bluuebunny/crossref_metadata_2025 huggingface dataset:
Media Credibility
Authors: Tsfati Yariv
Published: June 2011

Audience perceptions regarding the credibility of news media have been studied using several concepts, including “media credibility,” “trust in media,” “media skepticism,” and “media cynicism.” In general, researchers interested in the credibility concept are concerned with audience perceptions of news media, not with the actual credibility of journalists. Early research on media credibility conducted at Yale in the 1950s manipulated the credibility of communicators and measured the impact of this manipulation on audience persuasion. Only in the 1970s did scholars begin to treat it not as a static trait of the source but as a dynamic perception of the audience. A major line of research on media credibility has to do with a phenomenon called “hostile media perception,” which takes place when involved people with opposing opinions on an issue perceive the very same, seemingly objective coverage as biased against their respective points of view. Other lines of research have examined the factors underlying audience credibility perceptions and their consequences for various social phenomena. Recently, scholars have revisited early work on medium credibility to investigate audience perceptions of online versus traditional media.
Population Structure of Brown Rot Fungi on Stone Fruits in China
Authors: Zhu Xiao-qiong , Chen Xiao-yu , Guo Li-yun
Published: June 2011

In total, 455 Monilinia isolates from stone fruits collected from several provinces (cities) in China from 2003 to 2009 were identified to species based on morphological characteristics, molecular identification, and the sequence of the internal transcribed spacer (ITS) regions 1 and 2 and the 5.8S gene of the ribosomal RNA. Overall, four species were detected (Monilinia fructicola, M. fructigena, M. laxa, and Monilia polystroma). M. fructicola was the most prevalent (93.0%) followed by M. fructigena (4.8%), M. laxa (2.0%), and Monilia polystroma (0.2%). M. fructicola and M. fructigena were found on peach, plum, and apricot; M. laxa was found only on apricot, cherry (in an organic orchard), and wild peach; and Monilia polystroma was found only on plum in Heilongjiang. The pathogenicity of Monilinia fructicola, M. laxa, and M. fructigena did not significantly differ on wounded nectarine and apricot, indicating that the differences in frequency of occurrence were not linked to virulence. Phylogenetic analysis based on ITS sequences showed that the isolates of M. laxa and M. fructigena from China differed from isolates of these species from other countries, and that the difference led to the separation of the isolates from China and those from other countries into different phylogenetic groups. Further study is needed to determine whether they are cryptic species.
Analysis of Verticillium dahliae Suggests a Lack of Correlation Between Genotypic Diversity and Virulence Phenotypes
Authors: Atallah Zahi K. , Maruthachalam Karunakaran , Vallad Gary E. , Davis R. Michael , Klosterman Steven J. , Subbarao Krishna V.
Published: June 2011

Verticillium dahliae causes severe wilt and recurring losses in numerous agricultural and ornamental hosts worldwide. Two virulence phenotypes (races) have been identified based on the Ve resistance gene and its homologs but their distribution and evolutionary history are unknown. Sequence analyses of the intergenic spacer of the ribosomal DNA and amplified fragment length polymorphism markers suggested an absence of correlation between genotypic diversity and virulence phenotypes. Additionally, both race 1 and 2 phenotypes were isolated in various geographic regions and hosts. Sustained levels of migration of both virulence phenotypes among various geographic regions were evident, and the study also suggested that both virulence phenotypes infect a variety of hosts, regardless of the availability of resistant cultivars. Given the high genotypic diversity observed in V. dahliae, more than the two known virulence phenotypes may be present in nature but not yet identified because of the current lack of sources of resistance other than the Ve gene and its homologs. The inclusion of various genotypes exhibiting the same virulence phenotype may greatly improve the long-term effectiveness of resistance to race 2 of V. dahliae regardless of the host. This study also confirms the transcontinental gene flow and high genotypic diversity of V. dahliae affecting lettuce in coastal California regardless of the molecular markers employed.
First Report of Anthracnose Caused by Colletotrichum gloeosporioides on Pistachio (Pistacia vera) in China
Authors: Yang S. Y. , Su S. C. , Liu T. , Fan G. , Wang J. , Leng P. S.
Published: June 2011

