bluuebunny/crossref_metadata_2025 huggingface dataset:
How I Learned to Stop Worrying and Love the Market: Virtualism, Disavowal, and Public Secrecy in Neoliberal Environmental Conservation
Authors: Fletcher Robert
Published: September 2013

There is often a substantial gap between ‘vision’ and ‘execution’ in neoliberal governance, yet this gap is rarely acknowledged within neoliberal discourse. In the realm of environmental governance this has manifested in increased reliance on neoliberal conservation strategies despite mounting evidence concerning their common failure to perform as intended. This paper seeks to explain this contradictory situation, drawing on Foucaultian as well as Lacanian theorization via Žižek to suggest that neoliberal conservation's ‘virtualistic’ vision commonly necessitates antineoliberal regulation, for the deeply flawed understandings of human behavior and social action in which it is grounded frequently compel intervention contrary to free market principles in order to preserve the goals that market mechanisms are intended to achieve. I contend, further, that neglect of the characteristic disjuncture between vision and execution in neoliberal conservation may take the form of ‘fetishistic disavowal’, functioning as a ‘public secret’ (something generally known but not generally articulated) in terms of which explicit identification of the disjuncture, paradoxically, intensifies its obfuscation. This analysis is illustrated through discussion of prominent conservation strategies in Latin America, particularly ecotourism and payment for environmental services, which are commonly described as neoliberal market mechanisms yet in practice operate quite differently.
Jailbreak: a fishway releases the endangered Macquarie perch from confinement below an anthropogenic barrier
Authors: Broadhurst B. T. , Ebner B. C. , Lintermans M. , Thiem J. D. , Clear R. C.
Published: September 2013

Management interventions are often needed to facilitate the recovery of ecosystems affected as a result of human alteration. Population-level monitoring is often central to evaluating the effectiveness of specific on-ground actions. In the present study, we assessed the response of a remnant population of the endangered Macquarie perch (Macquaria australasica) to the construction of a rock ramp fishway on the Cotter River, Australia, over a 7-year period. Prior to fishway construction, this obligate riverine spawner had been previously confined to Cotter Reservoir and six kilometres of stream by a raised road-crossing. Surveys conducted in the 2 years following fishway completion failed to detect Macquarie perch upstream of the fishway. Subsequent surveys (6–7 years post-fishway completion) detected Macquarie perch up to 12 km upstream of the fishway. The number and distribution of smaller-sized individuals (0+ (<100-mm total length (TL) and 1+ (100- to >150-mm TL)) suggests that individuals found upstream of the fishway are resident stream fish and not fish that have migrated from known downstream spawning areas. The success of the fishway has been timely because enlargement of a downstream reservoir will inundate four kilometres of river and destroy the majority of spawning sites of this species downstream of the fishway in the Cotter River.
Conservation of an inauspicious endangered freshwater fish, Murray hardyhead (Craterocephalus fluviatilis), during drought and competing water demands in the Murray–Darling Basin, Australia
Authors: Ellis Iain M. , Stoessel Daniel , Hammer Michael P. , Wedderburn Scotte D. , Suitor Lara , Hall Arkellah
Published: September 2013

Approximately 40% of Australian freshwater fish species are of conservation concern, largely because of the impacts of river regulation, habitat fragmentation and alien fishes. Murray hardyhead is a threatened fish endemic to the southern Murray–Darling Basin in Australia, which has declined significantly in range and abundance since European settlement. Conservation of the species has relied largely on environmental watering of off-channel wetlands where isolated populations persist. This became problematic during recent drought (1997–2010) because of competing demands for limited water, and resentment towards environmental watering programs from communities that themselves were subject to reduced water entitlements. In response, emergency conservation measures prioritised the delivery of environmental water to minimise applied volumes. Captive maintenance programs were established for fish rescued from four genetically distinct conservation units, with varying levels of breeding success. Several translocations of wild and captive-bred fish to surrogate refuge sites were also conducted. Future recovery of the species should secure existing natural and stocked populations and translocate fish to additional appropriate sites to spread risk and reinstate natural pathways for dispersal. The approach to the conservation of Murray hardyhead during extreme environmental conditions provides insights to inform the management of fishes in other drought-prone regions of the world.
Let’s not forget the small fishes – conservation of two threatened species of pygmy perch in south-eastern Australia
Authors: Saddlier Stephen , Koehn John D. , Hammer Michael P.
Published: September 2013

