bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of daily- and annual- increment counts in otoliths of bigeye (Thunnus obesus), yellowfin (T. albacares), southern bluefin (T. maccoyii) and albacore (T. alalunga) tuna
Authors: Williams Ashley J. , Leroy Bruno M. , Nicol Simon J. , Farley Jessica H. , Clear Naomi P. , Krusic-Golub Kyne , Davies Campbell R.
Published: August 2013

Williams, A. J., Leroy, B. M., Nicol, S. J., Farley, J. H., Clear, N. P., Krusic-Golub, K., and Davies, C. R. Comparison of daily- and annual-increment counts in otoliths of bigeye (Thunnus obesus), yellowfin (T. albacares), southern bluefin (T. maccoyii) and albacore (T. alalunga) tuna. – ICES Journal of Marine Science, 70: . Information on the age of individuals is often required for models assessing the status of stocks. Techniques used to estimate age of tuna have varied across species and agencies, precluding meta-analyses of age and growth. We compared age estimates obtained from commonly used ageing techniques for four important tuna species: bigeye tuna, yellowfin tuna, southern bluefin tuna, and albacore tuna. Estimates of age from counts of annual increments in transverse-sectioned otoliths were generally higher than those from counts of daily increments in transverse and longitudinal sections for all species, particularly for fish older than two years. However, annual counts produced younger estimates, on average, relative to daily counts for bigeye and yellowfin tuna younger than one year. Estimates derived from daily increments in longitudinal and transverse sections were generally similar, although longitudinal sections produced relatively older age estimates for individuals older than two years. A linear or non-linear increase in the magnitude of differences between ageing methods was the best-approximating model in all cases except when comparing daily-increment counts between transverse and longitudinal otolith sections for southern bluefin tuna. These observations are consistent with a narrowing of daily increments with increasing age, resulting in underestimates of age relative to those derived from annual increments. We conclude that (i) daily increments are unsuitable for ageing individuals over two years, especially for southern bluefin and albacore, (ii) longitudinal sections are more precise and produce older age estimates than transverse sections for daily-age estimates, (iii) there are considerable differences in these trends between species, likely dependent on longevity, and (iv) parameter estimates and/or conclusions based on meta-analyses using age data derived from different ageing methods are likely confounded with methodological biases. This result demonstrates that greater effort is required to provide consistent, validated methods for routine age determination to support the assessment and management of these valuable populations.
Androgen changes and flexible rutting behaviour in male giraffes
Authors: Seeber Peter A. , Duncan Patrick , Fritz Hervé , Ganswindt André
Published: August 2013

The social organization of giraffes (Giraffa camelopardalis) imposes a high-cost reproductive strategy on bulls, which adopt a ‘roving male’ tactic. Our observations on wild giraffes confirm that bulls indeed have unsynchronized rut-like periods, not unlike another tropical megaherbivore, the elephant, but on a much shorter timescale. We found profound changes in male sexual and social activities at the scale of about two weeks. This so far undescribed rutting behaviour is closely correlated with changes in androgen concentrations and appears to be driven by them. The short time scale of the changes in sexual and social activity may explain why dominance and reproductive status in male giraffe in the field seem to be unstable.
Respiratory control in aquatic insects dictates their vulnerability to global warming
Authors: Verberk Wilco C. E. P. , Bilton David T.
Published: August 2013

Forecasting species responses to climatic warming requires knowledge of how temperature impacts may be exacerbated by other environmental stressors, hypoxia being a principal example in aquatic systems. Both stressors could interact directly as temperature affects both oxygen bioavailability and ectotherm oxygen demand. Insufficient oxygen has been shown to limit thermal tolerance in several aquatic ectotherms, although, the generality of this mechanism has been challenged for tracheated arthropods. Comparing species pairs spanning four different insect orders, we demonstrate that oxygen can indeed limit thermal tolerance in tracheates. Species that were poor at regulating oxygen uptake were consistently more vulnerable to the synergistic effects of warming and hypoxia, demonstrating the importance of respiratory control in setting thermal tolerance limits.
The Pyrexia transient receptor potential channel mediates circadian clock synchronization to low temperature cycles in
Drosophila melanogaster
Authors: Wolfgang Werner , Simoni Alekos , Gentile Carla , Stanewsky Ralf
Published: August 2013

Circadian clocks are endogenous approximately 24 h oscillators that temporally regulate many physiological and behavioural processes. In order to be beneficial for the organism, these clocks must be synchronized with the environmental cycles on a daily basis. Both light : dark and the concomitant daily temperature cycles (TCs) function as
Zeitgeber
(‘time giver’) and efficiently entrain circadian clocks. The temperature receptors mediating this synchronization have not been identified. Transient receptor potential (TRP) channels function as thermo-receptors in animals, and here we show that the Pyrexia (Pyx) TRP channel mediates temperature synchronization in
Drosophila melanogaster
. Pyx is expressed in peripheral sensory organs (chordotonal organs), which previously have been implicated in temperature synchronization. Flies deficient for Pyx function fail to synchronize their behaviour to TCs in the lower range (16–20°C), and this deficit can be partially rescued by introducing a wild-type copy of the
pyx
gene. Synchronization to higher TCs is not affected, demonstrating a specific role for Pyx at lower temperatures. In addition,
pyx
mutants speed up their clock after being exposed to TCs. Our results identify the first TRP channel involved in temperature synchronization of circadian clocks.
Tracking multi-generational colonization of the breeding grounds by monarch butterflies in eastern North America
Authors: Flockhart D. T. Tyler , Wassenaar Leonard I. , Martin Tara G. , Hobson Keith A. , Wunder Michael B. , Norris D. Ryan
Published: August 2013

