bluuebunny/crossref_metadata_2025 huggingface dataset:
Lake‐size dependency of wind shear and convection as controls on gas exchange
Authors: Read Jordan S. , Hamilton David P. , Desai Ankur R. , Rose Kevin C. , MacIntyre Sally , Lenters John D. , Smyth Robyn L. , Hanson Paul C. , Cole Jonathan J. , Staehr Peter A. , Rusak James A. , Pierson Donald C. , Brookes Justin D. , Laas Alo , Wu Chin H.
Published: April 2012

High‐frequency physical observations from 40 temperate lakes were used to examine the relative contributions of wind shear (u*) and convection (w*) to turbulence in the surface mixed layer. Seasonal patterns of u* and w* were dissimilar; u* was often highest in the spring, while w*increased throughout the summer to a maximum in early fall. Convection was a larger mixed‐layer turbulence source than wind shear (u*/w* < 0.75) for 18 of the 40 lakes, including all 11 lakes <10 ha. As a consequence, the relative contribution of convection to the gas transfer velocity (k, estimated by the surface renewal model) was greater for small lakes. The average k was 0.54 m day−1 for lakes <10 ha. Because u* and w*differ in temporal pattern and magnitude across lakes, both convection and wind shear should be considered in future formulations of lake‐air gas exchange, especially for small lakes.
An exact solution for equatorially trapped waves
Authors: Constantin Adrian
Published: April 2012

We present an exact solution of the nonlinear governing equations for geophysical water waves in theβ‐plane approximation near the Equator. The solution describes in the Lagrangian framework equatorially trapped waves propagating eastward in a stratified inviscid fluid.
Family Support in Early Hearing Detection and Intervention (EHDI) Systems
Authors: Martin Patti , Nicholson Nannette , Hall Charia
Published: April 2012

Family support has evolved from a buzzword of the 1990s to a concept founded in theory, mandated by federal law, valued across disciplines, and espoused by both parents and professionals. This emphasis on family-centered practices for families of young children with disabilities, coupled with federal policy initiatives and technological advances, served as the impetus for the development of Early Hearing Detection and Intervention (EHDI) programs (Nicholson & Martin, in press). White, Forsman, Eichwald, and Muñoz (2010) provide an excellent review of the evolution of EHDI systems, which include family support as one of their 9 components. The National Center for Hearing Assessment and Management (NCHAM), the Maternal and Child Health Bureau, and the Center for Disease Control Centers cosponsored the first National EHDI Conference. This conference brought stakeholders including parents, practitioners, and researchers from diverse backgrounds together to form a learning collaborative (Forsman, 2002). Attendees represented a variety of state, national, and/or federal agencies and organizations. This forum focused effort on the development of EHDI programs infused with translating research into practices and policy. When NCHAM, recognizing the critical role of family support in the improvement of outcomes for both children and families, created a think tank to investigate the concept of a conference centered on support for families of children who are deaf or hard of hearing in 2005, the “Investing in Family Support” (IFSC) conference was born. This conference was specifically designed to facilitate and enhance EHDI efforts within the family support arena. From this venue, a model of family support was conceptualized and has served as the cornerstone of the IFSC annual conference since 2006. Designed to be a functional framework, the IFSC model delineates where and how families find support. In this article, we will promote and encourage continued efforts towards defining operational measures and program components to ultimately quantify success as it relates to improved outcomes for these children and their families. The authors view this opportunity to revisit the theoretical underpinnings of family support, the emerging research in this area, and the basics of the IFSC Model of Family Support as a call to action. We challenge professionals who work with children identified as deaf or hard of hearing to move family support from conceptualization to practices that are grounded in evidence and ever mindful of the unique and dynamic nature of individual families.
Managing Problem Emotions and Behaviors in Children With ASD: An Assessment-Driven Three-Step Approach
Authors: Mazefsky Carla A.
Published: April 2012

Emotional and behavioral problems in children with autism spectrum disorders (ASD) interfere with daily functioning and their ability to learn new skills. Thus, promoting emotional and behavioral stability is often a necessary component of intervention with children with ASD. This article reviews an approach to managing emotional and behavioral problems in ASD that begins with a thorough assessment to identify the function of the behavior or source of distress. I review common contributors to problem emotions and behaviors in ASD, highlight the importance of matching the intervention to the results of the assessment, and describe a stepwise approach to intervention.
Categorization in ASD: The Role of Typicality and Development
Authors: Gastgeb Holly Zajac , Strauss Mark S.
Published: April 2012

There is a growing amount of evidence suggesting that individuals with autism spectrum disorders (ASD) differ in the way in which they cognitively process information. A critical aspect of cognitive processing that is receiving more attention in studies of ASD is categorization. The studies presented here examined the effect of typicality on categorization of objects and gender in high-functioning children, adolescents, and adults with ASD and matched controls. The ASD and control groups showed improved categorization throughout the lifespan for typical and somewhat typical object category members and typical gender faces. However, individuals with ASD took more time to categorize atypical object category members and were less accurate in categorizing atypical gender faces from age 8–12 years through adulthood. We will discuss the implications of these results for teaching categories and category labels to individuals with ASD.
Using Family Members or Close Friends as Informants About Participation Goals for Older Adults With and Without Aphasia
Authors: Haley Katarina L. , Wangerman Thomas
Published: April 2012