In the 1990s, pistachio (Pistacia vera L. ‘Kerman’ and ‘Peters’) was introduced in China. They are found in many orchards in Beijing and Gansu and Hebei provinces, northern China. In 2009, a new disease was observed on leaves, stems, and fruits in pistachio orchards in Gansu Province. Disease incidence in 8- to 12-year-old orchards was 30%. Yield losses reached 25%. Symptoms began as discrete, sunken, black spots, approximately 10 mm in diameter, followed by circular lesions that eventually coalesced with tissue death recorded and orange fructifications developed on lesions. Pieces of diseased leaves, stems, and fruits were surfaced sterilized and placed on 2% potato dextrose agar (PDA) at 25°C. A fungus was consistently isolated. After 10 days, cultures on PDA showed aerial, white mycelium that turned gray to grayish black with a salmon-to-orange conidial mass at 25°C and a 12-h photoperiod. Brown, 80 to 120 μm long setae were observed in the acervulus. Conidia were hyaline, fusiform to nearly straight, and averaged 12 to 18 × 3 to 5 μm. On the basis of morphological characteristics, the fungus was identified as Colletotrichum gloeosporioides (Penz.) Sacc. (2). On PDA, 0.5 μg/ml of benomyl was applied for the sensitivity test (3). Benomyl completely inhibited the growth of the fungus. Mycelial DNA was extracted, PCR amplified using ITS1 and ITS4 primers for the ribosomal DNA internal transcribed spacers 1 and 2, and sequenced. The DNA sequence was recorded in GenBank as No. HQ631378. The DNA sequence was blasted showing 99% identity with Accession Nos. GQ144454 and GU004376, for C. gloeosporioides. Pathogenicity tests were conducted under greenhouse conditions at 25°C. Three replicates of 2-year-old ‘Kerman’ plants were inoculated with mycelial PDA plugs placed on 0.5-cm2 stem wounds and then wrapped with Parafilm. Controls were inoculated with PDA plugs without the fungus. After 3 weeks, stem cankers were observed on inoculated plants. Control plants remained healthy. Pathogenicity was also tested on injured leaves and fruits. A 10-μl drop of a spore suspension of 104 conidia/ml was applied on ‘Kerman’ and ‘Peters’ leaves and ‘Kerman’ fruits and placed on plates with a wet filter paper at 25°C. Small, black lesions were observed at 2 days after inoculation. At 7 days, necrotic lesions covered the entire surface. C. gloeosporioides was reisolated from necrotic lesions. Controls did not develop symptoms. C. acutatum has been reported on pistachio in Australia (1), but to our knowledge, this is the first report of anthracnose caused by C. gloeosporioides on pistachio.

References: (1) G. J. Ash and V. M. Lanoiselet. Australas. Plant Pathol. 30:365, 2001. (2) J. Y. Lu. Plant Pathogenic Mycology. China Agricultural Press, Beijing, 2001. (3) N. A. R. Peres et al. Plant Dis. 86:620, 2002.
Identification of polymorphisms in the malic enzyme 1, NADP(+)‐dependent, cytosolic and nuclear receptor subfamily 0, group B, member 2 genes and their associations with meat and carcass quality traits in commercial Angus cattle
Authors: Gill J. L. , Bishop S. C. , McCorquodale C. , Williams J. L. , Wiener P.
Published: June 2011

Genes involved in the physiological control of energy and triglyceride synthesis, such as malic enzyme 1, NADP(+)‐dependent, cytosolic (ME1) and nuclear receptor subfamily 0, group B, member 2 (NR0B2), are key candidates that may have effects on meat and carcass quality traits. These genes were sequenced in Aberdeen Angus beef cattle, and the possibility of associations between SNPs and economically important carcass and meat quality traits was tested. Six novel SNPs, five in ME1 and one in NR0B2, were identified. A SNP in exon eight of ME1 resulted in a non‐synonymous amino acid change from valine to isoleucine. Phenotypic data were recorded on 536 commercial Aberdeen Angus‐cross beef cattle, which comprised 28 carcass quality, tenderness and sensory traits. The majority of the SNPs were associated with at least one of these traits, including an association between the NR0B2 SNP and fat class, and associations between at least one of the ME1 SNPs and eye muscle area, sirloin weight before maturation, sirloin steak tail length, and juiciness.
Barriers and facilitators to optimize function and prevent disability worsening: a content analysis of a nurse home visit intervention
Authors: Liebel Dianne V. , Powers Bethel Ann , Friedman Bruce , Watson Nancy M.
Published: June 2011

liebel d.v., powers b.a., friedman b. & watson n.m. (2012) Barriers and facilitators to optimize function and prevent disability worsening: a content analysis of a nurse home visit intervention. Journal of Advanced Nursing68(1), 80–93.

Aims.  This paper is a report of an analysis of how to better understand the results of the nurse home visit intervention in the Medicare Primary and Consumer‐Directed Care Demonstration in terms of facilitators and barriers to disability improvement/maintenance as compared with disability worsening.

Background.  There is a lack of literature describing how nurse home visit interventions are able to maintain/improve disability among older persons with disability. The present study is one of only six reporting beneficial disability outcomes.

Methods.  Cases were purposefully sampled to represent change in the disability construct leading to selection of ten cases each of disability maintenance/improvement (no change or decrease in total Activities of Daily Living score from baseline) and worsening (an increase in total Activities of Daily Living score from baseline). Data from nurses’ progress notes and case studies (collected in March 1998–June 2002) were analysed using qualitative descriptive analysis (May 2009). These results remain relevant because the present study is one of the few studies to identify select nurse activities instrumental in postponing/minimizing disability worsening.

Results/findings.  Three primary themes captured the facilitators and barriers to effective disability maintenance/improvement: (1) building and maintaining patient‐centred working relationships, (2) negotiating delivery of intervention components and (3) establishing balance between patients’ acute and chronic care needs. Sub‐themes illustrate nurse, patient and system factors associated with effective disability maintenance/improvement (e.g. nurse caring, communicating, facilitating interdisciplinary communication) and barriers associated with disability worsening (e.g. dementia, depression and recurring acute illnesses).