Insect migration may involve movements over multiple breeding generations at continental scales, resulting in formidable challenges to their conservation and management. Using distribution models generated from citizen scientist occurrence data and stable-carbon and -hydrogen isotope measurements, we tracked multi-generational colonization of the breeding grounds of monarch butterflies (
Danaus plexippus
) in eastern North America. We found that monarch breeding occurrence was best modelled with geographical and climatic variables resulting in an annual breeding distribution of greater than 12 million km
2
that encompassed 99% occurrence probability. Combining occurrence models with stable isotope measurements to estimate natal origin, we show that butterflies which overwintered in Mexico came from a wide breeding distribution, including southern portions of the range. There was a clear northward progression of monarchs over successive generations from May until August when reproductive butterflies began to change direction and moved south. Fifth-generation individuals breeding in Texas in the late summer/autumn tended to originate from northern breeding areas rather than regions further south. Although the Midwest was the most productive area during the breeding season, monarchs that re-colonized the Midwest were produced largely in Texas, suggesting that conserving breeding habitat in the Midwest alone is insufficient to ensure long-term persistence of the monarch butterfly population in eastern North America.
Environmental levels of oestrogenic and antiandrogenic compounds feminize digit ratios in male rats and their unexposed male progeny
Authors: Auger Jacques , Le Denmat Dominique , Berges Raymond , Doridot Ludivine , Salmon Benjamin , Canivenc-Lavier Marie Chantal , Eustache Florence
Published: August 2013

Digit length ratios, especially the second-to-fourth digit ratio (2D : 4D), are associated with various pathological and behavioural conditions in many species including humans and are dependent upon prenatal androgen to oestrogen balance. It is unknown whether digit ratios are modified by environmental exposure to ubiquitous endocrine disruptors
.
We studied the effect on adult male
Wistar
rat digit ratios of a gestational exposure to the oestrogenic and antiandrogenic compounds bisphenol A (BPA), genistein and vinclozolin, in low doses, and in combination with investigating in parallel a possible sexual dimorphism of this trait. We also investigated the effects on the male progeny not exposed during gestation. X-rays were taken of the left and right forepaws, and 2D–5D proximal to distal phalanx distances were measured by a standardized procedure based on semi-automatic image analysis. We provide evidence that there is a sexual dimorphism of digit ratios in the
Wistar
rat, and we found that BPA alone or in combination with genistein and vinclozolin significantly feminized digit ratios in male rats. Intriguingly, significant feminization of digit ratios was also found in the unexposed male progeny of males that had been exposed to compound mixtures. In conclusion, prenatal environmental levels of endocrine-active substances permanently disrupt digit ratios. Digit ratio measurement in adults is thus a promising biomarker of prenatal exposure to low-dose endocrine disruptors in rodents, with potential implications for future studies in humans.
A restatement of the natural science evidence base relevant to the control of bovine tuberculosis in Great Britain
†
Authors: Godfray H. Charles J. , Donnelly Christl A. , Kao Rowland R. , Macdonald David W. , McDonald Robbie A. , Petrokofsky Gillian , Wood James L. N. , Woodroffe Rosie , Young Douglas B. , McLean Angela R.
Published: August 2013

Bovine tuberculosis (bTB) is a very important disease of cattle in Great Britain, where it has been increasing in incidence and geographical distribution. In addition to cattle, it infects other species of domestic and wild animals, in particular the European badger (
Meles meles
). Policy to control bTB is vigorously debated and contentious because of its implications for the livestock industry and because some policy options involve culling badgers, the most important wildlife reservoir. This paper describes a project to provide a succinct summary of the natural science evidence base relevant to the control of bTB, couched in terms that are as policy-neutral as possible. Each evidence statement is placed into one of four categories describing the nature of the underlying information. The evidence summary forms the appendix to this paper and an annotated bibliography is provided in the electronic supplementary material.
Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring
Authors: Liu You-Cheng , Young Li-Sen , Lin Shih-Yao , Hameed Asif , Hsu Yi-Han , Lai Wei-An , Shen Fo-Ting , Young Chiu-Chung
Published: August 2013

