bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct Roles for Mitogen-Activated Protein Kinase Signaling and CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 in Regulating the Peak Time and Amplitude of the Plant General Stress Response
Authors: Bjornson Marta , Benn Geoffrey , Song Xingshun , Comai Luca , Franz Annaliese K. , Dandekar Abhaya M. , Drakakaki Georgia , Dehesh Katayoon
Published: August 2014

To survive environmental challenges, plants have evolved tightly regulated response networks, including a rapid and transient general stress response (GSR), followed by well-studied stress-specific responses. The mechanisms underpinning the GSR have remained elusive, but a functional cis-element, the rapid stress response element (RSRE), is known to confer transcription of GSR genes rapidly (5 min) and transiently (peaking 90–120 min after stress) in vivo. To investigate signal transduction events in the GSR, we used a 4xRSRE:LUCIFERASE reporter in Arabidopsis (Arabidopsis thaliana), employing complementary approaches of forward and chemical genetic screens, and identified components regulating peak time versus amplitude of RSRE activity. Specifically, we identified a mutant in CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) with reduced RSRE activation, verifying this transcription factor’s role in activation of the RSRE-mediated GSR. Furthermore, we isolated a mutant in MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) KINASE KINASE1 (mekk1-5), which displays increased basal and an approximately 60-min earlier peak of wound-induced RSRE activation. The double mekk1/camta3 mutant positioned CAMTA3 downstream of MEKK1 and verified their distinct roles in GSR regulation. mekk1-5 displays programmed cell death and overaccumulates reactive oxygen species and salicylic acid, hallmarks of the hypersensitive response, suggesting that the hypersensitive response may play a role in the RSRE phenotype in this mutant. In addition, chemical inhibition studies suggest that the MAPK network is required for the rapid peak of the RSRE response, distinguishing the impact of chronic (mekk1-5) from transient (chemical inhibition) loss of MAPK signaling. Collectively, these results reveal underlying regulatory components of the plant GSR and further define their distinct roles in the regulation of this key biological process.
The Role of a Potassium Transporter OsHAK5 in Potassium Acquisition and Transport from Roots to Shoots in Rice at Low Potassium Supply Levels
Authors: Yang Tianyuan , Zhang Song , Hu Yibing , Wu Fachi , Hu Qingdi , Chen Guang , Cai Jing , Wu Ting , Moran Nava , Yu Ling , Xu Guohua
Published: August 2014

In plants, K transporter (KT)/high affinity K transporter (HAK)/K uptake permease (KUP) is the largest potassium (K) transporter family; however, few of the members have had their physiological functions characterized in planta. Here, we studied OsHAK5 of the KT/HAK/KUP family in rice (Oryza sativa). We determined its cellular and tissue localization and analyzed its functions in rice using both OsHAK5 knockout mutants and overexpression lines in three genetic backgrounds. A β-glucuronidase reporter driven by the OsHAK5 native promoter indicated OsHAK5 expression in various tissue organs from root to seed, abundantly in root epidermis and stele, the vascular tissues, and mesophyll cells. Net K influx rate in roots and K transport from roots to aerial parts were severely impaired by OsHAK5 knockout but increased by OsHAK5 overexpression in 0.1 and 0.3 mm  K external solution. The contribution of OsHAK5 to K mobilization within the rice plant was confirmed further by the change of K concentration in the xylem sap and K distribution in the transgenic lines when K was removed completely from the external solution. Overexpression of OsHAK5 increased the K-sodium concentration ratio in the shoots and salt stress tolerance (shoot growth), while knockout of OsHAK5 decreased the K-sodium concentration ratio in the shoots, resulting in sensitivity to salt stress. Taken together, these results demonstrate that OsHAK5 plays a major role in K acquisition by roots faced with low external K and in K upward transport from roots to shoots in K-deficient rice plants.
DLSR design and plans: an international overview
Authors: Hettel Robert
Published: August 2014

It has been known for decades that the emittance of multi-GeV storage rings can be reduced to very small values using multi-bend achromat (MBA) lattices. However, a practical design of a ring having emittance approaching the diffraction limit for multi-keV photons,i.e.a diffraction-limited storage ring (DLSR), with a circumference of order 1 km or less was not possible before the development of small-aperture vacuum systems and other accelerator technology, together with an evolution in the understanding and accurate simulation of non-linear beam dynamics, had taken place. The 3-GeV MAX IV project in Sweden has initiated a new era of MBA storage ring light source design,i.e.a fourth generation, with the Sirius project in Brazil now following suit, each having an order of magnitude smaller horizontal emittance than third-generation machines. The ESRF, APS and SPring-8 are all exploring 6-GeV MBA lattice conversions in the imminent future while China is considering a similar-energy green-field machine. Other lower-energy facilities, including the ALS, SLS, Soleil, Diamond and others, are studying the possibility of such conversions. Future larger-circumference rings, possibly housed in >2-km tunnels made available by decommissioned high-energy physics accelerators, could have sub-10-pm-rad emittances, providing very high coherence for >10-keV X-rays. A review of fourth-generation ring design concepts and plans in the world is presented.
X-ray spectroscopy for chemical and energy sciences: the case of heterogeneous catalysis
Authors: Frenkel Anatoly I. , van Bokhoven Jeroen A.
Published: August 2014

