bluuebunny/crossref_metadata_2025 huggingface dataset:
Sublethal effects of fluctuating hypoxia on juvenile tropical Australian freshwater fish
Authors: Flint Nicole , Crossland Michael R. , Pearson Richard G.
Published: November 2014

Hypoxia in freshwater ecosystems of the Australian wet tropics occurs naturally, but is increasing as a result of anthropogenic influences. Diel cycling of dissolved oxygen (DO) concentration (fluctuating hypoxia) is common in the region. Laboratory experiments sought to identify relationships between severity of fluctuating hypoxia and sublethal effects on ventilation, feeding and growth for juvenile barramundi (Lates calcarifer), eastern rainbowfish (Melanotaenia splendida splendida) and sooty grunter (Hephaestus fuliginosus). Fish continued to feed and grow under daily exposure to severe fluctuating hypoxia treatments for several weeks. Ventilation rates increased in a significant direct quadratic relationship with the severity of hypoxia treatments and increasing hypoxia caused ventilatory behaviour changes in all species. Barramundi and rainbowfish attempted aquatic surface respiration and were more tolerant of severe hypoxia than was sooty grunter; barramundi and rainbowfish are also more likely to experience hypoxia in the wild. There was a significant quadratic relationship between growth and minimum DO saturation for barramundi. Although all three species were tolerant of hypoxia, anthropogenic stressors on tropical Australian aquatic ecosystems may increase the frequency and severity of hypoxic conditions causing a concomitant increase in fish kill events.
WemIQ: an accurate and robust isoform quantification method for RNA-seq data
Authors: Zhang Jing , Kuo C.-C. Jay , Chen Liang
Published: November 2014

Motivation: The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms.

Results: We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads among isoforms efficiently. The weight represents the oversampling or undersampling of sequence reads and is estimated through a generalized Poisson model without any presumption on the bias sources and formats. WemIQ significantly improves the quantification of isoform and gene expression as well as the derived exon inclusion rates. It provides robust expression estimates across different laboratories and protocols, which is valuable for the integrative analysis of RNA-seq. For the recent single-cell RNA-seq data, WemIQ also provides the opportunity to distinguish bias heterogeneity from true biological heterogeneity and uncovers smaller cell-to-cell expression variability.

Availability and implementation: WemIQ can be downloaded from http://www-rcf.usc.edu/~liangche/software.html

Contact:  liang.chen@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
EPGA: de novo assembly using the distributions of reads and insert size
Authors: Luo Junwei , Wang Jianxin , Zhang Zhen , Wu Fang-Xiang , Li Min , Pan Yi
Published: November 2014

Motivation: In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficulty of genome assembly. The universally accepted solution is choosing one based on read overlaps and paired-end (mate-pair) reads. However, this solution faces difficulties with regard to some complex repetitive regions. In addition, sequencing errors may produce false repetitive regions and uneven sequencing depth leads some sequence regions to have too few or too many reads. All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.

Results: In this article, we develop an algorithm, called extract paths for genome assembly (EPGA), which extracts paths from De Bruijn graph for genome assembly. EPGA uses a new score function to evaluate extension candidates based on the distributions of reads and insert size. The distribution of reads can solve problems caused by sequencing errors and short repetitive regions. Through assessing the variation of the distribution of insert size, EPGA can solve problems introduced by some complex repetitive regions. For solving uneven sequencing depth, EPGA uses relative mapping to evaluate extension candidates. On real datasets, we compare the performance of EPGA and other popular assemblers. The experimental results demonstrate that EPGA can effectively obtain longer and more accurate contigs and scaffolds.

Availability and implementation: EPGA is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA.

Contact:  jxwang@csu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
High-Density Lipoprotein-Mediated Cholesterol Efflux Capacity Is Improved by Treatment With Antiretroviral Therapy in Acute Human Immunodeficiency Virus Infection
Authors: Lo Janet , Rosenberg Eric S. , Fitzgerald Michael L. , Bazner Suzane B. , Ihenachor Ezinne J. , Hawxhurst Victoria , Borkowska Alison H. , Wei Jeffrey , Zimmerman Chloe O. , Burdo Tricia H. , Williams Kenneth C. , Freeman Mason W. , Grinspoon Steven K.
Published: November 2014

Background.  Individuals infected with human immunodeficiency virus (HIV) have decreased high-density lipoprotein (HDL)-cholesterol and increased cardiovascular disease (CVD). Reverse cholesterol transport from macrophages may be inhibited by HIV and contribute to increased CVD. Human studies have not investigated longitudinal effects of HIV and antiretroviral therapy (ART) on cholesterol efflux.