An aerobic, Gram-stain-negative, rod-shaped bacterium (designated strain CC-G9AT), motile by a polar-flagellum, was isolated from a hot spring water sample in Taiwan. Strain CC-G9ATcould grow at 20–42 °C, pH 6.0–10.0 and tolerate up to 7 % (w/v) NaCl. The 16S rRNA gene sequence analysis of strain CC-G9ATshowed pairwise sequence similarity toPseudomonas mendocinaLMG 1223T(97.7 %),Pseudomonas alcaligenesATCC 14909T(97.8 %),Pseudomonas alcaliphilaDSM 17744T(97.8 %),Pseudomonas toyotomiensisJCM 15604T(97.6 %),Pseudomonas oleovoranssubsp.lubricantisDSM 21016T(97.6 %) andPseudomonas argentinensisBCRC 17807T(97.5 %), and lower sequence similarity to other species of the genusPseudomonas. According to DNA–DNA association analysis, the relatedness of strain CC-G9ATtoP. mendocinaBCRC 10458T,P. alcaliphilaDSM 17744T,P. alcaligenesBCRC 11893T,P. oleovoranssubsp.lubricantisDSM 21016T,P. argentinensisBCRC 17807TandP. oleovoranssubsp.oleovoransBCRC 11902 was 55.1±3.1, 13.7±1.5, 14.1±1.8, 58.5±1.1, 28.9±2.0 and 28.6±1.8 %, respectively. The evolutionary trees reconstructed based on 16S rRNA,gyrBandrpoBgene sequences revealed varying phylogenetic neighbourhoods of strain CC-G9ATwith regard to the most closely related type strains. The predominant quinone system was ubiquinone (Q-9) and the DNA G+C content was 64.3±1.3 mol%. The major fatty acids were C10 : 03-OH, C12 : 0,C12 : 03-OH, C16 : 0and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6cand C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-G9ATis proposed to represent a novel species within the genusPseudomonasfor which the namePseudomonas guguanensissp. nov. is proposed. The type strain is CC-G9AT( = BCRC 80438T = JCM 18416T).
Efficient identification of Y chromosome sequences in the human and Drosophila genomes
Authors: Carvalho Antonio Bernardo , Clark Andrew G.
Published: August 2013

Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unmapped scaffolds. Identification of Y-linked genes among these fragments has yielded important insights about the origin and evolution of Y chromosomes, but the process is labor intensive, restricting studies to a small number of species. Apart from these fragmentary assemblies, in a few mammalian species, the euchromatic sequence of the Y is essentially complete, owing to painstaking BAC mapping and sequencing. Here we use female short-read sequencing and k-mer comparison to identify Y-linked sequences in two very different genomes, Drosophila virilis and human. Using this method, essentially all D. virilis scaffolds were unambiguously classified as Y-linked or not Y-linked. We found 800 new scaffolds (totaling 8.5 Mbp), and four new genes in the Y chromosome of D. virilis, including JYalpha, a gene involved in hybrid male sterility. Our results also strongly support the preponderance of gene gains over gene losses in the evolution of the Drosophila Y. In the intensively studied human genome, used here as a positive control, we recovered all previously known genes or gene families, plus a small amount (283 kb) of new, unfinished sequence. Hence, this method works in large and complex genomes and can be applied to any species with sex chromosomes.
Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
Authors: Mogno Ilaria , Kwasnieski Jamie C. , Cohen Barak A.
Published: August 2013

Gene promoters typically contain multiple transcription factor binding sites (TFBSs), which may vary in affinity for their cognate transcription factors (TFs). One major challenge in studying cis-regulation is to understand how TFBS variants affect gene expression. We studied the in vivo effects of TFBS variants on cis-regulation using synthetic promoters coupled with a thermodynamic model of TF binding. We measured expression driven by each promoter with RNA-seq of transcribed sequence barcodes. This allowed reporter genes to be highly multiplexed and increased our statistical power to detect the effects of TFBS variants. We analyzed the effects of TFBS variants using a thermodynamic framework that models both TF-DNA interactions and TF-TF interactions. We found that this system accurately estimates the in vivo relative affinities of TFBSs and predicts unexpected interactions between several TFBSs. Our results reveal that binding site variants can have complex effects on gene expression due to differences in TFBS affinity for cognate TFs and differences in TFBS specificity for noncognate TFs.
Calcium-Dependent Protein Kinase CPK6 Positively Functions in Induction by Yeast Elicitor of Stomatal Closure and Inhibition by Yeast Elicitor of Light-Induced Stomatal Opening in Arabidopsis
Authors: Ye Wenxiu , Muroyama Daichi , Munemasa Shintaro , Nakamura Yoshimasa , Mori Izumi C. , Murata Yoshiyuki
Published: August 2013