Heterogeneous catalysis is the enabling technology for much of the current and future processes relevant for energy conversion and chemicals synthesis. The development of new materials and processes is greatly helped by the understanding of the catalytic process at the molecular level on the macro/micro-kinetic time scale and on that of the actual bond breaking and bond making. The performance of heterogeneous catalysts is inherently the average over the ensemble of active sites. Much development aims at unravelling the structure of the active site; however, in general, these methods yield the ensemble-average structure. A benefit of X-ray-based methods is the large penetration depth of the X-rays, enablingin situandoperandomeasurements. The potential of X-ray absorption and emission spectroscopy methods (XANES, EXAFS, HERFD, RIXS and HEROS) to directly measure the structure of the catalytically active site at the single nanoparticle level using nanometer beams at diffraction-limited storage ring sources is highlighted. The use of pump–probe schemes coupled with single-shot experiments will extend the time range from the micro/macro-kinetic time domain to the time scale of bond breaking and making.
Magnet design for a low-emittance storage ring
Authors: Johansson Martin , Anderberg Bengt , Lindgren Lars-Johan
Published: August 2014

The MAX IV 3 GeV storage ring, currently under construction, pursues the goal of low electron beam emittance by using a multi-bend achromat magnet lattice, which is realised by having several consecutive magnet elements precision-machined out of a common solid iron block, 2.3–3.4 m long. With this magnet design solution, instead of having 1320 individual magnets, the MAX IV 3 GeV storage ring is built up using 140 integrated `magnet block' units, containing all these magnet elements. Major features of this magnet block design are compactness, vibration stability and that the alignment of magnet elements within each unit is given by the mechanical accuracy of the CNC machining rather than individual field measurement and adjustment. This article presents practical engineering details of implementing this magnet design solution, and mechanical + magnetic field measurement results from the magnet production series. At the time of writing (spring 2014), the production series, which is totally outsourced to industry, is roughly half way through, with mechanical/magnetic QA conforming to specifications. It is the conclusion of the authors that the MAX IV magnet block concept, which has sometimes been described as new or innovative, is from a manufacturing point of view simply a collection of known mature production methods and measurement procedures, which can be executed at fixed cost with a low level of risk.
Building access for people with intellectual disability, dubious past, uncertain future
Authors: Castell Lindsay
Published: August 2014

Purpose

– The purpose of this paper is to report on the under-representation of people with intellectual disability (ID) in Australian building guidelines. It presents a view about causes of this under-representation and offers opinion about the current status and future actions required to redress the situation.

Design/methodology/approach

– Electronic databases were searched to determine the extent of research about building access by people with ID and for references to both the historical treatment of people with ID and the nature of ID itself.

Findings

– The paper suggests the recently released Disability (Access to Premises) Standards and associated building code give no specific attention to the needs of people with ID. It suggests that poor historical treatment combined with difficulties with self-advocacy may have contributed to the lack of attention given to the needs of this building user group. It also suggests the need for evidence-based research to identify and substantiate inclusion of their needs in future building regulation.

Research limitations/implications

– There may be unpublished research and/or discussion covering the topic not retrievable through literature searches.

Practical implications

– While much has been written about adjustments to provide access for people with physical and sensory disabilities, more attention needs to be paid to the needs of those with ID to avoid inequities in building design.

Originality/value

– There is limited reference to building access for people with ID in literature and legislation. This paper adds to the literature and raises awareness of the ongoing need for greater inclusion.
Examination of student housing preferences, their similarities and differences
Authors: Khozaei Fatemeh , Hassan Ahmad Sanusi , Al Kodmany Kheir , Aarab Yasser
Published: August 2014

Purpose

– The aim of this paper is to identify the university student’s preferences for some important attributes of residence hall design. The study also attempts to highlight the differences and similarities in student’s preferences.

Design/methodology/approach

– The survey was distributed among students who were living in residence halls of a public university in Malaysia. A total of 752 students were recruited as participants. Data were collected using a self-administrated questionnaire. Students were asked to indicate their preferences rating a 4-point scale. The survey included questions concerning students’ preferences for residing in traditional and suite-style residence halls, single room and double room as well as rooms in which each student’s area is marked clearly. Collected data were analysed using PASW Statistics 17.

Findings

– The results indicated that, in total, students highly preferred residing in suite-style to traditional residence halls. Staying in a single room with shared bathroom was also preferred to double-sharing room. The results of study also indicated that living in a room in which each student ' s area is marked clearly is of great interest. The study proved significant differences in the students’ preferences based on their gender, nationality and study level.