Client-centered care is a stated focus for many rehabilitation programs, but personalized goal-setting presents unique challenges for people with aphasia (PWA). A potential solution for clinicians is to enlist the help of family members or close friends to determine what life activities should be addressed. In this article, we review two main reasons this solution is not ideal. First, we discuss how negative effects on autonomy and motivation may be instigated unintentionally. Next, we consider to what extent accurate input can be assumed by proxy responders. We conclude by reporting the results of a small study showing that congruence about activity choices among family members or friends not affected by aphasia is similar to previously reported congruence in families with a history of aphasia. These results suggest that ability to predict life activity preferences in others is limited, regardless of the presence of aphasia. We contend that although the input and participation of significant others is often critical to positive rehabilitation outcomes, the value of this input lies in its relationship to the priorities identified by the individual with aphasia, not in the potential for replacing it.
The Importance of Aphasia Community Programs in Supporting Self-Determination in PWA
Authors: Nicholas Marjorie
Published: April 2012

Aphasia support groups and aphasia community centers have been increasing in number over the past 2 decades in the United States and abroad. Participation in these innovative community programs can support the process of self-determination in people with aphasia. In this article, I discuss specific examples of how this occurs and, in addition, review the Living With Aphasia: Framework for Outcome Measurement (A-FROM) model (Kagan et al., 2008) as a useful way to conceptualize the individual benefits that people with aphasia (PWA) may receive from participation in aphasia community centers. The article concludes with a case presentation exemplifying the multi-level benefits achieved from participating in aphasia community programs.
Expression-based genome-wide association study links the receptor
CD44
in adipose tissue with type 2 diabetes
Authors: Kodama Keiichi , Horikoshi Momoko , Toda Kyoko , Yamada Satoru , Hara Kazuo , Irie Junichiro , Sirota Marina , Morgan Alexander A. , Chen Rong , Ohtsu Hiroshi , Maeda Shiro , Kadowaki Takashi , Butte Atul J.
Published: April 2012

Type 2 diabetes (T2D) is a complex, polygenic disease affecting nearly 300 million people worldwide. T2D is primarily characterized by insulin resistance, and growing evidence has indicated the causative link between adipose tissue inflammation and the development of insulin resistance. Genetic association studies have successfully revealed a number of important genes consistently associated with T2D to date. However, these robust T2D-associated genes do not fully elucidate the mechanisms underlying the development and progression of the disease. Here, we report an alternative approach, gene expression-based genome-wide association study (eGWAS): searching for genes repeatedly implicated in functional microarray experiments (often publicly available). We performed an eGWAS across 130 independent experiments (totally 1,175 T2D case-control microarrays) to find additional genes implicated in the molecular pathogenesis of T2D and identified the immune-cell receptor
CD44
as our top candidate (
P
= 8.5 × 10
−20
). We found
CD44
deficiency in a diabetic mouse model ameliorates insulin resistance and adipose tissue inflammation and also found that anti-CD44 antibody treatment decreases blood glucose levels and adipose tissue macrophage accumulation in a high-fat, diet-fed mouse model. Further, in humans, we observed CD44 is expressed in inflammatory cells in obese adipose tissue and discovered serum CD44 levels were positively correlated with insulin resistance and glycemic control.
CD44
likely plays a causative role in the development of adipose tissue inflammation and insulin resistance in rodents and humans. Genes repeatedly implicated in publicly available experimental data may have unique functionally important roles in T2D and other complex diseases.
Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions
Authors: de Alwis Ruklanthi , Smith Scott A. , Olivarez Nicholas P. , Messer William B. , Huynh Jeremy P. , Wahala Wahala M. P. B. , White Laura J. , Diamond Michael S. , Baric Ralph S. , Crowe James E. , de Silva Aravinda M.
Published: April 2012

Dengue is a mosquito-borne flavivirus that is spreading at an unprecedented rate and has developed into a major health and economic burden in over 50 countries. Even though infected individuals develop potent and long-lasting serotype-specific neutralizing antibodies (Abs), the epitopes engaged by human neutralizing Abs have not been identified. Here, we demonstrate that the dengue virus (DENV)-specific serum Ab response in humans consists of a large fraction of cross-reactive, poorly neutralizing Abs and a small fraction of serotype-specific, potently inhibitory Abs. Although many mouse-generated, strongly neutralizing monoclonal antibodies (mAbs) recognize epitopes that are present on recombinant DENV envelope (E) proteins, unexpectedly, the majority of neutralizing Abs in human immune sera bound to intact virions but not to the ectodomain of purified soluble E proteins. These conclusions with polyclonal Abs were confirmed with newly generated human mAbs derived from DENV-immune individuals. Two of three strongly neutralizing human mAbs bound to E protein epitopes that were preserved on the virion but not on recombinant E (rE) protein. We propose that humans produce Abs that neutralize DENV infection by binding a complex, quaternary structure epitope that is expressed only when E proteins are assembled on a virus particle. Mapping studies indicate that this epitope has a footprint that spans adjacent E protein dimers and includes residues at the hinge between domains I and II of E protein. These results have significant implications for the DENV Ab and vaccine field.
On De Giorgi’s conjecture and beyond
Authors: Del Pino Manuel , Kowalczyk Michal , Wei Juncheng
Published: April 2012

