bluuebunny/crossref_metadata_2025 huggingface dataset:
A new species ofExrima,synonymy of four species ofAphotopontius, StygiopontiusandRhogobius, and record of first copepodid stage of Dirivultidae (Copepoda: Siphonostomatoida) from deep-sea hydrothermal vents of the East Pacific Rise (13°N)
Authors: Ivanenko Viatcheslav N. , Defaye Danielle , Segonzac Michel , Khripounoff Alexis , Sarrazin Jozée , Ferrari Frank D.
Published: March 2011

Females of the new speciesExrima walterisp. nov. were found in sediment trap samples deployed over different sites of the East Pacific Rise (13°N) at 2600 m depth. Four traps were deposited during the HOPE99 cruise (1999) and recovered during the AMISTAD (1999) cruise on the research vessel ‘L'Atalante’. The new species is distinguished from congeners,E. singulaHumes, 1987 andE. dolichopusHumes, 1987, by the following derived characters: first somite of the urosome with 3 (one dorsal and two lateral) stout conical extensions; distal endopodal segment on the swimming leg 4 broad. In addition, many specimens of copepodids I and lecithotrophic nauplii, identified as belonging to Dirivultidae gen. sp., were found in the samples of all sediment traps. This is the first record of copepodids I and of a nauplius of dirivultids from the Pacific Ocean. Study of type and additional material collected during different Ifremer cruises at different vent sites (HERO91, EXOMAR, PHARE and MoMARETO) required synonymy of four species ofAphotopontiusHumes, 1987,StygiopontiusHumes, 1987 andRhogobiusHumes, 1987.Aphotopontius rapunculusHumes and Segonzac, 1998 is transferred to the genusRhogobiusbecause it possesses all presumed derived attributes of this genus: last abdominal somite with lobes at sides of anal operculum; second segment of antennal endopod elongate and slender. A new study of the type material suggests that:Aphotopontius temperatusHumes, 1997 is a synonym ofA. atlanteusHumes, 1996;Stygiopontius lumigerHumes, 1989 is a synonym ofS. sentiferHumes, 1987 whileS. bulbisetigerHumes, 1996 is a synonym ofS. pectinatusHumes, 1987. Females of the three synonymized species were found to be sub-adult females at copepodid V. Leg 6 on these specimens is one seta located dorsolaterally on the posterior part of the genital somite. This position for leg 6 is unknown for copepodid V of other siphonostomatoids whose leg 6 is located ventrally at copepodid V; the dorsolateral position is presumed derived and shared by the dirivultid generaAphotopontiusHumes, 1987 andStygiopontiusHumes, 1987. A new key to the Dirivultidae genera is presented.
Inaccuracies in routinely collected Atlantic herring (Clupea harengus) maturity data and correction using a gonadosomatic index model
Authors: McPherson Lindsay R. , Ganias Konstantinos , Marshall C. Tara
Published: March 2011

Macroscopic maturity staging data are widely used to distinguish between reproductive and non-reproductive individuals. The implicit assumption is that these data are accurate. The accuracy of macroscopic maturity staging of North Sea herring (Clupea harengus) has not been checked since the macroscopic scale was produced in 1961. The aim of this study was to assess the accuracy of macroscopic maturity staging of female North Sea herring by comparison to histological staging and the gonadosomatic index (GSI). Ovary samples were collected during the North Sea Herring Acoustic Survey in 2006 on-board FRV ‘Scotia’ (Scotland) and in 2007 on-board FRV ‘Scotia’ and RV ‘Johan Hjort’ (Norway). Commercial samples were also collected by Marine Scotland, Aberdeen in both years. The maturity staging error was relatively low in 2006 (21% error) but was much higher on-board FRV ‘Scotia’ (57%) and RV ‘Johan Hjort’ (47%) in 2007. There was estimated to be a 27% under-estimation of the spawning stock biomass (SSB) in 2007 due to the differences in the proportion mature but no change in SSB estimates in 2006. GSI cut-off scores, estimated by means of multinomial regression models were successfully able to separate immature females from both mature-active and recovering females; however, there was some overlap between the mature-active and recovering individuals. We conclude that an effective and low-cost means of reducing error in herring maturity studies is the combined use of a four-point macroscopic maturity scale with routinely collected GSI data, the latter acting to validate and fine tune macroscopic staging.
Seasonal and interannual variation of decapod larval abundance from two coastal locations in Scotland, UK
Authors: Pan Maria , Pierce Graham J. , Cunningham Carey O. , Hay Steve J.
Published: March 2011