Conclusion.  This study provides new insights about the facilitators and barriers to effective disability maintenance/improvement experienced by patients receiving home visits. Potential opportunities exist to integrate these insights into best‐practice models of nurse home visiting.
Should payments for biodiversity conservation be based on action or results?
Authors: Gibbons James M. , Nicholson Emily , Milner‐Gulland E. J. , Jones Julia P. G.
Published: June 2011

1. There is growing interest in the potential of payments for ecosystem services (PES) to encourage land managers to protect and enhance the environment. However, questions remain about how PES agreements should be designed. There is a division between schemes that structure payments by action or by results, with most biodiversity PES schemes, including European agri‐environment schemes, paying by action; for example incentivising land managers to carry out actions believed to increase biodiversity. Payment by results is a common incentive structure in the private sector (e.g. labourers doing piece work or no‐win no‐fee lawyers) but rarer in PES.

2. Using a theoretical modelling approach, we investigate the conditions under which each way of structuring payments may be more cost‐effective in a biodiversity PES.

3. Payment by action is favoured where there is a clear action that can be specified at an appropriate level and to which biodiversity is sensitive. We found that payment by results is favoured in degraded landscapes as incentives are created for managers to use their private knowledge and join the scheme only if they can produce the biodiversity services targeted by the scheme. Payment by results is also favoured where biodiversity is less sensitive to conservation action and when it is difficult for a central agency to determine an appropriate level of conservation action. This is because payment by results allows individual managers to optimise their level of action.

4. The relative cost of monitoring action (compliance with an agreement to manage in a certain way) versus results (the presence of biodiversity) has a substantial effect on which payment structure is more efficient only when the central agency can accurately set an appropriate level of action. We illustrate these principles with examples based on agri‐environment schemes.

5. Synthesis and applications. Payment by results deserves more attention from those designing biodiversity PES (be they agri‐environment schemes in agricultural landscapes or direct payment schemes in more intact ecosystems). This paper provides a formal framework to help policy makers identify the conditions under which payment by results or payment by action is most likely to yield cost‐effective biodiversity conservation.
Prioritising conservation areas using species surrogate measures: consistent with ecological theory?
Authors: Sætersdal Magne , Gjerde Ivar
Published: June 2011

1. Surrogate species measures of biodiversity (SSB) are used worldwide in conservation prioritisations. We address the important question whether the ideas behind SSB are consistent with current knowledge on distribution patterns of species, as reflected in theories of community assembly.

2. We investigated whether assumptions necessary for successful functioning of SSB (nested species assemblages, cross‐taxon congruence, spatio‐temporal consistency) were supported by predictions from either niche or neutral community models.

3. We found a general mismatch between ideas behind SSB and ecological community theory, except that SSB based on complementarity may be consistent with niche‐based theory when gradients in species composition are strong.

4. 
Synthesis and applications. The lack of a necessary scientific foundation may explain the disappointing results of empirical tests of SSB. We argue that site selection should be based on costs and opportunities within complementary environmental/land units, rather than expensive inventories of unfounded surrogate species.
Insights into Neogene Mediterranean biogeography based on phylogenetic relationships of mountain and lowland lineages of Narcissus (Amaryllidaceae)
Authors: Santos‐Gally Rocío , Vargas Pablo , Arroyo Juan
Published: June 2011

Aim  Our aims were: (1) to reconstruct the phylogenetic relationships of daffodils (Narcissus), focusing on the lowland subgenus Hermione and the mountain section Apodanthi; (2) to estimate the temporal setting of diversification; (3) to reconstruct the migration patterns of the lineages; and (4) to examine the microevolutionary differentiation of the wide‐ranging Narcissus tazetta group across the Mediterranean.

Location  The Mediterranean Basin.

Methods  Plastid (trnT–L, trnL–F and ndhF) sequences were obtained from 63 populations representing 23 species of Narcissus and combined with published data from 16 species. Phylogenetic relationships and dating were inferred by Bayesian analysis based on geological events and divergence estimates of closely related taxa. A dispersal–extinction–cladogenesis analysis was performed using maximum likelihood methods to infer ancestral geographical distributions, and phylogeographical reconstruction was performed using coalescence analysis.

Results  Subgenus Hermione is not recognized as a monophyletic group because two of the nine species were found to have a close relationship with the subgenus Narcissus. The results on section Apodanthi confirmed previous findings of its monophyly and phylogenetic relationships within this mountain group. Molecular dating and ancestral range reconstructions suggest that the ancestor of Narcissus originated in the Iberian Peninsula during the Late Oligocene–Early Miocene. Eastward expansion of the lineage range proceeded from the western Mediterranean and involved colonization of mountain ranges in northern Africa. The phylogeography of the N. tazetta group revealed a widespread distribution of certain haplotypes, suggesting wide dispersal and a high level of colonization in the Mediterranean Basin.

Main conclusions  Our study points to the role of three key historical events in Narcissus diversification: tectonic shifts of the Alboran domain in the western Mediterranean, the Messinian salinity crisis, and the onset of the Mediterranean climate followed by periods of repeated glaciation. Diversification of section Apodanthi probably resulted from allopatric speciation, while subgenus Hermione may have shown more sympatric speciation and high dispersal, despite the lack of apparent adaptations to long‐distance dispersal. This is best exemplified by the presence of both ancestral and recent haplotypes of N. tazetta across the Mediterranean.
Blueprint for a deliberative public forum on biobanking policy: were theoretical principles achievable in practice?
Authors: Molster Caron , Maxwell Susannah , Youngs Leanne , Kyne Gaenor , Hope Fiona , Dawkins Hugh , O’Leary Peter
Published: June 2011

Background:  Public deliberation is recommended for obtaining citizen input to policy development when policies involve contested ethical dimensions, diverse perspectives on how to trade‐off competing public interests and low public awareness of these perspectives. Several norms have been proposed for the design of deliberative methods. Evidence is scarce regarding whether such norms are achievable in practice.

