bluuebunny/crossref_metadata_2025 huggingface dataset:
A Call for Mini-Reviews: An Effective but Underutilized Method of Synthesizing Knowledge to Inform and Direct Fisheries Management, Policy, and Research
Authors: Donaldson M R , Aday D D , Cooke S J
Published: December 2011

Remaining current on emerging research in fisheries science is challenging. While review articles are often a go-to resource for managers and researchers alike, reviews in certain fisheries science subdisciplines are either dated or simply do not exist. Although there are a number of journals that publish lengthy reviews on topics relevant to fisheries, these are not always accessible and may not be read by managers, policymakers, and legislators. To address these concerns, there is a need for direct, concise, and timely review articles that tackle emerging issues (i.e., mini-reviews). Reviews of this type are rarely published in American Fisheries Society journals or fisheries journals in general, despite the fact that they have been widely successful and influential (in terms of both academic measures of research “impact” and in affecting change in management and policy) in ecological and conservation journals. We provide suggestions for developing high-quality mini-reviews and propose that Fisheries is an ideal outlet for these short and timely articles aimed at reaching a broad, multidisciplinary audience, including scientists, managers, policymakers, legislators, and other stakeholders.

Resumen

Mini-artículos de revisión: un método efectivo pero subutilizado para sintetizar el conocimiento e informar y dirigir el manejo, la política y la investigación en pesquerías

La vigencia del conocimiento de la nueva investigación en pesquerías representa un desafío. A pesar de que los artículos de revisión son una fuente obligada tanto para los manejadores como para los investigadores, en ciertas sub-disciplinas de la ciencia pesquera las revisiones son obsoletas o simplemente no existen. Si bien hay varias revistas que publican extensas revisiones en tópicos relevantes para las pesquerías, éstos no siempre son accesibles y pueden pasar desapercibidos por los manejadores, políticos y legisladores. Para atender estos problemas, existe la necesidad de producir artículos de revisión directos, concisos y oportunos que aborden temas emergentes (i.e. mini-artículos de revisión). Las revisiones de este tipo son rara vez publicadas por las revistas de la Sociedad Americana de Pesquerías pese a que han sido muy exitosas y trascendentes (en términos tanto de medida académica del impacto de la investigación como en la afectación en cuanto a cambios en el manejo y la política pesquera) en las revistas de ecología y conservación. Se hacen sugerencias para desarrollar mini-artículos de revisión de alta calidad y se propone la revista Fisheries como un sustrato ideal para este tipo de artículos cortos y oportunos, dirigidos a audiencias amplias y multidisciplinarias que incluyen científicos, manejadores, políticos, legisladores y otros interesados.
Legacy of New York State's Watershed Surveys, 1926–1939
Authors: Daniels Robert A
Published: December 2011

On 16 June 1926, A. L. Hazzard was casting flies into Dyke Creek, upper Genessee River, and reeled in two common shiners. That was the beginning of the watershed surveys of New York, which involved scores of individuals and stretched over 15 years. The state legislature authorized surveys of the aquatic life in streams and lakes with a $15,000 appropriation “to determine the most practical methods of increasing fish production.” Under the leadership and insight of Emmeline Moore, the surveys accomplished this mission by providing a basis for assessing the need and appropriateness of what previously had been a general stocking program. Groundwork for the surveys began under John Titcomb, and his writings and management activities influenced Dr. Moore. Her approach led to more than a refinement of stocking policy; she and her staff recognized the importance of assessing watersheds as systems and that policies affecting game fish required information on more than just the game fish. Staff conducted synoptic surveys of biota, assessed chemistry and hydrology, and paid particular attention to pollutants. The importance of vouchering specimens was recognized, and the surveys provided a steady stream of specimens that were used in several taxonomic studies. Finally, Titcomb and Moore recognized that in order to affect change in stocking policy, states needed well-trained biologists knowledgeable in all aspects of freshwater ecology. So, the surveys became the training school for a suite of biologists that dominated fisheries science in universities and in management agencies in the mid- and late 20th century. Perhaps the most important legacy of these surveys is not the reports, illustrations, specimens, or input from the well-trained fisheries scientists; it is a way of thinking about aquatic resources and the role of the manager in developing them
Assessing Risk of Extinction of Marine Fishes in Canada—The COSEWIC Experience
Authors: Powles Howard
Published: December 2011