The patterns of decapod larvae occurrence and abundance were studied from weekly time-series data of 8 years from Stonehaven (north-east Scotland) and 4 years and 8 months from Loch Ewe (north-west Scotland). The annual cycle observed was similar in the two locations and characterized by abundance peaks, the first in spring and another in the summer, extending into autumn. During the coldest months (December to February) decapod larvae were virtually absent in the plankton. Differences in abundance and occurrence of decapod larvae between locations and the influence of temperature, salinity and chlorophyll-a in the patterns observed, were analysed by generalized least-square functions. The results showed significant differences in the abundance of decapod larvae between locations, with higher larval abundances and an earlier appearance in the plankton in Loch Ewe (west coast). In Stonehaven (east coast), from 2003 onwards, a general increasing trend in the abundance of decapod larvae was observed, related to the increasing temperatures recorded at that site. The data demonstrate the high variability of decapod larval abundance on an annual basis and the high importance of temperature and chlorophyll-a to the occurrence and abundance of decapod larvae.
A new family, genus and species of apseudomorphan Tanaidacea (Crustacea: Peracarida) from the Caribbean Sea
Authors: Larsen Kim
Published: March 2011

A new family, of apseudomorphan Tanaidacea, Sphaeromapseudidae, is discovered and described from the Caribbean Sea. Sphaeromapseudidae is tentatively placed between the Metapseudidae and Tanzanapseudidae. A new genusSphaeromapseudesand species,S. plumosetosa, associated with intertidal coral rubble, are described.
New spectral multiplicities for mixing transformations
Authors: DANILENKO ALEXANDRE I.
Published: March 2011

It is shown that if E is a subset of $\Bbb N$ such that 1∈E or 2∈E then there is a mixing transformation whose set of spectral multiplicities is E.
Rigidity and mapping class group for abstract tiling spaces
Authors: KWAPISZ JAROSLAW
Published: March 2011

We study abstract self-affine tiling actions, which are an intrinsically defined class of minimal expansive actions of ℝdon a compact space. They include the translation actions on the compact spaces associated to aperiodic repetitive tilings or Delone sets in ℝd. In the self-similar case, we show that the existence of a homeomorphism between tiling spaces implies conjugacy of the actions up to a linear rescaling. We also introduce the general linear group of an (abstract) tiling, prove its discreteness, and show that it is naturally isomorphic with the (pointed) mapping class group of the tiling space. To illustrate our theory, we compute the mapping class group for a five-fold symmetric Penrose tiling.
A special case of effective equidistribution with explicit constants
Authors: MOHAMMADI A.
Published: March 2011

An effective equidistribution with explicit constants for the isometry group of rational forms with signature (2,1) is proved. As an application we get an effective discreteness of the Markov spectrum.
Seeking respite: issues around the use of day respite care for the carers of people with dementia
Authors: ROBINSON ANDREW , LEA EMMA , HEMMINGS LYNN , VOSPER GILLIAN , McCANN DAMHNAT , WEEDING FELICITY , RUMBLE ROGER
Published: March 2011

Ageing in Place policies have transferred responsibility for many frail elderly people and those living with dementia from residential to in-home care. Despite this placing a greater obligation on families, in Australia carers continue to under-use day respite services. This qualitative design study identified issues around the use of day respite care from the perspective of the family carer, focusing on barriers to attendance and strategies to facilitate attendance. Telephone interviews were held in 2007 with Tasmanian carers whose family member refused to attend day respite care (ten carers) and those whose family member attended (17). Carers considering day respite care were often overwhelmed by the quantity of information, confused about the process, and worried about the recipient's safety in an unfamiliar environment. They felt anxious about public acknowledgement of the condition leading to fear of embarrassment. Day respite care users appreciated the break it provided them and the opportunity for their family member to socialise. To facilitate a greater uptake of day respite care, reliable information sources and strategies to help carers deal with the emotions they face on a daily basis, together with a wider social acceptance of dementia, are important. Furthermore, carers need an opportunity to talk with others, enabling them to gain support from those who have successfully introduced a family member to day respite care.
A gendered lifecourse examination of sleep difficulties among older women
Authors: WALKER RUTH B. , LUSZCZ MARY A. , HISLOP JENNY , MOORE VIVIENNE
Published: March 2011

Recent research has suggested that understanding and addressing the high prevalence of sleep difficulties in older women requires going beyond a purely physiological focus to address the role of social contextual pressures and demands. We take a gendered lifecourse approach to explore how sleep difficulties have evolved and how their management might reflect the position of older women in society more broadly. We conducted in-depth interviews with 12 oldest-old (average age 86) community-dwelling women who currently experienced sleep difficulties. Five themes emerged from the analysis: significant life stages; contingent lives; daily concerns in relation to ageing; attitudes and responses of women and general practitioners; and stigma and sleeping pills, which provided a conceptual framework through which to explain the reality of sleep difficulties for these women. For all women, sleep difficulties were not related to physical aspects such as pain or discomfort, but were largely shaped by demands associated with family relationships at different times in the lifecourse. Furthermore, our findings suggest that responses by women themselves, and health professionals, reflect a sense of stigma around sleep difficulties and use of sleeping pills. More emphasis on the social contextual explanations underpinning sleep difficulties might lead to better prevention and treatment of such problems, and increase quality of life.
Bad data equals bad policy: how to trust estimates of ecosystem loss when there is so much uncertainty?
Authors: FRIESS D. A. , WEBB E. L.
Published: March 2011

