bluuebunny/crossref_metadata_2025 huggingface dataset:
miRCancer: a microRNA–cancer association database constructed by text mining on literature
Authors: Xie Boya , Ding Qin , Han Hongjin , Wu Di
Published: January 2013

Motivation: Research interests in microRNAs have increased rapidly in the past decade. Many studies have showed that microRNAs have close relationships with various human cancers, and they potentially could be used as cancer indicators in diagnosis or as a suppressor for treatment purposes. There are several databases that contain microRNA–cancer associations predicted by computational methods but few from empirical results. Despite the fact that abundant experiments investigating microRNA expressions in cancer cells have been carried out, the results have remain scattered in the literature. We propose to extract microRNA–cancer associations by text mining and store them in a database called miRCancer.

Results: The text mining is based on 75 rules we have constructed, which represent the common sentence structures typically used to state microRNA expressions in cancers. The microRNA–cancer association database, miRCancer, is updated regularly by running the text mining algorithm against PubMed. All miRNA–cancer associations are confirmed manually after automatic extraction. miRCancer currently documents 878 relationships between 236 microRNAs and 79 human cancers through the processing of >26 000 published articles.

Availability: miRCancer is freely available on the web at http://mircancer.ecu.edu/

Contact:  dingq@ecu.edu
Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
Authors: Busby Michele A. , Stewart Chip , Miller Chase A. , Grzeda Krzysztof R. , Marth Gabor T.
Published: January 2013

Motivation: A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?

Results: Scotty is an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives. This design can be based on data available from either pilot samples or publicly available datasets.

Availability: Scotty can be freely accessed on the web at http://euler.bc.edu/marthlab/scotty/scotty.php

Contact:  gabor.marth@bc.edu

Supplementary information:  Supplementary data are is available at Bioinformatics online.
Identification and Sensitivity Analysis for Multiple Causal Mechanisms: Revisiting Evidence from Framing Experiments
Authors: Imai Kosuke , Yamamoto Teppei
Published: January 2013

Social scientists are often interested in testing multiple causal mechanisms through which a treatment affects outcomes. A predominant approach has been to use linear structural equation models and examine the statistical significance of the corresponding path coefficients. However, this approach implicitly assumes that the multiple mechanisms are causally independent of one another. In this article, we consider a set of alternative assumptions that are sufficient to identify the average causal mediation effects when multiple, causally related mediators exist. We develop a new sensitivity analysis for examining the robustness of empirical findings to the potential violation of a key identification assumption. We apply the proposed methods to three political psychology experiments, which examine alternative causal pathways between media framing and public opinion. Our analysis reveals that the validity of original conclusions is highly reliant on the assumed independence of alternative causal mechanisms, highlighting the importance of proposed sensitivity analysis. All of the proposed methods can be implemented via an open source R package,mediation.
Effects of the Insect Growth Regulators Novaluron and Diflubenzuron on the Brown Marmorated Stink Bug
Authors: Kamminga Katherine L. , Kuhar Thomas P. , Wimer Adam , Herbert D. Ames
Published: January 2013

The brown marmorated stink bug (BMSB), Halyomorpha halys (Stål), is an invasive pest from China that causes economic damage to field crops, vegetables, and tree fruit. Due to its destructive potential, applications of broad-spectrum insecticides have escalated. Researchers are trying to identify options for controlling BMSB that have less of a negative impact on non-target species. Chitin biosynthesis inhibitors are more selective than the commonly used pyrethroids and organophosphates. They are active on the larval stage of the insect and are reported as having sublethal effects such as reducing adult fecundity. In our studies, bioassays were completed with chitin biosynthesis inhibitors novaluron and diflubenzuron to evaluate the effectiveness of these insecticides on adult mortality, nymphal growth, adult fecundity, and egg hatch. Our data indicate that treatments of novaluron at 362.2 g ai/ha or diflubenzuron at 280.2 g ai/ha effectively controlled BMSB nymphs. However, the insecticides were not effective at reducing egg hatch, adult fecundity, or adult life span. If novaluron or diflubenzuron are used in agriculture for BMSB control, then the nymphal stage should be targeted.

Accepted for publication 9 November 2012. Published 12 December 2012.
First Report of Pythium dissotocum Affecting Cilantro in Hydroponic Systems in Puerto Rico
Authors: Romero G. , de Jensen C. Estévez , Palmateer A. J.
Published: January 2013

Pythium dissotocum was detected on cilantro in hydroponic systems in Puerto Rico. Isolates from stem lesions were inoculated in cilantro ‘Lonestar’ and in pea ‘Sugar Baby,’ producing soft rot 21 and 15 days after inoculation, respectively. The pathogen was re-isolated from diseased plants and it was confirmed to be Pythium dissotocum by PCR.