Practical implications

– The outcome of this study can enhance the awareness of residence hall organizers and architects with regard to some of students’ priorities.

Originality/value

– The results give an important insight into student’s preferences towards their residence hall. The study provides statistic evidence unfavourably of traditional residence halls among the students of new generation. It also provides an insight into students ' greater needs and requirements for privacy.
Freedom and control: a state of balance in public space
Authors: Zhao Tianjiao , Siu Kin Wai Michael
Published: August 2014

Purpose

– The purpose of this study is to determine how to achieve a balance between freedom and control in public space. It analyses the relationship between freedom and control to identify phenomena and offer users and policymakers instructions for achieving that balance. Public space, including privately owned public space, is important to urban living. People have both the right to use public space and the responsibility to protect it. Both freedom and control should exist in public space in an appropriate combination. It is impossible and inappropriate for us to ask for absolute freedom or endure unreasonable control.

Design/methodology/approach

– A case study of Hong Kong’s Mass Transit Railway (MTR) reveals typical freedom/control relationships. Quantitative descriptions are given based on field observations.

Findings

– Freedom and control are primary factors affecting the quality of urban life and management of city space. They depend on and conflict with each other. The balance between freedom and control is a balance between diverse spaces. The “freedom space” belonging to both citizens and authorities determines whether freedom and control are balanced. Ethics and strategies constitute control. Only when each authority and user obtains a proper freedom space can freedom and control achieve balance in public space.

Research limitations/implications

– Freedom and control differ across cities because they are both affected by culture, history and tradition. As each city has its own characteristics, the freedom and control in each open space are distinctive. Balancing freedom and control requires an understanding of a city’s background and the era. While this paper does not attempt to achieve this understanding, further studies could devote more attention to dimensions of time and location.

Practical implications

– The findings provide recommendations for users, policymakers and construction and management companies that will allow the management of harmonious and high-quality open spaces.

Social implications

– Freedom and control are two main factors affecting quality of life. The balance between freedom and control may bring a harmony and stable society environment. It would benefit both the authority and the people a lot.

Originality/value

– This study provides a systematic analysis of freedom and control in public space and makes a valuable contribution to quality urban space policy, design and management.
Private finance initiative as a new way to manage public facilities
Authors: Wang Nannan
Published: August 2014

Purpose

– This paper aims to analyse the findings of the relevant studies, to summarise what has been done in this area, to direct future research and to improve private finance initiative (PFI) practice. PFI is a new form of contracting out public facilities to the private sector, where facility management was integrated with construction. There have been a large number of academic papers published on this subject; however, there is a lack of a systematic review of the PFI-related studies.

Design/methodology/approach

– The literature search focused on international peer-reviewed and published literature, with relevance to PFI. The search of literature, following the method of Tang et al. (2010) and Al-Sharif and Kaka (2004), involved the titles, keywords and abstracts, from some major electronic databases (Web of Science, Engineering Village, Science Direct (Elsevier) and Springer Link) of publications published between 1992 and 2011. The data were classified into six categories for further analysis.

Findings

– As a new way to procure public facility management, PFI projects have unique characteristics in comparison to conventional construction procurement. The review of the literature regarding PFI is important in terms of summarising the key findings and suggestions of studies for industry practitioners, as well as forecasting the future academic research trends in this area. The number of research works on PFI increased quickly in recent years; however, the review discovered there were still some issues not yet covered in the literature.

Research limitations/implications

– This review is not exhaustive in nature, as the criteria in selecting research papers only included English-written, peer-reviewed journals from some major electronic literature databases. This is the limitation of the research. Further review on a wider range of literature is recommended for researchers.

Originality/value

– Since PFI was introduced to the construction industry to fund infrastructure 20 years ago in the UK, it has gained interests from scholars. In this new form of contracting out public facilities to the private sector, facility management was integrated with construction. There have been a large number of academic papers published on this subject; however, there is a lack of a systematic review of the PFI studies.
Knowledge based governance, governance as learning: the leadership implications
Authors: Schwella Erwin
Published: August 2014

Purpose

– The purpose of this paper is to argue that effective and ethical governance and government can and should benefit from many influences and inputs. These influences and inputs, in the form of evidence, information, knowledge and informed public participation contribute to the quality and legitimacy of government analysis and action.

Design/methodology/approach

– The approach in this viewpoint is to use persuasive communication in an advocacy and illustrative way to introduce learning governance as an approach to governance.

Findings

– The viewpoint states the case for the usefulness and relevance of evidence and ideas based learning governance linked to learning leadership in governance for effective and ethical leadership in governance.