Yeast elicitor (YEL) induces stomatal closure that is mediated by a Ca2+-dependent signaling pathway. A Ca2+-dependent protein kinase, CPK6, positively regulates activation of ion channels in abscisic acid and methyl jasmonate signaling, leading to stomatal closure in Arabidopsis (Arabidopsis thaliana). YEL also inhibits light-induced stomatal opening. However, it remains unknown whether CPK6 is involved in induction by YEL of stomatal closure or in inhibition by YEL of light-induced stomatal opening. In this study, we investigated the roles of CPK6 in induction by YEL of stomatal closure and inhibition by YEL of light-induced stomatal opening in Arabidopsis. Disruption of CPK6 gene impaired induction by YEL of stomatal closure and inhibition by YEL of light-induced stomatal opening. Activation by YEL of nonselective Ca2+-permeable cation channels was impaired in cpk6-2 guard cells, and transient elevations elicited by YEL in cytosolic-free Ca2+ concentration were suppressed in cpk6-2 and cpk6-1 guard cells. YEL activated slow anion channels in wild-type guard cells but not in cpk6-2 or cpk6-1 and inhibited inward-rectifying K+ channels in wild-type guard cells but not in cpk6-2 or cpk6-1. The cpk6-2 and cpk6-1 mutations inhibited YEL-induced hydrogen peroxide accumulation in guard cells and apoplast of rosette leaves but did not affect YEL-induced hydrogen peroxide production in the apoplast of rosette leaves. These results suggest that CPK6 positively functions in induction by YEL of stomatal closure and inhibition by YEL of light-induced stomatal opening in Arabidopsis and is a convergent point of signaling pathways for stomatal closure in response to abiotic and biotic stress.
Thylakoid Membrane Maturation and PSII Activation Are Linked in Greening Synechocystis sp. PCC 6803 Cells
Authors: Barthel Sandra , Bernát Gábor , Seidel Tobias , Rupprecht Eva , Kahmann Uwe , Schneider Dirk
Published: August 2013

Thylakoid membranes are typical and essential features of both chloroplasts and cyanobacteria. While they are crucial for phototrophic growth of cyanobacterial cells, biogenesis of thylakoid membranes is not well understood yet. Dark-grown Synechocystis sp. PCC 6803 cells contain only rudimentary thylakoid membranes but still a relatively high amount of phycobilisomes, inactive photosystem II and active photosystem I centers. After shifting dark-grown Synechocystis sp. PCC 6803 cells into the light, “greening” of Synechocystis sp. PCC 6803 cells, i.e. thylakoid membrane formation and recovery of photosynthetic electron transport reactions, was monitored. Complete restoration of a typical thylakoid membrane system was observed within 24 hours after an initial lag phase of 6 to 8 hours. Furthermore, activation of photosystem II complexes and restoration of a functional photosynthetic electron transport chain appears to be linked to the biogenesis of organized thylakoid membrane pairs.
Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines
Authors: Roessler Christian G. , Kuczewski Anthony , Stearns Richard , Ellson Richard , Olechno Joseph , Orville Allen M. , Allaire Marc , Soares Alexei S. , Héroux Annie
Published: August 2013

To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide `conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.
Comparative genomics and transcriptomics analysis of experimentally evolved Escherichia coli MC1000 in complex environments
Authors: Puentes‐Téllez Pilar Eliana , Kovács Ákos T. , Kuipers Oscar P. , van Elsas Jan Dirk
Published: August 2013

It has recently become feasible to study the basis and nature of evolutionary changes in bacteria in an experimental setting using defined media. However, assessment of adaptive changes in complex environments has been scarce. In an effort to describe the responses in such environments, we unravel, in a comparative approach, the transcriptional and genetic profiles of 19 Escherichia coli strains that evolved in Luria Bertani medium under three different oxygen regimes over 1000 generations. A positive relationship between upregulation of gene expression and the number of mutations was observed, suggesting that a number of metabolic pathways were activated. Phenotypic polymorphisms were observed in parallel cultures, of which some were related with mutations at the regulatory level. Non‐parallel responses were observed at the intrapopulational level, which is indicative of diversifying selection. Parallel responses encompassed transcriptome diversity, and their effects were directly affected by differing genomic backgrounds. A fluctuating selective force produced higher phenotypic diversity compared with constant forces. This study demonstrates how phenotypic innovations may depend on the relationship between genomic changes and local ecological conditions. Using both comparative genomics and transcriptomics approaches, the results help elucidating various adaptive responses in cultures in unexplored complex environments.
Participative Leadership and the Organizational Commitment of Civil Servants in China: The Mediating Effects of Trust in Supervisor
Authors: Miao Qing , Newman Alexander , Schwarz Gary , Xu Lin
Published: August 2013

The present study examines whether participative leadership engenders organizational commitment amongst Chinese civil servants and analyses the mechanisms by which it transmits its effects. Confirmatory factor analysis and structural equation modelling revealed that there was a significant relationship between supervisor‐level participative leadership and the affective and normative commitment of subordinates, but no relationship with continuance commitment. Affective trust was also identified as the mediator variable underlying the relationship between participative leadership and organizational commitment. We show that participative leadership of supervisors elicits higher levels of trust and leads subordinates to reciprocate through exhibiting higher levels of organizational commitment. Our study also reveals that Chinese civil servants who accept an unequal distribution of power between supervisors and subordinates typically exhibit lower levels of affective and normative commitment to the organization than those who do not. Our results provide greater support for the deepening of administrative reforms and the dissemination of participative leadership practices in China's new civil service system.
The Changing Role of Tax Governance: Remaking the Large Corporate Taxpayer into a Visible Customer Partner
Authors: Tuck Penelope
Published: August 2013