Small species without commercial value are often overlooked in conservation management. Pygmy perches are minature percichthyid fishes from temperate southern Australia of significant conservation concern, with five of the seven described species being threatened nationally. The present paper examines the plight of Yarra pygmy perch Nannoperca obscura, and variegated pygmy perch N. variegata, and discusses the progress of national (and State) recovery-plan actions. Threats and risks to these species are considerable; however, overall, few recovery actions have been completed and the status of many populations is unknown following the recent ‘millenium drought’. Habitat restoration, fish rescues, environmental water delivery and research into distribution, ecology and population dynamics are largely driven by individuals within singular local management authorities. Like many small fishes, they receive less attention than do larger ones and a cross-jurisdictional national recovery team is required to prioritise, coordinate and implement conservation efforts before the continued persistence of these species can be assured. These two small fishes are representative of many similar species and the lessons from the present case study may be applied elsewhere throughout the world.
The rise and fall of a translocated population of the endangered Macquarie perch, Macquaria australasica, in south-eastern Australia
Authors: Lintermans Mark
Published: September 2013

Translocation is an increasingly popular conservation management activity worldwide, but the success of translocation is often not measured or reported. A population of the endangered Macquarie perch was imperilled by the damming in 1977 of the Queanbeyan River, near Canberra in south-eastern Australia. In November 1980, 66 adult Macquarie perch (309–389-mm total length) individuals were collected from the newlyformed reservoir, and translocated approximately 4 km upstream into the Queanbeyan River past a waterfall (which prevented access to spawning habitat). Five years of post-translocation monitoring at the release sites resulted in the capture of only a single individual in late 1981. Consequently, monitoring ceased because the translocation was assumed to have failed. However, subsequent angler reports and a preliminary survey in 1991 confirmed that some translocated fish had survived, and a small recruiting population had established. More intensive follow-up surveys and subsequent monitoring from 1996 to 2006 demonstrated an established population with consistent recruitment until 2001. However, after 2001, there was no evidence of recruitment and the population is now undetectable, with the prolonged ‘millennium drought’ (1997–2010) being the most plausible cause. The present study demonstrates the potentially ephemeral nature of assessments of success and failure, and the importance of targeted long-term monitoring programs.
A review of on-ground recovery actions for threatened freshwater fish in Australia
Authors: Lintermans Mark
Published: September 2013

Freshwater fish are a highly threatened group and recovery of these threatened species is an increasingly difficult ecological and social challenge. There are many different on-ground recovery actions available to managers, but no synthesis of what, how or why these recovery actions have been deployed. The present paper reviews 428 reported on-ground recovery actions from a survey of practitioners of threatened freshwater-fish recovery in Australia. Recovery actions were grouped into 12 categories, with the most commonly utilised recovery categories being harvest control, translocation, habitat enhancement and stock enhancement. Major drivers of recovery actions were general conservation concern, recovery plans and emergency responses. The number of recovery actions grew significantly in the decade beginning 2000 as the impacts of prolonged drought in south-eastern Australia intensified. In all, 58% of recovery actions occurred in the Murray–Darling Basin, although this region holds only 27% of the 74 listed threatened freshwater fish in Australia. Few or no recovery actions were reported for many species, and few actions occurred in northern or western parts of the country. More than 80% of recovery actions reportedly had some form of monitoring. The diversity of management interventions is reviewed, and patterns and issues are identified to guide future recovery efforts.
Predictive value of antral follicle count and anti-Müllerian hormone for follicle and oocyte developmental competence during the early prepubertal period in a sheep model
Authors: Torres-Rovira Laura , Gonzalez-Bulnes Antonio , Succu Sara , Spezzigu Antonio , Manca Maria E. , Leoni Giovanni G. , Sanna Marina , Pirino Salvatore , Gallus Marilia , Naitana Salvatore , Berlinguer Fiammetta
Published: September 2013

Circulating anti-Müllerian hormone (AMH) and antral follicle count (AFC) are addressed as suitable markers of oocyte quantity and quality during adulthood. To investigate whether AFC and circulating AMH could predict follicle development and oocyte quality during the prepubertal period we used 40-day-old ewe lambs with high, intermediate and low AFC (≥30, 16–29 and ≤15 follicles respectively). The analysis of the response to the exogenous FSH ovarian reserve test showed a positive correlation between AFC, AMH plasma levels, total follicle number and the number of large follicles (≥3 mm) grown after exogenous FSH administration. The incorporation of abattoir-derived oocytes collected from ovaries with different AFC in an in vitro embryo production system showed that a high AFC can predict oocyte quality in prepubertal ovaries, reflecting an ovarian status suitable for follicular development. The histological quantification of the ovarian reserve evidenced that AFC was not predictive of differences in either the number of healthy follicles or the size of the primordial follicle pool in prepubertal ovaries. Further studies are needed to investigate the implication on the reproductive performance of the significant inter-individual differences found in the present study in AFC and circulating AMH in the early prepubertal period.
Current status and future needs of the BehavePlus Fire Modeling System
Authors: Andrews Patricia L.
Published: September 2013