Canada's Species at Risk Act (SARA; 2003) legally established the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) with a mandate to assess the status of wildlife species it considers to be at risk. Species assessed by COSEWIC as at risk are then considered by the federal government for conservation action, including listing on SARA's Schedule I. COSEWIC‘s Marine Fishes Specialist Subcommittee focuses on five groups of high vulnerability: anadromous species, elasmobranchs, long‐lived species, species of large maximum size, and species that have shown severe decline. COSEWIC‘s assessment protocol uses quantitative criteria based on those developed by the International Union for Conservation of Nature (IUCN) but also considers life history and other biological information in assigning status. Published assessments cover 61 marine fish species: one extirpated, 14 endangered, 14 threatened, 16 special concern, 7 not at risk, and 9 data deficient. Questioned by some stakeholders, COSEWIC's assessment protocol represents a stable, documented framework that should give consistent results. Assessments show a broad pattern of severe declines across a wide range of species that might be expected to stimulate strong coordinated conservation action. Few marine fish species have been listed on SARA Schedule I. Conservation action for COSEWIC‐assessed species has been strong in some cases but not in others.
Comparative Evaluation of Molecular Diagnostic Tests for Nucleospora salmonis and Prevalence in Migrating Juvenile Salmonids from the Snake River, USA
Authors: Badil Samantha , Elliott Diane G. , Kurobe Tomofumi , Hedrick Ronald P. , Clemens Kathy , Blair Marilyn , Purcell Maureen K.
Published: December 2011

Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis: (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

Received September 14, 2010; accepted November 14, 2010
Evaluation of Emamectin Benzoate for the Control of Experimentally Induced Infestations of Argulus sp. in Goldfish and Koi Carp
Authors: Hanson Shari K. , Hill Jeffrey E. , Watson Craig A. , Yanong Roy P. E. , Endris Richard
Published: December 2011

The effect of 0.2% emamectin benzoate (SLICE; Intervet/ Schering-Plough Animal Health, Roseland, New Jersey) administered in top-dressed, pelleted commercial fish feed was evaluated for control of freshwater Argulus sp. in goldfish Carassius auratus and koi carp, a variant of common carp Cyprinus carpio, in freshwater aquaria at 24–25°C. Sixteen individually housed goldfish were each exposed to 37 Argulus. The number of fish lice attached to each fish at the start of the experiment was not determined; however, the total number of motile fish lice in each aquarium (on fish and in the water) was determined at the start and end of each experiment. Eight goldfish were fed the control diet (0 μg · kg fish biomass−1 · d−1) and eight were fed the medicated diet (50 μg · kg fish biomass−1 · d−1) for seven consecutive days. After treatment, fish louse infestation in controls was 20.5 ± 1.5 (mean ± SE) lice per fish. No Argulus were found on fish in the treated group. In a separate experiment, 10 individually housed koi were each exposed to 128 Argulus. Five koi were fed the control diet and five were fed a low-dose medicated diet (5 μg · kg fish biomass−1 · d−1) for 7 d. After treatment, fish louse infestation among the controls was 14.6 ± 3.8 lice per koi. No Argulus were found on koi in the treated group. Hence, a 7-d regimen of oral emamectin benzoate controlled experimental infestation of Argulus when administered to goldfish at 50 μg · kg fish biomass−1 · d−1 and to koi at 5 μg · kg fish biomass−1 · d−1.

Received March 24, 2010; accepted January 17, 2011
Nitrate-Induced Goiter in Captive Whitespotted Bamboo Sharks Chiloscyllium plagiosum
Authors: Morris Alexis L. , Hamlin Heather J. , Francis-Floyd Ruth , Sheppard Barbara J. , Guillette Louis J.
Published: December 2011

Elasmobranch susceptibility to goiter formation in captive environments has been well documented. Until recently, most public aquariums operated under the belief that the etiology of goiter in elasmobranchs was nutritional and specifically caused by insufficient dietary iodine. Recent studies have demonstrated that high environmental nitrate (NO3-N) inhibits the ability of the thyroid gland to utilize available iodide, resulting in thyroid gland overstimulation by thyroid stimulating hormone and ultimately leading to the development of goiter. The objective of this study was to evaluate the effects of high environmental nitrate concentrations on thyroid function in juvenile whitespotted bamboo sharks Chiloscyllium plagiosum. In July 2008, five juveniles (80–150 g) were exposed to a low-nitrate environment (NO3-N concentration < 1 mg/L of water) and five were exposed to an elevated-nitrate environment (NO3-N = 70 mg/L) for 29 d in a flow-through natural seawater system. Nitrate exposure did not affect growth rates (e.g., weight, length, and condition factor) and did not alter free plasma thyroxine concentrations during the 29-d experimental period. However, histological examination of thyroid glands from sharks exposed to elevated nitrate revealed the development of diffuse hyperplastic goiter. With increasing restrictions on water use, most modern aquaria operate as recirculating systems, which results in higher and more chronic nitrate exposure for captive animals. Goiter is one of the most common health problems in captive elasmobranchs, and this study suggests that nitrate exposure is an important factor in the etiology of this disease.