Neo‐liberalism encourages the rule of private interests coordinated by markets and arms'‐length regulation by central government and regulatory bodies, and also through the explosion of audit and scrutiny. Part of this approach is the reconceptualization of users of services or functions as customers even though a quasi supplier relationship does not seem to be involved, such as between a regulator and a regulatee. This empowerment of the customer has a consequential impact on the regulation process. This paper theorizes this dynamic of power as recursive governmentality. It examines the change and unintended consequences in a regulatory authority,HMRevenue and Customs, theUKtax administration, as it responds to this policy context and how this leads to a search for a new identity as a customer‐service provider.
Urban Geographies of Hesitant Transition: Tracing Socioeconomic Segregation in Post‐Ceauşescu Bucharest
Authors: Marcińczak Szymon , Gentile Michael , Rufat Samuel , Chelcea Liviu
Published: August 2013

Scholars have raised concerns about the social costs of the transition from state socialism to capitalism in Central and Eastern Europe, and geographers are particularly interested in the spatial expressions and implications of these costs, including apparently increasing residential segregation. Applying a range of segregation measures to 1992 and 2002 census data, this contribution studies socio‐occupational residential segregation in Bucharest. The conclusion is that Bucharest was relatively socio‐spatially mixed at both times; in fact, a modest, yet fully legible, decreasing overall trend is observable. This is at odds with many popular assumptions of the past 20 years.
Maternal and perinatal outcomes among nulliparous adolescents in low‐ and middle‐income countries: a multi‐country study
Authors: Ganchimeg T , Mori R , Ota E , Koyanagi A , Gilmour S , Shibuya K , Torloni MR , Betran AP , Seuc A , Vogel J , Souza JP
Published: August 2013

Objective

To investigate the risk of adverse pregnancy outcomes and caesarean section among adolescents in low‐ and middle‐income countries.

Design

Secondary analysis using facility‐based cross‐sectional data from the World Health Organization (WHO) Global Survey on Maternal and Perinatal Health.

Setting

Twenty‐three countries in Africa, Latin America, and Asia.

Population

Women admitted for delivery in 363 health facilities during 2–3 months between 2004 and 2008.

Methods

We constructed multilevel logistic regression models to estimate the effect of young maternal age on risks of adverse pregnancy outcomes.

Main outcome measures

Risk of adverse pregnancy outcomes among young mothers.

Results

A total of 78 646 nulliparous mothers aged ≤24 years and their singleton infants were included in the analysis. Compared with mothers aged 20–24 years, adolescents aged 16–19 years had a significantly lower risk of caesarean section (adjusted OR 0.75, 95% CI 0.71–0.79). When the analysis was restricted to caesarean section indicated for presumed cephalopelvic disproportion, the risk of caesarean section was significantly higher among mothers aged ≤15 years (aOR 1.27, 95% CI 1.07–1.49) than among those aged 20–24 years. Higher risks of low birthweight and preterm birth were found among adolescents aged 16–19 years (aOR 1.10, 95% CI 1.03–1.17; aOR 1.16, 95% CI 1.09–1.23, respectively) and ≤15 years (aOR 1.33, 95% CI 1.14–1.54; aOR 1.56, 95% CI 1.35–1.80, respectively).

Conclusions

Adolescent girls experiencing pregnancy at a very young age (i.e. <16 years) have an increased risk of adverse pregnancy outcomes.
Inhibition of Cronobacter sakazakii by Heat Labile Bacteriocins Produced by Probiotic LAB Isolated from Healthy Infants
Authors: Awaisheh Saddam S. , Al‐Nabulsi Anas A. , Osaili Tareq M. , Ibrahim Salam , Holley Richard
Published: August 2013

Cronobacter sakazakii is an opportunistic pathogen that can cause bacteremia, meningitis, and necrotizing enterocolitis, most often in neonates with case‐fatality rates that may reach 80%. The antimicrobial activity of lactic acid bacteria against a wide range of foodborne pathogens is well‐established in different types of food products. The objective of the current study was to investigate the antibacterial activity of Lactobacillus acidophilus and L. casei isolated from feces of healthy infants against different strains of C. sakazakii in agar and a rehydrated infant milk formula (RIMF) model. The inhibition zones of C. sakazakii around L. acidophilus or L. casei ranged from 22 to 32 mm on eMan Rogosa Sharpe (MRS) agar under aerobic conditions, while a slight reduction in antibacterial activity was noted on modified MRS (0.2% glucose) under anaerobic conditions. It was observed that pH‐neutralized cell‐free supernatant (CFS) of L. acidophilus or L. casei was inhibitory against tested C. sakazakii strains. The inhibition zones of neutralized CFS were lower than the antibacterial activities of live cultures. The antibacterial activity of CFS was abolished when CFS from L. acidophilus or L. casei was heated at 60 or 80 °C for either 10 min or 2 h, or treated with trypsin or pepsin. This was considered strong evidence that the inhibition was due to the production of bacteriocins by L. casei and L. acidophilus. Both the CFS and active growing cells of L. casei and L. acidophilus were able to reduce the viability of C. sakazakii in the RIMF model. The results may extend the use of natural antimicrobials instead of conventional preservation methods to improve the safety of RIMF.
DNA barcoding in Mexico: an introduction
Authors: Elías‐Gutiérrez M. , León‐Regagnon V.
Published: August 2013

DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega‐diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies.
The Timeliness of the Bond Market Reaction to Bad Earnings News
Authors: Defond Mark L. , Zhang Jieying
Published: August 2013