The BehavePlus Fire Modeling System is among the most widely used systems for wildland fire prediction. It is designed for use in a range of tasks including wildfire behaviour prediction, prescribed fire planning, fire investigation, fuel hazard assessment, fire model understanding, communication and research. BehavePlus is based on mathematical models for fire behaviour, fire effects and fire environment. It is a point system for which conditions are constant for each calculation, but is designed to encourage examination of the effect of a range of conditions through tables and graphs. BehavePlus is successor to BEHAVE, which was developed in 1977 and became available for field application in 1984. It was updated to BehavePlus in 2002. Updates through version 5 have added features and modelling capabilities. It is becoming increasingly difficult to expand the system. A redesign will address the need for consolidation with other systems and make it easier to incorporate new research results. This paper describes the development history and application of BehavePlus. The design, features and modelling foundation of the current system are described. Considerations for the next generation are presented.
Dislocation reactions, grain boundaries, and irreversibility in two-dimensional lattices using topological tweezers
Authors: Irvine William T. M. , Hollingsworth Andrew D. , Grier David G. , Chaikin Paul M.
Published: September 2013

Significance

The properties of real-world materials are typically determined by small collections of defects within them. One common defect––a dislocation––results from removing half a row of atoms from a crystal, leaving behind the other half that now ends abruptly at a tip in the crystal. The termination point behaves like a point “particle” that carries a topological charge, obeys dynamical laws, and interacts with other such particles to create grain boundaries. We report a method to precisely manipulate dislocations by using specially designed light fields (“topological tweezers”) to massage an experimental model system consisting of microscopic colloids. We use this tool to study their interactions and complex collective dynamics that are not always as reversible as one might think.
Origin and provenance of spherules and magnetic grains at the Younger Dryas boundary
Authors: Wu Yingzhe , Sharma Mukul , LeCompte Malcolm A. , Demitroff Mark N. , Landis Joshua D.
Published: September 2013

Significance

This study ties the spherules recovered in Pennsylvania and New Jersey to an impact in Quebec about 12,900 y ago at the onset of Younger Dryas. Our discovery resulted from an exhaustive search that examined the question of whether there is any evidence of extraterrestrial platinum group metals present in the bulk sediments, magnetic grains, and spherules recovered from the Younger Dryas boundary (YDB). We find that the spherules are likely quenched silicate melts produced following the impact at the YDB. The source of spherule osmium, however, is likely terrestrial and not meteorite derived.
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
Authors: Kamisetty Hetunandan , Ovchinnikov Sergey , Baker David
Published: September 2013

Significance

We develop an improved method for predicting residue–residue contacts in protein structures that achieves higher accuracy than previous methods by integrating structural context and sequence coevolution information. We then determine the conditions under which these predicted contacts are likely to be useful for structure modeling and identify more than 400 protein families where these conditions are currently met.
Abundance and Size Structure of Shortnose Sturgeon in the Altamaha River, Georgia
Authors: Peterson Douglas L. , Bednarski Michael S.
Published: September 2013

Endangered Shortnose Sturgeon Acipenser brevirostrum inhabit large tidal rivers along the Atlantic coastline of North America, ranging from the St. John River, Canada, southward to the St. Johns River, Florida. Currently, long‐term assessments of the abundance and age structure of southern populations are completely lacking. To address this information gap, we assessed recent changes in Shortnose Sturgeon abundance and age structure by sampling with anchored entanglement gear in the Altamaha River, Georgia, during summer in 2004–2010. To estimate abundance, we used the Huggins closed‐capture model in Program MARK. We assessed size structure by interpreting the first, second, and third quartiles of the FL of individuals captured during each year. In total, we captured 1,737 Shortnose Sturgeon (72 recaptures). Total estimated abundance was variable, ranging from 1,206 individuals (95% lognormal confidence interval [CI] = 566–2,759) in 2009 to 5,551 individuals (95% CI = 2,804–11,304) in 2006. Much of the annual variation in total abundance was attributable to wide variations in juvenile abundance, which ranged from a low of 62 individuals (95% CI = 24–181) in 2009 to a high of 3,467 individuals (95% CI = 1,744–7,095) in 2006. Annual shifts in size structure were indicative of rapid population turnover, probably resulting from a combination of mortality and permanent emigration. Although the Altamaha River Shortnose Sturgeon population shares several characteristics with northern populations (e.g., variable juvenile abundance and stable adult abundance), our results suggest that southern populations are more susceptible to decline because of their accelerated life cycle and inherently lower abundances.
Using Seasonal Variation in Otolith Microchemical Composition to Indicate Largemouth Bass and Southern Flounder Residency Patterns across an Estuarine Salinity Gradient
Authors: Farmer Troy M. , DeVries Dennis R. , Wright Russell A. , Gagnon Joel E.
Published: September 2013