Accepted for publication 5 December 2012. Published 14 December 2012.
Sunflower Diseases Remain Rare in California Seed Production Fields Compared to North Dakota
Authors: Gulya Thomas J. , Rooney-Latham Suzanne , Miller Jean S. , Kosta Kathleen , Murphy-Vierra Colleen , Larson Carrie , Vaccaro William , Kandel Hans , Nowatzki John F.
Published: January 2013

The majority of United States sunflower production is in seven Midwestern states, but hybrid planting seed is almost exclusively produced in California. Due to the lack of summer rains and furrow irrigation, California-produced seed is relatively disease free and thus it regularly meets phytosanitary restrictions imposed by many countries. For the 15-year period from 1997 to 2011, 7231 seed fields in northern California were inspected and samples processed at the state diagnostic laboratory (California Department of Food and Agriculture). Rust (Puccinia helianthi) was the most prevalent quarantine disease, found in 4.3% of fields. Stalk rot (Sclerotinia sclerotiorum) and downy mildew (Plasmopara halstedii) were the only other quarantine pathogens observed, found in 2.6% and 0.5% of the 7231 fields, respectively. Many sunflower pathogens have never been recorded in California, including Phoma macdonaldii, Phomopsis helianthi, or any virus. North Dakota, the state with the highest US sunflower production, had quarantine pathogens in 88% of 1263 fields surveyed from 1995 to 2011. Phoma macdonaldii, Sclerotinia sclerotiorum, Puccinia helianthi, Phomopsis helianthi, Plasmopara halstedii, and Verticillium dahliae were recorded in 62, 54, 37, 33, 14, and 12%, respectively, of North Dakota fields.

Accepted for publication 5 November 2012. Published 14 December 2012.
Accuracy of the actuator disc-RANS approach for predicting the performance and wake of tidal turbines
Authors: Batten W. M. J. , Harrison M. E. , Bahaj A. S.
Published: January 2013

The actuator disc-RANS model has widely been used in wind and tidal energy to predict the wake of a horizontal axis turbine. The model is appropriate where large-scale effects of the turbine on a flow are of interest, for example, when considering environmental impacts, or arrays of devices. The accuracy of the model for modelling the wake of tidal stream turbines has not been demonstrated, and flow predictions presented in the literature for similar modelled scenarios vary significantly. This paper compares the results of the actuator disc-RANS model, where the turbine forces have been derived using a blade-element approach, to experimental data measured in the wake of a scaled turbine. It also compares the results with those of a simpler uniform actuator disc model. The comparisons show that the model is accurate and can predict up to 94 per cent of the variation in the experimental velocity data measured on the centreline of the wake, therefore demonstrating that the actuator disc-RANS model is an accurate approach for modelling a turbine wake, and a conservative approach to predict performance and loads. It can therefore be applied to similar scenarios with confidence.
The FMRFamide-related neuropeptide FLP-20 is required in the mechanosensory neurons during memory for massed training in C. elegans
Authors: Li Chris , Timbers Tiffany A. , Rose Jacqueline K. , Bozorgmehr Tahereh , McEwan Andrea , Rankin Catharine H.
Published: January 2013

Lasting memories are likely to result from a lasting change in neurotransmission. In the nematode Caenorhabditis elegans, spaced training with a tap stimulus induces habituation to the tap that lasts for >24 h and is dependent on glutamate transmission, postsynaptic AMPA receptors, and CREB. Here we describe a distinct, presynaptic mechanism for a shorter lasting memory for tap habituation induced by massed training. We report that a FMRFamide-related peptide (FMRF = Phe-Met-Arg-Phe-NH2), FLP-20, is critical for memory lasting 12 h following massed training, but is not required for other forms of memory. Massed training correlated with a flp-20-dependent increase in synaptobrevin tagged with green fluorescent protein in the presynaptic terminals of the PLM mechanosensory neurons that followed the timeline of the memory trace. We also demonstrated that flp-20 is required specifically in the mechanosensory neurons for memory 12 h after massed training. These findings show that within the same species and form of learning, memory is induced by distinct mechanisms to create a lasting alteration in neurotransmission that is dependent upon the temporal pattern of training: memory of spaced training results from postsynaptic changes in the interneurons of the neural circuit, whereas memory of massed training results from presynaptic changes in the mechanosensory neurons of the neural circuit.
incurvata13, a Novel Allele of AUXIN RESISTANT6, Reveals a Specific Role for Auxin and the SCF Complex in Arabidopsis Embryogenesis, Vascular Specification, and Leaf Flatness
Authors: Esteve-Bruna David , Pérez-Pérez José Manuel , Ponce María Rosa , Micol José Luis
Published: January 2013