Received August 4, 2010; accepted February 22, 2011
Assessing the Suitability of a Partial Water Reuse System for Rearing Juvenile Chinook Salmon for Stocking in Washington State
Authors: Good Christopher , Vinci Brian , Summerfelt Steven , Snekvik Kevin , Adams Ian , Dilly Samuel
Published: December 2011

To assess the suitability of water reuse technology for raising Pacific salmon Oncorhynchus spp. for stocking purposes, fish health and welfare were compared between two groups of juvenile Chinook salmon O. tshawytscha from the same spawn: one group was reared in a pilot partial water reuse system (circular tanks), and the other group was reared in a flow-through raceway. This observational study was carried out over a 21-week period in Washington State. Reuse and raceway fish were sampled repeatedly for pathogen screening and histopathology; fin erosion and whole-blood characteristics were also evaluated. By the study's end, no listed pathogens were isolated from either cohort, and survival was 99.3% and 99.0% in the reuse and raceway groups, respectively. Condition factor was 1.28 in raceway fish and 1.14 in reuse fish; this difference may have been attributable to occasional differences in feeding rates between the cohorts. Fin indices (i.e., length of the longest dorsal or caudal fin ray, standardized by fork length) were lower in reuse fish than in raceway fish, but fin erosion was not grossly apparent in either cohort. The most consistent histological lesion was gill epithelial hypertrophy in reuse fish; however, blood analyses did not suggest any corresponding physiological imbalances. Overall, results suggest that water reuse technology can be employed in rearing juvenile anadromous salmonids for stocking purposes.

Received December 3, 2009; accepted February 14, 2011
Passive Immunization of Pacific Herring against Viral Hemorrhagic Septicemia
Authors: Hershberger P. K. , Gregg J. L. , Grady C. A. , LaPatra S. E. , Winton J. R.
Published: December 2011

The plasma of Pacific herring Clupea pallasii that survived laboratory-induced viral hemorrhagic septicemia (VHS) epizootics contained humoral substances that, when injected into naïve animals, conferred passive immunity against the disease. Among groups exposed to viral hemorrhagic septicemia virus (VHSV), injection of donor plasma from VHS survivors resulted in significantly greater survival (50%) and significantly lower tissue titers (1.5 × 105 plaque-forming units [PFU]/g) than the injection of plasma from VHSV-naïve donors (6% survival; 3.7 × 106 PFU/g). Additionally, the magnitude of the protective immune response increased during the postexposure period; plasma that was collected from survivors at 123 d postexposure (931 degree-days) provided greater protection than plasma collected from survivors at 60 d postexposure (409 degree-days). These results provide proof of concept that the VHSV exposure history of Pacific herring populations can be determined post hoc; furthermore, the results can be used as the foundation for developing additional high-throughput diagnostic techniques that may be effective at quantifying herd immunity and forecasting the potential for future VHS epizootics in populations of wild Pacific herring.

Received October 20, 2010; accepted April 7, 2011
Carbonic Anhydrase Activities from the Rainbow Trout Lens Correspond to the Development of Acute Gas Bubble Disease
Authors: Gültepe Nejdet , Ateş Orhan , Hisar Olcay , Beydemir Şükrü
Published: December 2011

Dissolved gas supersaturation is hazardous to fish and can result in gas bubble disease (GBD). Signs of GBD typically include bubbles in the eyes, fins, skin, lateral line, and gill filaments. Ocular abnormalities in diseased salmonids typically occur after aberrant gas production in the eyes. In this study, freshwater rainbow trout Oncorhynchus mykiss were exposed experimentally to percent total gas pressure (TGP%) levels of 104% (control) and 115%. No mortalities occurred during the 7-d experimental period. Effects of GBD were observed externally as a darkened skin, exophthalmia, localized hemorrhage in the eye, and gas bubbles on the operculum. Additional signs included increased swimming activity and, more frequently, panic episodes. Carbonic anhydrase (CA) enzyme activities from the lens and retina were determined at days 0, 1, 3, 5, and 7 of the study. Venous blood gases were also measured on day 7. Retinal pH did not differ between normal and affected fish, but blood characteristics such as the partial pressure of O2, partial pressure of CO2, carboxyhemoglobin level, and bicarbonate ion concentration were significantly elevated in affected fish relative to normal fish. Venous blood pH and oxyhemoglobin levels were not significantly different between affected and normal fish. Patterns of response to total dissolved gas levels differed between the lens and the retina. Mean CA activities in the lenses of fish exposed to a TGP% level of 115% were significantly below those of control fish. However, retinal CA activities did not significantly differ between the two groups over the course of the experiment. These findings show that dissolved gas supersaturation reduces CA activity in the rainbow trout lens.

Received June 17, 2010; accepted March 20, 2011
The phosphoinositide-associated protein Rush hour regulates endosomal trafficking inDrosophila
Authors: Gailite Ieva , Egger-Adam Diane , Wodarz Andreas
Published: December 2011