Estuaries are transitional zones where salinity largely controls the distribution of both freshwater and marine species. However, the degree to which freshwater and marine species use these variable habitats as year‐round residents or transient migrants is largely unknown. We used otolith strontium: calcium ratios (Sr: Ca) as a marker for salinity exposure to reconstruct lifetime salinity exposure plots for individual Largemouth Bass Micropterus salmoides and Southern Flounder Paralichthys lethostigma collected across a seasonally variable estuarine salinity gradient. Initially, we determined that a definable relationship existed between salinity, water chemistry, and otolith Sr: Ca for both species. We then used otolith Sr: Ca profiles to indicate lifetime salinity exposure and subsequently classified each fish as either a freshwater resident, transient (combination of freshwater and estuarine signals in otolith), or estuarine resident. For Southern Flounder we also used Sr: Ca profiles from the otolith core to classify each individual as having either a freshwater core or estuarine or marine core. For Largemouth Bass, most (88%) individuals in the lower estuary were estuarine residents, whereas most (77%) individuals in the upper estuary were freshwater residents. These data support the hypothesis that adult Largemouth Bass in lower portions of the estuary do not migrate to avoid salinity, but rather remain in lower portions of the estuary throughout life. For Southern Flounder, 45% of individuals had estuarine or marine core Sr: Ca signals, while 55% had freshwater Sr: Ca core signals. Combining core and residency classification patterns revealed that three patterns described 95% of the Southern Flounder collected: (1) freshwater core and freshwater resident (16%), (2) freshwater core and estuarine resident (37%), and (3) estuarine or marine core and estuarine resident (42%). These data demonstrate that both tidal freshwater and low‐salinity estuarine habitats are important nursery areas for Southern Flounder.
Evidence for Density‐Dependent Changes in Growth, Downstream Movement, and Size of Chinook Salmon Subyearlings in a Large‐River Landscape
Authors: Connor William P. , Tiffan Kenneth F. , Plumb John M. , Moffitt Christine M.
Published: September 2013

We studied the growth rate, downstream movement, and size of naturally produced fall Chinook Salmon Oncorhynchus tshawytscha subyearlings (age 0) for 20 years in an 8th‐order river landscape with regulated riverine upstream rearing areas and an impounded downstream migration corridor. The population transitioned from low to high abundance in association with U.S. Endangered Species Act and other federally mandated recovery efforts. The mean growth rate of parr in the river did not decline with increasing abundance, but during the period of higher abundance the timing of dispersal from riverine habitat into the reservoir averaged 17 d earlier and the average size at the time of downstream dispersal was smaller by 10 mm and 1.8 g. Changes in apparent abundance, measured by catch per unit effort, largely explained the time of dispersal, measured by median day of capture, in riverine habitat. The growth rate of smolts in the reservoir declined from an average of 0.6 to 0.2 g/d between the abundance periods because the reduction in size at reservoir entry was accompanied by a tendency to migrate rather than linger and by increasing concentrations of smolts in the reservoir. The median date of passage through the reservoir was 14 d earlier on average, and average smolt size was smaller by 38 mm and 22.0 g, in accordance with density‐dependent behavioral changes reflected by decreased smolt growth. Unexpectedly, smolts during the high‐abundance period had begun to reexpress the migration timing and size phenotypes observed before the river was impounded, when abundance was relatively high. Our findings provide evidence for density‐dependent phenotypic change in a large river that was influenced by the expansion of a recovery program. Thus, this study shows that efforts to recover native fishes can have detectable effects in large‐river landscapes. The outcome of such phenotypic change, which will be an important area of future research, can only be fully judged by examining the effect of the change on population viability and productivity.
Use of Laparoscopy for Sex Identification of Asp Aspius aspius
Authors: Falahatkar Bahram , Tolouei Gilani Mohammad H.
Published: September 2013

Asp Aspius aspius is an endangered rheophilic cyprinid species. This study describes a laparoscopic technique for Asp sex identification that also permits observations of the gonads. Seventeen fish (790–3,020 g, 41.4–73.6 cm TL, age 2–5) were examined using a laparoscope for gender determination. The cystoscope sheath was inserted into the body cavity through a small (0.9–1 cm) incision in the left flank, after which the gonads were visualized using a monitor. All fish but one were correctly sexed using this procedure in a minimal amount of time. Histological preparations showed the gonads to be at different stages of maturity in both sexes. This study demonstrated that laparoscopy can be used as an effective and minimally invasive diagnostic technique for sex identification and maturity stage determination in Asp that are under propagation and used for stock rehabilitation.