Auxin plays a pivotal role in plant development by modulating the activity of SCF ubiquitin ligase complexes. Here, we positionally cloned Arabidopsis (Arabidopsis thaliana) incurvata13 (icu13), a mutation that causes leaf hyponasty and reduces leaf venation pattern complexity and auxin responsiveness. We found that icu13 is a novel recessive allele of AUXIN RESISTANT6 (AXR6), which encodes CULLIN1, an invariable component of the SCF complex. Consistent with a role for auxin in vascular specification, the vascular defects in the icu13 mutant were accompanied by reduced expression of auxin transport and auxin perception markers in provascular cells. This observation is consistent with the expression pattern of AXR6, which we found to be restricted to vascular precursors and hydathodes in wild-type leaf primordia. AXR1, RELATED TO UBIQUITIN1-CONJUGATING ENZYME1, CONSTITUTIVE PHOTOMORPHOGENIC9 SIGNALOSOME5A, and CULLIN-ASSOCIATED NEDD8-DISSOCIATED1 participate in the covalent modification of CULLIN1 by RELATED TO UBIQUITIN. Hypomorphic alleles of these genes also display simple venation patterns, and their double mutant combinations with icu13 exhibited a synergistic, rootless phenotype reminiscent of that caused by loss of function of MONOPTEROS (MP), which forms an auxin-signaling module with BODENLOS (BDL). The phenotypes of double mutant combinations of icu13 with either a gain-of-function allele of BDL or a loss-of-function allele of MP were synergistic. In addition, a BDL:green fluorescent protein fusion protein accumulated in icu13, and BDL loss of function or MP overexpression suppressed the phenotype of icu13. Our results demonstrate that the MP-BDL module is required not only for root specification in embryogenesis and vascular postembryonic development but also for leaf flatness.
The Arabidopsis Rho of Plants GTPase AtROP6 Functions in Developmental and Pathogen Response Pathways
Authors: Poraty-Gavra Limor , Zimmermann Philip , Haigis Sabine , Bednarek Paweł , Hazak Ora , Stelmakh Oksana Rogovoy , Sadot Einat , Schulze-Lefert Paul , Gruissem Wilhelm , Yalovsky Shaul
Published: January 2013

How plants coordinate developmental processes and environmental stress responses is a pressing question. Here, we show that Arabidopsis (Arabidopsis thaliana) Rho of Plants6 (AtROP6) integrates developmental and pathogen response signaling. AtROP6 expression is induced by auxin and detected in the root meristem, lateral root initials, and leaf hydathodes. Plants expressing a dominant negative AtROP6 (rop6DN) under the regulation of its endogenous promoter are small and have multiple inflorescence stems, twisted leaves, deformed leaf epidermis pavement cells, and differentially organized cytoskeleton. Microarray analyses of rop6DN plants revealed that major changes in gene expression are associated with constitutive salicylic acid (SA)-mediated defense responses. In agreement, their free and total SA levels resembled those of wild-type plants inoculated with a virulent powdery mildew pathogen. The constitutive SA-associated response in rop6DN was suppressed in mutant backgrounds defective in SA signaling (nonexpresser of PR genes1 [npr1]) or biosynthesis (salicylic acid induction deficient2 [sid2]). However, the rop6DN npr1 and rop6DN sid2 double mutants retained the aberrant developmental phenotypes, indicating that the constitutive SA response can be uncoupled from ROP function(s) in development. rop6DN plants exhibited enhanced preinvasive defense responses to a host-adapted virulent powdery mildew fungus but were impaired in preinvasive defenses upon inoculation with a nonadapted powdery mildew. The host-adapted powdery mildew had a reduced reproductive fitness on rop6DN plants, which was retained in mutant backgrounds defective in SA biosynthesis or signaling. Our findings indicate that both the morphological aberrations and altered sensitivity to powdery mildews of rop6DN plants result from perturbations that are independent from the SA-associated response. These perturbations uncouple SA-dependent defense signaling from disease resistance execution.
Telaprevir: helical chains based on three-point hydrogen-bond connections
Authors: Gelbrich Thomas , Kahlenberg Volker , Langes Christoph , Griesser Ulrich J.
Published: January 2013

The crystal structure of the title compound [systematic name: (1S,3aR,6aS)-2-((2S)-2-{[(2S)-2-cyclohexyl-2-(pyrazine-2-carbonylamino)acetyl]amino}-3,3-dimethylbutanoyl)-N-[(3S)-1-(cyclopropylamino)-1,2-dioxohexan-3-yl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrole-1-carboxamide], C36H53N7O6, contains two independent molecules, which possess distinct conformations and a disordered cyclopenta[c]pyrrolidine unit. In the crystal, molecules are linked into helical chainsviathree-point N—H...O hydrogen-bond connections in which three NH and three carbonyl groups per molecule are utilized. The chiralities of the six stereocentres per molecule inferred from this study are in agreement with the synthetic procedure.
1-Phenyl-2-[4-(trifluoromethyl)phenyl]-1H-benzimidazole
Authors: Jayamoorthy K. , Mohandas T. , Sakthivel P. , Jayabharathi J.
Published: January 2013