Methods.  Subjects with acute HIV infection were randomized to ART or not. Cholesterol efflux capacity was determined ex vivo after exposure of murine macrophages to apolipoprotein B-depleted patient sera obtained at baseline and after 12 weeks.

Results.  After 12 weeks, HIV RNA decreased most in subjects randomized to ART. Available data on cholesterol demonstrated that efflux capacity from Abca1+/+ macrophages was increased most by sera obtained from ART-treated subjects (20.5% ± 5.0% to 24.3 % ± 6.9%, baseline to 12 weeks, P = .007; ART group [n = 6] vs 18.0 % ± 3.9% to 19.1 % ± 2.9%, baseline to 12 weeks, P = .30; untreated group [n = 6] [P = .04 ART vs untreated group]). Change in HIV RNA was negatively associated with change in Abca1+/+ macrophage cholesterol efflux (r = − 0.62, P = .03), and this finding remained significant (P = .03) after controlling for changes in HDL-cholesterol, CD4+ cells, and markers of monocyte or macrophage activation.

Conclusions.  In subjects acutely infected with HIV, ATP-binding cassette transporter A1-mediated cholesterol efflux was stimulated to a greater degree over time by apolipoprotein B-depleted serum from subjects randomized to ART. The improvement in cholesterol efflux capacity is independently related to reduction in viral load.
A coronal hole jet observed with Hinode and the Solar Dynamics Observatory
Authors: Young Peter R. , Muglach Karin
Published: November 2014

A small blowout jet was observed at the boundary of the south polar coronal hole on 2011 February 8 at around 21:00 UT. Images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO) revealed an expanding loop rising from one footpoint of a compact, bipolar bright point. Magnetograms from the Helioseismic Magnetic Imager (HMI) on board SDO showed that the jet was triggered by the cancelation of a parasitic positive polarity feature near the negative pole of the bright point. The jet emission was present for 25 min and it extended 30 Mm from the bright point. Spectra from the Extreme Ultraviolet Imaging Spectrometer on board Hinode yielded a temperature and density of 1.6 MK and 0.9–1.7 × 108 cm−3 for the ejected plasma. Line-of-sight velocities reached up to 250 km s−1 and were found to increase with height, suggesting plasma acceleration within the body of the jet. Evidence was found for twisting motions within the jet based on variations of the line-of-sight velocities across the jet width. The derived angular speed was in the range (9–12) × 10−3 rad s−1, consistent with previous measurements from jets. The density of the bright point was 7.6 × 108 cm−3, and the peak of the bright point's emission measure occurred at 1.3 MK, with no plasma above 3 MK.
Multi-scale mechanical characterization of highly swollen photo-activated collagen hydrogels
Authors: Tronci Giuseppe , Grant Colin A. , Thomson Neil H. , Russell Stephen J. , Wood David J.
Published: November 2014

Biological hydrogels have been increasingly sought after as wound dressings or scaffolds for regenerative medicine, owing to their inherent biofunctionality in biological environments. Especially in moist wound healing, the ideal material should absorb large amounts of wound exudate while remaining mechanically competentin situ. Despite their large hydration, however, current biological hydrogels still leave much to be desired in terms of mechanical properties in physiological conditions. To address this challenge, a multi-scale approach is presented for the synthetic design of cyto-compatible collagen hydrogels with tunable mechanical properties (from the nano- up to the macro-scale), uniquely high swelling ratios and retained (more than 70%) triple helical features. Type I collagen was covalently functionalized with three different monomers, i.e. 4-vinylbenzyl chloride, glycidyl methacrylate and methacrylic anhydride, respectively. Backbone rigidity, hydrogen-bonding capability and degree of functionalization (F: 16 ± 12–91 ± 7 mol%) of introduced moieties governed the structure–property relationships in resulting collagen networks, so that the swelling ratio (SR: 707 ± 51–1996 ± 182 wt%), bulk compressive modulus (Ec: 30 ± 7–168 ± 40 kPa) and atomic force microscopy elastic modulus (EAFM: 16 ± 2–387 ± 66 kPa) were readily adjusted. Because of their remarkably high swellingandmechanical properties, these tunable collagen hydrogels may be further exploited for the design of advanced dressings for chronic wound care.
Dynamics and optimal control of flexible solar updraft towers
Authors: Chi Michael , Gay-Balmaz François , Putkaradze Vakhtang , Vorobieff Peter
Published: November 2014