Scientific evidence will be better incorporated into conservation action and environmental policy if it is deemed credible by decision-makers. However, huge uncertainties are inherent in large-scale ecosystem statistics. Two wetland case studies relating to mangrove areal extent in Peninsular Malaysia and saltmarsh loss in the UK indicate the major causes of information uncertainty, relating to poor methodological description, traceability and assumptions associated with the use of grey literature. Furthermore, potentially inaccurate information can be propagated throughout the research community and gain ‘proof by assertion’, especially if the information originates from an authoritative source. Researchers must better consider implicit and explicit uncertainty and be critical of secondary information. Future information production requires the use of rigorous peer-reviewed methodologies in order to decrease and quantify error. Such steps will increase the credibility of scientific evidence, so researchers can better contribute to a two-way science and policy deliberation approach.
Resolving management conflicts: could agricultural land provide the answer for an endangered species in a habitat classified as a World Heritage Site?
Authors: SMITH REBECCA K. , RYAN EMMA , MORLEY EMMA , HILL RUSSELL A.
Published: March 2011

The short-interval fires required to promote grazing for large herbivores within the Cape Floristic Region World Heritage Site are detrimental to plant diversity. At the same time, longer interval fires significantly reduce graze quality. Conservation managers thus face an enormous challenge when the herbivores are also a conservation priority, since the competing conservation objectives are difficult to reconcile. Population growth rates of genetically important populations of endangered Cape mountain zebra (Equus zebra zebra) are low or declining following management focused on their fynbos habitat. Investigation of spatial and temporal habitat use and the diet of Cape mountain zebra, focusing on the use of land historically converted to agricultural grassland within fynbos in De Hoop Nature Reserve (South Africa), determined factors limiting populations and facilitated development of management strategies. Zebras selected grassland over other habitat types, despite grassland accounting for only a small proportion of the reserve. Grasses also made up the greatest proportion of diet for zebras throughout the year. Time spent on grasslands increased with grass height and was likely to have been influenced by grass protein levels. It is likely that grazing resources are a limiting factor for zebra, and so options for improving and/or increasing grassland at De Hoop should be considered. Translocation of surplus males to other conservation areas, reductions in other herbivore populations and targeted burns to increase grassland availability all offer short-term solutions. However, the acquisition of agricultural grassland adjacent to reserves is likely to be a viable long-term management strategy for this and other genetically important Cape mountain zebra populations. Low conservation priority habitats, such as farmland, should be considered for other management conflicts, as they have the potential to play a vital role in conservation.
Entamoeba species associated with chronic diarrhoea in Pakistan
Authors: YAKOOB J. , ABBAS Z. , BEG M. A. , NAZ S. , KHAN R. , JAFRI W.
Published: March 2011

We determined the prevalence of Entamoeba (E.) histolytica, E. dispar and E. moshkovskii in patients with chronic diarrhoea associated with abdominal pain or discomfort mimicking irritable bowel syndrome. Stool samples were collected from 161 patients with chronic diarrhoea and from 157 healthy controls. Stool microscopy with modified trichrome stain, culture and polymerase chain reaction (PCR) for Entamoeba spp. differentiation was performed. Microscopy demonstrated Entamoeba cysts in 44% (57/129) of patients with diarrhoea compared to 29% (44/151) of controls (P=0·009). In patients with diarrhoea, PCR for E. histolytica was positive in 9% (11/129) (P=0·008), E. dispar in 19% (24/129) (P=0·117) and E. moshkovskii in 19% (24/129) (P<0·001). E. histolytica and E. moshkovskii were significantly associated with diarrhoea while E. dispar was found equally in both groups.
Psittacosis outbreak after participation in a bird fair, Western France, December 2008
Authors: BELCHIOR E. , BARATAUD D. , OLLIVIER R. , CAPEK I. , LAROUCAU K. , DE BARBEYRAC B. , HUBERT B.
Published: March 2011

In December 2008, three hospitalized cases of suspected psittacosis infection were notified by respiratory disease clinicians from a local hospital to the Regional Epidemiology Unit of Pays de la Loire, France. They all had attended a bird fair. A retrospective cohort study was conducted among exhibitors and organizers to identify potential risk factors in relation to this fair. Environmental and veterinary investigations were implemented to trace potential sources of infection. We identified two confirmed, two probable and 44 possible cases among participants. The attack rate in exhibitors and organizers was 38% (33/86). The median incubation period was 11 days (range 6–22 days). Individuals located in two particular sectors of the showroom were found to be at double the risk of developing psittacosis (relative rate 2·1, 95% confidence interval 1·03–4·18) than those in other sectors. Pooled faecal samples of birds belonging to a possible case exhibitor tested positive for Chlamydiaceae by PCR. Ventilation conditions in the showroom were inadequate. This investigation allowed the formulation of recommendations to prevent psittacosis in bird exhibitions which are held weekly in France.
Banking crises and the international monetary system in the Great Depression and now
Authors: Moessner Richhild , Allen William A.
Published: March 2011

