bluuebunny/crossref_metadata_2025 huggingface dataset:
Dispersal and upstream migration of an amphidromous neritid snail: implications for restoring migratory pathways in tropical streams
Authors: GORBACH KATHLEEN R. , BENBOW M. ERIC , McINTOSH MOLLIE D. , BURKY ALBERT J.
Published: June 2012

1. The amphidromous life cycle of several species of neritid snails, shrimp and gobies throughout the tropics includes juveniles that migrate from the ocean to breed in fresh water. In many Hawaiian streams, the decline of Neritina granosa, an endemic gastropod, has been associated with habitat degradation and water withdrawal, which are common factors affecting tropical rivers around the world.

2. We investigated the effects of water withdrawal and density on dispersal and upstream migration of N. granosa using three experimental treatments: (i) reduced flow (RF) owing to a stream diversion, (ii) natural flow (NF) and (iii) natural flow with artificially increased snail density. For each treatment, snails were differentially tagged and released in a stream without a natural, extant population of N. granosa.

3. Capture rates ranged from 17 to 65% over a 63‐day period following release. Captures on 2–6 days after release measured initial dispersal and migration, whereas longer‐term migration rates were calculated from snails captured 16–63 days after release. Snails under NF displayed positive rheotactic behaviour, with only 3–12% demonstrating initial downstream movement. Under RF, 22–77% of snails moved downstream or showed no bias either way.

4. Initial mean upstream migration rate (UMR) was 0.25, 0.66 and 1.16 m day−1 under RF, NF and natural flow with increased snail density, respectively. Longer‐term migration rates did not differ significantly between treatments, and the overall mean was 0.62 m day−1.

5. Principal component analysis and generalised linear models were used to identify habitat characteristics important to UMR, with habitat and reach‐scale hydraulics as the most important factors. The relationship between discharge and UMR suggested it would take 11–35 years for snails to migrate past the most upstream water diversion. However, rates from published studies of neritid snail species migrating en masse or in long lines under natural situations suggested that N. granosa could migrate above stream diversions within 72 days–2.5 years (when in an aggregation) and 29 days–1.1 years (when following in long lines of individuals).

6. An understanding of upstream neritid snail migration can be used for the management and conservation of this and other migratory species in tropical streams.
Sea anemones may thrive in a high CO2 world
Authors: Suggett David J. , Hall‐Spencer Jason M. , Rodolfo‐Metalpa Riccardo , Boatman Toby G. , Payton Ross , Tye Pettay D. , Johnson Vivienne R. , Warner Mark E. , Lawson Tracy
Published: June 2012

Increased seawater pCO2, and in turn ‘ocean acidification’ (OA), is predicted to profoundly impact marine ecosystem diversity and function this century. Much research has already focussed on calcifying reef‐forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA‐like conditions can simultaneously enhance the ecological success of non‐calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft‐bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone (Anemonia viridis) population was observed along a natural CO2 gradient at Vulcano, Italy. Both gross photosynthesis (PG) and respiration (R) increased with pCO2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO2 stimulation) of metabolism. The increase of PG outweighed that of R and the genetic identity of the symbiotic microalgae (Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with pCO2, which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non‐calcifying anthozoans to thrive in future environments, i.e. higher seawater pCO2. Understanding how CO2‐enhanced productivity of non‐ (and less‐) calcifying anthozoans applies more widely to tropical ecosystems is a priority where such organisms can dominate benthic ecosystems, in particular following localized anthropogenic stress.
Benign mesenchymal tumours and tumour‐like lesions in end‐stage renal disease
Authors: Büttner Maike , Kufer Verena , Brunner Kathrin , Hartmann Arndt , Amann Kerstin , Agaimy Abbas
Published: June 2012

Aims:  Mesenchymal neoplasms of the kidney are rare, and most represent sporadic angiomyolipomas. A few haemangiomas have been reported in end‐stage renal disease (ESRD) but, to date, no study has focused on the frequency and morphological spectrum of mesenchymal lesions in ESRD.

Methods and results:  We evaluated retrospectively 90 nephrectomy specimens with ESRD. Haemangiomas were detected in eight cases (8.8%; six males and two females; mean age: 55 years); four were multifocal and four had concurrent renal epithelial neoplasms. Lesions involved the medulla (three), cortex (two) or both (three), and the size range was 1–25 mm (mean 4.8 mm). Histologically, all were capillary haemangiomas with an at least focally detectable spleen‐like anastomosing pattern. All tumours stained positively for CD31 and FLI‐1, but none expressed pankeratin (KL‐1), podoplanin/D2‐40, HHV8 or GLUT‐1. Minute angiomyolipomas (mean size 2.3 mm) were detected in four patients (mean age 49.5 years). Tumour‐like smooth muscle proliferations were seen surrounding muscular arteries (eight), occasionally admixed with fat extending from the renal sinus mimicking angiomyolipoma. No similar tumours were found in 105 control kidneys.

