externa only. In 54 out of 139 samples, fungi were found in the auditory canal, in five on the tympanic membrane, and in five in the middle ear. Two‐thirds were isolated as moulds and one‐third as yeasts. Dominating species were Aspergillus niger and Candida parapsilosis. Samples of 15 patients suspected of having mastoiditis or cholesteatoma were examined histologically. Fungal hyphae were observed in the middle ear cavity and/or between horny lamellae of cholesteatoma in 4 patients. In the middle ear of immunocompetent patients chronic‐hyperplastic (polypous) inflammation was detected with increased production of mucus, which probably promotes the colonization with pathogenic fungi as in the middle ear just like in the auditory canal.
Fluconazole: optimized antifungal therapy based on pharmacokinetics
Authors: Silling G. 
Published: April 2011

Summary. Fluconazole, a triazole, inhibits synthesis of ergosterol. The key enzyme of antifungal activity is C‐14‐Demethylase, which itself depends on Cytochrom‐P‐450. So drugs that inhibit or induce this enzyme lead to interactions that have to be considered when dosing fluconazole. Oral bioavailability is more than 90% after a 50mg dose, peak levels are reached after 0.5–1.5 h (empty stomach) or 4 h (with nutritition). A loading dose on the first day leads to steady state levels on the second day. Because of the hydrophilic properties fluconazole penetrates very well into body fluids and tissues. With the M27 method conditions regarding susceptibility testing have been standardized and minimal inhibitory concentrations (MICs) have been established for fluconazole. The linear relation between dose and concentration offers the possibility to treat less susceptible fungi with higher doses, but only when MICs correlate with efficacy and higher doses are tolerated as well. Prospectively randomized studies are rare. With the limited data indications as consensus recommendations are demonstrated. Data regarding high dose therapy with fluconazole in surgical or intensive care patients demonstrate efficacy and tolerability. In addition dosage has to be adjusted in case of haemofiltration or haemodialysis. At last future options for high dose fluconazole are discussed.Zusammenfassung. Fluconazol ist ein Triazol, das die Ergosterol‐Biosynthese hemmt. Das Schlüsselenzym der antimykotischen Wirkung ist die C‐14‐Demethylase, die wiederum vom Coenzym Cytochrom‐P‐450 abhängig ist. Medikamente, die über eine Hemmung oder Induktion dieses Enzyms wirken, führen zu Interaktionen, die in der Dosierung berücksichtigt werden müssen. Die orale Bioverfügbarkeit beträgt mehr als 90% nach Einnahme von 50 mg, Spitzenspiegel werden nach 0,5–1,5 h (nüchtern) bzw 4 h (bei Nahrungsaufnahme) erreicht. Eine „loading dose” am ersten Tag führt zu „steady state” Bedingungen am 2. Tag. Aufgrund der Hydrophilie ist die Penetration in flüssige Kompartimente und Körpergewebe gut. Mit der M27‐Methode wurden die Testbedingungen zur Empfindlichkeitstestung standardisiert und minimale Hemmkonzentrationen (MIC) für Fluconazol festgelegt. Die lineare Beziehung zwischen Dosis und Serumkonzentration ermöglicht es, weniger sensible Pilze durch eine Dosiserhöhung von Fluconazol zu therapieren. Voraussetzungen dafür sind, dass die MIC mit der Wirkung korreliert und das Nebenwirkungsprofil der Substanz diese Dosissteigerung zulässt. Prospektiv randomisierte Studien zu dieser Fragestellung sind limitiert. Anhand der verfügbaren Daten sollen Indikationen und Konsensus‐Empfehlungen dargestellt werden. Die Daten zur Hochdosistherapie bei chirurgischen und Intensivpatienten sollen die Wirksamkeit und Tolerabilität aufzeigen sowie die Komplexität in der Dosierung und Therapie bei Einsatz von Nierenersatzverfahren. Abgeleitet werden soll ein Ausblick auf zukünftige Therapieoptionen.
Are you hungry? Are you thirsty? – fasting times in elective outpatient pediatric patients
Authors: Engelhardt Thomas , Wilson Graham , Horne Lesley , Weiss Markus , Schmitz Achim 
Published: April 2011

SummaryObjective:  This study assessed the duration of pre‐operative fasting in children and its impact on the subjective feeling of hunger and thirst prior to elective outpatient anesthesia.Background:  Pediatric fasting guidelines are designed to reduce the risk of pulmonary aspiration of gastric contents during general anesthesia, and a fasting regimen of 6–8 h for solids, 4 h for breast milk, and 2 h for clear fluids is commonly used. Anecdotal evidence suggests that fasting times are often excessive.Methods:  A total of 1350 consecutive healthy children aged <16 (median 7.7, range 2–16) presenting for elective dental treatment under general anesthesia were enrolled in this prospective study. On hospital arrival, all children were asked when they last ate or drank and to rate their degree of hunger and thirst.Results:  The median (range) fasting times were 12:05 (00:45–21:50) hours and 07:57 (00:05–20:50) hours for solids and fluids, respectively. The majority of children were very hungry or starving (756/1350 = 56%), but less than third of all children were very thirsty (361/1350 = 27%). Duration of solid food fast and severity of hunger correlated for patients fasted from before midnight (r = 0.92) but not for food after midnight. No correlation was found for fluid intake and perception of thirst.Conclusion:  This study shows that children presenting for elective outpatient surgery are suffering from a considerable amount of pre‐operative discomfort because of excessive fasting. Strategies to guarantee minimal fasting at hospital admission are urgently needed.
Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs
Authors: Cramer Nina , Klockgether Jens , Wrasman Kristie , Schmidt Mario , Davenport Colin F. , Tümmler Burkhard 
Published: April 2011