We consider the problem of existence of entire solutions to the Allen–Cahn equation Δ
u
 + 
u
 - 
u
3
 = 0 in

, usually regarded as a prototype for the modeling of phase transition phenomena. In particular, exploiting the link between the Allen–Cahn equation and minimal surface theory in dimensions
N
≥9, we find a solution,
u
, with ∂

x

N

u
 > 0, such that its level sets are close to a nonplanar, minimal, entire graph. This counterexample provides a negative answer to a celebrated question by Ennio de Giorgi [De Giorgi E (1979)
Proceedings of the International Meeting on Recent Methods in Nonlinear Analysis (Rome, 1978)
, 131–188, Pitagora, Bologna]. Our results suggest parallels of De Giorgi’s conjecture for finite Morse index solutions in two and three dimensions and suggest a possible program of classification of all entire solutions.
Breeding for disease resistance in livestock and fish.
Authors: Stear M. J. , Nikbakht G. , Matthews L. , Jonsson N. N.
Published: April 2012

Breeding for disease resistance offers improved animal welfare and increased returns for breeders. It is now practised in cattle, sheep, pig, chicken and fish farming. This review provides an overview for the non-specialist of the strategies to breed for disease resistance, with equal weighting on traditional phenotypic methods and the changes being introduced by modern genomic tests. It starts by explaining four key concepts in selective breeding: heritability, estimated breeding value (EBV), repeatability and genetic correlation. It then explains the decisions required to create selection objectives, selection criteria and selection indices. The response to selection is then considered with emphasis on the factors that constrain the response to selection: generation interval, variation in breeding values, selection intensity, effective population size and the accuracy of selection. Quantitative genetic theory can accurately predict the response to selective breeding of production traits, but is less effective at predicting the response to selection for resistance to microbial and parasitic diseases because selecting resistant animals and culling susceptible animals can alter the rate of disease transmission. Mathematical models are therefore required to predict the effect of genetic and epidemiological changes on disease incidence.
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
Authors: Shah T. S. , Liu J. Z. , Floyd J. A. B. , Morris J. A. , Wirth N. , Barrett J. C. , Anderson C. A.
Published: April 2012

Motivation: Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants.

Results: Using data from 4537 individuals from the 1958 British Birth Cohort genotyped on the Immunochip, we estimate the proportion of SNPs lost to downstream analysis due to false quality control failures, and rare variants misclassified as monomorphic, is only 1.38% with optiCall, in comparison to 3.87, 7.85 and 4.09% for Illuminus, GenoSNP and GenCall, respectively. We show that optiCall accurately captures rare variants and can correctly account for SNPs where probe intensity clouds are shifted from their expected positions.

Availability and implementation: optiCall is implemented in C++ for use on UNIX operating systems and is available for download at http://www.sanger.ac.uk/resources/software/opticall/.

Contact:  optiCall@sanger.ac.uk
Management and outcomes following an acute coronary event in patients with chronic heart failure 1999–2007
Authors: Ranasinghe Isuru , Naoum Chris , Aliprandi‐Costa Bernadette , Sindone Andrew P. , Steg P. Gabriel , Elliott John , McGarity Bruce , Lefkovits Jeffrey , Brieger David ,   on behalf of the Australia–New Zealand GRACE
Published: April 2012

Aim

The outcome of patients with chronic heart failure (CHF) following an ischaemic event is poorly understood. We evaluated the management and outcomes of CHF patients presenting with an acute coronary syndrome (ACS) and explored changes in outcomes over time.

Method and results

A total of 5556 patients enrolled in the Australia–New Zealand population of the Global Registry of Acute Coronary Events (GRACE) between 1999 and 2007 were included. Patients with CHF (n = 609) were compared with those without CHF (n = 4947). Patients with CHF were on average 10 years older, were more likely to be female, had more co‐morbidities and cardiac risk factors, and were more likely to have a prior history of angina, myocardial infarction, and revascularization by coronary artery bypass graft (CABG) when compared with those without CHF. CHF was associated with a substantial increase in in‐hospital renal failure [odds ratio (OR) 1.76, 95% confidence interval (CI) 1.15–2.71], readmission post‐discharge (OR 1.47, 95% CI 1.17–1.90), and 6‐month mortality (OR 2.25, 95% CI 1.55–3.27). Over the 9 year study period, in‐hospital and 6 month mortality in those with CHF declined by absolute rates of 7.5% and 14%, respectively. This was temporally associated with an increase in prescription of thienopyridines, beta‐blockers, statins, and angiotensin II receptor blockers, increased rates of coronary angiography, and 31.8% absolute increase in referral rates for cardiac rehabilitation.