Purpose:  This paper refers to principles of deliberative democracy theory to describe a deliberative public forum on biobanking. Practical challenges and contextual facilitators of achieving deliberative ideals are discussed, along with factors that influenced use of the forum output in policy development.

Method:  The forum ran for 4 days over two weekends in Perth, Western Australia. Key methodological features were socio‐demographic stratification to randomly recruit a mini‐public of citizens for discursive representation, provision of information inclusive of diverse perspectives and framed for difference, provision of a fair way for reasoning and collective decision making and adoption of processes to achieve publicity, accountability and independence from undue institutional influence.

Results:  Most design principles were achieved in practice, with the fundamental exception of representativeness. Factors influencing these outcomes, and the use of deliberated outputs to develop policy, included institutional characteristics, the design involvement of deliberative experts and quality of the outputs when compared to other consultation methods.

Conclusions:  Public deliberations can achieve design ideals and influence (ethics‐based) public health policy. The representation of ‘hard to reach’ citizens and their views needs further consideration, particularly as this relates to the procedural legitimacy of ethical analyses and the just inclusion of deliberative citizen advice within the broader policy‐making process.
HLA‐B35 correlates with a favorable outcome following adjuvant administration of an HLA‐matched allogeneic melanoma vaccine
Authors: Lotem M. , Kadouri L. , Merims S. , Ospovat I. , Nissan A. , Ron I. , Frankenburg S. , Machlenkin A. , Israel S. , Steinberg H. , Hamburger T. , Peretz T.
Published: June 2011

This work presents survival data of 42 melanoma patients at high risk for disease recurrence who received an allogeneic melanoma vaccine composed of three cell lines, each matching at least one allele of the recipient's human leukocyte antigen (HLA)‐A and ‐B loci. The 5‐year overall survival (OS) rate and disease‐free survival (DFS) compared favorably with the standard interferon‐α regimen. Interestingly, patients bearing HLA‐B35 had significantly better OS and DFS (OS of 100% and DFS of 90% for HLA‐B35 vs 56% and 23%, for the non‐B35 patients). In contrast, patients expressing HLA‐B07 did not fare well with the vaccine. Although the data include a relatively small cohort of patients, it strongly hints toward a correlation between HLA types and potential benefit from anticancer immunotherapy.
Massive icebergs, alteration in primary food resources and change in benthic communities at Cape Evans, Antarctica
Authors: Thrush Simon F. , Cummings Vonda J.
Published: June 2011

The presence of massive icebergs in the Southwestern Ross Sea (Antarctica) in the early‐to‐mid‐2000s changed the regional sea ice regime and phytoplankton productivity. We exploit data on benthic macro‐ and megafaunal communities collected on six occasions between 2001 and 2009 in the shallow waters adjacent to Cape Evans to link these oceanographic shifts to changes in benthic ecology. Changes in the abundance of individual species and community composition were generally strongest, and mostly negative, in 2002 and 2003, which exhibited the largest decrease in water column productivity and thick and persistent sea ice. This pattern of decreasing numbers from the start of sampling in 2001 to the lowest values in 2003 is consistent with the impact of the icebergs and a lagged response on the part of the benthic populations in response to food shortage. The patterns of stronger effects on macrofauna than on megafauna, and on abundance rather than species richness, are consistent with a change in food supply and/or recruitment for short‐lived species, rather than a physical disturbance effect. Nevertheless, recovery patterns are likely to reflect changes in benthic communities associated with larval supply and changes in top‐down control after the years of predicted lowest food supply. There are many potential manifestations of climate change in Antarctica, and many of the ecological responses to environmental change are likely to be mediated through the foodweb. Long‐term studies in different locations are essential if we are to understand and forecast changes in sea‐floor ecosystems.
Identification of two portal vein tumor thrombosis associated proteins in hepatocellular carcinoma: Protein disulfide‐isomerase A6 and apolipoprotein A‐I
Authors: Xu Xiao , Wei Xuyong , Ling Qi , Cheng Jun , Zhou Bin , Xie Haiyang , Zhou Lin , Zheng Shusen
Published: June 2011

Background and Aim:  Portal vein tumor thrombus (PVTT) is one of the factors that can affect prognosis and survival of hepatocellular carcinoma (HCC). In the present study, we aimed to find out some biomarkers associated with vascular invasion features of HCC with the method of comparative proteomic analysis.

Methods:  The proteins were extracted from a pair of HCC tissues with PVTT and without PVTT, and then separated by two‐dimensional polyacrylamide gel electrophoresis. Differentially expressed protein spots were identified by matrix assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Further analysis of two proteins were completed using real‐time fluorescence quantitative polymerase chain reaction and western‐blot in 40 HCC tissues with PVTT (n = 20) and without PVTT (n = 20).

Results:  Among 465 protein spots displayed on the gels, 33 unique proteins (> twofold change, P < 0.01) were identified, including 24 upregulated in HCC tissue without PVTT and nine upregulated in HCC tissue with PVTT. The real‐time fluorescence quantitative PCR showed no statistically significant difference between HCC tissues with PVTT and without PVTT for mRNA expressions of protein disulfide‐isomerase, A6 (PDI A6) (P = 0.137) and apolipoprotein A‐I (Apo A‐I) (P = 0.718). However, compared with HCC tissues without PVTT, protein expression of PDI A6 was higher in HCC tissues with PVTT (P < 0.001), while protein expression of Apo A‐I was lower in HCC tissues with PVTT (P = 0.012).