We identify similarities and differences in the scale and nature of the banking crises in 2008-9 and the Great Depression, and analyse differences in the policy response to the two crises in light of the prevailing international monetary systems. We find that the scale of the banking crisis, as measured by falls in international short-term indebtedness and total bank deposits, was smaller in 2008-9 than in 1931. However, central bank liquidity provision was larger in the flexible exchange rate environment of 2008-9 than in 1931, when it had been constrained in many countries by the gold standard.
COMPACT DIFFERENCES OF COMPOSITION OPERATORS ON BERGMAN SPACES IN THE BALL
Authors: YANG XIANG DONG , KHOI LE HAI
Published: March 2011

We obtain necessary and sufficient conditions for the compactness of differences of composition operators acting on the weighted Bergman spaces in the unit ball. A representation of a composition operator as a finite sum of composition operators modulo compact operators is also studied.
Combining current land use and farmers' knowledge to design land-use requirements and improve land suitability evaluation
Authors: Ziadat Feras M. , Sultan Kais A.
Published: March 2011

Land suitability analysis is very important to assess and propose the most suitable land-use options. The reliability of land suitability evaluation is controlled by choosing the most limiting land characteristics and their ratings for the proposed land utilization types (LUTs). This study aims at examining the possibility of using current land use and farmers' knowledge as a starting point to suggest and/or modify land evaluation criteria, and to improve the land suitability evaluation process. The potential suitability of land for five LUTs (open range, improved range, rainfed barley, drip-irrigated vegetables and drip-irrigated trees) was evaluated near Al-Mafraq in Jordan using the maximum limitation method. The results indicated variable agreement levels between potential land suitability and current land use for different LUTs. Sixteen farms were selected to represent different cases of disagreement between potential suitability and current land use and were visited to explore the farmers' improved management practices adopted to overcome land-use limitations. Using proposed criteria, only 1% of the study area was highly suitable for drip irrigation, whereas most of the area was moderately or marginally suitable for other uses. This represents the conventional land evaluation procedures, which, in most cases, overlook the farmers' knowledge and practices that are adopted in a particular area to overcome biophysical limitations. The ratings for different land characteristics were modified based on comparisons with current land use, and by referring to farmers’ adopted management practices. Using modified criteria, the highly suitable area for drip-irrigated vegetables increased by 18% and the highly suitable area for drip-irrigated trees increased by 25%. The results emphasized that the consideration of the farmer's indigenous knowledge and current land use improve the land evaluation process, which leads to better utilization of limited land resources in fragile environments.
Two‐dimensional ionospheric tomography over the low‐latitude Indian region: An intercomparison of ART and MART algorithms
Authors: Das Sukanta Kumar , Shukla Ashish Kumar
Published: March 2011

Single‐frequency users of a satellite‐based augmentation system (SBAS) rely on ionospheric models to mitigate the delay due to the ionosphere. The ionosphere is the major source of range and range rate errors for users of the Global Positioning System (GPS) who require high‐accuracy positioning. The purpose of the present study is to develop a tomography model to reconstruct the total electron content (TEC) over the low‐latitude Indian region which lies in the equatorial ionospheric anomaly belt. In the present study, the TEC data collected from the six TEC collection stations along a longitudinal belt of around 77 degrees are used. The main objective of the study is to find out optimum pixel size which supports a better reconstruction of the electron density and hence the TEC over the low‐latitude Indian region. Performance of two reconstruction algorithms Algebraic Reconstruction Technique (ART) and Multiplicative Algebraic Reconstruction Technique (MART) is analyzed for different pixel sizes varying from 1 to 6 degrees in latitude. It is found from the analysis that the optimum pixel size is 5° × 50 km over the Indian region using both ART and MART algorithms.
Pidgin-creoles as a scattered sprachbund
Authors: Kihm Alain
Published: March 2011

That creole languages resemble each other beyond the diversity of their lexifiers and formative environments is a fact. Similarity should not be overstated, however, as creole languages also differ from each other in important ways. Hence the fundamental issues of creole studies: why are Creoles similar and what makes them different? What kind of a language group do they constitute? A genetic family they certainly are not, nor are they a typological group: creole languages do not constitute a type of their own. Assuming universal grammar viewed as a language bioprogram (LB) to be the principle of creole similarity strongly overstates this similarity. Moreover there are reasons to doubt the reality of the LB.
Actually the kind of partial similarities exhibited by creole languages looks rather like what languages in a sprachbund or linguistic area have in common. How can languages scattered all over the world constitute an area, though? An answer is proposed in this study, which rests on two assumptions. First, creole languages constitute a virtual (non-spatial) area by virtue of their very similar origins, namely strong punctuations (catastrophes in a technical sense) involving Basic Variety (pidgin) episodes. Secondly, the (by no means necessary) aftermath of the catastrophe was an exceptional and limited repairing recourse to default grammar, whereby is meant a non-innate (at least not genetically coded), usage-based organization of the sound-meaning interface ensuring semantic transparency, that is the most direct mapping possible given (a) the organization of language sound; (b) the nature of meaning; (c) human preferred ways of associating forms and notions, also relevant for drawing, tool making, and so forth. Beyond that, creole languages are free to differ according to their lexifiers, substrates, adstrates, and so forth.
Creolization and admixture
Authors: Plag Ingo
Published: March 2011