We find that bond price quotes impound bad earnings news on a more timely basis than good earnings news and that the bond market impounds bad news on a more timely basis than the stock market. We also find that the timeliness of the bond market reaction to bad news is concentrated primarily among speculative‐grade bonds, consistent with earnings news having a larger effect on bond price quotes when default risk is high. In addition, we find that a portion of the bad news impounded by the bond market reverses following the earnings announcement. Overall, our findings are consistent with bondholders’ asymmetric payoff function having important implications for the valuation role of accounting information in the bond market. Specifically, our findings indicate that bond quotes impound bad earnings news much earlier in the pre‐earnings announcement period than stock prices. In addition, bondholders appear to overreact to the bad earnings news initially and correct this overreaction subsequent to the earnings announcement.
Auditors’ Professional Skepticism: Neutrality versus Presumptive Doubt
Authors: Quadackers Luc , Groot Tom , Wright Arnold
Published: August 2013

Although skepticism is widely viewed as essential to audit quality, there is a debate about what form is optimal. The two prevailing perspectives that have surfaced are “neutrality” and “presumptive doubt.” With neutrality, auditors neither believe nor disbelieve client management. With presumptive doubt, auditors assume some level of dishonesty by management, unless evidence indicates otherwise. The purpose of this study is to examine which of these perspectives is most descriptive of auditors’ skeptical judgments and decisions, in higher and lower control environment risk settings. This issue is important, since there is a lack of empirical evidence as to which perspective is optimal in addressing client risks. An experimental study is conducted involving a sample of 96 auditors from one of the Big 4 auditing firms in the Netherlands, with experience ranging from senior to partner. One of the skepticism measures is reflective of neutrality, the Hurtt Professional Skepticism Scale (HPSS), whereas the other reflects presumptive doubt, the inverse of the Rotter Interpersonal Trust Scale (RIT). The findings suggest that the presumptive doubt perspective of professional skepticism is more predictive of auditor skeptical judgments and decisions than neutrality, particularly in higher‐risk settings. Since auditing standards prescribe greater skepticism in higher‐risk settings, the findings support the appropriateness of a presumptive doubt perspective and have important implications for auditor recruitment and training, guidance in audit tools, and future research.
Mitochondrial energetics is impaired in vivo in aged skeletal muscle
Authors: Gouspillou Gilles , Bourdel‐Marchasson Isabelle , Rouland Richard , Calmettes Guillaume , Biran Marc , Deschodt‐Arsac Véronique , Miraux Sylvain , Thiaudiere Eric , Pasdois Philippe , Detaille Dominique , Franconi Jean‐Michel , Babot Marion , Trézéguet Véronique , Arsac Laurent , Diolez Philippe
Published: August 2013

With aging, most skeletal muscles undergo a progressive loss of mass and strength, a process termed sarcopenia. Aging‐related defects in mitochondrial energetics have been proposed to be causally involved in sarcopenia. However, changes in muscle mitochondrial oxidative phosphorylation with aging remain a highly controversial issue, creating a pressing need for integrative approaches to determine whether mitochondrial bioenergetics are impaired in aged skeletal muscle. To address this issue, mitochondrial bioenergetics was first investigated in vivo in the gastrocnemius muscle of adult (6 months) and aged (21 months) male Wistar rats by combining a modular control analysis approach with 31P magnetic resonance spectroscopy measurements of energetic metabolites. Using this innovative approach, we revealed that the in vivo responsiveness (‘elasticity’) of mitochondrial oxidative phosphorylation to contraction‐induced increase in ATP demand is significantly reduced in aged skeletal muscle, a reduction especially pronounced under low contractile activities. In line with this in vivo aging‐related defect in mitochondrial energetics, we found that the mitochondrial affinity for ADP is significantly decreased in mitochondria isolated from aged skeletal muscle. Collectively, the results of this study demonstrate that mitochondrial bioenergetics are effectively altered in vivo in aged skeletal muscle and provide a novel cellular basis for this phenomenon.
Chemical, morphological and microhardness changes of dentine after chemomechanical caries removal
Authors: Hamama HH , Yiu CKY , Burrow MF , King NM
Published: August 2013

Background

This study compared the chemical, morphological and microhardness changes in carious dentine following application of NaOCl‐based (Carisolv), papain‐based (Papacarie) chemomechanical caries removal agents with conventional rotary method.

Methods

Thirty‐two carious and eight non‐carious human permanent molars were used. The carious molars were randomly distributed into four groups: Group 1 (positive control) – molars were left without caries removal; Group 2 – caries excavated with rotary method; Group 3 – caries excavated with Carisolv; Group 4 – caries excavated with Papacarie. Group 5 (negative control) consisted of eight sound molars. After caries excavation, all specimens were prepared for chemical, morphological analysis and Vickers hardness testing.

Results

EDX analysis showed no significant difference in Ca wt%, P wt% and Ca/P ratio among Groups 2 to 5. Vickers hardness of dentine from Groups 3 and 4 was significantly lower (p < 0.05) than for Groups 2 and 5. The use of Papacarie resulted in a dentine surface without smear layer and patent tubules, while Carisolv resulted in a dentine surface exhibiting two patterns: (1) the presence of smear layer or (2) patent tubules with partial smear layer formation.