In the title molecule, C20H13F3N2, the benzimidazole unit is close to being planar [maximum deviation = 0.012 (1) Å] and forms dihedral angles of 31.43 (7) and 61.45 (9)° with the 4-(trifluoromethyl)phenyl and 1-phenyl rings, respectively; the dihedral angle between these rings is 60.94 (10)°. In the crystal, C—H...F hydrogen bonds link the molecules into chains along thec-axis direction. The CF3group is rotationally disordered with an occupancy ratio of 0.557 (8):0.443 (8) for the F atoms.
[8-(4-Phenoxybenzoyl)-2,7-bis(propan-2-yloxy)naphthalen-1-yl](4-phenoxyphenyl)methanone
Authors: Yoshiwaka Sayaka , Hijikata Daichi , Sasagawa Kosuke , Okamoto Akiko , Yonezawa Noriyuki
Published: January 2013

The entire title molecule, C42H36O6, is completed by the application of a twofold axis. The 4-phenoxybenzoyl groups at the 1- and 8-positions of the naphthalene ring system are aligned almost antiparallel. The dihedral angle between the best planes of the benzene rings of the benzoyl moieties and the naphthalene ring system is 70.52 (5)° and that between the best planes of the benzene rings of the phenoxy groups and the naphthalene ring system is 27.80 (6)°. In the crystal, molecules are linked into a three-dimensional architecture by C—H...O and C—H...π interactions.
Key CSR dimensions for the food chain
Authors: Forsman‐Hugg Sari , Katajajuuri Juha‐Matti , Riipi Inkeri , Mäkelä Johanna , Järvelä Katja , Timonen Päivi
Published: January 2013

Purpose

This paper aims to identify and define the content of corporate social responsibility (CSR) for the food chain.

Design/methodology/approach

A qualitative research approach was applied in the study, based on participatory and case study research methodologies. The study drew on three different case food products and their supply chains: rye bread, broiler chicken products and margarine. The content of CSR was built through participatory workshops, the aim of which was to elicit the ideas of different stakeholder groups.

Findings

The study identified seven key dimensions of food chain CSR: environment, product safety, corporate nutritional responsibility, occupational welfare, animal health and welfare, local market presence and economic responsibility.

Originality/value

The results provide food and agribusiness companies with a better understanding of core CSR issues and their relevance in complex chains and networks. This may encourage the companies to promote their activities in a more responsible and sustainable direction and offer elements to build sustainable business cases. In addition, the results may indicate a change towards broader understanding of what is meant by corporate social responsibility.
Disclosure strategies regarding ethically questionable business practices
Authors: Aktar Ipek
Published: January 2013

Purpose

The author's objective is to reveal the consumer responses to information disclosure strategies regarding controversial ethical issues.

Design/methodology/approach

The author is interested in how voluntary disclosure of questionable business practices by chocolate manufacturers regarding child labor exploitation at cocoa plantations influences consumer behavior. A total of 120 students participated in an experimental study in which the author manipulated awareness of ethical issues in the chocolate industry and corporate disclosure strategy. The author measured willingness to pay (WTP) and consumer perceptions about the firm's commitment to corporate social responsibility.

Findings

The study found that voluntary disclosure of unethical business practices by a firm was not damaging in terms of consumer perceptions. When public awareness was limited, disclosing participation in unethical behavior did not influence WTP for the firm's products. When public awareness was high, disclosing this negative information is even more beneficial than no disclosure and generates similar responses to including only positive elements in the firm's communication, provided that the firm commits to eliminate its unethical practices.

Research limitations/implications

Voluntary negative social disclosure will not hurt a firm's performance in terms of sales, given the disclosure is transparent and this suggests a credible commitment to improve its practices regarding the issue.

Originality/value

The author investigates the optimal strategy for a firm to disclose ethical infractions. She demonstrates that being open about them does not necessarily damage a firm's reputation and suggests under which conditions this is the case.
Does hope moderate the impact of job burnout on frontline bank employees’ in‐role and extra‐role performances?
Authors: Yavas Ugur , Babakus Emin , Karatepe Osman M.
Published: January 2013

Purpose

The purpose of this paper is to examine whether hope as a personal resource moderates the relationships between job burnout and frontline bank employees’ in‐role and extra‐role performances.

Design/methodology/approach

Frontline employees of several banks throughout the Turkish Republic of Northern Cyprus serve as the study setting.

Findings

Results of the study reveal that burnout is significantly related to frontline employees’ in‐role and extra‐role performances and that hope moderates these relationships.

Research limitations/implications

Though common method bias does not appear to be a potential threat to the magnitude of relationships, in future studies using multiple‐informants (e.g. performance data from supervisors or customers) would be useful. In addition, replication studies among front employees in other countries would be beneficial for further generalizations.

Practical implications

Management of the banks should consider the personality traits of the individuals during the selection process. This is important, since hope reduces the detrimental impact of burnout on performance outcomes. Management should also retain employees high in hope, because such employees can create a positive work environment and serve as role models to their colleagues with low hope.