Proponents of a ‘feature pool’ approach to creolization (e.g. Mufwene 2001, Aboh & Ansaldo 2006) have claimed that the emergence of the new grammar is driven by the syntax-discourse prominence, markedness, and frequency of available features, with typological similarity or dissimilarity of the languages involved playing a crucial role in the competition and selection process. This paper takes a closer look at the predictions of a feature pool-based approach to creolization and tests whether these predictions are borne out by the facts. Three case studies from the Surinamese creoles and Sri Lanka Malay show that the feature pool approach suffers from a number of conceptual, theoretical, and empirical problems. The typology alone of the languages involved in the contact is not a good predictor for the outcome of language contact. The feature pool approach neglects processing constraints: one can only select from what one can process. ‘Creolization’, as in the case of the emergence of the Surinamese Creoles, is not ‘exceptional’, but happens in contact situations in which second language acquisition plays a significant role. The processing restrictions inherent in second language acquisition play an important role in shaping the structural outcome. ’Admixture’, as in the case of Sri Lanka Malay, is not ‘exceptional’ either, but happens in different situations and shows different processes at work. And these processes allow structural outcomes that are very different from those found under the conditions of second language acquisition.
The typology of Caribbean Creole reduplication
Authors: Kouwenberg Silvia , LaCharité Darlene
Published: March 2011

Although many aspects of Creole languages remain relatively unexplored, the morphology of Creole languages has been especially neglected. This is largely because it is still widely believed that Creoles have very little in the way of morphology, even compared to an inflection-poor language such as English. Moreover, the morphology that Creoles do have is often assumed to be quite similar from one Creole language to another and is further thought to be predictable and transparent. However, there is an emerging body of research on Pidgin and Creole morphology showing that the hypothesis of semantic transparency and regularity in Creole morphology does not stand up to scrutiny.
The purpose of this paper is to explore the typological characteristics of morphological reduplication in Caribbean Creole (CC) languages, and to assess these characteristics against this background. To this purpose, we will examine reduplication in a sample of CC languages of different lexifiers (Dutch, English, French, Portuguese and Spanish), with respect to their form, semantics and distribution. Our research confirms that morphological reduplication is not uniform across these languages. Moreover, it shows that reduplication is surprisingly complex within a single language.
Comparative graphematics
Authors: Weingarten Rüdiger
Published: March 2011

This paper seeks to outline comparative graphematics as a linguistic approach within writing systems research and typology. In addition to providing a general outline of the approach and its benefits, it is exemplified through a discussion of the relation between the gemination of consonant letters and the graphemic representation of long consonants. Two different approaches within comparative graphematics are applied, one that asks about the meaning or function of the units of writing systems and one that starts with linguistic (e.g. phonological or morphological) units or structures and looks at whether they are represented (and, if so, how) in various writing systems. Consequently, two different typological matrices are presented. Moreover, through a combination of historical and comparative perspectives, the paper investigates the diachronic transitions in the functions of a graphemic construction, as observed within the history of a single writing system or in its adoption within several systems. It is shown that an inherited construction, such as the germination of consonant letters, can be reanalysed; if it loses its former representational function during the course of language change, it may subsequently be utilized for different purposes. A construction may also remain as an ‘evolutionary vestige’ within a writing system, at least for some time. Similar forms of reanalysis can be found if a construction is applied to a new language. Keywords: graphematics; orthography; writing system; script; comparative linguistics; cross-linguistic studies; typology; germination
Writing in Portuguese chats :)
Authors: Silva Cláudia
Published: March 2011

This paper aims at determining the relationship between writing in chats and features from different writing systems. Although net users do not realise it, they recreate features mainly from morphographic systems and consonantal scripts and, consequently, they seem to be searching for a more economical way of conveying meaning through writing. When carrying out a corpus-based study, involving 90 minutes of real-time conversations in a Portuguese chat programme, we observed tendencies concerning spelling changes: the syllable onset is usually preserved, which resembles consonantal scripts; the number of syllables is frequently maintained, in common with syllabaries; the use of emoticons reminds us of morphographic systems, and spelling words as they are heard imitates phonemically transparent orthographies. This paper aims to reflect on the phenomenon that net users unconsciously recreate features which make spelling more efficient. Tracing the deviations occuring in chats may be seen as a way of accessing the speakers’ intuitive knowledge. Keywords: chat; writing system; spelling; deviation; syllable; corpus study; Portuguese
Voters and leaders in the mirror of politics: Similarity in personality and voting choice in Italy and Spain
Authors: Vecchione Michele , González Castro José Luis , Caprara Gian Vittorio
Published: March 2011