Endocytosis regulates multiple cellular processes, including the protein composition of the plasma membrane, intercellular signaling, and cell polarity. We have identified the highly conserved protein Rush hour (Rush) and show that it participates in the regulation of endocytosis. Rush localizes to endosomes via direct binding of its FYVE (Fab1p, YOTB, Vac1p, EEA1) domain to phosphatidylinositol 3-phosphate. Rush also directly binds to Rab GDP dissociation inhibitor (Gdi), which is involved in the activation of Rab proteins. Homozygous rush mutant flies are viable but show genetic interactions with mutations in Gdi, Rab5, hrs, and carnation, the fly homologue of Vps33. Overexpression of Rush disrupts progression of endocytosed cargo and increases late endosome size. Lysosomal marker staining is decreased in Rush-overexpressing cells, pointing to a defect in the transition between late endosomes and lysosomes. Rush also causes formation of endosome clusters, possibly by affecting fusion of endosomes via an interaction with the class C Vps/homotypic fusion and vacuole protein-sorting (HOPS) complex. These results indicate that Rush controls trafficking from early to late endosomes and from late endosomes to lysosomes by modulating the activity of Rab proteins.
Three-dimensional ultrastructure of the septin filament network inSaccharomyces cerevisiae
Authors: Bertin Aurélie , McMurray Michael A. , Pierson Jason , Thai Luong , McDonald Kent L. , Zehr Elena A. , García Galo , Peters Peter , Thorner Jeremy , Nogales Eva
Published: December 2011

Septins are conserved GTP-binding proteins involved in membrane compartmentalization and remodeling. In budding yeast, five mitotic septins localize at the bud neck, where the plasma membrane is enriched in phosphatidylinositol-4,5-bisphosphate (PtdIns4,5P2). We previously established the subunit organization within purified yeast septin complexes and how these hetero-octamers polymerize into filaments in solution and on PtdIns4,5P2-containing lipid monolayers. How septin ultrastructure in vitro relates to the septin-containing filaments observed at the neck in fixed cells by thin-section electron microscopy was unclear. A morphological description of these filaments in the crowded space of the cell is challenging, given their small cross section. To examine septin organization in situ, sections of dividing yeast cells were analyzed by electron tomography of freeze-substituted cells, as well as by cryo–electron tomography. We found networks of filaments both perpendicular and parallel to the mother–bud axis that resemble septin arrays on lipid monolayers, displaying a repeat pattern that mirrors the molecular dimensions of the corresponding septin preparations in vitro. Thus these in situ structures most likely represent septin filaments. In viable mutants lacking a single septin, in situ filaments are still present, although more disordered, consistent with other evidence that the in vivo function of septins requires filament formation.
Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter
Authors: Whelan Christopher , Sönmez Kemal
Published: December 2011

Summary: Biological network analysis can be enhanced by examining the connections between nodes and the rest of the network. For this purpose we have developed GraphletCounter, an open-source software tool for computing graphlet degree signatures that can operate on its own or as a plug-in to the network analysis environment Cytoscape. A unique characteristic of GraphletCounter is its ability to compute the graphlet signatures of network motifs, which can be specified by files generated by the motif-finding tool mfinder. GraphletCounter displays graphlet signatures for visual inspection within Cytoscape, and can output graphlet data for integration with larger workflows.

Availability and implementation: GraphletCounter is implemented in Java. It can be downloaded from the Cytoscape plugin repository, and is also available at http://sonmezsysbio.org/software/ graphletcounter.

Contact:  whelanch@ohsu.edu
Identification and removal of ribosomal RNA sequences from metatranscriptomes
Authors: Schmieder Robert , Lim Yan Wei , Edwards Robert
Published: December 2011

Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.

Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/.

Contact:  rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Chronic pulmonary cavitary tuberculosis in rabbits: a failed host immune response
Authors: Subbian Selvakumar , Tsenova Liana , Yang Guibin , O'Brien Paul , Parsons Sven , Peixoto Blas , Taylor Leslie , Fallows Dorothy , Kaplan Gilla
Published: December 2011

The molecular determinants of the immune response to
Mycobacterium tuberculosis
HN878 infection in a rabbit model of pulmonary cavitary tuberculosis were studied. Aerosol infection of rabbits resulted in a highly differentially expressed global transcriptome in the lungs at 2 weeks, which dropped at 4 weeks and then gradually increased. While
IFNγ
was progressively upregulated throughout the infection, several other genes in the
IFNγ
network were not. T-cell activation network genes were gradually upregulated and maximally induced at 12 weeks. Similarly, the
IL4
and B-cell activation networks were progressively upregulated, many reaching high levels between 12 and 16 weeks. Delayed peak expression of genes associated with macrophage activation and Th1 type immunity was noted. Although spleen CD4
+
and CD8
+
T cells showed maximal tuberculosis antigen-specific activation by 8 weeks, macrophage activation in lungs, lymph nodes and spleen did not peak until 12 weeks. In the lungs, infecting bacilli grew exponentially up to 4 weeks, followed by a steady-state high bacillary load to 12 weeks that moderately increased during cavitation at 16 weeks. Thus, the outcome of HN878 infection of rabbits was determined early during infection by a suboptimal activation of innate immunity and delayed T-cell activation.
2,2′′,3,3′′,4,4′′,5,5′′-Octaphenyl-1,1′:4′,1′′-terphenyl and 2′,3′,5′,6′-tetrafluoro-2,2′′,3,3′′,4,4′′,5,5′′-octaphenyl-1,1′:4′,1′′-terphenyl
Authors: Budy Stephen M. , Nichol Gary S. , Loy Douglas A.
Published: December 2011