Originality/value

– The value of the viewpoint is to stimulate and elicit discussion and debate on learning governance and leadership as approach to governance leadership.
Information systems an alternative to modernization to achieve in the control of management of municipal public services
Authors: Patiño Israel
Published: August 2014

Purpose

– Information systems (IS) in the public environment largely depend on a needs analysis for their successful integration. This is more likely lead to an improvement in the management control of municipal public services (MPSs) with the help of scientific and technological methodologies, based on both qualitative and quantitative methods. The paper aims to discuss these issues.

Design/methodology/approach

– The data were obtained through field research techniques such as interviews and observation and applying this in each of the municipalities, and complemented by 196 citizen surveys.

Findings

– An outcome of this research is the implementation of a specific IS to improve administrative and operational processes based on data collected in six municipalities. This implies not only technological but also cultural evolution, since the incorporation of the IS impacts both municipal authorities and society as a whole.

Originality/value

– This research is based on the need to develop IS to improve management control of MPSs and thus meet the needs of population, and in turn, support the municipal authorities.
Implementation of quality management system based on ISO9001:2008 and its effects on customer satisfaction case study
Authors: Nabavi Vahid , Azizi Majid , Faezipour Mehdi
Published: August 2014

Purpose

– The purpose of this paper is to discuss the effect of the ISO 9001 quality management system on customer satisfaction and show an application of an analytic hierarchy process (AHP)-based method for measuring the customer satisfaction index (CSI). This will be useful to anyone who wants to have an ISO 9001 quality management system in his or her organization.

Design/methodology/approach

– This paper describes an ISO 9001 quality management implementation process based on ISO 9001 requirements, and uses the AHP method for weighting effective criteria on customer satisfaction. All data were obtained via questionnaires and assessed with EXPERT CHOICE 11 software.

Findings

– According to the results of the weighting, the factors influencing the satisfaction of a kitchen worktops customer, price and sales terms of this product has a significant impact on customer satisfaction and, in competitive conditions, this criterion has a determining role in the creation of utility for customers. ISO 9001 quality management system has been able to increase the CSI within an 11-month period of study.

Originality/value

– This paper is the first to use the AHP method with a new approach in a case study, offering a complete, comprehensive method for assessing customer implications.
Implementing total quality management (TQM) in the Palestinian construction industry
Authors: Maher Altayeb Mustafa , Bashir Alhasanat Mahmoud
Published: August 2014

Purpose

– The construction industry has been one of the most important industries for the development of the Palestinian infrastructure and economy. Total quality management (TQM) is considered one of the most important approaches to the success of construction industry. The purpose of this paper is to determine the success factors necessary for the implementation of TQM at various phases of project planning, design and construction in the Gaza Strip.

Design/methodology/approach

– A computer model was developed to assess the current strengths and weaknesses of each component of the construction industry, such as owner, consultant and contractor, regarding their use of quality management methodologies.

Findings

– The research determined a total of eight major factors and 81 sub-factors. It was identified that seven critical success factors with 38 significant sub-factors were required for the successful implementation of TQM in Gaza Strip construction organizations.

Originality/value

– An original assessment of the importance of TQM in the construction industry in Palestine. The computer model shows the strengths and weaknesses of stakeholders within the industry.
Determination of Bayesian reliability sampling plans based on exponential-inverted gamma distribution
Authors: Appaia Loganathan , Muthu Krishnan Padmanaban , Kalaiselvi Sankaran
Published: August 2014

Purpose

– The purpose of this paper is the determination of reliability sampling plans in the Bayesian approach assuming that the lifetime distribution is exponential.

Design/methodology/approach

– Sampling plans are used in manufacturing companies as a tool for carrying out sampling inspections, in order to make decisions about the disposition of many finished products. If the quality characteristic is considered as the lifetime of the products, the plan is known as a reliability sampling plan. In life testing, censoring schemes are adopted in order to save time and cost of life test. The inverted gamma distribution is employed as the natural conjugate prior to the average lifetime of the products. The sampling plans are developed assuming various probability distributions to the lifetime of the products.

Findings

– The optimum plansnandcare obtained for some sets of values of (p1,a,p2,ß). The selection of sampling plans is illustrated through numerical examples.

Originality/value

– Results obtained in this paper are original and the study has been done for the first time in this regard. Reliability sampling plans are essential for making decisions either to accept or reject based on the inspection of the sample.
Critical thinking, information literacy and quality enhancement plans
Authors: E. Bryan Jacalyn
Published: August 2014

Purpose

– This paper aims to investigate the relationship between information literacy and critical thinking. Specifically, the connection between the elements of critical thinking as expressed in one university’s Quality Enhancement Plan (QEP) and the advancing learning transforming scholarship (ACRL) Information Literacy Competency Standards (ACRL IL Standards). Concrete examples of how librarians support information literacy and critical thinking were examined.

Design/methodology/approach

– Following a literature review, the ACRL IL Standards were mapped to the elements of a university’s QEP (critical thinking + core values = decision-making). A wiki was then created to illicit specific examples from librarians regarding how they incorporate the elements of critical thinking in their reference/instruction work.