Conclusions:  Benign haemangiomas are not uncommon in ESRD, but may be under‐recognized. They display distinctive morphology and should be distinguished from angiosarcomas and capillary‐rich renal cell carcinomas.
Does the proliferation fraction help identify mature B cell lymphomas with double‐ and triple‐hit translocations?
Authors: Mationg‐Kalaw Emarene , Tan Leonard H C , Tay Kevin , Lim Soon Thye , Tang Tiffany , Lee Yvonne Y L , Tan Soo Yong
Published: June 2012

Mationg‐Kalaw E, Tan L H C, Tay K, Lim S T, Tang T, Lee Y Y L & Tan S Y  (2012) Histopathology Does the proliferation fraction help identify mature B cell lymphomas with double‐ and triple‐hit translocations?

Aims:  The entity ‘B cell lymphoma, unclassifiable, with features intermediate between diffuse large B cell lymphoma (DLBCL) and Burkitt lymphoma (BL)’ refers to B cell neoplasms that share overlapping characteristics of BL and DLBCL. A subset of these ‘grey‐zone lymphomas’ possesses C‐MYC and IGH translocations but, in addition, contains additional rearrangements of BCL2 and/or BCL6 genes. The aim of this study was to investigate if the proliferation fraction by Ki67 immunostaining can be used to identify such double‐/triple‐hit lymphomas.

Methods and results:  We studied 492 cases of mature aggressive B cell neoplasms by histology, immunohistochemistry and interphase fluorescence in‐situ hybridization (FISH) using break‐apart probes against C‐MYC, BCL2, BCL6, IGH, MALT1, PAX5 and CCND1. Forty Burkitt lymphomas and 28 cases of MYC+ double‐/triple‐hit lymphomas were identified. Of the latter, 77% and 54% displayed proliferation fractions exceeding 75% and 90%, respectively. With a cut‐off of >75% by Ki67 immunostaining, the sensitivity and specificity for detection of MYC+ double/triple translocations was 0.77 and 0.36. Raising the proliferation fraction criterion to >90% improved the specificity to 0.62 at the expense of a low sensitivity of 0.54.

Conclusions:  Immunostaining for Ki67 is not a useful approach to prescreen B cell lymphomas for MYC+ double/triple translocations.
Optical coherence tomography
Authors: PODOLEANU A. Gh.
Published: June 2012

The review provides a concise explanation of principles of operation of different optical coherence tomography methods. A comparative analysis of their advantages and disadvantages is presented in relation to specific applications. The review will assist the reader in making an educated choice on the most suitable optical coherence tomography method to be used in a particular application.
Effect of tick saliva on signalling pathways activated by TLR‐2 ligand and Borrelia afzelii in dendritic cells
Authors: LIESKOVSKA J. , KOPECKY J.
Published: June 2012

Dendritic cells are a sentinel in defending against pathogens and tick saliva facilitates transmission of tick‐borne pathogens by modulating the host immune response. The maturation of dendritic cells is inhibited by tick saliva. To elucidate the mechanism of this inhibition, we tested the impact of Ixodes ricinus tick saliva on signalling pathways activated by Toll‐like receptor (TLR‐2) ligand and Borrelia afzelii in spleen dendritic cells. The activation of nuclear factor‐κB (NF‐κB) p65 and phosphatidylinositol‐3 kinase (PI3K)/Akt pathways was decreased by tick saliva upon both TLR‐2 and Borrelia stimulation. Among the mitogen‐activated protein kinases (MAPK), the activation of extracellular matrix‐regulated kinase (Erk1/2) was suppressed by tick saliva, but not p38. In response to spirochaetes, the amount of TNF‐α decreased in the presence of tick saliva which was mediated by selective suppression of Erk1/2, NF‐κB and Akt as tick saliva mimicked the effect of their specific inhibitors, UO126, IKK‐IV and LY294002, respectively. Saliva‐induced enhancement of IL‐10 was not observed in the presence of specific inhibitor of Protein Kinase A (PKA), H‐89, suggesting the involvement of PKA pathway in IL‐10 production. Our cumulative data show that tick saliva interferes with several signalling pathways, thus modulating the immune functions of dendritic cells.
SUB1A‐dependent and ‐independent mechanisms are involved in the flooding tolerance of wild rice species
Authors: Niroula Raj Kumar , Pucciariello Chiara , Ho Viet The , Novi Giacomo , Fukao Takeshi , Perata Pierdomenico
Published: June 2012

Crop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood‐tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A‐genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance‐related SUB1A‐1 and the intolerance‐related SUB1A‐2 alleles were found in tolerant and sensitive accessions, respectively. Flooding‐tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C‐genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence‐induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A‐1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C‐genome group, which show instead a SUB1A‐independent response to submergence.
Homologous RXLR effectors from Hyaloperonospora arabidopsidis and Phytophthora sojae suppress immunity in distantly related plants
Authors: Anderson Ryan G. , Casady Megan S. , Fee Rachel A. , Vaughan Martha M. , Deb Devdutta , Fedkenheuer Kevin , Huffaker Alisa , Schmelz Eric A. , Tyler Brett M. , McDowell John M.
Published: June 2012