Received March 26, 2013; accepted June 13, 2013
The Southern European Welfare model in the post-industrial order
Authors: Marí-Klose Pau , Moreno-Fuentes Francisco Javier
Published: September 2013

The discussion on the existence of a distinctive ‘Mediterranean’ welfare model has focused on the historical and politico-institutional dynamics, as well as on the policy traits of the welfare arrangements found in Southern European countries. Particular attention has been given to the external pressures and internal constraints faced by the welfare systems of these countries, as well as to what extent there is a common response to such challenges. In this article, we claim that while researchers were embarked in this scholarly effort, Southern European societies kept changing, transforming the nature of existing arrangements in not always forecasted directions, to the point of questioning the adequacy of clustering them under a common type. The current context of economic and financial crisis introduces additional factors in the process of transformation and reform of the welfare schemes of these countries, placed at the epicentre of the turmoil shattering European economies and societies.
Female employment and the economic crisis
Authors: Andreotti Alberta , Mingione Enzo , Pratschke Jonathan
Published: September 2013

One of the characteristics of the Italian peninsula is a sharp North-South gradient on many economic and labour market variables. This gradient is particularly marked in relation to female employment, making Italy a particularly useful ‘laboratory’ for studying changes in gender roles. Esping-Andersen's description of the decline of the ‘male breadwinner’ model and the search for a ‘new equilibrium’ in gender roles is suggestive, but the assumption that current processes will inevitably converge towards a relatively homogeneous social configuration (exemplified by the Scandinavian countries) is rather unconvincing. We will show in this article that the Italian case comprises macro-regions with very different female employment rates and highly differentiated welfare systems. Furthermore, one of the effects of the economic crisis has been to obstruct the entry of women into paid work, particularly in the South where employment rates are already at a very low level. When discussing trends and changes in women's roles, it is important to remember that the resulting transformations are plural, contingent and discontinuous and strongly shaped by prevailing socio-economic conditions. In the context of a prolonged and severe crisis, the differences between Northern and Southern Italy have been further accentuated, impeding the development of coherent policy responses and obstructing change in gender roles.
Is social protection in Greece at a crossroads?
Authors: Petmesidou Maria
Published: September 2013

This paper critically examines the limitations and deadlocks of welfare patterns embedded in the statist-familialist regime that for a long-time has been pivotal for the institutional set up and processes of social redistribution in Greece. Changes to social protection under the combined effect of conflicts and impasses of this regime, and of an intractable sovereign debt crisis (largely due to accumulated deadlocks) that has engulfed the country since the late 2000s are our main focus. Current welfare reforms across major policy areas are examined, with the aim to foreshadow the direction of impending change; and, particularly, to trace any indications of whether reform can bolster ‘inclusive solidarity’ and improve redistribution or, instead, will bring about heightened insecurity.
Compensatory Growth of the Sandbar Shark in the Western North Atlantic Including the Gulf of Mexico
Authors: Romine J. G. , Musick J. A. , Johnson R. A.
Published: September 2013

The number of Sandbar Sharks Carcharhinus plumbeus in the western North Atlantic Ocean has experienced a drastic decline since the early 1980s, reaching a minimum during the early 1990s. Catch rates in the early 1990s were a mere 25% of those during the 1980s. According to several fishery-independent surveys, the low point in Sandbar Shark abundance followed a period of high exploitation. Growth models fit to age–length data collected from 1980 to 1983 and from 2001 to 2004 were compared to investigate potential changes in parameter estimates that might reveal compensatory responses in the Sandbar Shark population. Statistical differences were found between the model parameters for the two time periods, but the differences in growth rates were minimal. The parameters from the three-parameter von Bertalanffy growth model for female sharks during the 1980–1983 and 2000–2004 time periods were as follows: L∞ = 188.4 and 178.3 cm FL; k = 0.084 and 0.106; and t  0 = −4.097 and −3.41. For males the growth parameters were as follows: L∞ = 164.63 and 173.66 cm; k = 0.11 and 0.11; and t  0 = −3.62 and −3.33. The estimated age at 50% maturity for female Sandbar Sharks changed from 15 years to 12.49 years between the two time periods.

Received December 21, 2012; accepted March 28, 2013
Reproductive Biology of the Cownose Ray in the Charlotte Harbor Estuarine System, Florida
Authors: Poulakis Gregg R.
Published: September 2013

The Cownose Ray Rhinoptera bonasus is an abundant species in the western Atlantic Ocean, including the Gulf of Mexico, but its reproductive biology is not completely known because of the difficulty of obtaining year-round samples in large portions of its range where the species is migratory. To address this knowledge gap, Cownose Rays were studied in a subtropical estuarine system where rays are available year-round. Size at maturity and reproductive cyclicity were assessed using 140 females and 151 males. For females, the size at 50% maturity was 701 mm disk width (DW) based on ovary length and weight, maximum follicle diameter, and mating wounds and scars; the size at 100% maturity was 712 mm DW. For males, the size at 50% maturity was 681 mm DW based on clasper morphology, testis length and weight, and epididymis width; the size at 100% maturity was 712 mm DW. Overall testis size (length and weight) and mean testis lobe diameter peaked up to 2 months prior to ovary size and maximum follicle diameter, indicating that males were preparing to inseminate females during the entire parturition and mating period. Mating behaviors and fresh mating wounds were observed mostly between April and June. Ovulation peaked in May, and parturition occurred primarily in March and April after an 11–12 month, single-embryo gestation period, suggesting that females are synchronous in Charlotte Harbor. Size at birth was 202–383 mm DW. Concurrent vitellogenesis and gestation indicated a clearly defined annual reproductive cycle that may be completed within the estuary. Understanding reproductive life history in wide-ranging species such as the Cownose Ray is useful in the short term for making sound management decisions and for future comparison as the effects of global climate change are realized.