Findings

– Considerable correspondence was found between the ACRL IL Standards and the elements of critical thinking in the QEP, but this varied with the specific standard and the specific QEP component. Wiki results revealed that librarians used many concrete activities that supported QEP critical-thinking elements.

Research limitations/implications

– In this study, mapping the ACRL IL Standards to QEP components was subjective, performed by only one individual. Future research, perhaps involving the forthcoming ACRL IL Standards, might be better carried out by a larger group, thereby enhancing objectivity.

Originality/value

– The literature review showed a lack of specificity in how critical thinking is defined and integrated into library reference/instruction work. The present study compared eight specific elements of critical thinking to the ACRL IL Standards and found 108 concrete examples of their application.
Old wine in a new bottle: customer orientation in librarianship
Authors: Matteson Miriam , Boyden Cynthia
Published: August 2014

Purpose

– The purpose of the paper is to explore the research on the personality trait of customer orientation (CO) and consider how it may be applicable to customer service work in libraries.

Design/methodology/approach

– The paper reviews business research literature on CO and relates it to library science literature on customer service.

Findings

– CO is a measurable personality trait that is shown to predict customer service behaviors in service employees. Research also shows that CO is associated with customers’ perceptions of service quality.

Practical implications

– Libraries should prioritize CO in their hiring, training and recognition processes.

Originality/value

– CO is a well-researched personality trait in the business literature. The original contribution of this paper is to report the research on customer orientation, relate it to similar concepts in librarianship and suggest ways libraries can integrate an awareness of CO in their human resources processes.
Reference inquiries received through different channels
Authors: Emmanuel Baro Ebikabowei , U. Efe Bueaty , K. Oyeniran Gboyega
Published: August 2014

Purpose

– This study aims to investigate the different channels reference librarians receive reference inquiries from patrons in university libraries in Nigeria.

Design/methodology/approach

– A questionnaire was used to collect data on the various channels through which reference librarians received reference inquiries in Nigerian university libraries. The questionnaire was administered using an online method.

Findings

– It emerged that the face-to-face traditional reference desk was rated as the highest channel through which librarians receive reference inquiries in Nigeria, followed by library Facebook page and phone/short message service (SMS). Instant messaging (IM) and e-mail were identified as the least used channels by the patrons. The challenges mentioned include the absence of policy statements concerning virtual reference services; the lack of information and communications technology (ICT) skills on the part of librarians; slow Internet connectivity; power failures; management’s lack of support for emerging technologies; IM’s limitations; user’s expectations of instant answer; inarticulate requests; and lack of adequate current reference materials.

Research limitations/implications

– The findings are from a small sample size; therefore, the findings may not be substantial enough to generalize. Further study is necessary to determine if these results are consistent throughout other university libraries in Nigeria.

Originality/value

– The findings will inform university libraries in developing countries that are planning to adopt virtual reference services to deliver reference services to users anywhere, anytime.
Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment
Authors: Hilker Rolf , Munder Antje , Klockgether Jens , Losada Patricia Moran , Chouvarine Philippe , Cramer Nina , Davenport Colin F. , Dethlefsen Sarah , Fischer Sebastian , Peng Huiming , Schönfelder Torben , Türk Oliver , Wiehlmann Lutz , Wölbeling Florian , Gulbins Erich , Goesmann Alexander , Tümmler Burkhard
Published: August 2014

The population genomics of Pseudomonas aeruginosa was analysed by genome sequencing of representative strains of the 15 most frequent clonal complexes in the P. aeruginosa population and of the five most common clones from the environment of which so far no isolate from a human infection has been detected. Gene annotation identified 5892–7187 open reading frame (ORFs; median 6381 ORFs) in the 20 6.4–7.4 Mbp large genomes. The P. aeruginosa pangenome consists of a conserved core of at least 4000 genes, a combinatorial accessory genome of a further 10 000 genes and 30 000 or more rare genes that are present in only a few strains or clonal complexes. Whole genome comparisons of single nucleotide polymorphism synteny indicated unrestricted gene flow between clonal complexes by recombination. Using standardized acute lettuce, Galleria mellonella and murine airway infection models the full spectrum of possible host responses to P. aeruginosa was observed with the 20 strains ranging from unimpaired health following infection to 100% lethality. Genome comparisons indicate that the differential genetic repertoire of clones maintains a habitat‐independent gradient of virulence in the P. aeruginosa population.
The novel catabolic pathway of 3,6‐anhydro‐L‐galactose, the main component of red macroalgae, in a marine bacterium
Authors: Yun Eun Ju , Lee Saeyoung , Kim Hee Taek , Pelton Jeffrey G. , Kim Sooah , Ko Hyeok‐Jin , Choi In‐Geol , Kim Kyoung Heon
Published: August 2014