Conclusions

Papain‐based (Papacarie) chemomechanical caries removal method is a reliable alternative to conventional rotary and NaOCl‐based (Carisolv) caries removal.
Validation and further characterization of a major quantitative trait locus associated with host response to experimental infection with porcine reproductive and respiratory syndrome virus
Authors: Boddicker N. J. , Garrick D. J. , Rowland R. R. R. , Lunney J. K. , Reecy J. M. , Dekkers J. C. M.
Published: August 2013

Infectious diseases are costly to the swine industry; porcine reproductive and respiratory syndrome (PRRS) is the most devastating. In earlier work, a quantitative trait locus associated with resistance/susceptibility to PRRS virus was identified on Sus scrofa chromosome 4 using approximately 560 experimentally infected animals from a commercial cross. The favorable genotype was associated with decreased virus load and increased weight gain (WG). The objective here was to validate and further characterize the association of the chromosome 4 region with PRRS resistance using data from two unrelated commercial crossbred populations. The validation populations consisted of two trials each of approximately 200 pigs sourced from different breeding companies that were infected with PRRS virus and followed for 42 days post‐infection. Across all five trials, heritability estimates were 0.39 and 0.34 for viral load (VL; area under the curve of log‐transformed viremia from 0 to 21 days post‐infection) and WG to 42 days post‐infection respectively. Effect estimates of SNP WUR10000125 in the chromosome 4 region were in the same directions and of similar magnitudes in the two new trials as had been observed in the first three trials. Across all five trials, the 1‐Mb region on chromosome 4 explained 15 percent of genetic variance for VL and 11 percent for WG. The effect of the favorable minor allele at SNP WUR10000125 was dominant. Ordered genotypes for SNP WUR10000125 showed that the effect was present irrespective of whether the favorable allele was paternally or maternally inherited. These results demonstrate that selection for host response to PRRS virus infection could reduce the economic impact of PRRS.
Causes of SLIT discontinuation and strategies to improve the adherence: a pragmatic approach
Authors: Savi E. , Peveri S. , Senna G. , Passalacqua G.
Published: August 2013

Sublingual immunotherapy (SLIT) is often discontinued, and many patients do not renew the prescription. We evaluated the reasons for discontinuation and set up an educational/follow‐up plan to improve the adherence. In a first phase, the adherence at 4 months was directly assessed. Based on those results, an action plan (education, frequent contacts, and strictly scheduled visits) was developed and tested in other patients. A group of matched patients did not undergo the follow‐up plan (controls). In the first phase, involving 252 subjects, at 4 months, there were 30% dropouts, mainly due to side‐effects. In the second phase, 149 patients underwent education/follow‐up and 90 received no intervention. In the first group, discontinuations at 4 months were 5%, vs 18% in the controls (P = 0.01). After one year, 12% of patients were lost in the first group and 35% in the control group (P < 0.001). An adequate education and a strict follow‐up can significantly reduce SLIT's discontinuations.
Modulation of allergen‐induced bronchoconstriction by fluticasone furoate and vilanterol alone or in combination
Authors: Oliver A. , Bjermer L. , Quinn D. , Saggu P. , Thomas P. , Yarnall K. , Lötvall J.
Published: August 2013

Background

This placebo‐controlled study assessed the effects of the once‐daily inhaled corticosteroid (ICS) fluticasone furoate (FF) and long‐acting beta2‐agonist (LABA) vilanterol (VI) on early and late asthmatic responses (EAR/LAR) and airway hyper‐responsiveness (AHR).

Methods

Patients (n = 27) were randomized to FF (100 μg), VI (25 μg), FF/VI (100/25 μg), and placebo for 21 days (four periods). Allergen challenge was performed 1 h post‐dose on day 21. AHR was assessed on day 22 using methacholine.

Results

Allergen challenge caused an early change (0–2 h) in minimum forced expiratory volume in 1 s (FEV1) of −1.091 l (95% CI: −1.344; −0.837) following placebo therapy; changes were −0.955 l (−1.209; −0.702), −0.826 l (−1.070; −0.581), and −0.614 l (−0.858; −0.370) following VI, FF, or FF/VI therapy, respectively. Treatment differences were significant for all comparisons between therapies. Mean changes in 0–2 h %FEV1 were as follows: −28.05 (placebo), −23.10 (VI), −22.33 (FF), and −16.10 (FF/VI). Following placebo, the late change (4–10 h) in weighted mean FEV1 was −0.466 l (−0.589; −0.343) and −0.298 l (−0.415; −0.181) after VI, and was +0.018 l with both FF/VI (−0.089; 0.124) and FF (−0.089; 0.125). Treatment differences were significant for all comparisons between therapies except FF/VI vs FF. Mean changes in 4–10 h %FEV1 were as follows: −21.08 (placebo), −14.30 (VI), −5.02 (FF), and −5.83 (FF/VI). AHR 24 h after allergen challenge was significantly reduced with FF/VI and FF vs placebo, and FF/VI was superior to either component.