Received September 30, 2012; accepted March 21, 2013
Occurrence of an Intersexual Blacktip Shark in the Northern Gulf of Mexico, with Notes on the Standardization of Classifications for This Condition in Elasmobranchs
Authors: Hendon Jill M. , Koester David M. , Hoffmayer Eric R. , Driggers William B. , Cicia Angela M.
Published: September 2013

An intersexual Blacktip Shark Carcharhinus limbatus with a testis, immature female reproductive tracts (embedded), and claspers was caught in the Gulf of Mexico. Histology of the single gonad revealed that all stages of spermatogenesis were occurring; however, the absence of ovaries and a male duct system suggests that neither sex would have been functional in this individual. Intersexuality has been reported in 17 families and 36 species of elasmobranchs. The degree to which the different sexes are present in a given individual is often difficult to categorize by normal hermaphroditic standards, as this is typically an anomalous presentation in elasmobranchs. Therefore, this report provides three categories for classification (basic, incomplete, and complete intersexuality) to standardize terminology and allow for more precise comparisons to be made among elasmobranch examples. Basic intersexuals have gonadal tissue of only one sex and a combination of other male and female characters with neither or only one sex being complete. Incomplete intersexuals have gonadal tissue of both sexes and a combination of other male and female characters; however, neither or only one sex is complete. Complete intersexuals have claspers as well as gonadal tissue and tracts for both sexes. The majority of the reported intersexual elasmobranchs, including the shark described here, are basic intersexuals.

Received September 30, 2012; accepted April 17, 2013
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets
Authors: Crowell Kevin L. , Slysz Gordon W. , Baker Erin S. , LaMarche Brian L. , Monroe Matthew E. , Ibrahim Yehia M. , Payne Samuel H. , Anderson Gordon A. , Smith Richard D.
Published: September 2013

Motivation: The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing.

Results: We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.

Availability: LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README).

Contact:  rds@pnnl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data
Authors: McClellan Elizabeth A. , Moerland Perry D. , van der Spek Peter J. , Stubbs Andrew P.
Published: September 2013

Summary: The discovery of functionally related groups in a set of significantly abundant proteins from a mass spectrometry experiment is an important step in a proteomics analysis pipeline. Here we describe NetWeAvers (Network Weighted Averages) for analyzing groups of regulated proteins in a network context, e.g. as defined by clusters of protein–protein interactions. NetWeAvers is an R package that provides a novel method for analyzing proteomics data integrated with biological networks. The method includes an algorithm for finding dense clusters of proteins and a permutation algorithm to calculate cluster P-values. Optional steps include summarizing quantified peptide values to single protein values and testing for differential expression, such that the data input can simply be a list of identified and quantified peaks.

Availability and implementation: The NetWeAvers package is written in R, is open source and is freely available on CRAN and from netweavers.erasmusmc.nl under the GPL-v2 license.

Contact: e.mcclellan@erasmusmc.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Does copepod size determine food consumption of particulate feeding fish?
Authors: van Deurs Mikael , Koski Marja , Rindorf Anna
Published: September 2013

van Deurs, M., Koski, M., and Rindorf, A. Does copepod size determine food consumption of particulate feeding fish? – ICES Journal of Marine Science, 71: . The climate-induced reduction in the mean copepod size, mainly driven by a decrease in the abundance of the large Calanus finmarchicus around 1987, has been linked to the low survival of fish larvae in the North Sea. However, to what extent this sort of reduction in copepod size has any influence on adult particulate feeding fish is unknown. In the present study, we investigated the hypothesis that the availability of the large copepods determines food consumption and growth conditions of lesser sandeel (Ammodytes marinus) in the North Sea. Analysis of stomach content suggested that food consumption is higher for fish feeding on large copepods, and additional calculations revealed how handling time limitation may provide part of the explanation for this relationship. Comparing stomach data and zooplankton samples indicated that lesser sandeel actively target large copepods when these are available. Finally, we observed that the length of lesser sandeel began to decrease in the late 1980s, simultaneously with the C. finmarchicus decline.
Long-term effects of addition of mineralocorticoid receptor antagonist to angiotensin II receptor blocker in patients with diabetic nephropathy: a randomized clinical trial
Authors: Esteghamati Alireza , Noshad Sina , Jarrah Sorour , Mousavizadeh Mostafa , Khoee Seyed Hamid , Nakhjavani Manouchehr
Published: September 2013

Background

Addition of spironolactone (SPR) to angiotensin-converting enzyme (ACE) inhibitors or angiotensin II receptor blockers (ARBs) might provide antiproteinuric effects beyond what is gained by either medication alone. This study was designed to assess the long-term efficacy of SPR/ARB combination in comparison with the standard ACE/ARB regimen in diabetic nephropathy.