Relations between voting choice and similarity in traits between voters and political candidates are examined in two studies. The first study was conducted in Spain, where the personalities of Mariano Rajoy and José Luis Rodríguez Zapatero were assessed. The second study was conducted in Italy, where the politicians assessed were Walter Veltroni and Silvio Berlusconi. Results show in both cases a similarity between voters’ self‐reported personality and their appraisals of the leaders of the party for which they voted. Similarity is generally higher with respect to traits that are the most distinctive for each platform and its leader. The findings show a higher similarity between voters and their leaders on the markers of agreeableness, such as “loyal” and “sincere.” Findings hold across countries and political figures, demonstrating the role that personal characteristics of both voters and candidates play in orienting political preference.
International education and the employability of UK students
Authors: Brooks Rachel , Waters Johanna , Pimlott‐Wilson Helena
Published: March 2011

A common theme within the literature on higher education is the congested nature of the graduate labour market. Researchers have highlighted the lengths to which many students now go, in response to this congestion, to ‘distinguish themselves’ from other graduates: paying increased attention to university status; engaging in a range of extra‐curricular activities; and pursuing postgraduate qualifications. Studies that have focused on the strategies of Asian students, specifically, have pointed to the important place of studying abroad as a further strategy in this pursuit of distinction. Given that there is now some evidence that the number of UK students enrolling on a degree programme overseas is increasing, this article explores the extent to which an overseas education can be seen as part of a broader strategy on the part of British students to seek distinction within the labour market and whether such an education does indeed offer tangible employment benefits.
Teaching writing: A situated dynamic
Authors: Fisher Ros
Published: March 2011

The paper is theoretically grounded in Cultural Historical Activity Theory, which holds that human development is founded within participation in social and cultural practices. In particular, the teaching of literacy is shaped not only by the curriculum as designated by policy makers and the institution in which it is located, but also by the individuals' understanding of what literacy and learning involves and how they act to achieve their goals. The paper explores data from a project that investigated the relationship between classroom talk and the teaching of writing in six early‐years classrooms. Participants' own understandings of teaching and learning need to be taken into account by researchers and policy makers. Cultural Historical Activity Theory has been used to explore the dynamic relationship between activity at societal, institutional and individual levels. It is argued that researchers and policy makers need to take account of the wider socio‐cultural context in planning and evaluating curriculum development initiatives.
Finite generation of Tate cohomology
Authors: Carlson Jon , Chebolu Sunil , Mináč Ján
Published: March 2011

Let

G
G

be a finite group and let

k
k

be a field of characteristic

p
p

. Given a finitely generated indecomposable nonprojective

k
G

kG

-module

M
M

, we conjecture that if the Tate cohomology

H
^

∗

(
G
,
M
)

\hat {H}^*(G, M)

of

G
G

with coefficients in

M
M

is finitely generated over the Tate cohomology ring

H
^

∗

(
G
,
k
)

\hat {H}^*(G, k)

, then the support variety

V
G

(
M
)

V_G(M)

of

M
M

is equal to the entire maximal ideal spectrum

V
G

(
k
)

V_G(k)

. We prove various results which support this conjecture. The converse of this conjecture is established for modules in the connected component of

k
k

in the stable Auslander-Reiten quiver for

k
G

kG

, but it is shown to be false in general. It is also shown that all finitely generated

k
G

kG

-modules over a group

G
G

have finitely generated Tate cohomology if and only if

G
G

has periodic cohomology.
PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies
Authors: Huang Jie , Johnson Andrew D. , O'Donnell Christopher J.
Published: March 2011

Motivation: The concept of pleiotropy was proposed a century ago, though up to now there have been insufficient efforts to design robust statistics and software aimed at visualizing and evaluating pleiotropy at a regional level. The Pleiotropic Region Identification Method (PRIMe) was developed to evaluate potentially pleiotropic loci based upon data from multiple genome-wide association studies (GWAS).

Methods: We first provide a software tool to systematically identify and characterize genomic regions where low association P-values are observed with multiple traits. We use the term Pleiotropy Index to denote the number of traits with low association P-values at a particular genomic region. For GWAS assumed to be uncorrelated, we adopted the binomial distribution to approximate the statistical significance of the Pleiotropy Index. For GWAS conducted on traits with known correlation coefficients, simulations are performed to derive the statistical distribution of the Pleiotropy Index under the null hypothesis of no genotype–phenotype association. For six hematologic and three blood pressure traits where full GWAS results were available from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, we estimated the trait correlations and applied the simulation approach to examine genomic regions with statistical evidence of pleiotropy. We then applied the approximation approach to explore GWAS summarized in the National Human Genome Research Institute (NHGRI) GWAS Catalog.

Results: By simulation, we identified pleiotropic regions including SH2B3 and BRAP (12q24.12) for hematologic and blood pressure traits. By approximation, we confirmed the genome-wide significant pleiotropy of these two regions based on the GWAS Catalog data, together with an exploration on other regions which highlights the FTO, GCKR and ABO regions.