The title compounds, C66H46, (I), and C66H42F4, (II), are polyphenylated arylenes synthesized by one-step Diels–Alder cycloaddition reactions. In both structures, all molecules lie on crystallographic inversion centers. In the case of (I), there are two half-molecules present in the asymmetric unit, (IA) and (IB); the geometry of each half-molecule differs principally in the magnitudes of the dihedral angles between mean planes fitted through the central aryl ring and the pendant phenyl rings. The crystal used was a non-merohedral twin, with a refined twin scale factor of 0.460 (8). The dihedral angle between the plane of the central tetrafluorinated ring and the adjacent tetraphenylated ring in (II) is 83.87 (4)°, significantly greater than the dihedral angles of 49.89 (12) and 54.38 (10)° found in the two half-molecules in (IA) and (IB), respectively, and attributed to intermolecular C—H...F hydrogen bonding in (II). Intermolecular C—H...π bonding is found in (I). Two interactions have the C—H bond oriented towards the centroid (Cg) of a butadiene fragment of a phenyl ring; both H...Cgdistances are approximately 2.68 Å and the interactions connect adjacent molecules into stacks in thec-axis direction. The composition of the stacks alternates,i.e.(IA)–(IB)–(IA)–(IB)etc. A third, weaker, C—H...π interaction and a phenyl–phenyl close contact connect each end of the long molecular axes of (IB) with an adjacent molecule of (IA) into chains which run perpendicular to the (140) and (\overline{1}40) planes. C—H...F interactions in (II) have the most profound influence on the molecular and crystal structure, the main effect of which is the above-mentioned increase in the dihedral angle between the plane of the central tetrafluorinated ring and the adjacent tetraphenylated ring. C—H...F interactions have refined H...F distances of 2.572 (15) and 2.642 (16) Å, with approximate C—H...F angles of 123 and 157°, respectively. These form a hydrogen-bonded ribbon structure which propagates in theb-axis direction.
Recombination rates across porcine autosomes inferred from high‐density linkage maps
Authors: Muñoz M. , Alves E. , Ramayo‐Caldas Y. , Casellas J. , Rodríguez C. , Folch J. M. , Silió L. , Fernández A. I.
Published: December 2011

Studies of the variation in recombination rate across the genome provide a better understanding of evolutionary genomics and are also an important step towards mapping and dissecting complex traits in domestic animals. With the recent completion of the porcine genome sequence and the availability of a high‐density porcine single nucleotide polymorphism (SNP) array, it is now possible to construct a high‐density porcine linkage map and estimate recombination rate across the genome. A total of 416 animals were genotyped with the Porcine SNP60BeadChip, and high‐density chromosome linkage maps were constructed using CRI‐MAP, assuming the physical order of the Sscrofa10 assembly. The total linkage map length was 2018.79 cM, using 658 meioses and 14 503 SNPs. The estimated average recombination rate across the porcine autosomes was 0.86 cM/Mb. However, a large variation in recombination rate was observed among chromosomes. The estimated average recombination rates (cM/Mb) per chromosome ranged from 0.48 in SSC1 to 1.48 in SSC10, displaying a significant negative correlation with the chromosome sizes. In addition, the analysis of the variation in the recombination rates taking 1‐Mb sliding windows has allowed us to demonstrate the variation in recombination rates within chromosomes. In general, a larger recombination rate was observed in the extremes than in the centre of the chromosome. Finally, the ratio between female and male recombination rates was also inferred, obtaining a value of 1.38, with the heterogametic sex having the least recombination.
Compliance with focused antenatal care services: do health workers in rural Burkina Faso, Uganda and Tanzania perform all ANC procedures?
Authors: Conrad Paul , Schmid Gerhrd , Tientrebeogo Justin , Moses Arinaitwe , Kirenga Silvia , Neuhann Florian , Müller Olaf , Sarker Malabika
Published: December 2011

Objective  To assess health workers’ compliance with the procedures set in the focused antenatal care (ANC) guidelines in rural Uganda, Tanzania and Burkina Faso; to compare the compliance within and among the three study sites; and to appraise the logistic and supply of the respective health facilities (HF).

Methods  The cross‐sectional study was conducted in the rural HF in three African countries. This descriptive observational study took place in HF in Nouna, Burkina Faso (5), Iganga, Uganda (6) and Rufiji, Tanzania (7). In total, 788 ANC sessions and service provisions were observed, the duration of each ANC service provision was calculated, and the infrastructures of the respective HF were assessed.

Results  Health workers in all HF performed most of the procedures but also omitted certain practices stipulated in the focused ANC guidelines. There was a substantial variation in provision of ANC services among HF within and among the country sites. The findings also revealed that the duration of first visits was <15 min and health workers spent even less time in subsequent visits in all three sites. Reagents for laboratory tests and drugs as outlined in the focus ANC guidelines were often out of stock in most facilities.