Diverse pathogens secrete effector proteins into plant cells to manipulate host cellular processes. Oomycete pathogens contain large complements of predicted effector genes defined by an RXLR host cell entry motif. The genome of Hyaloperonospora arabidopsidis (Hpa, downy mildew of Arabidopsis) contains at least 134 candidate RXLR effector genes. Only a small subset of these genes is conserved in related oomycetes from the Phytophthora genus. Here, we describe a comparative functional characterization of the Hpa RXLR effector gene HaRxL96 and a homologous gene, PsAvh163, from the Glycine max (soybean) pathogen Phytophthora sojae. HaRxL96 and PsAvh163 are induced during the early stages of infection and carry a functional RXLR motif that is sufficient for protein uptake into plant cells. Both effectors can suppress immune responses in soybean. HaRxL96 suppresses immunity in Nicotiana benthamiana, whereas PsAvh163 induces an HR‐like cell death response in Nicotiana that is dependent on RAR1 and Hsp90.1. Transgenic Arabidopsis plants expressing HaRxL96 or PsAvh163 exhibit elevated susceptibility to virulent and avirulent Hpa, as well as decreased callose deposition in response to non‐pathogenic Pseudomonas syringae. Both effectors interfere with defense marker gene induction, but do not affect salicylic acid biosynthesis. Together, these experiments demonstrate that evolutionarily conserved effectors from different oomycete species can suppress immunity in plant species that are divergent from the source pathogen’s host.
Association of 14 bp insertion/deletion polymorphism of the HLA‐G gene in father with severe preeclampsia in Chinese
Authors: Zhang Z. , Li Y. , Zhang L. L. , Jia L. T. , Yang X. Q.
Published: June 2012

Preeclampsia (PE), especially severePEincluding early (before 34 weeks' gestation) and late (after 34 weeks' gestation) onsetPE, is one of the leading causes of maternal and fetal mortality and morbidity. It is well known that abnormal human leukocyte antigen subtype G (HLA‐G) expression may contribute toPE. In this study, we investigated allelic and genotypic frequencies of the 14 bp deletion/insert polymorphism in the 3′‐untranslated region (3′‐UTR) of theHLA‐G gene in cases (120 pairs of mother–offspring, 82 couples, and 67 pairs of father–offspring with severePE) and controls (158 pairs of mother–offspring, 87 couples, and 75 pairs of father–offspring with normal pregnancy). We found that the frequencies of the +14 bp/+14 bpHLA‐G genotype of the offspring were significantly higher in the severe and early onset severePEcases compared with controls, and the frequencies of the −14 bp/−14 bpHLA‐G genotype of the offspring were significantly lower in the early onset severePEcases compared with controls. The frequency of combined −14 bp/+14 bp mother/ +14 bp/+14 bp offspring genotypes was significantly higher in the severe and early onset severePEcases compared with controls, and the frequency of combined −14 bp/+14 bp mother/ −14 bp/−14 bp offspring genotypes was significantly lower in the early onset severePEcases compared with late onset severePEcases. The frequency of combined −14 bp/−14 bp father/−14 bp/−14 bp offspring genotypes was significantly lower in the early onset severePEcases compared with late onset severePEcases and controls. In overview, theHLA‐G 14 bp deletion/insert polymorphism is associated with severePEin father–offspring, and its distribution is different between the early and late onset severePE.
Assessment of copy‐number variation in the NKG2C receptor gene in a single‐tube and characterization of a reference cell panel, using standard polymerase chain reaction
Authors: Moraru M. , Cañizares M. , Muntasell A. , de Pablo R. , López‐Botet M. , Vilches C.
Published: June 2012

Natural killer (NK) and T‐lymphocytes monitor human leukocyte antigen (HLA)‐E expression through CD94:NKG2 heterodimers. Structural polymorphism is not a hallmark for NK‐complex genes on chromosome 12, except for complete NKG2C deletion in some humans. We present a method for fast, simple and accurate assessment of NKG2C copy‐number variation – presence or absence in the genome of an NKG2C gene, in homo‐ or heterozygosis, is detected by a single conventional polymerase chain reaction that yields amplicons of different lengths in each genotype. We have also determined the NKG2C genotypes of a reference cell panel comprising 13 NK‐ and tumour‐cell lines and 39 Epstein‐Barr virus transformed cells from the International Histocompatibility Workshop. Our results should facilitate research on the importance of NKG2C and its deletion for immunity.
Oxygenation index predicts mortality in pediatric stem cell transplant recipients requiring mechanical ventilation
Authors: Rowan Courtney M. , Hege Kerry M. , Speicher Richard H. , Goodman Michael , Perkins Susan M. , Slaven James E. , Westenkirchner David F. , Haut Paul R. , Nitu Mara E.
Published: June 2012

Rowan CM, Hege KM, Speicher RH, Goodman M, Perkins SM, Slaven JE, Westenkirchner DF, Haut PR, Nitu ME. Oxygenation index predicts mortality in pediatric stem cell transplant recipients requiring mechanical ventilation.