Conclusions:  PDI A6 and Apo A‐I are closely related to vascular invasion feature of HCC.
Variation in human genetic polymorphisms, their association with Helicobacter pylori acquisition and gastric cancer in a multi‐ethnic country
Authors: Schmidt Heather‐Marie A , Ha Dung Mai , Taylor Elizabeth F , Kovach Zsuzsanna , Goh Khean‐Lee , Fock Kwong Ming , Barrett Jennifer H , Forman David , Mitchell Hazel
Published: June 2011

Background and Aim:  The contribution of human genetic polymorphisms to Helicobacter pylori infection and gastric cancer (GC) development remains unclear due to geographic variation in the association between specific host genetic polymorphisms and GC. In the current study we investigated the association between polymorphisms related to immune and cancer‐related pathways and H. pylori infection among the major ethnicities, Chinese, Malay and Indian, resident in Singapore and Malaysia as well as the association between these polymorphisms and GC development in ethnic Chinese patients.

Methods:  Thirty‐four polymorphisms in 26 genes were typed by mass spectrometry in 422 patients undergoing endoscopy (162 Chinese, 113 Indian and 87 Malay controls and 60 Chinese GC cases). Patients were assessed for evidence of H. pylori infection. Odds ratios (OR) and confidence intervals (CI) were obtained using logistic regression models.

Result:  The prevalence of 16 polymorphisms varied significantly among the ethnicities. In the Chinese subgroup, nominally significant associations were shown between (i) EBBR2+1963G (rs1801200) and H. pylori infection (per‐allele OR: 0.48, 95% CI 0.23, 0.98, P = 0.04), (ii) PTGS2‐1195G (rs689466) and an increased risk of GC on adjusting for H. pylori status (OR: 1.53, 95% CI 0.99, 2.37, P = 0.05), and (iii) IL1B‐1473C (rs1143623) and a decreased risk of GC (OR: 0.64, 95% CI 0.41, 0.99, P = 0.05). Borderline significant associations were seen between IL2‐330G (rs2069762) (OR 1.45, 95% CI 0.95, 2.15, P = 0.06) and IL13‐1111T (rs1800925) (OR 0.65, 95% CI 0.42, 1.01, P = 0.06) and H. pylori infection.

Conclusion:  These findings contribute to the understanding of the genetic variation between ethnicities, which may influence H. pylori susceptibility and the outcome of infection.
Helicobacter pylori induces promoter hypermethylation and downregulates gene expression of IRX1 transcription factor on human gastric mucosa
Authors: Guo Xiao Bo , Guo Lei , Zhi Qiao Ming , Ji Jun , Jiang Jin Ling , Zhang Rong Juan , Zhang Jia Nian , Zhang Jun , Chen Xue Hua , Cai Qu , Li Jian Fang , Yan Min , Gu Qin Long , Liu Bing Ya , Zhu Zheng Gang , Yu Ying Yan
Published: June 2011

Background and Aim:  Gene silence of IRX1 tumor suppressor by promoter CpG methylation combined with loss of heterozygosity (LOH) has been identified in human gastric cancer. This study investigated the association between methylation of IRX1 and Helicobacter pylori infection in gastric mucosa tissues and cell line.

Methods:  IRX1 methylation was studied by methylation specific polymerase chain reaction (MSP) and bisulfate sequencing polymerase chain reaction (BSP) methods in gastric mucosa tissues from H. pylori‐positive chronic gastritis patients or H. pylori‐negative chronic gastritis patients. Promoter activity, methylation status and gene expressing level of IRX1 were evaluated by persistent infecting H. pylori on human gastric cells GES‐1 in vitro. Electron microscopy was used to observe the effect of H. pylori infection on GES‐1 gastric mucosa cells.

Results:  The methylation level of IRX1 promoter in H. pylori positive chronic gastritis and H. pylori negative chronic gastritis was 55.30% ± 13.17 versus 5.20% ± 6.31, respectively (P < 0.01). H. pylori infection stimulated increased microvillus, and mucous secretion on GES‐1 cells. Infection of H. pylori induced IRX1 promoter methylation and downregulation of the promoter activity as well as gene expression significantly.

Conclusions:  This study firstly demonstrated that H. pylori infection contributes to IRX1 promoter methylation on gastric mucosa.
Capital structure and business cycles
Authors: Akhtar Shumi
Published: June 2011

This study investigates the relationship between business cycles and capital structure. Specifically, it extends the work of Lemmon et al. (2008), by incorporating the effect of four different stages of the business cycle – peak, contraction, trough and expansion – on the relative importance of the unobserved permanent component of the capital structure. Results indicate that business cycles play an important role in explaining the unobserved permanent component of leverage ratios after controlling for firm fixed effects. In particular, the model becomes much stronger in explaining the variation in leverage ratios after accounting for business cycle phases.
Enhancing the expression of starch synthase class IV results in increased levels of both transitory and long‐term storage starch
Authors: Gámez‐Arjona Francisco M. , Li Jun , Raynaud Sandy , Baroja‐Fernández Edurne , Muñoz Francisco J. , Ovecka Miroslav , Ragel Paula , Bahaji Abdellatif , Pozueta‐Romero Javier , Mérida Ángel
Published: June 2011