The catabolic fate of the major monomeric sugar of red macroalgae, 3,6‐anhydro‐L‐galactose (AHG), is completely unknown in any organisms. AHG is not catabolized by ordinary fermentative microorganisms, and it hampers the utilization of red macroalgae as renewable biomass for biofuel and chemical production. In this study, metabolite and transcriptomic analyses of Vibrio sp., a marine bacterium capable of catabolizing AHG as a sole carbon source, revealed two key metabolic intermediates of AHG, 3,6‐anhydrogalactonate (AHGA) and 2‐keto‐3‐deoxy‐galactonate; the corresponding genes were verified in vitro enzymatic reactions using their recombinant proteins. Oxidation by an NADP+‐dependent AHG dehydrogenase and isomerization by an AHGA cycloisomerase are the two key AHG metabolic processes. This newly discovered metabolic route was verified in vivo by demonstrating the growth of Escherichia coli harbouring the genes of these two enzymes on AHG as a sole carbon source. Also, the introduction of only these two enzymes into an ethanologenic E. coli strain increased the ethanol production in E. coli by fermenting both AHG and galactose in an agarose hydrolysate. These findings provide not only insights for the evolutionary adaptation of a central metabolic pathway to utilize uncommon substrates in microbes, but also a metabolic design principle for bioconversion of red macroalgal biomass into biofuels or industrial chemicals.
A vapBC‐type toxin–antitoxin module of Sinorhizobium meliloti influences symbiotic efficiency and nodule senescence of Medicago sativa
Authors: Lipuma Justine , Cinege Gyöngyi , Bodogai Monica , Oláh Boglárka , Kiers Aurélie , Endre Gabriella , Dupont Laurence , Dusha Ilona
Published: August 2014

The symbiotic nitrogen‐fixing soil bacterium Sinorhizobium meliloti carries a large number of toxin–antitoxin (TA) modules both on the chromosome and megaplasmids. One of them, the vapBC‐5 module that belongs to the type II systems was characterized here. It encodes an active toxin vapC‐5, and was shown to be controlled negatively by the complex of its own proteins. Different mutants of the vapBC‐5 genes exhibited diverse effects on symbiotic efficiency during interaction with the host plant Medicago sativa. The absence of the entire vapBC‐5 region had no influence on nodule formation and nitrogen fixation properties. The strain carrying an insertion in the antitoxin gene showed a reduced nitrogen fixation capacity resulting in a lower plant yield. In contrast, when the toxin gene was mutated, the strain developed more efficient symbiosis with the host plant. The nitrogen fixing root nodules had a delayed senescent phenotype and contained elevated level of plant‐derived molecules characteristic of later steps of nodule development. The longer bacteroid viability and abundance of active nitrogen fixing zone resulted in increased production of plant material. These data indicate that modification of the toxin/antitoxin production may influence bacteroid metabolism and may have an impact on the adaptation to changing environmental conditions.
The heat shock transcription factor PsHSF1 of Phytophthora sojae is required for oxidative stress tolerance and detoxifying the plant oxidative burst
Authors: Sheng Yuting , Wang Yonglin , Meijer Harold J. G. , Yang Xinyu , Hua Chenlei , Ye Wenwu , Tao Kai , Liu Xiaoyun , Govers Francine , Wang Yuanchao
Published: August 2014

In the interaction between plant and microbial pathogens, reactive oxygen species (ROS) rapidly accumulate upon pathogen recognition at the infection site and play a central role in plant defence. However, the mechanisms that plant pathogens use to counteract ROS are still poorly understood especially in oomycetes, filamentous organisms that evolved independently from fungi. ROS detoxification depends on transcription factors (TFs) that are highly conserved in fungi but much less conserved in oomycetes. In this study, we identified the TF PsHSF1 that acts as a modulator of the oxidative stress response in the soybean stem and root rot pathogen Phytophthora sojae. We found that PsHSF1 is critical for pathogenicity in P. sojae by detoxifying the plant oxidative burst. ROS produced in plant defence can be detoxified by extracellular peroxidases and laccases which might be regulated by PsHSF1. Our study extends the understanding of ROS detoxification mechanism mediated by a heat shock TF in oomycetes.
Cold‐active bacteriophages from the Baltic Sea ice have diverse genomes and virus–host interactions
Authors: Senčilo Ana , Luhtanen Anne‐Mari , Saarijärvi Mikko , Bamford Dennis H. , Roine Elina
Published: August 2014