Abstract:  The mortality in the ICU for pediatric HSCT recipients remains high. Early pulmonary complications continue to be an obstacle to the survival. We hypothesize OI is a predictor for mortality in critically ill pediatric HSCT recipients. Retrospective review of pediatric HSCT recipients between 2002 and 2010 who required intensive care during the same hospital admission as their transplant. Twenty‐eight patients accounted for 31 ICU admissions. Twenty‐six (84%) admissions required mechanical ventilation. Ten (38%) mechanically ventilated admissions were placed on HFOV. Mortality of those mechanically ventilated was 70%. An OI ≥ 20 at any point during ventilation was associated with 94% mortality, while an OI ≥ 25 had 100% mortality. There was a significant association between maximum OI at any point during mechanical ventilation and ICU mortality, with the odds of dying increasing by 13% for each unit increase of max OI (OR = 1.13, 95% CI = 1.01–1.26, p = 0.03). An OI of 20 had a sensitivity of 0.89 and specificity of 0.83 for predicting mortality. OI has a strong association with ICU mortality among pediatric stem cell recipients.
Identification of Taxus microRNAs and their targets with high‐throughput sequencing and degradome analysis
Authors: Hao Da‐Cheng , Yang Ling , Xiao Pei‐Gen , Liu Ming
Published: June 2012

Plant microRNAs (miRNAs) have an impact in the regulation of several biological processes such as development, growth and metabolism by negatively controlling gene expression at the post‐transcriptional level. However, the role of these small molecules in the medicinal gymnosperm species Taxus remained elusive. To elucidate the role of miRNAs in Taxus we used a deep sequencing approach to analyze the small RNA and degradome sequence tags of Taxus mairei leaves. For miRNAs, the sequencing library generated 14.9 million short sequences, resulting in 13.1 million clean reads. The library contains predominantly small RNAs with 21 nucleotide length, followed by 19‐nt and 20‐nt small RNAs. Around 29% of total small RNAs are matched to the T. mairei transcriptome. By sequence alignment, we identified 871 mature miRNAs, 15 miRNA* and 869 miRNA precursors representing known plant miRNA families. There are 547 unique small RNA matching the miRNA precursors. We predict 37 candidate novel miRNAs from the unannotated small RNAs that could be mapped to the reference transcriptome. The expression of the selected candidates was for the first time quantified by real‐time reverse transcription polymerase chain reaction. The novel miRNA m0034 turns out to be from the intron sequence of the paclitaxel biosynthetic gene taxadiene synthase. The 21 potential targets of nine novel miRNAs are also predicted. Additionally, 56 targets for known miRNA families and 15 targets for novel candidate miRNA families were identified by high‐throughput degradome‐sequencing approach. It is found that two paclitaxel biosynthetic genes, taxane 13α hydroxylase and taxane 2α‐O‐benzoyltransferase, are the cleavage targets of miR164 and miR171, respectively. This study represents the first transcriptome‐based analysis of miRNAs and degradome in gymnosperms.
Twelve‐hour days in the brain and behavior of split hamsters
Authors: Butler Matthew P. , Rainbow Megan N. , Rodriguez Elizabeth , Lyon Sarah M. , Silver Rae
Published: June 2012

Hamsters will spontaneously ‘split’ and exhibit two rest–activity cycles each day when housed in constant light (LL). The suprachiasmatic nucleus (SCN) is the locus of a brain clock organizing circadian rhythmicity. In split hamsters, the right and left SCN oscillate 12 h out of phase with each other, and the twice‐daily locomotor bouts alternately correspond to one or the other. This unique configuration of the circadian system is useful for investigation of SCN communication to efferent targets. To track phase and period in the SCN and its targets, we measured wheel‐running and FOS expression in the brains of split and unsplit hamsters housed in LL or light–dark cycles. The amount and duration of activity before splitting were correlated with latency to split, suggesting behavioral feedback to circadian organization. LL induced a robust rhythm in the SCN core, regardless of splitting. The split hamsters’ SCN exhibited 24‐h rhythms of FOS that cycled in antiphase between left and right sides and between core and shell subregions. In contrast, the medial preoptic area, paraventricular nucleus of the hypothalamus, dorsomedial hypothalamus and orexin‐A neurons all exhibited 12‐h rhythms of FOS expression, in‐phase between hemispheres, with some detectable right–left differences in amplitude. Importantly, in all conditions studied, the onset of FOS expression in targets occurred at a common phase reference point of the SCN oscillation, suggesting that each SCN may signal these targets once daily. Finally, the transduction of 24‐h SCN rhythms to 12‐h extra‐SCN rhythms indicates that each SCN signals both ipsilateral and contralateral targets.
Management and short‐term outcome of malignant colorectal polyps in the north of England1
Authors: Gill M. D. , Rutter M. D. , Holtham S. J.
Published: June 2012

Aim  Management of malignant colorectal polyps (MCP) is contentious, with no randomized controlled trials comparing endoscopic with surgical management. This study reviews the management and outcomes of MCPs across a UK region.