Methods

In an open-label, parallel-group, single-center, randomized clinical trial (NCT01667614), 136 patients with diabetes and proteinuria, already treated with enalapril and losartan, were included. In 74 patients, ACE inhibitors were discontinued. After a wash-out period of 2 weeks, 25 mg SPR daily was initiated. The remainder of the patients (n = 62) received ACE inhibitors and ARBs as before. Patients were followed every 3 months for 18 months. During each visit, systolic and diastolic blood pressure (BP), urinary albumin excretion (UAE), serum creatinine, estimated glomerular filtration rate (eGFR) and serum potassium concentrations were determined.

Results

After 18 months, three patients in the SPR/ARB group developed asymptomatic hyperkalemia. SPR/ARB significantly reduced both systolic and diastolic BP (P < 0.001 and 0.001, respectively). SPR/ARB decreased UAE by 46, 72 and 59% after 3, 12 and 18 months, respectively. Compared with the continuation regimen, SPR/ARB was superior in UAE reduction (P = 0.017 after 18 months), independent of BP change. In both groups, eGFR declined significantly over the trial course and the decline rate did not differ significantly between the two groups.

Conclusions

Addition of SPR to ARB provides added benefits with respect to BP control and proteinuria diminution. These antiproteinuric effects are not accompanied by prevention of eGFR loss compared with conventional therapy with ACE/ARB.
Clinical outcomes and macrolide resistance in Mycoplasma pneumoniae infection in Scotland, UK
Authors: Ferguson Graeme D. , Gadsby Naomi J. , Henderson Sarah S. , Hardie Alison , Kalima Pota , Morris Andrew Conway , Hill Adam T. , Cunningham Steve , Templeton Kate E.
Published: September 2013

Mycoplasma pneumoniaehas a cyclical, epidemic pattern of infection and the most recent epidemic occurred in Europe in 2011. Macrolides are recommended for the treatment ofM. pneumoniaerespiratory tract infection, but macrolide resistance has been reported at low levels in Europe. The aim of the study was to examine the clinical impact of the recentM. pneumoniaeepidemic in a hospital setting in Scotland and to determine whether macrolide-resistant strains are present. Data were analysed retrospectively for 307 patients withM. pneumoniaerespiratory infection diagnosed in 2010 and 2011 in Edinburgh, UK. Genotypic macrolide resistance testing was also carried out in 32 patients in whom resistance was considered most likely, based on their clinical picture. We found that 175 patients (59 %) were admitted to hospital, 20 (7 %) were admitted to critical care and 97 (38 %) required oxygen. All 48 adult patients (100 %) were admitted to hospital, compared with 127 children (51 %). Adults were also more likely to require oxygen [odds ratio (OR) 4.964,P<0.001, 95 % confidence interval (CI) 2.129–11.803] and to be admitted to critical care (OR 4.909,P = 0.001, 95 % CI 1.735–13.829), compared with children. Macrolide resistance conferred by the 23S rRNA gene mutation was found in samples from 6 out of 32 patients (19 %) in the subset tested. The results suggest that the recentM. pneumoniaeepidemic was associated with a significant burden of hospital admission locally. The study also describes the first case series of macrolide-resistantM. pneumoniaein the UK, indicating that macrolide resistance surveillance is warranted in preparation for the next epidemic.
Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries
Authors: Wang Jiyong , Tadeo Xavier , Hou Haitong , Tu Patricia G. , Thompson James , Yates John R. , Jia Songtao
Published: September 2013

Heterochromatin spreading leads to the silencing of genes within its path, and boundary elements have evolved to constrain such spreading. In fission yeast, heterochromatin at centromeres I and III is flanked by inverted repeats termed IRCs, which are required for proper boundary functions. However, the mechanisms by which IRCs prevent heterochromatin spreading are unknown. Here, we identified Bdf2, which is homologous to the mammalian bromodomain and extraterminal (BET) family double bromodomain proteins involved in diverse types of cancers, as a factor required for proper boundary function at IRCs. Bdf2 is enriched at IRCs through its interaction with the boundary protein Epe1. The bromodomains of Bdf2 recognize acetylated histone H4 tails and antagonize Sir2-mediated deacetylation of histone H4K16. Furthermore, abolishing H4K16 acetylation (H4K16ac) with an H4K16R mutation promotes heterochromatin spreading, and mimicking H4K16ac by an H4K16Q mutation blocks heterochromatin spreading at IRCs. Our results thus illustrate a mechanism of establishing chromosome boundaries at specific sites through the recruitment of a factor that protects euchromatic histone modifications. They also reveal a previously unappreciated function of H4K16ac in cooperation with H3K9 methylation to regulate heterochromatin spreading.
A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism
Authors: Marina Diana B. , Shankar Smita , Natarajan Prashanthi , Finn Kenneth J. , Madhani Hiten D.
Published: September 2013