Conclusions

Acute coronary syndrome patients with pre‐existing CHF are a very high risk group and carry a disproportionate mortality burden. Encouragingly, there was a marked temporal improvement in outcomes over a 9 year period with an increase in evidence‐based treatments and secondary preventative measures.
Endoscopic Retrograde Cholangiopancreatography in Neonatal Cholestasis
Authors: Shteyer Eyal , Wengrower Dov , Benuri‐Silbiger Ishay , Gozal David , Wilschanski Michael , Goldin Eran
Published: April 2012

Background:

Endoscopic retrograde cholangiopancreatography (ERCP) is not as widely used in children as in adults and is performed in few specialized centers. The aim of the present study was to review the experience of ERCP in children younger than 3 months in a national referral center.

Methods:

A retrospective chart review was performed of all of the babies younger than 3 months who underwent ERCP between 2000 and 2010. Data on demographics, diagnosis, type of anesthesia, treatments, and complications were collected.

Results:

A total of 27 babies, 14 boys, were examined. Median age was 55 days (range 33–89). Ultrasound was normal in 16 infants, whereas others included small gallbladder (4), biliary stones (3), and dilated bile ducts (3). Thirteen infants underwent earlier liver biopsy, which was inconclusive. ERCP led to the diagnosis of biliary atresia in 13 infants who had subsequent surgery. In others, ERCP showed choledochal cyst (1), biliary stones (2), dilated bile ducts (1), and normal examination (6); there were 5 failures. The final diagnoses in our cohort were extrahepatic biliary atresia (15), biliary stones (5), neonatal hepatitis (4), choledochal cyst (1), paucity of intrahepatic bile duct (1), and congenital hepatic fibrosis (1). Diagnoses in the failed ERCP group included biliary atresia (2), bile duct paucity (1), and biliary stones (2). In 4 (19%) infants with clinical suspicion of extrahepatic biliary atresia, a normal ERCP ruled out the diagnosis and avoided an intraoperative cholangiogram. No complications, including pancreatitis, were reported.

Conclusions:

ERCP in infants is feasible and has no complications. It may serve as an additional diagnostic tool in neonatal cholestasis in inconclusive cases and may prevent more invasive procedures. ERCP may be part of the algorithm of neonatal cholestasis when it is available and other investigations fail to confirm a diagnosis.
Systematic identification of edited microRNAs in the human brain
Authors: Alon Shahar , Mor Eyal , Vigneault Francois , Church George M. , Locatelli Franco , Galeano Federica , Gallo Angela , Shomron Noam , Eisenberg Eli
Published: April 2012

Adenosine-to-inosine (A-to-I) editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Editing of miRNAs has the potential to add another layer of complexity to gene regulation pathways, especially if editing occurs within the miRNA–mRNA recognition site. Thus, it is of interest to study the extent of this phenomenon. Current reports in the literature disagree on its extent; while some reports claim that it may be widespread, others deem the reported events as rare. Utilizing a next-generation sequencing (NGS) approach supplemented by an extensive bioinformatic analysis, we were able to systematically identify A-to-I editing events in mature miRNAs derived from human brain tissues. Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in vitro ADAR overexpression assays. The editing efficiency of most sites identified is very low. Similar results are obtained for publicly available data sets of mouse brain-regions tissues. Thus, we find that A-to-I editing does alter several miRNAs, but it is not widespread.
Reorganization of the host epigenome by a viral oncogene
Authors: Ferrari Roberto , Su Trent , Li Bing , Bonora Giancarlo , Oberai Amit , Chan Yvonne , Sasidharan Rajkumar , Berk Arnold J. , Pellegrini Matteo , Kurdistani Siavash K.
Published: April 2012

Adenovirus small e1a oncoprotein causes ∼70% reduction in cellular levels of histone H3 lysine 18 acetylation (H3K18ac). It is unclear, however, where this dramatic reduction occurs genome-wide. ChIP-sequencing revealed that by 24 h after expression, e1a erases 95% of H3K18ac peaks in normal, contact-inhibited fibroblasts and replaces them with one-third as many at new genomic locations. The H3K18ac peaks at promoters and intergenic regions of genes with fibroblast-related functions are eliminated after infection, and new H3K18ac peaks are established at promoters of highly induced genes that regulate cell cycling and at new putative enhancers. Strikingly, the regions bound by the retinoblastoma family of proteins in contact-inhibited fibroblasts gain new peaks of H3K18ac in the e1a-expressing cells, including 55% of RB1-bound loci. In contrast, over half of H3K9ac peaks are similarly distributed before and after infection, independently of RB1. The strategic redistribution of H3K18ac by e1a highlights the importance of this modification for transcriptional activation and cellular transformation as well as functional differences between the RB-family member proteins.
An overview on the role of Hexanchiformes in marine ecosystems: biology, ecology and conservation status of a primitive order of modern sharks
Authors: Barnett A. , Braccini J. M. , Awruch C. A. , Ebert D. A.
Published: April 2012