Conclusion  Health workers in all three country sites failed to perform all procedures stipulated in the focused ANC guideline; this could not be always explained by the lack of supplies. It is crucial to point out the necessity of the core procedures of ANC repeatedly.
Ureteral replacement with appendix in pediatric renal transplantation
Authors: Corbetta Juan P. , Weller Santiago , Bortagaray Juan I. , Durán Victor , Burek Carol , Sager Cristian , Lopez Juan C.
Published: December 2011

Corbetta JP, Weller S, Bortagaray JI, Durán V, Burek C, Sager C, Lopez JC. Ureteral replacement with appendix in pediatric renal transplantation.

Abstract:  Ureteral necrosis is an uncommon complication following RT which can adversely affect outcome. Even though authors agree that the native ureter ought to be preserved, there are cases in which graft function can only be salvaged by ureteral substitution. The scant references in the literature on the use of the appendix for left ureteral replacement in children prompted us to report the following two cases in whom the technique was employed and to assess the evolution of graft function in these patients.
Parental Investment Theory and Nest Defence by Imperial Shags: Effects of Offspring Number, Offspring Age, Laying Date and Parent Sex
Authors: Svagelj Walter S. , Magdalena Trivellini María , Quintana Flavio
Published: December 2011

Nest defence is a common form of parental care employed by birds to improve the survival of their offspring. Theory predicts that parents should adjust their nest defence according to the value of the brood at stake, defending more intensively broods with high survival and reproductive prospects. We evaluated the influence of offspring number, offspring age, laying date and parent sex on nest‐defence intensity (NDI) of the Imperial Shag Phalacrocorax atriceps, a sexually dimorphic seabird with seasonal decline in offspring survival and very limited renesting potential. We also evaluated whether NDI was correlated within pairs and whether NDI of both members of the pair was correlated with incubation and breeding success. To elicit defensive behaviour, we simulated predation attempts using a Kelp Gull Larus dominicanus model. As predicted by theory, NDI was positively correlated with the number of offspring in the nest and offspring age. NDI during chick rearing was higher than that at early and late incubation, while no differences were found between incubation stages. Contrary to our prediction, we did not find differences in NDI according to laying date. NDI for males was higher than females, while NDI was also positively correlated within pairs. NDI was not statistically related to incubation or breeding success. These results suggest that other factors, such as laying date or parental quality and age, play a much larger role in determining the outcome and productivity of a nesting attempt. Our results provide partial support for parental investment theory; while parental defence increased with brood value according to offspring number and age, parental defence was not related to laying date, a factor strongly affecting offspring survival and recruitment probabilities in this species.
Adjustment to loss of the driving role following traumatic brain injury: A qualitative exploration with key stakeholders
Authors: Liddle Jacki , Fleming Jennifer , McKenna Kryss , Turpin Merrill , Whitelaw Penny , Allen Shelley
Published: December 2011

Background/aims:  Community mobility is affected by an interruption to or cessation of driving following traumatic brain injury (TBI). This study aimed to examine loss of the driving role and to explore the outcomes associated with driving cessation from the perspectives of key people involved within the process: people with TBI, their family members and involved health professionals.

Methods:  A qualitative methodology was used, employing semi‐structured interviews with 15 individuals with TBI who had experienced driving cessation, 10 family members and 10 health professionals working with this population.

Results:  This article focuses on two themes, each with three subthemes. Being stuck: needs related to driving cessation had subthemes: (i) an emotional time, (ii) being normal and (iii) participation without driving. The second theme, A better way: suggestions to improve outcomes had subthemes: (i) information, (ii) support and trying it out and (iii) their family member’s roles and needs.

Conclusions:  Driving cessation following TBI is associated with emotional, identity, transport and participation‐related needs. An ongoing, individualised approach involving information, support and practical experiences may improve outcomes of driving cessation for people with TBI and their family members.
Using Short Message Service (SMS) to teach English idioms to EFL students
Authors: Hayati Abdolmajid , Jalilifar Alireza , Mashhadi Amir
Published: December 2011

This study aimed to gauge the efficacy of three modes of instruction of English idioms, ie, Short Message Service (SMS)‐based learning, contextual learning and self‐study learning. More precisely, this study capitalized on the push aspect of SMS affordance to deliver bite‐sized English idiom lessons on spaced intervals to the learners irrespective of the traditionally inherent problems in most teaching classrooms of English as a Foreign Language learning contexts and thus promote regular study. Students' perceptions and attitudes toward mobile learning and the application of SMS in teaching and learning English (idioms) were also sought by conducting a poststudy survey. Overall, the results revealed that students receiving short mini‐lessons on their mobile phones via SMS were more enthusiastic and learned more than their counterparts on paper or contextual groups.

Practitioner Notes

What is already known about this topic

Among different functions a mobile phone can afford, its Short Message Service (SMS) has been widely used to transmit and receive general and educational contents.

SMS affordance of mobile phones has been used to teach language components such as grammar and vocabulary.

The efficiency of teaching English idioms via SMS in comparison with other methods (eg, contextual learning and self‐study approaches) has not been examined in the Mobile Assisted Language Learning practices simultaneously.