Originality/value

Empirical research in the banks services literature pertaining to the effect of hope on extra‐role performance and hope as a moderator of the impact of burnout on in‐role and extra‐role performances is scarce. Therefore, this study adds to the literature in this research stream by investigating the aforementioned relationships.
Microwave permittivity and permeability of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 thick films using superstrate method
Authors: Kashid P.B. , Kulkarni D.C. , Surve V.G. , Puri Vijaya
Published: January 2013

Purpose

The purpose of this paper is to study thickness dependent variation in microwave properties of the MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films and enhancement of power efficiency of Ag thick film EMC patch antenna.

Design/methodology/approach

X‐band microwave properties of the MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films were measured by superstrate technique using Ag thick film EMC patch antenna as the resonant element. The complex permittivity and permeability of these thick films were also measured by this technique. The microwave response of the EMC patch, complex permeability and permittivity of Mg0.8Mn0.1Al0.1Zn0.8Fe1.2O4 and Mg0.9Al0.1Zn0.8Fe1.2O4 thick films and their thickness dependency were investigated.

Findings

The XRD patterns reveal the cubic spinel crystal system was obtained for both compositions. The crystallite size obtained was 134.68 nm for Mg0.8Mn0.1Al0.1Zn0.8Fe1.2O4 and 155.99 nm for Mg0.9Al0.1Zn0.8Fe1.2O4 The superstrate technique has been used successfully to evaluate the complex permittivity and permeability of the ferrite thick films in the X band. The EMC patch also show thickness and composition dependent frequency agility and enhancement of power efficiency.

Originality/value

The complex permeability of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films measured by superstrate technique is reported in this paper. The superstrate of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films makes the Ag thick film EMC patch antenna frequency agile and power amplification is obtained.
Mobile cloud computing: state of the art and outlook
Authors: Dihal Soebhaash , Bouwman Harry , de Reuver Mark , Warnier Martijn , Carlsson Christer
Published: January 2013

Purpose

The purpose of this conceptual paper is to explore the meaning of cloud computing for mobile communication. The paper answers the question “what is mobile cloud computing?” and how is it related to the generic cloud computing concept?

Design/methodology/approach

This is an explanatory conceptual paper, based on literature review and exploring potential use cases, focused on the use of mobile cloud for service, platform or infrastructure access. The authors exclude the discussion of the traditional cloud concept in back office processes of telecom operators, and service providers.

Findings

Where cloud computing is focused on pooling of resources, mobile technology is focused on pooling and sharing of resources locally enabling alternative use cases for mobile infrastructure, platforms and service delivery. The paper discusses relevant concepts and offers examples of use cases.

Research limitations/implications

The value of mobile cloud solutions is not yet explicit, but needs further attention. Research should focus on the relation between mobile cloud computing, platforms and eco systems. From a user perspective the willingness to share pooled resources needs further attention.

Practical implications

Mobile cloud computing offers the possibility that disruptive applications might impact the mobile eco system; reinforcing or weakening business models of core players like handset providers, telecom operators, and service providers.

Originality/value

A lot of attention is paid to cloud computing and to platform discussions, papers on mobile cloud are scarce. This paper offers the current state of the art and a research outlook.
Economic reforms, determinants and stability of dividends in a dynamic setting
Authors: Subhash Kamat Manoj , Kamat Manasvi M.
Published: January 2013

Purpose

This study aims to find whether the Indian private corporate sector follow stable cash dividend policies, whether dividends smoothen earnings, estimate the implicit target dividend ratio, and examine the determinants along with speed of adjustment of dividends towards a long run target ratio.

Design/methodology/approach

The study uses the instrumental variable (IV) approach for dynamic panel data for 1971‐2010 periods controlling for economic reforms. The GMM‐in‐levels model, GMM‐in‐first‐differences and GMM‐in‐systems are alternatively estimated to include other lag structures.

Findings

In the post‐reform period lower dividends are consistent with rapid growth in the economic environment and the tendency to smoothen dividends has considerably decreased over time. The estimated model suggests dividends substitute for less opportunity for internal growth and increased general likening to relatively retain their earnings and finance their growth, unlike the past.

Research limitations/implications

Limitation to capture substitution, ownership and self selection effects stems up from data as the Annual Studies RBI does not include such variables, does not capture qualitative data and disallows identification of the firm.

Practical implications

The paper documents long run trends and inter‐temporal dividend patterns controlling economic reforms for a relatively larger number of public limited firms nearing four decades for an emerging economy.

Originality/value

This is a first attempt to take a holistic view of dividend using rich set of unexplored dynamic panel data on Indian firms controlling for reforms using contemporary econometric models and analyzes issues relating determinants, smoothening and stability of the corporate dividend structure.
Intra‐ and interpopulational variation in the ability of a solitary bee species to develop on non‐host pollen: implications for host range expansion
Authors: Haider Mare , Dorn Silvia , Müller Andreas
Published: January 2013

Pollen host choice in bees is in many cases highly conserved, which might partly be due to physiological limitations of bee larvae to digest non‐host pollen. These limitations need to be overcome in order to incorporate new pollen hosts; however, the mechanisms underlying such host expansion are poorly understood.