Starch is an important renewable raw material with an increasing number of applications. Several attempts have been made to obtain plants that produce modified versions of starch or higher starch yield. Most of the approaches designed to increase the levels of starch have focused on the increment of the amount of ADP‐glucose or ATP available for starch biosynthesis. In this work, we show that the overexpression of starch synthase class IV (SSIV) increases the levels of starch accumulated in the leaves of Arabidopsis by 30%–40%. In addition, SSIV‐overexpressing lines display a higher rate of growth. The increase in starch content as a consequence of enhanced SSIV expression is also observed in long‐term storage starch organs such as potato tubers. Overexpression of SSIV in potato leads to increased tuber starch content on a dry weight basis and to increased yield of starch production in terms of tons of starch/hectare. These results identify SSIV as one of the regulatory steps involved in the control of the amount of starch accumulated in plastids.
Discovery of polymorphisms in starch‐related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing†
Authors: Kharabian‐Masouleh Ardashir , Waters Daniel L. E. , Reinke Russell F. , Henry Robert J.
Published: June 2011

High‐throughput sequencing of pooled DNA was applied to polymorphism discovery in candidate genes involved in starch synthesis. This approach employed semi‐ to long‐range PCR (LR‐PCR) followed by next‐generation sequencing technology. A total of 17 rice starch synthesis genes encoding seven classes of enzymes, including ADP‐glucose pyrophosphorylase (AGPase), granule starch synthase (GBSS), soluble starch synthase (SS), starch branching enzyme (BE), starch debranching enzyme (DBE) and starch phosphorylase (SPHOL) and phosphate translocator (GPT1) from 233 genotypes were PCR amplified using semi‐ to long‐range PCR. The amplification products were equimolarly pooled and sequenced using massively parallel sequencing technology (MPS). By detecting single nucleotide polymorphism (SNP)/Indels in both coding and noncoding areas of the genes, we identified genetic differences and characterized the SNP/Indel variation and distribution patterns among individual starch candidate genes. Approximately, 60.9 million reads were generated, of which 54.8 million (90%) mapped to the reference sequences. The average coverage rate ranged from 12 708 to 38 300 times for SSIIa and SSIIIb, respectively. SNPs and single/multiple‐base Indels were analysed in a total assembled length of 116 403 bp. In total, 501 SNPs and 113 Indels were detected across the 17 starch‐related loci. The ratio of synonymous to nonsynonymous SNPs (Ka/Ks) test indicated GBSSI and isoamylase 1 (ISA1) as the least diversified (most purified) and conservative genes as the studied populations have been through cycles of selection. This report demonstrates a useful strategy for screening germplasm by MPS to discover variants in a specific target group of genes.
A Dynamic Route Choice Model Considering Uncertain Capacities
Authors: Ng ManWo , Waller S. Travis
Published: June 2011

Abstract:  The standard assumption in (dynamic) traffic assignment models is that route choice is solely determined by a (perceived) deterministic travel time. However, recently, there is a growing interest in (dynamic) equilibrium route choice models in which travelers not only select their paths based on an estimated deterministic travel time, but also based on travel time reliability, in this article defined as the probability that the actual travel time deviates from the anticipated value. We extend the linear programming cell transmission model‐based dynamic traffic assignment (LP CTM‐DTA) model to account for travelers’ consideration of uncertainty regarding saturation flow rates (in this article referred to as capacities). It is shown that these reliability considerations can be accounted for by simply reducing the road capacities appearing in the constraint set of the classical LP CTM‐DTA model. More importantly, we provide results on the amount of capacity reduction necessary to ensure a certain reliability level. Although in the proposed model any probability distribution can be used to model the uncertainty, the selection of a specific probability distribution can potentially be burdensome for the modeler. To this end, we also present results on the class of symmetric probability distributions that has been particularly popular in the robust optimization literature. Properties for this broad class of distributions will be derived within the context of the introduced model. In numerical case studies, the model predicts that travel patterns can be significantly different when accounting for travelers’ reliability considerations.
Visualization of 3D osteon morphology by synchrotron radiation micro‐CT
Authors: Cooper D. M. L. , Erickson B. , Peele A.G. , Hannah K. , Thomas C. D. L. , Clement J. G.
Published: June 2011