What this paper adds

Gauging the comparative efficacy of SMS‐based instruction of English idioms in contrast with two other instruction modes, ie, contextual learning and self‐study simultaneously.

Delivering bite‐sized SMS‐based English idiom lessons to the learners beyond the constraints of the traditional classrooms and promoting regular study.

Seeking students' perceptions and attitudes toward mobile learning and the application of SMS in teaching and learning English idioms by conducting a poststudy survey.

Implications for practice and/or policy

Insights gathered from the comparative integration of mobile devices, particularly mobile phones and its different affordances into teaching classrooms of English as a Foreign Language learning contexts, are considered to have important implications for the educators and technologists to harness the potential of mobile technologies and design appropriate tasks that pave the way for the widespread use of this platform for language learning on a large scale.

A deep understanding of the mobile devices used and the possibilities associated with them is needed in order to better design the mobile learning (m‐learning) activities.

Embarking on an m‐learning project entails designing particular activities tailored to the needs of students involved in the learning process.
Towards Understanding Variations in Social Care for Older People in England
Authors: Brand Christian , Hughes Jane , Challis David
Published: December 2011

Indicators of the public provision of old age social care are routinely recorded in England and have been used for diverse purposes including performance monitoring. Despite long‐term policy guidance promoting more homogeneous service provision, large variations can still be observed between local authorities (the providers of state‐funded social care). Our aim is to better understand such variations in a small selection of key aggregate indicators. Drawing on multiple data sources and pursuing a two‐step strategy, we first assess the explanatory power of a set of structural predictors and then add to the models a set of specific care management ‘process’ predictors. We find that structural factors beyond the control of local authorities explain a considerable share of the observable variation. The additional explanatory power of care management characteristics is small in comparison. Therefore, our findings suggest that caution must be taken when aggregate indicators of service provision are used for performance monitoring purposes, as a degree of autonomy over outcomes may be implied which in light of the empirical evidence is unrealistic. Past attempts to influence the aggregate pattern of service provision – apparently seeking greater ‘territorial justice’– are likely to have had adverse implications for service users and the uniformity of service delivery across England. Questions are raised about the adequate role of central government in a policy environment characterized by longstanding local government responsibility.
HIV‐related stigma and NGO‐isation in India: a historico‐empirical analysis
Authors: Nambiar Devaki
Published: December 2011

In response to World Bank critiques in 2007, the Indian Ministry of Health and Family Welfare declared that human immunodeficiency virus (HIV)‐related stigma was a barrier to the participation of non‐governmental organisations (NGOs) in the implementation of HIV prevention targeted interventions. Taking a deeper view of HIV‐related stigma as a historically inflected process of devaluation, this article details the history and transformation of NGO involvement in the HIV epidemic from 1986 through economic liberalisation in the 1990s up to the Second National AIDS Control Programme (NACP II 1999–2006). It additionally examines findings from interviews and participant observation of NGO workers (N = 24) from four targeted intervention NGOs in Delhi funded under NACP II. Analysis reveals that a second wave of HIV‐related NGO involvement has mushroomed in the past two decades, affording NGO workers multiple pathways to credibility in the Indian response to the epidemic. Contradictions embedded in the overlap of these pathways produce stigma, reflecting ‘adverse incorporation’ of the NGO workers. Drawing upon noteworthy exceptions to this trend from the first wave of Indian HIV‐related NGOs, the article calls for NGO participation as an explicitly political project of addressing the social inequalities that shape stigma as well as vulnerability to illness writ large.
Cued Recall and Other Cognitive Tasks to Facilitate Dementia Recognition in Primary Care
Authors: Fuchs Angela , Wiese Birgitt , Altiner Attila , Wollny Anja , Pentzek Michael
Published: December 2011

Objectives

To compare the accuracy of commonly used tasks with that of the Visual Association Test (VAT), a conceptually different test involving cued recall of pictorial stimuli, in the recognition of dementia within primary care.

Design

A cross‐sectional diagnostic study of concurrent validity.

Setting

Twenty‐nine German primary care practices.

Participants

Four hundred twenty‐three individuals in primary care participating in a longitudinal cohort study.

Measurements

Participants underwent a comprehensive neuropsychological interview. The validated clinical dementia diagnosis was used as reference standard. Index tests comprised the VAT, Mini‐Cog, clock drawing, verbal fluency, episodic memory, and subjective complaints. Validity parameters were calculated; possible confounders of test performance (age, sex, education, comorbidity, depression, language) were evaluated.

Results

Twenty‐one participants (5%) had dementia according to the reference standard. The VAT distinguished dementia from nondementia with a sensitivity of 95.2% (95% confidence interval (CI) = 86.1–100.0), a specificity of 96.0% (95% CI = 94.1–97.9), a positive predictive value (PPV) of 55.6% (95% CI = 39.3–71.8), and a negative predictive value (NPV) of 99.7% (95% CI = 99.2–100.0). The next‐most‐accurate tasks were the Mini‐Cog and immediate and delayed recall. Their sensitivity and NPV are similar to those of the VAT, but their PPV and specificity were significantly lower than those of the VAT. Age and depression affected all test scores.