Method  Patients with a malignant polyp were identified using the NORCCAG (NORthern Colorectal Cancer Audit Group) database between April 2006 and July 2010. All histopathology reports and follow‐up procedures were reviewed.

Results  Of 386 patients identified, 165 (42.7%) had the polyp biopsied and 221 (57.3%) had an endoscopic local excision (37 piecemeal excision, 184 polypectomy). All patients having an endoscopic biopsy underwent surgery. 103 (46.6%) having a local excision had follow‐up surgery, of whom 79 (76.7%) had no residual cancer. Of the 118 patients managed endoscopically, none had residual cancer on follow‐up endoscopy. The 21 (5.4%) Dukes C cancers were associated with Kikuchi SM3/Haggitt 4 lesions (χ2 = 10.85, P = 0.005) and lesions with an involved/unsure excision margin (χ2 = 7.44, P = 0.017). Predictors of finding residual tumour at surgery after local excision were Kikuchi SM3/Haggitt Level 4 (χ2 = 17.07, P < 0.001) and an involved/unsure excision margin (χ2 = 20.45, P < 0.001). An excision margin > 0 mm was associated with the finding of no residual tumour (χ2 = 25.21, P < 0.001). There was no difference in survival between surgical and endoscopic management (χ2 = 0.634, P = 0.426) after a mean follow‐up of 25.1 months.

Conclusion  Endoscopic management of a subgroup of MCPs appears safe. A clear resection margin (> 0 mm) appears sufficient to avoid surgery, except in locally advanced lesions (Kikuchi 3/Haggitt 4) which have a greater risk of residual cancer at surgery and lymph node metastasis.
A critical analysis of undergraduate students' cultural immersion experiences
Authors: Harrowing J.N. , Gregory D.M. , O'Sullivan P.S. , Lee B. , Doolittle L.
Published: June 2012

HARROWING J.N., GREGORY D.M., O'SULLIVAN P.S., LEE B. & DOOLITTLE L. (2012) A critical analysis of undergraduate students' cultural immersion experiences. International Nursing Review

Purpose:  This paper is concerned with the impact of an international health promotion experience on the understanding of culture among university students. Such immersion experiences are often cited as a strategy to prepare nurses for culturally appropriate practice. We describe students' epistemic movements over time with respect to cultural perspectives prior to, during and after a field study in Malawi.

Design:  Data were collected at three time points from students in undergraduate nursing (n = 14) and non‐nursing (n = 8) programs at a Canadian university. Two essays narrating participants' understanding of culture were submitted by consenting class members. A subgroup of nine participants (four nursing students, five from other disciplines) completed a third narrative following a subsequent field study course in Malawi.

Method:  Using narrative analysis, themes and structures in the participants' writing were identified and located within a constructivist or essentialist paradigm of cultural understanding.

Findings:  Overwhelmingly, students' narratives were initially portrayed and informed by an essentialist understanding of culture. Later narratives demonstrated varying degrees of epistemic movement towards more constructivist viewpoints. Narratives that initially exhibited constructivist characteristics tended to display strengthened convictions in that paradigm.

Conclusion:  We challenge the claim that an international immersion experience immediately transforms participants into cultural experts; our evidence suggests that students experienced existential growth, but their understanding of culture did not change as a result of their brief stay in a different cultural context. Cultural immersion is a phenomenon that requires more critical analysis and systematic investigation to determine how such experiences contribute to learning about culture among nursing students.
Targeted re‐sequencing of the allohexaploid wheat exome
Authors: Winfield Mark O. , Wilkinson Paul A. , Allen Alexandra M. , Barker Gary L. A. , Coghill Jane A. , Burridge Amanda , Hall Anthony , Brenchley Rachael C. , D’Amore Rosalinda , Hall Neil , Bevan Michael W. , Richmond Todd , Gerhardt Daniel J. , Jeddeloh Jeffrey A. , Edwards Keith J.
Published: June 2012

Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of sequence data required for whole genome studies. Even with the advent of next‐generation sequencing technology, it is still relatively expensive to generate whole genome sequences for more than a few wheat genomes at any one time. To overcome this problem, we have developed a targeted‐capture re‐sequencing protocol based upon NimbleGen array technology to capture and characterize 56.5 Mb of genomic DNA with sequence similarity to over 100 000 transcripts from eight different UK allohexaploid wheat varieties. Using this procedure in conjunction with a carefully designed bioinformatic procedure, we have identified more than 500 000 putative single‐nucleotide polymorphisms (SNPs). While 80% of these were variants between the homoeologous genomes, A, B and D, a significant number (20%) were putative varietal SNPs between the eight varieties studied. A small number of these latter polymorphisms were experimentally validated using KASPar technology and 94% proved to be genuine. The procedures described here to sequence a large proportion of the wheat genome, and the various SNPs identified should be of considerable use to the wider wheat community.
Bayesian face recognition and perceptual narrowing in face‐space
Authors: Balas Benjamin
Published: June 2012