In this study, we examined intra‐ and interpopulational variation in the ability of larvae of the solitary bee species Osmia cornuta (Megachilidae) to develop on a non‐host pollen diet of Ranunculus acris (Ranunculaceae) by comparing larval performance within and between five geographically distant European populations.

The majority of bee larvae from all tested populations died when reared on the Ranunculus pollen diet. Between 10% and 43·5% of all larvae per population reached the cocoon stage, and 48% of these emerged as viable adults from the cocoons, indicating that the physiological ability to cope with the unfavourable properties of Ranunculus pollen exists in each population.

The bee larvae of one population exhibited significantly reduced survival on the Ranunculus pollen diet compared with three of the four other populations.

Although bees that successfully developed on the Ranunculus pollen diet showed a distinctly prolonged development time, exhibited higher mortality during diapause and reached a considerably lower adult weight compared with individuals fed the control pollen diet, several of the Ranunculus fed individuals were able to reproduce and to sire viable offspring.

This study provides the first evidence for both intra‐ and interpopulational variation in the physiological ability of solitary bees to digest non‐host pollen. This variation might enable host expansion and subsequent host shifts in response to natural selection.
The marine controlled source electromagnetic response of a steel borehole casing: applications for the NEPTUNE Canada gas hydrate observatory
Authors: Swidinsky Andrei , Edwards R. Nigel , Jegen Marion
Published: January 2013

Gas hydrates are a potential energy resource, a possible factor in climate change and an exploration geohazard. The University of Toronto has deployed a permanent seafloor time‐domain controlled source electromagnetic (CSEM) system offshore Vancouver Island, within the framework of the NEPTUNE Canada underwater cabled observatory. Hydrates are known to be present in the area and due to their electrically resistive nature can be monitored by 5 permanent electric field receivers. However, two cased boreholes may be drilled near the CSEM site in the near future. To understand any potential distortions of the electric fields due to the metal, we model the marine electromagnetic response of a conductive steel borehole casing. First, we consider the commonly used canonical model consisting of a 100 Ωm, 100 m thick resistive hydrocarbon layer embedded at a depth of 1000 m in a 1 Ωm conductive host medium, with the addition of a typical steel production casing extending from the seafloor to the resistive zone. Results show that in both the frequency and time domains the distortion produced by the casing occurs at smaller transmitter‐receiver offsets than the offsets required to detect the resistive layer. Second, we consider the experimentally determined model of the offshore Vancouver Island hydrate zone, consisting of a 5.5 Ωm, 36 m thick hydrate layer overlying a 0.7 Ωm sedimentary half‐space, with the addition of two borehole casings extending 300 m into the seafloor. In this case, results show that the distortion produced by casings located within a 100 m safety zone of the CSEM system will be measured at 4 of the 5 receivers. We conclude that the boreholes must be positioned at least 200 m away from the CSEM array so as to minimize the effects of the casings.
Food production vs. biodiversity: comparing organic and conventional agriculture
Authors: Gabriel Doreen , Sait Steven M. , Kunin William E. , Benton Tim G.
Published: January 2013

A substantial proportion of the global land surface is used for agricultural production. Agricultural land serves multiple societal purposes; it provides food, fuel and fibre and also acts as habitat for organisms and supports the services they provide. Biodiversity conservation and food production need to be balanced: production needs to be sustainable, while conservation cannot be totally at the expense of crop yield.

To identify the benefits (in terms of biodiversity conservation) and costs (in terms of reduction in yields) of agricultural management, we examined the relationship between crop yield and abundance and species density of important taxa in winter cereal fields on both organic and conventional farms in lowland England.

Of eight species groups examined, five (farmland plants, bumblebees, butterflies, solitary bees and epigeal arthropods) were negatively associated with crop yield, but the shape of this relationship varied between taxa. It was linear for the abundance of bumblebees and species density of butterflies, concave up for the abundance of epigeal arthropods and butterflies and concave down for species density of plants and bumblebees.

Grain production per unit area was 54% lower in organic compared with conventional fields. When controlling for yield, diversity of bumblebees, butterflies, hoverflies and epigeal arthropods did not differ between farming systems, indicating that observed differences in biodiversity between organic and conventional fields are explained by lower yields in organic fields and not by different management practices per se. Only percentage cover and species density of plants were increased by organic field management after controlling for yield. The abundance of solitary wild bees and hoverflies was increased in landscapes with high amount of organic land.