Availability and Implementation: The Perl and R scripts are available at http://www.framinghamheartstudy.org/research/gwas_pleiotropictool.html.

Contact:  odonnellc@nhlbi.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
TEQC: an R package for quality control in target capture experiments
Authors: Hummel Manuela , Bonnin Sarah , Lowy Ernesto , Roma Guglielmo
Published: March 2011

Summary:  TEQC is an R/Bioconductor package for quality assessment of target enrichment experiments. Quality measures comprise specificity and sensitivity of the capture, enrichment, per-target read coverage and its relation to hybridization probe characteristics, coverage uniformity and reproducibility, and read duplicate analysis. Several diagnostic plots allow visual inspection of the data quality.

Availability and implementation:  TEQC is implemented in the R language (version >2.12.0) and is available as a Bioconductor package for Linux, Windows and MacOS from www.bioconductor.org.

Contact:  manuela.hummel@crg.es
The lens: a classical model of embryonic induction providing new insights into cell determination in early development
Authors: Gunhaga Lena
Published: March 2011

The lens was the first tissue in which the concept of embryonic induction was demonstrated. For many years lens induction was thought to occur at the time the optic vesicle and lens placode came in contact. Since then, studies have revealed that lens placodal progenitor cells are specified already at gastrula stages, much earlier than previously believed, and independent of optic vesicle interactions. In this review, I will focus on how individual signalling molecules, in particular BMP, FGF, Wnt and Shh, regulate the initial specification of lens placodal cells and the progressive development of lens cells. I will discuss recent work that has shed light on the combination of signalling molecules and the molecular interactions that affect lens specification and proper lens formation. I will also discuss proposed tissue interactions important for lens development. A greater knowledge of the molecular interactions during lens induction is likely to have practical benefits in understanding the causes and consequences of lens diseases. Moreover, knowledge regarding lens induction is providing fundamental important insights into inductive processes in development in general.
Homeostasis in the vertebrate lens: mechanisms of solute exchange
Authors: Dahm Ralf , van Marle Jan , Quinlan Roy A. , Prescott Alan R. , Vrensen Gijs F. J. M.
Published: March 2011

The eye lens is avascular, deriving nutrients from the aqueous and vitreous humours. It is, however, unclear which mechanisms mediate the transfer of solutes between these humours and the lens' fibre cells (FCs). In this review, we integrate the published data with the previously unpublished ultrastructural, dye loading and magnetic resonance imaging results. The picture emerging is that solute transfer between the humours and the fibre mass is determined by four processes: (i) paracellular transport of ions, water and small molecules along the intercellular spaces between epithelial and FCs, driven by Na+-leak conductance; (ii) membrane transport of such solutes from the intercellular spaces into the fibre cytoplasm by specific carriers and transporters; (iii) gap-junctional coupling mediating solute flux between superficial and deeper fibres, Na+/K+-ATPase-driven efflux of waste products in the equator, and electrical coupling of fibres; and (iv) transcellular transfer via caveoli and coated vesicles for the uptake of macromolecules and cholesterol. There is evidence that the Na+-driven influx of solutes occurs via paracellular and membrane transport and the Na+/K+-ATPase-driven efflux of waste products via gap junctions. This micro-circulation is likely restricted to the superficial cortex and nearly absent beyond the zone of organelle loss, forming a solute exchange barrier in the lens.
Biological glass: structural determinants of eye lens transparency
Authors: Bassnett Steven , Shi Yanrong , Vrensen Gijs F. J. M.
Published: March 2011

The purpose of the lens is to project a sharply focused, undistorted image of the visual surround onto the neural retina. The first pre-requisite, therefore, is that the tissue should be transparent. Despite the presence of remarkably high levels of protein, the lens cytosol remains transparent as a result of short-range-order interactions between the proteins. At a cellular level, the programmed elimination of nuclei and other light-scattering organelles from cells located within the pupillary space contributes directly to tissue transparency. Scattering at the cell borders is minimized by the close apposition of lens fibre cells facilitated by a plethora of adhesive proteins, some expressed only in the lens. Similarly, refractive index matching between lens membranes and cytosol is believed to minimize scatter. Refractive index matching between the cytoplasm of adjacent cells is achieved through the formation of cellular fusions that allow the intermingling of proteins. Together, these structural adaptations serve to minimize light scatter and enable this living, cellular structure to function as ‘biological glass’.
The ocular lens: a classic model for development, physiology and disease
Authors: Wormstone I. Michael , Wride Michael A.
Published: March 2011