Cortical bone histology has been the subject of scientific inquiry since the advent of the earliest microscopes. Histology – literally the study of tissue – is a field nearly synonymous with 2D thin sections. That said, progressive developments in high‐resolution X‐ray imaging are enabling 3D visualization to reach ever smaller structures. Micro‐computed tomography (micro‐CT), employing conventional X‐ray sources, has become the gold standard for 3D analysis of trabecular bone and is capable of detecting the structure of vascular (osteonal) porosity in cortical bone. To date, however, direct 3D visualization of secondary osteons has eluded micro‐CT based upon absorption‐derived contrast. Synchrotron radiation micro‐CT, through greater image quality, resolution and alternative contrast mechanisms (e.g. phase contrast), holds great potential for non‐destructive 3D visualization of secondary osteons. Our objective was to demonstrate this potential and to discuss areas of bone research that can be advanced through the application of this approach. We imaged human mid‐femoral cortical bone specimens derived from a 20‐year‐old male (Melbourne Femur Collection) at the Advanced Photon Source synchrotron (Chicago, IL, USA) using the 2BM beam line. A 60‐mm distance between the target and the detector was employed to enhance visualization of internal structures through propagation phase contrast. Scan times were 1 h and images were acquired with 1.4‐μm nominal isotropic resolution. Computer‐aided manual segmentation and volumetric 3D rendering were employed to visualize secondary osteons and porous structures, respectively. Osteonal borders were evident via two contrast mechanisms. First, relatively new (hypomineralized) osteons were evident due to differences in X‐ray attenuation relative to the surrounding bone. Second, osteon boundaries (cement lines) were delineated by phase contrast. Phase contrast also enabled the detection of soft tissue remnants within the vascular pores. The ability to discern osteon boundaries in conjunction with vascular and cellular porosity revealed a number of secondary osteon morphologies and provided a unique 3D perspective of the superimposition of secondary osteons on existing structures. Improvements in resolution and optimization of the propagation phase contrast promise to provide further improvements in structural detail in the future.
Introduction to a Virtual Special Issue on plant respiration in variable environments
Authors: Atkin Owen K.
Published: June 2011

Link to the Virtual Special Issue
Scan patterns when viewing natural scenes: Emotion, complexity, and repetition
Authors: Bradley Margaret M. , Houbova Petra , Miccoli Laura , Costa Vincent D. , Lang Peter J.
Published: June 2011

Eye movements were monitored during picture viewing, and effects of hedonic content, perceptual composition, and repetition on scanning assessed. InExperiment 1, emotional and neutral pictures that were figure‐ground compositions or more complex scenes were presented for a 6‐s free viewing period. Viewing emotional pictures or complex scenes prompted more fixations and broader scanning of the visual array, compared to neutral pictures or simple figure‐ground compositions. Effects of emotion and composition were independent, supporting the hypothesis that these oculomotor indices reflect enhanced information seeking.Experiment 2tested an orienting hypothesis by repeatedly presenting the same pictures. Although repetition altered specific scan patterns, emotional, compared to neutral, picture viewing continued to prompt oculomotor differences, suggesting that motivationally relevant cues enhance information seeking in appetitive and defensive contexts.
The local universality of veterinary expertise and the geography of animal disease
Authors: Enticott Gareth
Published: June 2011

This paper explores the concept of local universality in relation to the regulation of animal health. Protocols have come to play an important role in medical practice, standardising diseases and the expertise required to identify them. Focusing on the use of protocols to identify bovine tuberculosis (bTB) in England and Wales, it is argued that the decontextualised expertise inherent to protocols comes unstuck in practice. Using ethnographies of two veterinary practices, the paper instead shows how forms of situated veterinary expertise emerge in response to practical contingencies, thereby enacting different ontological versions of bTB. The development of these skills stems from the relationships that organise bTB testing as well as through informal work‐based modes of learning. Although these practices vary from place to place and depart from the bTB testing protocol, it is variation in practice rather than uniformity that effectively allows the protocol to work. In conclusion, the paper discusses how the management of animal health may be assisted by a flexible rather than uniform approach to disease and veterinary expertise.
Human geography without time‐space1
Authors: Merriman Peter
Published: June 2011

In this paper I challenge the obsession of many Anglophone human geographers with time‐space and space‐time. While acknowledging that spacing and timing are important dimensions of the unfolding of many events, I question the logic of positioning them as the primordial, foundational, a priori measures for thinking about events, position, extension and context, and I suggest that their prioritisation reflects the continuing power of space and time as concepts in both classical and modern science and significant strands of philosophy. The paper traces how space and time have increasingly been thought together by human geographers since the late 1960s, examining how discussions of time‐space and space‐time have underpinned the writings of thinkers such as Torsten Hägerstrand, Nigel Thrift, Anthony Giddens, David Harvey and Doreen Massey. The paper draws upon strands of processual, poststructuralist and post‐phenomenological thinking in an attempt to map out a different way of thinking about the unfolding of events, in which spacing and timing should not be seen a priori to be any more important than other constitutive measures – e.g. movement, rhythm, force, energy, affect or sensation – in the unfolding and turbulence of the world. The paper then describes how certain practices like driving and dancing may be characterised by an apprehension and inhabitation of movement‐space rather than space‐time.
Calcitonin and calcitonin receptor‐like receptors: common themes with family B GPCRs?
Authors: Barwell James , Gingell Joseph J , Watkins Harriet A , Archbold Julia K , Poyner David R , Hay Debbie L
Published: June 2011

The calcitonin receptor (CTR) and calcitonin receptor‐like receptor (CLR) are two of the 15 human family B (or Secretin‐like) GPCRs. CTR and CLR are of considerable biological interest as their pharmacology is moulded by interactions with receptor activity‐modifying proteins. They also have therapeutic relevance for many conditions, such as osteoporosis, diabetes, obesity, lymphatic insufficiency, migraine and cardiovascular disease. In light of recent advances in understanding ligand docking and receptor activation in both the family as a whole and in CLR and CTR specifically, this review reflects how applicable general family B GPCR themes are to these two idiosyncratic receptors. We review the main functional domains of the receptors; the N‐terminal extracellular domain, the juxtamembrane domain and ligand interface, the transmembrane domain and the intracellular C‐terminal domain. Structural and functional findings from the CLR and CTR along with other family B GPCRs are critically appraised to gain insight into how these domains may function. The ability for CTR and CLR to interact with receptor activity‐modifying proteins adds another level of sophistication to these receptor systems but means careful consideration is needed when trying to apply generic GPCR principles. This review encapsulates current thinking in the realm of family B GPCR research by highlighting both conflicting and recurring themes and how such findings relate to two unusual but important receptors, CTR and CLR.