The large size, high trophic level and wide distribution of Hexanchiformes (cow and frilled sharks) should position this order as important apex predators in coastal and deep‐water ecosystems. This review synthesizes available information on Hexanchiformes, including information not yet published, with the purpose of evaluating their conservation status and assessing their ecological roles in the dynamics of marine ecosystems. Comprising six species, this group has a wide global distribution, with members occurring from shallow coastal areas to depths of c. 2500 m. The limited information available on their reproductive biology suggests that they could be vulnerable to overexploitation (e.g. small litter sizes for most species and suspected long gestation periods). Most of the fishing pressure exerted on Hexanchiformes is in the form of commercial by‐catch or recreational fishing. Comprehensive stock and impact assessments are unavailable for most species in most regions due to limited information on life history and catch and abundance time series. When hexanchiform species have been commercially harvested, however, they have been unable to sustain targeted fisheries for long periods. The potentially high vulnerability to intense fishing pressure warrants a conservative exploitation of this order until thorough quantitative assessments are conducted. At least some species have been shown to be significant apex predators in the systems they inhabit. Should Hexanchiformes be removed from coastal and deep‐water systems, the lack of sympatric shark species that share the same resources suggests no other species would be capable of fulfilling their apex predator role in the short term. This has potential ecosystem consequences such as meso‐predator release or trophic cascades. This review proposes some hypotheses on the ecology of Hexanchiformes and their role in ecosystem dynamics, highlighting the areas where critical information is required to stimulate research directions.
Biology of the Greenland shark Somniosus microcephalus
Authors: MacNeil M. A. , McMeans B. C. , Hussey N. E. , Vecsei P. , Svavarsson J. , Kovacs K. M. , Lydersen C. , Treble M. A. , Skomal G. B. , Ramsey M. , Fisk A. T.
Published: April 2012

Greenland shark Somniosus microcephalus is a potentially important yet poorly studied cold‐water species inhabiting the North Atlantic and Arctic Oceans. Broad‐scale changes in the Arctic ecosystem as a consequence of climate change have led to increased attention on trophic dynamics and the role of potential apex predators such as S. microcephalus in the structure of Arctic marine food webs. Although Nordic and Inuit populations have caught S. microcephalus for centuries, the species is of limited commercial interest among modern industrial fisheries. Here, the limited historical information available on S. microcephalus occurrence and ecology is reviewed and new catch, biological and life‐history information from the Arctic and North Atlantic Ocean region is provided. Given the considerable by‐catch rates in high North Atlantic Ocean latitudes it is suggested that S. microcephalus is an abundant predator that plays an important, yet unrecognized, role in Arctic marine ecosystems. Slow growth and large pup sizes, however, may make S. microcephalus vulnerable to increased fishing pressure in a warming Arctic environment.
Patterns in composition, abundance and scarring of whale sharks Rhincodon typus near Holbox Island, Mexico
Authors: Ramírez‐Macías D. , Meekan M. , De La Parra‐Venegas R. , Remolina‐Suárez F. , Trigo‐Mendoza M. , Vázquez‐Juárez R.
Published: April 2012

Photo‐identification and conventional tagging were used to estimate population size and structure of the whale shark Rhincodon typus near Holbox Island, Mexico. From 2005 to 2008, photographs of spot patterns behind the last gill slit and in a lateral view on the left side of each animal were used to identify individuals. Additionally, 578 R. typus were tagged using conventional marker tags. Of these and the 350 R. typus that were identified from 1184 photographs, 65% were male; 27%, female and 8%, indeterminate sex. Photographed R. typus ranged in size from 2·5 to 9·5 m total length. Size was bimodal with a large peak at 6 m and a smaller peak at 7 m. Photo‐identification showed that there was considerable loss of marker tags. Few of these remained on the animals for more than a year, so that interannual re‐sights using tagging could not be used in population modelling. Forty six interannual re‐sightings were found in the photographic library; the interval between these re‐sightings was typically 1 year. It was estimated that the R. typus aggregation near Holbox Island ranged from 521 to 809 individuals, based on mark–recapture models. From 13 to 33% of R. typus photographed had scars that were attributable to boat strikes. This study provides a baseline for assessing the status of R. typus near Holbox Island. This information is useful to understand drivers of local population size and distribution and potential concerns about increasing effects of tourism on R. typus in this area and for designing better management programmes for R. typus conservation.
Biennial reproductive cycle in an extensive matrotrophic viviparous batoid: the sandyback stingaree Urolophus bucculentus from south‐eastern Australia
Authors: Trinnie F. I. , Walker T. I. , Jones P. L. , Laurenson L. J.
Published: April 2012