The use of solar chimneys for energy production was suggested more than 100 years ago. Unfortunately, this technology has not been realized on a commercial scale, in large part due to the high cost of erecting tall towers using traditional methods of construction. Recent works have suggested a radical decrease in tower cost by using an inflatable self-supported tower consisting of stacked toroidal bladders. While the statics deflections of such towers under constant wind have been investigated before, the key for further development of this technology lies in the analysis of dynamics, which is the main point of this paper. Using Lagrangian reduction by symmetry, we develop a fully three-dimensional theory of motion for such towers and study the tower's stability and dynamics. Next, we derive a geometric theory of optimal control for the tower dynamics using variable pressure inside the bladders and perform detailed analytical and numerical studies of the control in two dimensions. Finally, we report on the results of experiments demonstrating the remarkable stability of the tower in real-life conditions, showing good agreement with theoretical results.
Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil
Authors: Liu Qin , Ren Min , Zhang Li-Li
Published: November 2014

Two halophilic archaeal strains, TRM20010T and TRM20345T, were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010T and TRM20345T were able to grow at 30–62 °C (optimum 37 °C), 0.9–5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0–10.0 (optimum pH 7.0−7.5) and neither strain required Mg2+ for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB′ genes revealed that strains TRM20010T and TRM20345T clustered together and formed a distinct clade separated from the related genera

Halovivax

,

Haloterrigena

,

Halostagnicola

,

Natronolimnobius

and

Natrinema

. The DNA G+C contents of strains TRM20010T and TRM20345T were 63.9 and 63.8 mol%, respectively. The DNA–DNA hybridization value between strain TRM20010T and strain TRM20345T was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010T and TRM20345T represent two novel species in a new genus within the family

Halobacteriaceae

, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010T = CCTCC AB2013112T = NRRL B-59996T) and Natribaculum longum sp. nov. (type strain TRM20345T = CCTCC AB2013113T = NRRL B-59997T) are proposed.
Legionella norrlandica sp. nov., isolated from the biopurification systems of wood processing plants
Authors: Rizzardi Kristina , Winiecka-Krusnell Jadwiga , Ramliden Miriam , Alm Erik , Andersson Sabina , Byfors Sara
Published: November 2014

Fourteen isolates of an unknown species identified as belonging to the genus

Legionella

by selective growth on BCYE agar were isolated from the biopurification systems of three different wood processing plants. The mip gene sequence of all 14 isolates was identical and a close match alignment revealed 86 % sequence similarity with

Legionella pneumophila

serogroup 8. The whole genome of isolate LEGNT was sequenced, and a phylogenetic tree based on the alignment of 16S rRNA, mip, rpoB, rnpB and the 23S–5S intergenic region clustered LEGNT with

L. pneumophila

ATCC 33152T. Analysis of virulence factors showed that strain LEGNT carries the majority of known

L. pneumophila

virulence factors. An amoeba infection assay performed to assess the pathogenicity of strain LEGNT towards Acanthamoeba castellanii showed that it can establish a replication vacuole in A. castellanii but does not significantly affect replication of amoebae. Taken together, the results confirm that strain LEGNT represents a novel species of the genus

Legionella

, for which the name Legionella norrlandica sp. nov. is proposed. The type strain is LEGNT ( = ATCC BAA-2678T = CCUG 65936T).
Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species
Authors: Yassin A. F. , Spröer C. , Pukall R. , Sylvester M. , Siering C. , Schumann P.
Published: November 2014

The remarkable host specificity of the species of the genus

Actinobaculum

led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus

Actinobaculum

. The proposals of this study include the reclassification of

Actinobaculum schaalii

and

Actinobaculum urinale

as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541T = CCUG 27420T) and Actinotignum urinale comb. nov. (type strain DSM 15805T = CCUG 46093T), respectively. Emended descriptions of the genus

Actinobaculum

and

Actinomyces suis

are also provided. The results of 16S rRNA gene sequence analysis and DNA–DNA hybridization also indicated that the type strain of

Actinobaculum massiliense

deposited as CCUG 47753T ( = DSM 19118T) should in fact be considered a member of the species

Actinobaculum schaalii

. In addition, comparative 16S rRNA gene sequencing and DNA–DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199T ( = DSM 26039T = CCUG 64068T).
Proposal for ‘Candidatus Mycoplasma haemomuris subsp. musculi’ in mice, and ‘Candidatus Mycoplasma haemomuris subsp. ratti’ in rats
Authors: Harasawa Ryô , Fujita Hiromi , Kadosaka Teruki , Ando Shuji , Rikihisa Yasuko
Published: November 2014

Mycoplasma haemomuris

is causative of infectious anaemia or splenomegaly in rodents. We examined the nucleotide sequences of the non-ribosomal genes, rnpB and dnaK, in strains of the species

M. haemomuris

detected in small field mice and black rats. rnpB nucleotide sequences in strains of the species