Heterotrophic bacteria are the major prokaryotic component of the Baltic Sea ice microbiome, and it is postulated that phages are among their major parasites. In this study, we sequenced the complete genomes of six earlier reported phage isolates from the Baltic Sea ice infecting Shewanella sp. and Flavobacterium sp. hosts as well as characterized the phage–host interactions. Based on the genome sequences, the six phages were classified into five new genera. Only two phages, 1/4 and 1/40, both infecting Shewanella sp. strains, showed significant nucleotide sequence similarity to each other and could be grouped into the same genus. These two phages are also related to Vibrio‐specific phages sharing approximately 25% of the predicted gene products. Nevertheless, cross‐titrations showed that the cold‐active phages studied are host specific: none of the seven additionally tested, closely related Shewanella strains served as hosts for the phages. Adsorption experiments of two Shewanella phages, 1/4 and 3/49, conducted at 4°C and at 15°C revealed relatively fast adsorption rates that are, for example, comparable with those of phages infective in mesophilic conditions. Despite the small number of Shewanella phages characterized here, we could already find different types of phage–host interactions including a putative abortive infection.
Stereotactic body radiotherapy for primary prostate cancer: A systematic review
Authors: Tan Tze‐Jian , Siva Shankar , Foroudi Farshad , Gill Suki
Published: August 2014

Stereotactic body radiotherapy (SBRT) for prostate cancer allows overall treatment times to be reduced to as little as 1 week while maintaining a non‐invasive approach. This study provides a comprehensive summary of the literature relating to SBRT in prostate cancer. A systematic review of the relevant literature was performed using structured search terms. Fourteen phase I–II trials and retrospective studies using SBRT for the treatment of prostate cancer were used. Three studies were identified which addressed cost. Dose fractionation, radiotherapy procedures, biochemical progression‐free survival, toxicity, cost and quality of life were critically appraised. A total of 1472 patients were examined across studies. Median follow‐up ranged from 11 to 60 months. The most common dose fractionation was 35–36.25 Gy in five fractions, used in nine out of 14 studies. Ten of 14 studies used CyberKnife. The overall biochemical progression‐free survival ranged 81–100%. Acute grade 2 urinary and rectal toxicities were reported in 5–42% and 0–27% of patients, respectively. Acute grade 3 or more urinary and rectal toxicity were 0.5% and 0%, respectively. Late grade 2 urinary toxicity was reported in 0–29% of patients, while 1.3% had a late grade 3 urinary toxicity. There were no late grade 4 urinary toxicities seen. Late grade 2 rectal toxicity was reported in 0–11%, while 0.5% had a late grade 3 rectal toxicity. Late grade 4 rectal toxicity was reported in 0.2% of patients.
Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China
Authors: Chen Juan , Zhao Jietang , Erickson David L. , Xia Nianhe , Kress W. John
Published: August 2014

The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear‐cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH‐psbA and trnL‐F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra‐ and inter‐specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH‐psbA (100%), trnL‐F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH‐psbA and trnL‐F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.
A generalized residual technique for analysing complex movement models using earth mover's distance
Authors: Potts Jonathan R. , Auger‐Méthé Marie , Mokross Karl , Lewis Mark A.
Published: August 2014

Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences. Predicting their behaviour often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity. Although tools exist to determine which of a set of candidate models is best relative to the others, there is currently no generic goodness‐of‐fit framework for testing how close the best model is to the real complex stochastic system.

We propose such a framework, using a novel application of the Earth mover's distance, also known as the Wasserstein metric. It is applicable to any stochastic process where the probability of the model's state at time t is a function of the state at previous times. It generalizes the concept of a residual, often used to analyse 1D summary statistics, to situations where the complexity of the underlying model's probability distribution makes standard residual analysis too imprecise for practical use.

We give a scheme for testing the hypothesis that a model is an accurate description of a data set. We demonstrate the tractability and usefulness of our approach by application to animal movement models in complex, heterogeneous environments. We detail methods for visualizing results and extracting a variety of information on a given model's quality, such as whether there is any inherent bias in the model, or in which situations, it is most accurate. We demonstrate our techniques by application to data on multispecies flocks of insectivore birds in the Amazon rain forest.

This work provides a usable toolkit to assess the quality of generic movement models of complex systems, in an absolute rather than a relative sense.
Statistics for citizen science: extracting signals of change from noisy ecological data
Authors: Isaac Nick J. B. , van Strien Arco J. , August Tom A. , de Zeeuw Marnix P. , Roy David B.
Published: August 2014

Policy‐makers increasingly demand robust measures of biodiversity change over short time periods. Long‐term monitoring schemes provide high‐quality data, often on an annual basis, but are taxonomically and geographically restricted. By contrast, opportunistic biological records are relatively unstructured but vast in quantity. Recently, these data have been applied to increasingly elaborate science and policy questions, using a range of methods. At present, we lack a firm understanding of which methods, if any, are capable of delivering unbiased trend estimates on policy‐relevant time‐scales.

We identified a set of candidate methods that employ data filtering criteria and/or correction factors to deal with variation in recorder activity. We designed a computer simulation to compare the statistical properties of these methods under a suite of realistic data collection scenarios. We measured the Type I error rates of each method–scenario combination, as well as the power to detect genuine trends.