Long noncoding RNAs (lncRNAs) can trigger repressive chromatin, but how they recruit silencing factors remains unclear. In Schizosaccharomyces pombe, heterochromatin assembly on transcribed noncoding pericentromeric repeats requires both RNAi and RNAi-independent mechanisms. In Saccharomyces cerevisiae, which lacks a repressive chromatin mark (H3K9me [methylated Lys9 on histone H3]), unstable ncRNAs are recognized by the RNA-binding protein Nrd1. We show that the S. pombe ortholog Seb1 is associated with pericentromeric lncRNAs. Individual mutation of dcr1+ (Dicer) or seb1+ results in equivalent partial reductions of pericentromeric H3K9me levels, but a double mutation eliminates this mark. Seb1 functions independently of RNAi by recruiting the NuRD (nucleosome remodeling and deacetylase)-related chromatin-modifying complex SHREC (Snf2–HDAC [histone deacetylase] repressor complex).
Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues
Authors: Smith Graham , Wermuth Urs D.
Published: September 2013

The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O+·C2HO4−·2H2O, (I), and with adipic acid, bis(4-carbamoylpiperidinium) adipate dihydrate, 2C6H13N2O+·C6H8O42−·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carboxylic acid O—H...Ocarboxylhydrogen-bonding interactions, formingC(5) chain substructures which extend alonga. The isonipecotamide cations also give parallel chain substructures through amide N—H...O hydrogen bonds, the chains being linked acrossband downcby alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N—H...Ocarboxylhydrogen bonds, generating cyclicR43(10) andR32(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion-related cations are interlinked through the two water molecules, which act as acceptors in dual amide N—H...Owaterhydrogen bonds, to give a cyclicR42(8) association which is conjoined with anR44(12) motif. Further N—H...Owater, water O—H...Oamideand piperidinium N—H...Ocarboxylhydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide–amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.
Anisotropic model for the numerical computation of magnetostriction in grain-oriented electrical steel sheets
Authors: Kaltenbacher Manfred , Volk Adrian , Ertl Michael
Published: September 2013

Purpose

– The modeling of magnetostrictive effects is a topic of intensive research. The authors' goal is the precise modeling and numerical simulation of the magnetic field and resulting mechanical vibrations caused by magnetostriction along the joint regions of electric transformers.

Design/methodology/approach

– The authors apply the finite element (FE) method to efficiently solve the arising coupled system of partial differential equations describing magnetostriction. Hereby, they fully take the anisotropic behavior of the material into account, both in the computation of the nonlinear electromagnetic field as well as the induced magnetostrictive strains. To support their material models, the authors measure the magnetic as well as the mechanical hysteresis curves of the grain-oriented electrical steel sheets with different orientations (w.r.t the rolling direction). From these curves they then extract for each orientation the corresponding commutation curve, so that the hysteretic behavior is simplified to a nonlinear one.

Findings

– The numerical simulations show strong differences both in the magnetic field as well as mechanical vibrations when comparing this newly developed anisotropic model to an isotropic one, which just uses measured curves in rolling direction of the steel sheets. Therefore, a realistic modeling of the magnetostrictive behavior, especially for grain-oriented electrical steel as used in transformers, needs to take into account the anisotropic material behavior.

Originality/value

– The authors have developed an enhanced material model for describing magnetostrictive effects along the joint regions of electric transformers, which fully considers the anisotropic material behavior. This model has been integrated into a FE scheme to numerically simulate the mechanical vibrations in transformer cores caused by magnetostriction.
Building organizational advantage: social capital in multinational enterprises
Authors: Lehtimäki Hanna , Karintaus Katja
Published: September 2013

Purpose

This paper aims to advance the authors' understanding about the functioning of intra‐organizational social connections in creating organizational advantage and operational efficiency in multinational enterprises (MNEs). The focus is on the structural dimension of social capital.

Design/methodology/approach

The study is an empirically grounded case research with three internationally operating manufacturing companies. Each company had set a strategic initiative to exploit customer knowledge more effectively and increase global sales. The study has been conducted in close collaboration with the participating companies. The data comprise interviews and social network surveys.

Findings

The study shows that the structure of relationships constituting social capital consists of not only ties of knowledge transfer but also of sociability and trust. High level of social capital provides for solving complex customer problems, combining expert knowledge, and creation of novel innovations. Trust is needed to build shared understanding and sense of ownership in the subunits. Highly centralized social structure does not allow for solving complex problems and creating new knowledge across organizational boundaries.

Practical implications

For the managers, this study offers insight into the functioning of the social networks as an integral part of operational efficiency in MNEs.

Originality/value

Focusing on the behaviour of the entire network allows for discussing the impact of social structure on the knowledge flows within the firm. The study contributes to the call for empirical work at the systemic level of analysis on knowledge flows in MNEs.