Millions are rendered blind or exhibit visual impairment due to pathologies of the lens of the eye. Lens research therefore addresses the direct need to gain insights into the cellular and molecular basis of disease, but, moreover, serves as a valuable experimental system to answer fundamental biological questions. This themed issue showcases the scientific knowledge of the processes involved in the development, structure, ultrastructure, physiology and pathology of the lens and how this information has the potential to significantly further knowledge in various fields of research. The issue is divided into three main areas. Firstly, the lens is discussed as a developmental model for embryonic induction, as an elegant system for studying the role of growth factors in development, and for analysis of the molecular control and cellular basis of cellular differentiation. The genetic basis of disorders of lens development, including paediatric cataract (lens opacity), are also discussed in this section. Secondly, adult lens structure and ultrastructure are covered, as well as the lens as a model for homeostasis and solute exchange. Finally, the papers in the latter part of the special issue review lens pathology, including the lens as a model for normal and pathological ageing, vitreoretinal influences on lens function and cataract and the lens as a model for fibrotic disease. Overall, the articles highlight the lens as a continuing, very important and attractive model system for biologists working in many different research areas.
Legionella nagasakiensis sp. nov., isolated from water samples and from a patient with pneumonia
Authors: Yang Genyan , Benson Robert F. , Ratcliff Rodney M. , Brown Ellen W. , Steigerwalt Arnold G. , Thacker W. Lanier , Daneshvar Maryam I. , Morey Roger E. , Saito Atsushi , Fields Barry S.
Published: March 2011

A novel Legionella species was identified based on analysis of 16S rRNA and mip (macrophage infectivity potentiator) gene sequences, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens and quantitative DNA–DNA hybridization. Strain CDC-1796-JAP-ET was isolated from well water at the Nagasaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. Strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires’ disease in the US. Cells from these four strains were Gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, β-lactamase and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of members of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described members of the Legionellaceae. DNA–DNA hybridization studies indicated that DNAs from the four strains were highly related (78–84 %) but they showed 29 % relatedness to Legionella oakridgensis ATCC 33761T and less than 10 % to strains of other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov. is proposed; the type strain is CDC-1796-JAP-ET ( = ATCC BAA-1557T = JCM 15315T).
Natribacillus halophilus gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium isolated from soil
Authors: Echigo Akinobu , Minegishi Hiroaki , Shimane Yasuhiro , Kamekura Masahiro , Usami Ron
Published: March 2011

A moderately halophilic and alkalitolerant bacterium, designated strain HN30T, was isolated from garden soil in Japan. Cells of strain HN30T were motile, endospore-forming, aerobic, rod-shaped and Gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7–23 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.5–10.0 (optimum, pH 8.0–8.5) and at 20–40 °C (optimum, 30 °C). The isoprenoid quinone was menaquinone-7. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of strain HN30T was 47 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN30T was most closely related to Geomicrobium halophilum BH1T (93 % sequence similarity). 16S rRNA gene sequence similarities with other recognized species were less than 89 %. Phylogenetic and phenotypic characteristics indicated that strain HN30T represents a novel species in a new genus, for which the name Natribacillus halophilus gen. nov., sp. nov. is proposed; the type strain is HN30T ( = JCM 15649T = DSM 21771T).
Actinomadura meridiana sp. nov., isolated from mountain soil
Authors: Lee Soon Dong
Published: March 2011

A novel actinomycete, designated strain DLS-45T, was isolated from soil from the surface of a rock collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Substrate mycelium was well developed, but aerial mycelium was scant on most of the media tested. Spherical to subspherical spores on the aerial mycelium were in chains that were arranged in hooks and their surfaces were warty. The combination of morphological and chemical features supported the classification of the new isolate in the genus Actinomadura. The neighbour-joining tree based on 16S rRNA gene sequences showed that the strain belonged to the family Thermomonosporaceae and formed a coherent cluster with Actinomadura pelletieri IMSNU 22169T (98.0 % sequence similarity). The other closest relatives were Actinomadura bangladeshensis 3-46-b(3)T (98.2 %) and Actinomadura chokoriensis 3-25-a(11)T (97.9 %). Levels of DNA–DNA relatedness between strain DLS-45T and the type strains of the phylogenetic relatives were less than 17 %. A battery of phenotypic, genotypic and DNA–DNA relatedness data indicated that strain DLS-45T represented a novel species of the genus Actinomadura, for which the name Actinomadura meridiana sp. nov. is proposed. The type strain is strain DLS-45T ( = KCTC 19558T = DSM 45252T).
Candida cellulosicola sp. nov., a xylose-utilizing anamorphic yeast from rotten wood
Authors: Guo Xinyan , Zhu Hongkun , Bai Feng-Yan
Published: March 2011

Two xylose-utilizing yeast strains isolated from rotten wood collected in the rainforest in different mountains of Hainan province, southern China, were studied. Sequence analysis of the large subunit rDNA D1/D2 domain and internal transcribed spacer region revealed that the strains represent a novel anamorphic yeast species, for which the name Candida cellulosicola sp. nov. is proposed; the type strain is HNX16-2T ( = CGMCC 2.3503T = CBS 11952T). Phylogenetically, the novel species was closely related to a xylose-utilizing teleomorphic ascomycetous yeast species Spencermartinsiella europaea in the family Trichomonascaceae, but differed from the latter by 3.0 % mismatches in the D1/D2 domain.