During the first year of life, infants’ face recognition abilities are subject to ‘perceptual narrowing’, the end result of which is that observers lose the ability to distinguish previously discriminable faces (e.g. other‐race faces) from one another. Perceptual narrowing has been reported for faces of different species and different races, in developing humans and primates. Though the phenomenon is highly robust and replicable, there have been few efforts to model the emergence of perceptual narrowing as a function of the accumulation of experience with faces during infancy. The goal of the current study is to examine how perceptual narrowing might manifest as statistical estimation in ‘face‐space’, a geometric framework for describing face recognition that has been successfully applied to adult face perception. Here, I use a computer vision algorithm for Bayesian face recognition to study how the acquisition of experience in face‐space and the presence of race categories affect performance for own and other‐race faces. Perceptual narrowing follows from the establishment of distinct race categories, suggesting that the acquisition of category boundaries for race is a key computational mechanism in developing face expertise.
Connecting neural coding to number cognition: a computational account
Authors: Prather Richard W.
Published: June 2012

The current study presents a series of computational simulations that demonstrate how the neural coding of numerical magnitude may influence number cognition and development. This includes behavioral phenomena cataloged in cognitive literature such as the development of numerical estimation and operational momentum. Though neural research has begun to describe neural coding of number, it is unclear how specific characteristics of the neural coding may relate to the expansive list of behavioral phenomena in the development of number cognition. The following study considers several possibilities.
Politics is Still an Adversarial Business: Minority Government and Mixed-Member Proportional Representation in Scotland and in New Zealand
Authors: Lundberg Thomas Carl
Published: June 2012

Both Scotland and New Zealand, small nations with a British political heritage, implemented mixed-member proportional (MMP) electoral systems in the 1990s. Minority government characterises most of the New Zealand experience since the introduction of MMP in 1996, while Scotland's only such experience occurred between 2007 and 2011. The Scottish experience differed significantly from that of New Zealand because Scotland has a different party system (characterised by two major cleavages) and exists in a system of multi-level governance, resulting in a more conflict-laden relationship between parties. The centre-periphery cleavage in the Scottish case results from being part of the United Kingdom, while New Zealand is an independent state. Both nations introduced MMP as part of an effort to bring about a ‘new politics’, but the impact of institutional engineering upon the behaviour of politicians has been limited.
We Are the World—and They Are Not: Prototypicality for the World Community, Legitimacy, and Responses to Global Inequality
Authors: Reese Gerhard , Berthold Anne , Steffens Melanie C.
Published: June 2012

The relation between developed and developing countries is characterized by inequalities that sometimes hinder actions against worldwide problems. The current research presents an intergroup approach, based on the ingroup projection model, towards an analysis of psychological processes that perpetuate global inequality on a social group level. Precisely, we argue that people from developed countries perceive their group as more prototypical for the world population than they perceive people from developing countries. These perceptions of ingroup prototypicality should in turn relate to legitimacy beliefs and predict unfavorable behavioral intentions towards developing countries. We present two studies that corroborate our hypotheses: In Study 1, participants from a developed country perceived their ingroup as more prototypical for the superordinate group (i.e., world population) than the outgroup (i.e., developing countries), which in turn was related to beliefs that global inequality is legitimate. This finding was replicated in Study 2, and the predicted effect of ingroup prototypicality on behavioral intentions was mediated by legitimacy beliefs. These findings demonstrate that intergroup processes can contribute to perpetuating global inequality.
The Intergenerational Transmission of Contending Place Identities
Authors: Rico Guillem , Jennings M. Kent
Published: June 2012

Although a considerable amount of research exists regarding the transfer of political orientations within the family, little systematic attention has been devoted to studying the transmission of place (territorial) identities in contexts where such identities constitute a basic cleavage of political competition. This article examines the transfer of place identities in Catalonia, Spain, where contending identities, along with left‐right ideology, give shape to a distinctive regional political life. Using data from region‐wide household surveys, we analyze the reproduction of place identities as observed in parent‐child pairs and triads and find that it exceeds the reproduction of other political orientations, including left‐right self‐location and party preference. The direct transmission model fares well against the rival hypothesis of indirect transmission via parental social characteristics and the competing impact of the local context. Parent‐child congruence varies according to the homogeneity of parental place identities, the same‐sex and cross‐sex combinations of parents and their children, and the ethnic composition of neighborhoods.
Areal Typology of Proto‐Indo‐European: The Case for Caucasian Connections
Authors: Matasović Ranko
Published: June 2012

This paper re‐examines the evidence for early contacts between Proto‐Indo‐European (PIE) and the languages of the Caucasus. Although we were not able to find certain proofs of lexical borrowing between PIE and North Caucasian, there are a few undeniable areal‐typological parallels in phonology and grammar. Some features generally attributed to PIE are not found in the majority of languages of North and Northeastern Eurasia, while they are common, or universally present, in the languages of the Caucasus (especially North Caucasus). Those features include the high consonant‐to‐vowel ratio, tonal accent, number suppletion in personal pronouns, the presence of gender and the morphological optative and, possibly, the presence of glottalized consonants and ergativity.
The Trade and Welfare Impacts of Australian Quarantine Policies: The Case of Pigmeat
Authors: Beghin John , Melatos Mark
Published: June 2012