We found that simple methods produce biased trend estimates, and/or had low power. Most methods are robust to variation in sampling effort, but biases in spatial coverage, sampling effort per visit, and detectability, as well as turnover in community composition, all induced some methods to fail. No method was wholly unaffected by all forms of variation in recorder activity, although some performed well enough to be useful.

We warn against the use of simple methods. Sophisticated methods that model the data collection process offer the greatest potential to estimate timely trends, notably Frescalo and occupancy–detection models.

The potential of these methods and the value of opportunistic data would be further enhanced by assessing the validity of model assumptions and by capturing small amounts of information about sampling intensity at the point of data collection.
Overweight and Obesity Among Children and Adolescents with Fetal Alcohol Spectrum Disorders
Authors: Fuglestad Anita J. , Boys Christopher J. , Chang Pi‐Nian , Miller Bradley S. , Eckerle Judith K. , Deling Lindsay , Fink Birgit A. , Hoecker Heather L. , Hickey Marie K. , Jimenez‐Vega Jose M. , Wozniak Jeffrey R.
Published: August 2014

Background

Because prenatal alcohol exposure is associated with growth deficiency, little attention has been paid to the potential for overweight and obesity in children with fetal alcohol spectrum disorders (FASD). This study examined the prevalence of overweight/obesity (body mass index [BMI]) in a large clinical sample of children with FASD.

Methods

Children, aged 2 to 19 years, who were evaluated for FASD at University Clinics, included 445 with an FASD diagnosis and 171 with No‐FASD diagnosis. Prevalence of overweight/obesity (BMI ≥85 percentile) was compared to national and state prevalence. BMI was examined in relation to FASD diagnosis, gender, and age. Dietary intake data were examined for a young subsample (n = 42).

Results

Thirty‐four percent with any FASD diagnosis were overweight or obese, which did not differ from the No‐FASD group or U.S. prevalence. Underweight was prevalent in those with fetal alcohol syndrome (FAS) (17%). However, increased rates of overweight/obesity were seen in those with partial FAS (40%). Among adolescents, those with any FASD diagnosis had increased overweight/obesity (42%), particularly among females (50%). The rate in adolescent females with FASD (50%) was nearly 3 times higher than state prevalence for adolescent females (17 to 18%), p < 0.001. In the young subsample, those who were overweight/obese consumed more calories, protein, and total fat per day than those who were not overweight or obese.

Conclusions

Rates of overweight/obesity are increased in children with partial FAS. In adolescents, rates are increased for any FASD diagnosis (particularly in females). Results are suggestive of possible metabolic/endocrine disruption in FASD—a hypothesis for which there is evidence from animal models. These data suggest that clinicians may consider prenatal alcohol exposure as a risk factor for metabolic/endocrine disruption, should evaluate diet as a risk in this population, and may need to target interventions to females prior to puberty to effect changes in overweight‐related outcomes.
Antecedent Predictors of Children's Initiation of Sipping/Tasting Alcohol
Authors: Donovan John E. , Molina Brooke S. G.
Published: August 2014

Background

Sipping or tasting alcohol is one of the earliest alcohol‐use behaviors in which young children engage, yet there is relatively little research on this behavior. Previous cross‐sectional analyses determined that child sipping or tasting is associated with the child's attitude toward sipping and with a family environment supportive of alcohol use, but not with variables reflecting psychosocial proneness for problem behavior as formulated in Problem Behavior Theory (Jessor and Jessor, Problem Behavior and Psychosocial Development: A Longitudinal Study of Youth, 1977, Academic Press, New York). This study extended these analyses longitudinally to identify antecedent predictors of the childhood initiation of sipping or tasting alcohol in a multiwave study.

Methods

A sample of 452 children (238 girls) aged 8 or 10 and their families was drawn from Allegheny County, PA, using targeted‐age directory sampling and random digit dialing procedures. Children were interviewed using computer‐assisted interviews. Antecedent variables collected at baseline (Wave 1) were examined as predictors of the initiation of sipping/tasting alcohol in childhood (before age 12) among Wave 1 abstainers (n = 286).

Results

Ninety‐four children initiated sipping/tasting alcohol in a nonreligious context between baseline and turning age 12. Initiation of sipping/tasting did not generally relate to baseline variables reflecting psychosocial proneness for problem behavior. Instead, as found in the previous cross‐sectional analyses, the variables most predictive of initiating sipping/tasting were perceived parents' approval for child sipping, parents' reported approval for child sipping, parents' current drinking status, and children's attitudes toward sipping/tasting alcohol.

Conclusions

These longitudinal analyses replicate the earlier cross‐sectional results. Young children's sipping/tasting of alcohol reflects parental modeling of drinking and parental approval of child sipping and does not represent a precocious manifestation of a psychosocial proneness to engage in problem behavior.