LINKED ARTICLES This article is part of a themed section on Secretin Family (Class B) G Protein‐Coupled Receptors. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.166.issue‐1
Rapid healing of chronic venous stasis leg ulcers treated by the application of a novel serum‐free cultured autologous epidermis
Authors: Wille John J. , Burdge Jeremy J. , Pitttelkow Mark R.
Published: June 2011

The efficacy and durability of wound closure was examined in a prospective randomized unbalanced clinical trial using the application of a living serum‐free cultured epidermal autograft in conjunction with wound‐area debridement and a four‐layer compression wrap (N=10) compared with wound‐area debridement and a four‐layer compression wrap in patients with hard‐to‐heal leg ulcers arising from confirmed venous stasis (N=5). All 15 patients who presented with full‐thickness venous ulceration were treated weekly for 8 weeks, with a 12‐week final evaluation. The average time to wound closure for the grafted wounds was 4.1 weeks for 80% (8/10) of the cases that closed in 12 weeks compared with 12 weeks for the one closed in the control case. All of the grafted wounds remained closed at 12‐month follow‐up and one more healed at 30 weeks postenrollment. In the control group, one additional wound healed at 21 weeks postenrollment after the placement of an autograft. No serious adverse events were reported and subjective pain assessment was substantially reduced immediately after graft application. The graft treatment significantly improved outcome and provided durable wound closure. The data suggest that this adaption of this procedure may reduce the management costs of these wound types.
Enhancement of flap survival and changes in angiogenic gene expression after AAV2‐mediated VEGF gene transfer to rat ischemic flaps
Authors: Wang Xiao Tian , Avanessian Bella , Ma Qiangzhong , Durfee Heather , Tang Yu Qing , Liu Paul Y.
Published: June 2011

Necrosis of surgically transferred flaps due to ischemia is a serious wound problem. We evaluated the improvement of flap survival and changes in angiogenic gene expression profiles after transfer of the VEGF gene by means of adeno‐associated virus type 2 (AAV2) vector to rat ischemic flaps. Thirty rats were divided into one experimental group, one AAV2‐GFP group, and one saline group. AAV2‐VEGF or AAV2‐GFP were injected intradermally into the rat dorsum in the AAV2‐VEGF or AAV2‐GFP group. The saline group received saline injection. A 3 × 10 cm flap was raised in each rat two weeks post‐injection. One week after surgery, flap viability was evaluated. Angiogenesis real‐time PCR array was performed to analyze the expression of angiogenesis‐associated genes. The AAV2‐VEGF treatment significantly improved flap survival (p<0.05). Immunohistochemical staining showed increased VEGF expression in AAV2‐VEGF treated flaps. The PCR array identified remarkable changes in 6 out of the 84 angiogenesis‐associated genes in AAV2‐VEGF treated flaps. Particularly, EGF, PDGF‐A and VEGF‐B genes were up‐regulated in these flaps. In contrast, FGF2 gene expression was down‐regulated. In conclusion, AAV2‐VEGF improves flap survival and affects the expression of a series of endogenous growth factor genes, which likely play critical roles in the enhancement of ischemic flap survival.
Associations Between Early Life Stress, Child Maltreatment, and Pubertal Development Among Girls in Foster Care
Authors: Mendle Jane , Leve Leslie D. , Van Ryzin Mark , Natsuaki Misaki N. , Ge Xiaojia
Published: June 2011

The present study investigated pubertal development in girls with maltreatment histories (N=100), assessed at 4 time points over 2 years, beginning in the spring of their final year of elementary school. This sample is unique in that participants were subject to an unusual level of environmental risk early in life and resided in foster care at the start of the study. Analyses replicated the previously established association between sexual abuse and earlier onset of maturation and earlier age at menarche. Physical abuse was related to a more rapid tempo of pubertal development across the period assessed. These results strengthen previous investigations of childhood maltreatment and puberty, highlighting the complexity and specificity of early life experiences for later development.
Risk Taking in Late Adolescence: Relations Between Sociomoral Reasoning, Risk Stance, and Behavior
Authors: Shaw Leigh A. , Amsel Eric , Schillo Joshua
Published: June 2011

This study explored relations among late adolescents' sociomoral reasoning about risk taking, risk stance, and behavior. One‐hundred and thirty‐two participants (18–20‐year‐olds) were surveyed about their own risk stance (Avoidant, Opportunistic, Curious, Risk Seeking) and behavior in three realms (Alcohol Use, Drug Use, Reckless Driving), and sociomoral reasoning about hypothetical risk taking in a baseline scenario with no social domain information and a final scenario that highlighted the moral (i.e., harmful consequences for others), conventional (i.e., sociolegal consequences), personal (i.e., personal prerogative), and prudential (i.e., harmful consequences for self) domains bearing on risk taking. The complex relations among sociomoral reasoning about risk taking, risk stance, and behavior are discussed in terms of social domain theory and dual‐process theories of risk taking.