We analyse the trade and welfare impact of quarantine measures imposed by Australia on imports of pigmeat. In particular, we account for changes to Australia’s pigmeat quarantine policy over time including those changes related to the recent resolution of a WTO dispute between Australia and the European Union. Using a random utility model, and applying it to corner solutions in import decisions, tariff equivalents (by major trading partner) are estimated for the different pigmeat quarantine regimes implemented by Australia during the period 1988–2009. The welfare impact on consumers, producers and foreign exporters is computed using a partial equilibrium model calibrated on the econometric estimates. The quarantine regimes had a strong effect on trade and welfare with a tariff equivalent above 113 per cent of average real‐world prices over the period analysed.
Private Standards, Trade and Poverty: GlobalGAP and Horticultural Employment in Senegal
Authors: Colen Liesbeth , Maertens Miet , Swinnen Johan
Published: June 2012

There is a growing body of literature that analyses the implications of private food standards for developing countries. Most of this literature has focused on the trade effects of standards and on the effects on exporters and producers. Very few studies have looked at the effect of standards for workers in export supply chains – although this is important for poverty reduction. In this paper, we use original panel data from surveys among workers in the horticultural export industry in Senegal to analyse the effects of GlobalGAP certification of exporter–producer companies on the employment conditions of workers in these companies. The results suggest that GlobalGAP certification is associated with an increase in workers’ daily wages and with longer employment periods. We put forward different explanations for the mechanism through which these effects on employment conditions can emerge.
Uncovering the Benefits of Participatory Research: Implications of a Realist Review for Health Research and Practice
Authors: JAGOSH JUSTIN , MACAULAY ANN C. , PLUYE PIERRE , SALSBERG JON , BUSH PAULA L. , HENDERSON JIM , SIRETT ERIN , WONG GEOFF , CARGO MARGARET , HERBERT CAROL P. , SEIFER SARENA D. , GREEN LAWRENCE W. , GREENHALGH TRISHA
Published: June 2012

Context: Participatory research (PR) is the co‐construction of research through partnerships between researchers and people affected by and/or responsible for action on the issues under study. Evaluating the benefits of PR is challenging for a number of reasons: the research topics, methods, and study designs are heterogeneous; the extent of collaborative involvement may vary over the duration of a project and from one project to the next; and partnership activities may generate a complex array of both short‐ and long‐term outcomes.

Methods: Our review team consisted of a collaboration among researchers and decision makers in public health, research funding, ethics review, and community‐engaged scholarship. We identified, selected, and appraised a large‐variety sample of primary studies describing PR partnerships, and in each stage, two team members independently reviewed and coded the literature. We used key realist review concepts (middle‐range theory, demi‐regularity, and context‐mechanism‐outcome configurations [CMO]) to analyze and synthesize the data, using the PR partnership as the main unit of analysis.

Findings: From 7,167 abstracts and 591 full‐text papers, we distilled for synthesis a final sample of twenty‐three PR partnerships described in 276 publications. The link between process and outcome in these partnerships was best explained using the middle‐range theory of partnership synergy, which demonstrates how PR can (1) ensure culturally and logistically appropriate research, (2) enhance recruitment capacity, (3) generate professional capacity and competence in stakeholder groups, (4) result in productive conflicts followed by useful negotiation, (5) increase the quality of outputs and outcomes over time, (6) increase the sustainability of project goals beyond funded time frames and during gaps in external funding, and (7) create system changes and new unanticipated projects and activities. Negative examples illustrated why these outcomes were not a guaranteed product of PR partnerships but were contingent on key aspects of context.

Conclusions: We used a realist approach to embrace the heterogeneity and complexity of the PR literature. This theory‐driven synthesis identified mechanisms by which PR may add value to the research process. Using the middle‐range theory of partnership synergy, our review confirmed findings from previous PR reviews, documented and explained some negative outcomes, and generated new insights into the benefits of PR regarding conflicts and negotiation between stakeholders, program sustainability and advancement, unanticipated project activity, and the generation of systemic change.
Moving from Intersection to Integration: Public Health Law Research and Public Health Systems and Services Research
Authors: BURRIS SCOTT , MAYS GLEN P. , DOUGLAS SCUTCHFIELD F. , IBRAHIM JENNIFER K.
Published: June 2012

Context:For three decades, experts have been stressing the importance of law to the effective operation of public health systems. Most recently, in a 2011 report, the Institute of Medicine recommended a review of state and local public health laws to ensure appropriate authority for public health agencies; adequate access to legal counsel for public health agencies; evaluations of the health effects and costs associated with legislation, regulations, and policies; and enhancement of research methods to assess the strength of evidence regarding the health effects of public policies. These recommendations, and the continued interest in law as a determinant of health system performance, speak to the need for integrating the emerging fields of Public Health Law Research (PHLR) and Public Health Systems and Services Research (PHSSR).