SummaryClones C and PA14 are the worldwide most abundant clonal complexes in the Pseudomonas aeruginosa population. The microevolution of clones C and PA14 was investigated in serial cystic fibrosis (CF) airway isolates collected over 20 years since the onset of colonization. Intraclonal evolution in CF lungs was resolved by genome sequencing of first, intermediate and late isolates and subsequent multimarker SNP genotyping of the whole strain panel. Mapping of sequence reads onto the P. aeruginosa PA14 reference genome unravelled an intraclonal and interclonal sequence diversity of 0.0035% and 0.68% respectively. Clone PA14 diversified into three branches in the patient's lungs, and the PA14 population acquired 15 nucleotide substitutions and a large deletion during the observation period. The clone C genome remained invariant during the first 3 years in CF lungs; however, 15 years later 947 transitions and 12 transversions were detected in a clone C mutL mutant strain. Key mutations occurred in retS, RNA polymerase, multidrug transporter, virulence and denitrification genes. Late clone C and PA14 persistors in the CF lungs were compromised in growth and cytotoxicity, but their mutation frequency was normal even in mutL mutant clades.
Inequality, Imbalance, Instability: Reflections on a Structural Crisis
Authors: Saith Ashwani 
Published: April 2011

ABSTRACTGlobalization has been accompanied by worsening inequality within core countries of global accumulation processes, as exemplified by China and the USA, where income and wealth inequalities have regained the stratospheric heights of the 1920s. In parallel, there are significantly diverging life chances for the rich and the poor. Extreme inequalities are deemed intrinsically toxic due to their potential for the subversion of regulatory and accountability institutions, the corrosion of societal norms, and the quality of democracy. The present conjuncture of crises provides credible evidence that inequality, especially extreme inequality, is not just a contextual feature or a downstream outcome issue, but a crucial upstream, causal factor in the pathology of the financial meltdown. This article introduces contributions elaborating causal pathologies connecting inequality, imbalances and instability, emphasizing the centrality of global interdependence. Beyond surviving the crisis through assorted fiscal stimuli packages of emergency resuscitation and life support, there are deeper structural policy issues to consider. The crisis briefly opened up democratic space for short‐term protective, and long‐term corrective interventions. However, this space was equally quickly shut down again, as the political and financial establishment resisted yielding permanent ground: witness the return to fiscal conservatism, the revival of the culture of bankers’ bonuses, and persisting international divisions over coordinated global action. There is an imperative to regulate rampant and dysfunctional financialization; to cooperate internationally for sustainable balanced economic growth; for an alternative politics to pull back from an inexorable slide into plutocracy, to let the people back in. Otherwise we risk lurching from one crisis episode to another, from tragedy to farce, and back again.
CHANGES IN SPATIAL PATTERNS OF THE IMMIGRANT POPULATION OF A SOUTHERN EUROPEAN METROPOLIS: THE CASE OF THE BARCELONA METROPOLITAN AREA (2001–2008)
Authors: MARTORI JOAN CARLES , APPARICIO PHILIPPE 
Published: April 2011

ABSTRACTTo date, the evolution of residential segregation patterns in southern European cities has received little attention. The case of Barcelona metropolitan area (BMA) is particularly relevant following a rapid growth of immigrant population over a very short period. This empirical study seeks to see if this rapid growth has changed the spatial segregation patterns of immigrant groups and led to the emergence of ethnic enclaves. First, we calculate five indices according to the classic dimensions of residential segregation. Then, we use an adapted version of the Poulsen et al. typology in order to identify ethnic enclaves. In the period under study, there was a general increase in two dimensions: Exposure and clustering. There was a decline in evenness and concentration, and a variety of situations in terms of centralization. The evolution of the segregation indices indicates a diversity of segregation patterns: an increase of segregation according to exposure and clustering dimensions, a decline in evenness and concentration, and a variety of situations in terms of centralization. Finally, the findings confirm the presence of ethnic enclaves following seven years of growth in the immigrant population.
Downward Nominal Wage Rigidity and Gender
Authors: Anspal Sten , Järve Janno 
Published: April 2011

AbstractWe test whether there are gender differences in downward rigidity, using Kahn's histogram‐location method and longitudinal registry data on all formally employed persons from the Estonian Tax and Customs Board. The results show that women resist pay cuts less than men. Also, in circumstances of increasing unemployment women's opposition to pay cuts decreases substantially, whereas men's attitudes towards pay cuts are not significantly affected by labour market conditions.
WHEN THE BOUGH BREAKS: CHILDHOOD MORTALITY AND BURIAL PRACTICE IN LATE NEOLITHIC ATLANTIC EUROPE
Authors: WATERMAN ANNA J. , THOMAS JONATHAN T. 
Published: April 2011

SummaryTowards the end of the fifth millennium BC, a new funerary tradition developed in Iberia and elsewhere in Atlantic Europe involving the use of megalithic tombs and natural or artificially constructed caves for the collective burial of the dead. Ancestor worship has been the most common theoretical framework used to explain this Neolithic burial tradition, despite demographic information which indicates that these burials house the remains of a significant percentage of children and adolescents. Using data from Late Neolithic (3500–2500 BC) tombs in south‐western Iberia as a departure point, in this paper we suggest that by reconsidering the impact that childhood mortality had upon burial and grave visitation practices in Neolithic communities, archaeologists can gain valuable phenomenological information which will allow for a more robust, multivocal interpretative approach.