Synthesis and applications. Our results indicate that considerable gains in biodiversity require roughly proportionate reductions in yield in highly productive agricultural systems. They suggest that conservation efforts may be more cost effective in low‐productivity agricultural systems or on non‐agricultural land. In less productive agricultural landscapes, biodiversity benefit can be gained by concentrating organic farms into hotspots without a commensurate reduction in yield.
Laparoscopic lymphocele fenestration in gynaecological cancer patients after retroperitoneal lymph node dissection as a first‐line treatment option
Authors: Radosa MP , Diebolder H , Camara O , Mothes A , Anschuetz J , Runnebaum IB
Published: January 2013

Objective

To evaluate laparoscopic lymphocele fenestration (LLF) as a first‐line treatment in gynaecological cancer patients with a history of retroperitoneal lymph node dissection (LND).

Design

Retrospective cohort study.

Setting

A tertiary referral centre.

Population

Patients who underwent LLF between January 2001 and December 2010 for a symptomatic lymphocele following retroperitoneal LND.

Methods

Surgical outcomes of 102 patients who underwent LLF at our hospital between January 2001 and December 2010 were analysed. Patients were identified using hospital database search software, and hand‐written and electronic charts were reviewed.

Main outcome measures

Outcomes included operating time, blood loss, conversion rate, intra‐ and postoperative complication rates, hospital stay and relapse rate.

Results

A total of 132 lymphoceles were fenestrated in 102 patients. The mean duration of surgery was 115.6 minutes and the average intraoperative blood loss per patient was 146 ml. The overall conversion rate to laparotomy was 7.8%. Intra‐ and postoperative complication rates were estimated at 9.8 and 5.9%, respectively. The rate of intraoperative and postoperative complications was significantly higher in patients after pelvic plus paraaortic LND (23.8%), compared with those after pelvic LND only (3.6%; P > 0.01). The mean follow‐up time was 60.4 months and a total of seven symptomatic recurrences of lymphoceles were observed (a recurrence rate of 6.9%).

Conclusions

For the treatment of symptomatic lymphoceles, LLF has previously been established as an efficient first‐line treatment option in a post‐transplant context. Our data suggest that these favourable results for LLF may be transferable to gynaecological cancer patients.
Outcome of severe placental insufficiency with abnormal umbilical artery Doppler prior to fetal viability
Authors: Simonazzi G , Curti A , Cattani L , Rizzo N , Pilu G
Published: January 2013

Objective

To evaluate the outcome of pregnancies complicated by placental insufficiency and abnormal umbilical artery Doppler prior to viability.

Design

A retrospective cohort study.

Setting

Italy.

Population

Singleton pregnancies with fetal growth restriction and absence of end‐diastolic velocities (AEDVs) in the umbilical arteries prior to 24 weeks.

Methods

A retrospective cohort study of singleton pregnancies with fetal growth restriction and AEDVs in the umbilical arteries prior to 24 weeks.

Main outcome measures

Fetal growth restriction and AEDVs in the umbilical arteries prior to 24 weeks.

Results

Of 16 fetuses first seen at 20–23 weeks, only 12 survived and one of these developed cerebral palsy. Severe hypertensive disorders occurred in three mothers. In four women, the Doppler waveforms progressively improved and developed a normal pulsatility. These fetuses had a better outcome than those that had persistent alterations: they were delivered later (34 versus 28 weeks), had a larger birthweight (1598 versus 630 g) and developed fewer complications.

Conclusions

Placental insufficiency with AEDV in the umbilical arteries prior to fetal viability is associated with a high probability of perinatal death and neonatal complications. However, progressive amelioration of Doppler indices occurs in a subset of women, and these fetuses have a much better outcome.
Diapause development in early and late emerging phenotypes of Delia floralis
Authors: Johansen Tor J. , Meadow Richard
Published: January 2013

The turnip fly, Delia floralis Fallén (Diptera: Anthomyiidae) is an important insect pest of brassica vegetable crops in the holarctic region. Different populations have strongly varying temperature requirements for fly emergence, a challenge for accurate prediction of activity. This study focused on diapause development in one early and one late emerging phenotype. The physiological state after various treatments was deduced from emergence data. Our results showed a slow diapause progression at chilling conditions for both populations and diapause ended about 7 months after pupae were formed for the early population. For the late population held at 4°C diapause did not end, no matter how long the duration of chilling. These pupae required a period with elevated temperatures above 6°C to continue development. At constant non‐chilling conditions (18°C) from the time pupae were formed both populations completed diapause most rapidly. These results indicate that chilling delayed, rather than accelerated development and was not a prerequisite for diapause development. For post‐diapause, results indicated a linear relationship between rate of development and temperature within the range of 6–18°C and a theoretical base temperature for development of about 2°C for both populations. In conclusion, D. floralis pupae are in diapause throughout a long winter period, and delayed emergence of the late population appears to be caused by prolonged diapause regulated by a developmental temperature threshold. The study has added information on the biology of turnip fly populations, a prerequisite for improved pest control.
Ion Torrent‐based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high‐performance liquid chromatography a promising rRNA depletion method
Authors: Castro Thiago L. P. , Seyffert Nubia , Ramos Rommel T. J. , Barbosa Silvanira , Carvalho Rodrigo D. O. , Pinto Anne Cybelle , Carneiro Adriana Ribeiro , Silva Wanderson Marques , Pacheco Luis G. C. , Downson Christopher , Schneider Maria P. C. , Miyoshi Anderson , Azevedo Vasco , Silva Artur
Published: January 2013