Methods:Expert commentary.

Findings:This article sets out a unified framework for the two fields and a shared research agenda built around three broad inquiries: (1) the structural role of law in shaping the organization, powers, prerogatives, duties, and limitations of public health agencies and thereby their functioning and ultimately their impact on public health (“infrastructure”); (2) the mechanisms through which public health system characteristics influence the implementation of interventional public health laws (“implementation”); and (3) the individual and system characteristics that influence the ability of public health systems and their community partners to develop and secure enactment of legal initiatives to advance public health (“innovation”). Research to date has laid a foundation of evidence, but progress requires better and more accessible data, a new generation of researchers comfortable in both law and health research, and more rigorous methods.

Conclusions:The routine integration of law as a salient factor in broader PHSSR studies of public health system functioning and health outcomes will enhance the usefulness of research in supporting practice and the long‐term improvement of system performance.
Regional variations in the distribution and colocalization of extracellular matrix proteins in the juvenile bovine meniscus
Authors: Vanderploeg Eric J. , Wilson Christopher G. , Imler Stacy M. , Ling Carrie Hang‐Yin , Levenston Marc E.
Published: June 2012

A deeper understanding of the composition and organization of extracellular matrix molecules in native, healthy meniscus tissue is required to fully appreciate the degeneration that occurs in joint disease and the intricate environment in which an engineered meniscal graft would need to function. In this study, regional variations in the tissue‐level and pericellular distributions of collagen types I, II and VI and the proteoglycans aggrecan, biglycan and decorin were examined in the juvenile bovine meniscus. The collagen networks were extensively, but not completely, colocalized, with tissue‐level organization that varied with radial position across the meniscus. Type VI collagen exhibited close association with large bundles composed of type I and II collagen and, in contrast to type I and II collagen, was further concentrated in the pericellular matrix. Aggrecan was detected throughout the inner region of the meniscus but was restricted to the pericellular matrix and sheaths of collagen bundles in the middle and outer regions. The small proteoglycans biglycan and decorin exhibited regional variations in staining intensity but were consistently localized in the intra‐ and/or peri‐cellular compartments. These results provide insight into the complex hierarchy of extracellular matrix organization in the meniscus and provide a framework for better understanding meniscal degeneration and disease progression and evaluating potential repair and regeneration strategies.
How cellulose‐based leaf toughness and lamina density contribute to long leaf lifespans of shade‐tolerant species
Authors: Kitajima Kaoru , Llorens Anna‐Maria , Stefanescu Carla , Timchenko Marta Vargas , Lucas Peter W. , Wright S. Joseph
Published: June 2012

See also the Commentary by Onoda and Lusk
Glucocorticoid treatment does not alter early cardiac adaptations to growth restriction in preterm sheep fetuses
Authors: Tare M , Miller SL , Wallace EM , Sutherland AE , Yawno T , Coleman HA , Jenkin G , Parkington HC
Published: June 2012

Please cite this paper as: Tare M, Miller S, Wallace E, Sutherland A, Yawno T, Coleman H, Jenkin G, Parkington H. Glucocorticoid treatment does not alter early cardiac adaptations to growth restriction in preterm sheep fetuses. BJOG 2012;119:906–914.

Objective  To study the consequences of glucocorticoid treatment in fetal growth restriction (FGR) on cardiac function.

Setting  Laboratory.

Sample  Sheep.

Methods  Growth restriction was induced in sheep fetuses using single umbilical artery ligation (SUAL) on days 105–110 of gestation (term 147). Control fetuses were not ligated. Betamethasone (BM) (11.4 mg intramuscularly) or saline was administered to ewes on days 5 and 6 after surgery. Ewes were anaesthetised on day 7, the fetuses were removed, and their hearts were mounted on a Langendorff apparatus. Balloon catheters were inserted into the right and left ventricles.

Outcome measures  Ventricular contractile function and infarct area following ischaemia/reperfusion.

Results  The SUAL resulted in FGR (body weight 77% of control). The FGR was associated with increases in basal left ventricular pressure development and rates of contraction and relaxation. Right ventricular contraction was unaffected. Following brief ischaemia/reperfusion, the infarct area in FGR hearts was increased four‐fold compared with controls. Antenatal BM resulted in a proportional increase in heart size and coronary flow, especially in FGR fetuses, and left ventricular pressure and heart rate responses to β‐adrenoceptor activation were increased.

Conclusions  Fetal hearts rapidly adapt to FGR to maintain substrate delivery to the brain and heart. The FGR greatly enhanced the area of ischaemia, with implications for susceptibility in postnatal life. Antenatal BM treatment does not interfere with these cardiac changes but appears to increase left ventricle β‐adrenoceptor responsiveness, which may render the offspring vulnerable to subsequent cardiac dysfunction.