Conclusion

Combined treatment with FF/VI provides additive protection from the EAR relative to its components, significant protection over VI alone from the LAR, and confers sustained protection from hyper‐responsiveness 24 h post‐dose.
Indirect comparison analysis of efficacy and safety between olanzapine and aripiprazole for schizophrenia
Authors: Kunitomi Taro , Hashiguchi Masayuki , Mochizuki Mayumi
Published: August 2013

Aims

Indirect comparison (IC) and direct comparison (DC) between aripiprazole and olanzapine for schizophrenia were conducted to compare their efficacy and safety. The objective was to determine the usability of IC and consistency of results delivered by the two comparisons. Factors that might influence the inconsistency of results were also investigated.

Methods

ICs and DCs were conducted using the change from baseline of the Positive and Negative Syndrome Scale (PANSS) total score as an efficacy endpoint and the dropout rate was selected as a safety endpoint. Placebo and risperidone were used as common comparators for ICs.

Results

A literature search identified 20 articles. The efficacy analysis gave results on the mean difference in PANSS change (95% CI) of −5.72 (−10.22, −1.22) in ICs using placebo as a common comparator and −7.41 (−15.96, 1.14) in DCs. When using risperidone as a common comparator, it was −9.15 (−20.12, 1.82). In rate ratio analysis of the all cause dropout rate, the IC result was 1.17 (0.83, 1.65) using placebo as a common comparator and 1.56 (0.57, 4.26) using risperidone as a common comparator. Both analyses gave consistent results between ICs and DCs. A slightly lower estimated value was observed in ICs using placebo.

Conclusions

This study demonstrated that ICs between olanzapine and aripiprazole can deliver results consistent with those of DCs. It is also suggested that the selection of a common comparator is important when control group bias is suspected in the data set.
Percutaneous suprapubic tube bladder drainage after robot‐assisted radical prostatectomy: a step‐by‐step guide
Authors: Ghani Khurshid R. , Trinh Quoc‐Dien , Sammon Jesse D. , Jeong Wooju , Simone Andrea , Dabaja Ali , Dusik Stacey , Peabody James O. , Menon Mani
Published: August 2013

Objective

To describe our technique of maintaining bladder drainage after robot‐assisted radical prostatectomy (RARP) using a percutaneous suprapubic tube (PST) in place of a urethral catheter.

Methods

A watertight anastomosis permits placement of the PST. Contraindications include morbid obesity, concomitant inguinal hernia mesh repair, anticoagulation therapy, limited hand dexterity in the patient, bladder neck reconstruction and extensive adhesiolysis at RARP.

The necessary equipment includes a 14‐F PST balloon catheter set, a three‐way connector, a connecting tube, a suture passer, 1/0 polypropylene sutures on a CT1 needle, a sterile plastic button, adhesive and steri‐strips.

Results

The important steps for PST placement are: Step 1: robot‐assisted placement of a bladder wall anchor suture; Step 2: transferring the bladder wall suture to anterior abdominal skin; Step 3: guided placement of the PST under robotic vision; Step 4: securing the PST within the bladder and abdominal wall; Step 5. postoperative care: clamping the PST on postoperative day 5, recording each void and post‐void residual urine volumes in a patient diary, removal of the PST on postoperative day 7 after 48 h of voiding with residual urine <100 mL per void.

Conclusion

We provide a concise step‐by‐step guide for placement of a PST during RARP as well as important management aspects for the successful adoption of this technique.
The ‘Our Say, Our Rights’ quilt
Authors: Keating Lorraine , Sheerin Fintan K.
Published: August 2013

Accessible summary

This article is about the rights of people with intellectual disabilities.

People with intellectual disabilities in Ireland made quilt squares with pictures on them. The pictures were about their rights.

People want to be able to choose and to do the same things as everyone else.
Comparative Kinetics of Qi Site Inhibitors of Cytochrome bc1 Complex: Picomolar Antimycin and Micromolar Cyazofamid
Authors: Li Hui , Zhu Xiao‐Lei , Yang Wen‐Chao , Yang Guang‐Fu
Published: August 2013

Antimycin and cyazofamid are specific inhibitors of the mitochondrial respiratory chain and bind to the Qi site of the cytochrome bc1 complex. With the aim to understand the detailed molecular inhibition mechanism of Qi inhibitors, we performed a comparative investigation of the inhibitory kinetics of them against the porcine bc1 complex. The results showed that antimycin is a slow tight‐binding inhibitor of succinate–cytochrome c reductase (SCR) with Ki = 0.033 ± 0.00027 nm and non‐competitive inhibition with respect to cytochrome c. Cyazofamid is a classical inhibitor of SCR with Ki = 12.90 ± 0.91 μm and a non‐competitive inhibitor with respect to cytochrome c. Both of them show competitive inhibition with respect to substrate DBH2. Further molecular docking and quantum mechanics calculations were performed. The results showed that antimycin underwent significant conformational change upon the binding. The energy barrier between the conformations in the crystal and in the binding pocket is ~13.63 kcal/mol. Antimycin formed an H‐bond with Asp228 and two water‐bridged H‐bonds with Lys227 and His201, whereas cyazofamid formed only one H‐bond with Asp228. The conformational change and the different hydrogen bonding network might account for why antimycin is a slow tight‐binding inhibitor, whereas cyazofamid is a classic inhibitor.