Corynebacterium pseudotuberculosis equi is a Gram‐positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse‐breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large‐scale assessment of genes throughout distinct isolates. Meanwhile, the RNA‐seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high‐performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.
Carbon Isotopic Evolution of the Late Ediacaran Gaojiashan Biota on the Northern Yangtze Platform, South China
Authors: Qingjun GUO , Yinan DENG , Xinglian YANG
Published: January 2013

Metazoan fossils in the Gaojiashan Biota are famous for being well preserved and may provide new insights into the early evolution and skeletonization of Metazoans. We are studying the isotopic compositions of organic and carbonate carbon from a sequence of sedimentary rocks at the Gaojiashan section, northern Yangtze Platform, Shaanxi Province of China. Organic carbon isotope values display a range between −30.8‰ and −24.7‰ with clear stratigraphic variations. Carbonate carbon isotope data vary between 0.1‰ and +6‰. Positive δ13C values from sediments with Gaojiashan biota reflect temporal variations in carbon turnover, i.e. an increasing in photosynthetic carbon fixation followed by an increasing subsequent fractional organic carbon burial, and that related to bio‐radiation such as increasing algae, bacteria, and original creatures productivity in biomass. These secular variations are interpreted to reflect perturbations of the regional carbon cycle, specifically changes in the fractional burial of organic carbon, and discuss the relationship between Gaojiashan biota and paleoenvrionmental variation.
Helium, Argon and Carbon Isotopic Compositions of Spring Gases in the Hainan Island, China
Authors: Sheng XU , Guodong ZHENG , Yongchang XU
Published: January 2013

Chemical and isotopic compositions have been measured for N2‐He‐rich bubbling gases discharging from hot springs in the Hainan Island, Southern China. Observed 3He/4He ratios (0.1–1.3 RA) indicate the occurrence of a mantle component throughout the island, which has been highly diluted by a crustal radiogenic 4He component. The occurrence of mantle‐derived helium is high in the northern island (12%–16% of total He) and gradually decreases towards southern coast (l%–3% of total He). Such a distribution pattern is most likely controlled by the Pleocene‐Quaternary volcanic activities in the northern island and groundwater circulation along the deep major faults. The 40Ar/36Ar and N2/Ar ratios suggest that N2 and Ar of the hot spring gases are mostly meteoric. Although δ13C values of CO2 (–20‰ to −27‰) with low concentrations are consistent with the biogenic origin, the combination of 3He/4He and δ13CCO2 suggests a two end‐member mixing of mantle and crustal components with CO2/3He ratios of 2×109 and 8×1011, respectively. However, the low CO2/3He ratios (1–22×106) can not be ascribed in terms of the simple mixing but has to be explained by the addition of radiogenic 4He and loss of CO2 by calcite precipitation in the hydrothermal system, which is most likely controlled by the degree of gas‐water‐rock interaction.
The depositional Environment at Shuidonggou Locality 2 in Northwest China at ∼72–18 kaBP
Authors: Decheng LIU , Xing GAO , Enfa LIU , Shuwen PEI , Fuyou CHEN , Shuqin ZHANG
Published: January 2013

Shuidonggou site has abundant Paleolithic remains of Late Pleistocene deposition. Studying the evolution of depositional environments is essential to the comprehensive understanding of the living conditions of ancient populations. To reconstruct the depositional environment at Shuidonggou, we carried out archaeological excavations and collected systematic deposition samples at the key position of Shuidonggou Locality 2 for grain size analysis and sporopollen statistics. The environmental evolution around the Shuidonggou site generally underwent four stages at ∼72–18 kaBP. During the first stage (∼72–41 kaBP), the river developed with gravel and sand stratums. During the second stage (41∼34 kaBP), a swamp with numerous aquatic plants formed. In the third stage (34–29 kaBP), site formation was characterized by shallow lake depositional conditions; the climate was relatively warm and humid. The marginal bank depositional conditions deteriorated during the fourth stage (29–18 kaBP), and the site underwent several dry events; the climate also became drier and colder.
Dismantling the Mantel tests
Authors: Guillot Gilles , Rousset François
Published: January 2013

The simple and partial Mantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two or more matrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables displaying some form of structure.

We show that contrary to a widely shared belief, partial Mantel tests are not valid in this case, and their bias remains close to that of the simple Mantel test.

We confirm that strong biases are expected under a sampling design and spatial correlation parameter drawn from an actual study.

The Mantel tests should not be used in case autocorrelation is suspected in both variables compared under the null hypothesis. We outline alternative strategies. The R code used for our computer simulations is distributed as supporting material.