Urolophus bucculentus, the largest urolophid species found in southern Australia, exhibits a biennial reproductive cycle. Ovulation occurs during October to January followed by a 15–19 month period of gestation followed by parturition during April to May and a short rest period while the ovarian follicles continue to develop for subsequent ovulation. Male breeding condition peaks during April to June to coincide with the period of parturition. Urolophus bucculentus has the highest matrotrophic contribution reported for any urolophid species, with a mean wet mass gain from egg in utero (4 g) to full‐term embryo in utero (250 g) of c. 6250% (maximum c. 7200%), and perhaps explains the biennial female reproductive cycle where 50% of females contribute to each year's recruitment. Litter size (one to five) increases with total length (LT). Females reach a longer maximum LT (LTmax) than do males (885 v. 660 mm). The LT at maturity for males and females at 50% mature (LT50) is c. 414 mm (63% of LTmax) for males and c. 502 mm (57% of LTmax) for females, length at maternity indicates that recruitment production occurs later in life at c. 632 mm LT (71% of LTmax).
Skate assemblage on the eastern Patagonian Shelf and Slope: structure, diversity and abundance
Authors: Arkhipkin A. , Brickle P. , Laptikhovsky V. , Pompert J. , Winter A.
Published: April 2012

The eastern Patagonian Shelf and continental slope of the south‐west Atlantic Ocean support a high biodiversity and abundance of skates. In this study, meso‐scale differences in the assemblages, spatial and seasonal distributions of skates are revealed among six habitat zones of the eastern Patagonian Shelf characterized by distinctive oceanographic conditions. Most skates belonged to temperate fauna, and their abundance was much greater in habitats occupied by temperate waters (north‐western outer shelf) or mixed waters (northern slope) than in habitats occupied by sub‐Antarctic waters (SASW) (south‐eastern outer shelf and southern slope). Sub‐Antarctic skates were not abundant on the shelf even in habitats occupied by SASW, occurring mainly in deep areas of the lower continental slope. The majority of temperate skates migrated seasonally, shifting northward in winter and spreading southward with warming waters in summer. Most temperate species had two peaks in female maturity (mainly spring and autumn) and spawned in the same habitats where they fed. It is hypothesized that the high biodiversity and abundance of skates on the Patagonian Shelf and Slope are due to the practical absence of their natural competitors, flatfishes, which occupy similar eco‐niches elsewhere.
Biology, ecology and conservation of the Mobulidae
Authors: Couturier L. I. E. , Marshall A. D. , Jaine F. R. A. , Kashiwagi T. , Pierce S. J. , Townsend K. A. , Weeks S. J. , Bennett M. B. , Richardson A. J.
Published: April 2012

The Mobulidae are zooplanktivorous elasmobranchs comprising two recognized species of manta rays (Mantaspp.) and nine recognized species of devil rays (Mobulaspp.). They are found circumglobally in tropical, subtropical and temperate coastal waters. Although mobulids have been recorded for over 400 years, critical knowledge gaps still compromise the ability to assess the status of these species. On the basis of a review of 263 publications, a comparative synthesis of the biology and ecology of mobulids was conducted to examine their evolution, taxonomy, distribution, population trends, movements and aggregation, reproduction, growth and longevity, feeding, natural mortality and direct and indirect anthropogenic threats. There has been a marked increase in the number of published studies on mobulids sincec. 1990, particularly for the genusManta, although the genusMobularemains poorly understood. Mobulid species have many common biological characteristics although their ecologies appear to be species‐specific, and sometimes region‐specific. Movement studies suggest that mobulids are highly mobile and have the potential to rapidly travel large distances. Fishing pressure is the major threat to many mobulid populations, with current levels of exploitation in target fisheries unlikely to be sustainable. Advances in the fields of population genetics, acoustic and satellite tracking, and stable‐isotope and fatty‐acid analyses will provide new insights into the biology and ecology of these species. Future research should focus on the uncertain taxonomy of mobulid species, the degree of overlap between their large‐scale movement and human activities such as fisheries and pollution, and the need for management of inter‐jurisdictional fisheries in developing nations to ensure their long‐term sustainability. Closer collaboration among researchers worldwide is necessary to ensure standardized sampling and modelling methodologies to underpin global population estimates and status.
Muscle function and swimming in sharks
Authors: Shadwick R. E. , Goldbogen J. A.
Published: April 2012

The locomotor system in sharks has been investigated for many decades, starting with the earliest kinematic studies by Sir James Gray in the 1930s. Early work on axial muscle anatomy also included sharks, and the first demonstration of the functional significance of red and white muscle fibre types was made on spinal preparations in sharks. Nevertheless, studies on teleosts dominate the literature on fish swimming. The purpose of this article is to review the current knowledge of muscle function and swimming in sharks, by considering their morphological features related to swimming, the anatomy and physiology of the axial musculature, kinematics and muscle dynamics, and special features of warm‐bodied lamnids. In addition, new data are presented on muscle activation in fast‐starts. Finally, recent developments in tracking technology that provide insights into shark swimming performance in their natural environment are highlighted.
Gibbsiella dentisursi sp. nov., isolated from the bear oral cavity
Authors: Saito Masanori , Shinozaki‐Kuwahara Noriko , Takada Kazuko
Published: April 2012