Conclusion

The VAT (cued recall of pictorial material) is superior to other tasks for the recognition of dementia in terms of higher specificity and PPV. Age‐specific cutoff scores may improve the validity of all tests.
Caudal Mediastinal Paraesophageal Abscesses in 7 Dogs
Authors: Brissot Hervé N. , Burton Carolyn A. , Doyle Ronan S. , Bray Jonathan P.
Published: December 2011

Objective

To report clinical, imaging, and surgical findings associated with caudal mediastinal paraesophageal abscesses (CMPA) in dogs and outcome after surgical treatment.

Study design

Case series.

Animals

Dogs (n = 7) with CMPA.

Methods

Medical records (April 2005–January 2010) were reviewed for dogs with CMPA treated surgically. Retrieved data were signalment, history, clinical findings, diagnostic investigations, surgical findings, surgical procedures performed, and postoperative recovery. Long‐term follow‐up information was obtained by telephone questionnaire of owners and referring veterinarians.

Results

Median sternotomy (5 dogs) or lateral thoracotomy (2 dogs) was used for access to CMPA, which were drained and partially debrided surgically. In 5 dogs, omentalization of the abscess cavity was performed through a diaphragmatic incision. Foreign material was not identified within any abscess. All dogs were discharged from the hospital and had full recovery.

Conclusions

CMPA should be suspected when there is regurgitation and pyrexia associated with a mass or enlargement in the caudal mediastinum. CMPA appears to have a good prognosis after aggressive surgical therapy.
Treatment of Meralgia Paresthetica with Ultrasound‐Guided Pulsed Radiofrequency Ablation of the Lateral Femoral Cutaneous Nerve
Authors: Fowler Ian M. , Tucker Anthony A. , Mendez Robert J.
Published: December 2011

Abstract:  A 23‐year‐old female with an 18‐month history of left anterolateral thigh paresthesias and burning pain consistent with meralgia paresthetica was referred to our clinic after failing trials of physical therapy, nonsteroidal anti‐inflammatories, gabapentin, and amitriptyline. We performed 3 lateral femoral cutaneous nerve blocks with corticosteroid over a 4‐month period; however, each block provided only temporary relief. As this pain was limiting the patient’s ability to perform her functions as an active duty service member, we elected to perform a pulsed radiofrequency treatment of the lateral femoral cutaneous nerve with ultrasound guidance and nerve stimulation. After locating the lateral femoral cutaneous nerve with ultrasound and reproducing the patient’s dysthesia with stimulation, pulsed radiofrequency treatment was performed at 42°C for 120 seconds. The needle was then rotated 180° and an additional cycle of pulsed radiofrequency treatment was performed followed by injection of 0.25% ropivacaine with 4 mg of dexamethasone. At 1.5 and 3 month follow‐up visits, the patient reported excellent pain relief with activity and improved ability to perform her duties as an active duty service member. ▪
The Formation of Early Stage Adipocere in Submerged Remains: A Preliminary Experimental Study*
Authors: Widya Marcella , Moffatt Colin , Simmons Tal
Published: December 2011

Abstract:  In some circumstances, the presence of adipocere may retard decomposition and complicate postmortem interval estimation. This article explores the correlation between Accumulated Degree Days (ADD) and early stage formation of adipocere. Sixty wild rabbit (Oryctolagus cuniculus) carcasses were used in this experiment; a control group (N = 30) deposited directly on the ground surface and an experimental group (N = 30) completely submersed in water in individual buckets. Data (water and inner body temperature, pH, and total body score) were collected every 100 ADD. Results indicated that early stage adipocere is correlated to ADD and that its formation on submersed remains is more likely to occur after 630 ADD. Skin sloughing promoted the formation of adipocere. No adipocere was formed on any of the control group rabbits. This study also highlights the fact that multiple factors influence adipocere formation and it is suggested that further research needs to be conducted into this area.
Investigative Studies into the Recovery of DNA from Improvised Explosive Device Containers*,‡
Authors: Hoffmann Shane G. , Stallworth Shawn E. , Foran David R.
Published: December 2011

Abstract:  Apprehending those who utilize improvised explosive devices (IEDs) is a national priority owing to their use both domestically and abroad. IEDs are often concealed in bags, boxes, or backpacks to prevent their detection. Given this, the goal of the research presented was to identify IED handlers through postblast DNA recovery from IED containers. Study participants were asked to use backpacks for 11 days, after which they served as containers for pipe bombs. Eleven postdeflagration backpack regions likely to be handled were swabbed and analyzed via mini‐short tandem repeats (miniSTRs) and alleles were called blind. An experimental consensus method was examined in which profiles from all regions were considered, to help identify spurious drop‐in/out. Results were correct for all loci, except one that remained ambiguous. The results show that recovering DNA from IED containers is a viable approach for aiding in the identification of those who may have been involved in an IED event.