A Gram‐negative, rod‐shaped, non‐spore forming and non‐motile bacterium, designated strain NUM 1720T, was isolated from the oral cavity of bears. Based on 16S rRNA gene sequence similarity, strain NUM 1720T was shown to be related to Gibbsiella quercinecans (99.4%). The gyrB and rpoB gene sequences of strain NUM 1720T showed 98.0% and 98.2% similarity with those of G. quercinecans. The DNA‐DNA hybridization value of strain NUM 1720T with G. quercinecans was 63.8%. The G + C content of the genomic DNA of the isolates was 55.0 mol%. Fatty acid analysis data supported the affiliation of strain NUM 1720T to the genus Gibbsiella. The major menaquinone and ubiquinone were MK‐8 and Q‐8, respectively. Strain NUM 1720T can be differed from G. quercinecans by the reactions to acetoin, inositol and D‐arabinose. Strain NUM 1720T therefore represents a novel species, for which the name Gibbsiella dentisursi sp. nov. is proposed, with type strain NUM 1720T (= JCM 17201T = DSM 23818T).
Safety and efficacy of icatibant self-administration for acute hereditary angioedema
Authors: Boccon-Gibod I , Bouillet L
Published: April 2012

We evaluated the efficacy and safety of icatibant self-administration in 15 patients with hereditary angioedema (HAE) types I or III, for 55 acute attacks (mostly severe or very severe). Icatibant self-administration was generally effective: first symptom improvement occurred in 5 min–2 h (HAE type I; n = 17) and 8 min–1 h (HAE type III; n = 9) for abdominal attacks and 5–30 min (HAE type I; n = 4) and 10 min–12 h (HAE type III; n = 6) for laryngeal attacks. Complete symptom resolution occurred in 15 min–19 h (HAE type I; n = 8) and 15 min–48 h (HAE type III; n = 9) for abdominal attacks and 5–48 h (HAE type I; n = 3) and 8–48 h (HAE type III; n = 5) for laryngeal attacks. No patient required emergency hospitalization. The only adverse events were mild, spontaneously resolving injection site reactions. Patients reported that carrying icatibant with them gave them greater confidence in managing their condition.
Foraging guild membership explains variation in waterbird responses to the hydrological regime of an arid‐region flood‐pulse river in Namibia
Authors: CUMMING GRAEME S. , PAXTON MARK , KING JACKIE , BEUSTER HANS
Published: April 2012

1. Little is known about hydrological influences on tropical waterbird communities. We used a 16‐year data set (1991–2007) of waterbird censuses, together with a classification of observed species into foraging guilds, to explore the relationships between natural variations in flow regime, foraging guild and the community composition of waterbirds at the Okavango River in the Caprivi Strip of north‐eastern Namibia, southern Africa.

2. We addressed three hypotheses to explain variation in waterbird community composition: (i) exploitation (birds move towards resource‐rich patches to exploit periods of high food abundance); (ii) escapism (declines in regional habitat quality force birds to aggregate in perennial waterbodies); and (iii) interaction (bird assemblages are dominated by intra‐ and interspecific interactions, such as flock formation for breeding or moulting, that can be explained better by life history demands or competition than by resource availability).

3. Waterbirds in different foraging guilds responded strongly but at different periods to changes in the hydrological environment, creating a complex but predictable successional pattern in community composition through time. Deep‐water feeders responded fastest (abundance peaking 2 months post‐flood), followed by shallow‐water feeders (4 months) and emergent vegetation feeders (7 months). Species that forage on short vegetation or in mud showed a bimodal response with peaks in abundance at 3 and 8 months post‐flood.

4. Our results indicated a strong effect of the local flow regime and hence supported the exploitation hypothesis. The foraging guild approach allowed us to identify clear patterns in a highly complex ecosystem and shows considerable promise as an analytical tool for similar data sets. Our results further suggest that while the entire bird community will be affected by hydrological alterations such as impoundments, water extraction and climate change, deep‐water feeders may be one of the most vulnerable groups.
Floral classification of Yucatan Peninsula honeys by PCA & HS‐SPME/GC–MS of volatile compounds
Authors: Cuevas‐Glory Luis , Ortiz‐Vázquez Elizabeth , Pino Jorge A. , Sauri‐Duch Enrique
Published: April 2012

In the current work, we focus on the application of principal component analysis (PCA) to differentiate the floral origin of three types of honeys of the Yucatan Peninsula, Mexico [Tahonal (Viguiera dentata Blake, var. heliantoides), Dzidzilché (Gymnopodium floribundum Rolfen) and Haabín (Piscidia piscipula L.)], by using the volatile compounds of the honey obtained by HS‐SPME/GC–MS with PDMS/DVB fibres. About 70 peaks were detected in each honey sample, many of them were found with similar retention times in the analysed honeys. The PCA with three factors (nearly 68% of the total variance) discriminates between the three types of honeys, which leads us to conclude that it is possible to successfully differentiate samples from different unifloral honeys according to their volatile composition.
The missing link in coenzyme A biosynthesis: PanM (formerly YhhK), a yeast GCN5 acetyltransferase homologue triggers aspartate decarboxylase (PanD) maturation in Salmonella enterica
Authors: Stuecker Tara N. , Hodge Kelsey M. , Escalante‐Semerena Jorge C.
Published: April 2012

Coenzyme A (CoA) is an essential cofactor for all forms of life. The biochemistry underpinning the assembly of CoA in Escherichia coli and other enterobacteria is well understood, except for the events leading to maturation of the L‐aspartate‐α‐decarboxylase (PanD) enzyme that converts pantothenate to β‐alanine. PanD is synthesized as pro‐PanD, which undergoes an auto‐proteolytic cleavage at residue Ser25 to yield the catalytic pyruvoyl moiety of the enzyme. Since 1990, it has been known that E. coli yhhK strains are pantothenate auxotrophs, but the role of YhhK in pantothenate biosynthesis remained an enigma. Here we show that Salmonella enterica yhhK strains are also pantothenate auxotrophs. In vivo and in vitro evidence shows that YhhK interacts directly with PanD, and that such interactions accelerate pro‐PanD maturation. We also show that S. enterica yhhK strains accumulate pro‐PanD, and that not all pro‐PanD proteins require YhhK for maturation. For example, the Corynebacterium glutamicum panD+ gene corrected the pantothenate auxotrophy of a S. enterica yhhK strain, supporting in vitro evidence obtained by others that some pro‐PanD proteins autocleave at faster rates. We propose the name PanM for YhhK to reflect its role as a trigger of pro‐PanD maturation by stabilizing pro‐PanD in an autocleavage‐prone conformation.
Is symptom relief associated with reduction in gastric retention after gastric electrical stimulation treatment in patients with gastroparesis? A sensitivity analysis with logistic regression models
Authors: Hou Q. , Lin Z. , Mayo M. S. , Sarosiek I. , Gajewski B. J. , McCallum R. W.
Published: April 2012

Background  Enterra gastric electrical stimulation (GES) is an alternative treatment for gastroparesis (GP) when standard medical therapy fails. The aims of this study were to evaluate the association between total symptom score (TSS) and reduction in gastric retention (GR) after GES by GP etiology and to examine the sensitivity of the association to varying cutpoints used to define GR and TSS improvement.

Methods  Gastric retention assessed with a standardized 99mTc radio‐labeled egg meal and TSS measured by a five‐point Likert scale in 221 GP patients treated with Enterra GES therapy for at least 1 year were analyzed. Bivariate chi‐square test and multivariable logistic regression with all possible cutpoints were used to assess the consistency of association and quantitate the relationship across three GP etiologies.

Key Results  Symptom relief in diabetic GP was more likely attributable to GR reduction as indicated by the consistently significant odds ratios (P < 0.01) across all cutpoints. The association in idiopathic GP was inconclusive because odds ratios were sensitive to cutpoints with P‐values ranging from 0.01 to 0.47. No association was found for patients with post surgical gastroparesis (P > 0.1 for all cutpoints). Patient age, gender, baseline TSS and baseline GR had no significant effect at 5% level on clinical improvement regardless of cutpoints for GR.

Conclusions & Inferences  Association between clinical improvements and GR reduction following GES treatment depends on patient etiology and was able to be demonstrated in diabetic GP. The association for idiopathic GP was inconclusive and no such association was found for post surgical GP across all possible cutpoint combinations.
Metabolic profiling reveals metabolic shifts in Arabidopsis plants grown under different light conditions
Authors: JÄNKÄNPÄÄ HANNA JOHANSSON , MISHRA YOGESH , SCHRÖDER WOLFGANG P. , JANSSON STEFAN
Published: April 2012

Plants have tremendous capacity to adjust their morphology, physiology and metabolism in response to changes in growing conditions. Thus, analysis solely of plants grown under constant conditions may give partial or misleading indications of their responses to the fluctuating natural conditions in which they evolved. To obtain data on growth condition‐dependent differences in metabolite levels, we compared leaf metabolite profiles of Arabidopsis thaliana growing under three constant laboratory light conditions: 30 [low light (LL)], 300 [normal light (NL)] and 600 [high light (HL)]µmol photons m−2 s−1. We also shifted plants to the field and followed their metabolite composition for 3 d. Numerous compounds showed light intensity‐dependent accumulation, including: many sugars and sugar derivatives (fructose, sucrose, glucose, galactose and raffinose); tricarboxylic acid (TCA) cycle intermediates; and amino acids (ca. 30% of which were more abundant under HL and 60% under LL). However, the patterns differed after shifting NL plants to field conditions. Levels of most identified metabolites (mainly amino acids, sugars and TCA cycle intermediates) rose after 2 h and peaked after 73 h, indicative of a ‘biphasic response’ and ‘circadian’ effects. The results provide new insight into metabolomic level mechanisms of plant acclimation, and highlight the role of known protectants under natural conditions.