M. haemomuris

isolated from small field mice and black rats had only 89 % sequence similarity, suggesting their separation into two distinct subgroups. dnaK had a nucleotide sequence similarity of 84 % between the subgroups. These results support the classification of

M. haemomuris

into two genetically distinct subgroups. Here we propose the establishment of these subgroups as ‘Candidatus Mycoplasma haemomuris subsp. musculi’, detected in small field mice (Apodemus argenteus), and ‘Candidatus Mycoplasma haemomuris subsp. ratti’, detected in black rats (Rattus rattus).
Reclassification of Bacteriovorax marinus as Halobacteriovorax marinus gen. nov., comb. nov. and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov.; description of Halobacteriovoraceae fam. nov. in the class Deltaproteobacteria
Authors: Koval Susan F. , Williams Henry N. , Stine O. Colin
Published: November 2014

The taxonomic status of saltwater

Bdellovibrio

-like prokaryotic predators has been revised to assign species to Halobacteriovorax gen. nov. A reclassification of

Bacteriovorax marinus

as Halobacteriovorax marinus comb. nov. (type strain ATCC BAA-682T = DSM 15412T) and

Bacteriovorax litoralis

as Halobacteriovorax litoralis comb. nov. (type strain ATCC BAA-684T = DSM 15409T) is proposed. This revision is necessary because a previous proposal to retain saltwater isolates as species of

Bacteriovorax

and reclassify

Bacteriovorax stolpii

as

Bacteriolyticum stolpii

was not approved. The type species of a genus cannot be reassigned to another genus.

Bacteriovorax stolpii

is thus retained as the type species of

Bacteriovorax

and Halobacteriovorax marinus is the type species of Halobacteriovorax and of Halobacteriovoraceae fam. nov.
Arabidopsis PIAL1 and 2 Promote SUMO Chain Formation as E4-Type SUMO Ligases and Are Involved in Stress Responses and Sulfur Metabolism
Authors: Tomanov Konstantin , Zeschmann Anja , Hermkes Rebecca , Eifler Karolin , Ziba Ionida , Grieco Michele , Novatchkova Maria , Hofmann Kay , Hesse Holger , Bachmair Andreas
Published: November 2014

The Arabidopsis thaliana genes PROTEIN INHIBITOR OF ACTIVATED STAT LIKE1 (PIAL1) and PIAL2 encode proteins with SP-RING domains, which occur in many ligases of the small ubiquitin-related modifier (SUMO) conjugation pathway. We show that PIAL1 and PIAL2 function as SUMO ligases capable of SUMO chain formation and require the SUMO-modified SUMO-conjugating enzyme SCE1 for optimal activity. Mutant analysis indicates a role for PIAL1 and 2 in salt stress and osmotic stress responses, whereas under standard conditions, the mutants show close to normal growth. Mutations in PIAL1 and 2 also lead to altered sulfur metabolism. We propose that, together with SUMO chain binding ubiquitin ligases, these enzymes establish a pathway for proteolytic removal of sumoylation substrates.
Boosting consumers’ self-efficacy by repositioning the self
Authors: Ben-Ami Michal , Hornik Jacob , Eden Dov , Kaplan Oren
Published: November 2014

Purpose

– This article aims to lend insight into the consumption situation wherein consumers are unmotivated to try new products or behaviors that they perceive as too difficult to adopt as a result of low self-efficacy.

Design/methodology/approach

– Two experiments were introduced to test hypotheses. In Studies 1 and 2, we demonstrated that enhancing specific self-efficacy (SSE) by repositioning the self, through marketing messages, increased participants’ behavioral intentions toward difficult to adopt (DTA) products.

Findings

– In this research, an important issue is elucidated in consumer behavior: a phenomenon wherein consumers lack the motivation, as a result of low self-efficacy (i.e. assessing the disparity between their current situation and some desired goals as too wide to bridge over), to try a product that would benefit them. Thus, the marketer’s role in this case is to convince the consumers that they are able to achieve these goals.

Research limitations/implications

– This study focuses on health and fitness products and on the effectiveness of messages targeted at raising SSE among undergraduate students through verbal persuasion. For better generalizability, it is recommended that future research focus on other product categories (e.g. do-it-yourself products, technological products) aimed at other segments (e.g. elderly consumers) and use other means of boosting consumers’ self-efficacy.

Practical implications

– The practical importance of the findings is especially relevant in DTA situations in which marketers aim to motivate consumers to engage in effortful consumption tasks.

Originality/value

– The uniqueness of our approach is, in addition to introducing the theoretical concepts, to demonstrate that marketers can boost individuals’ self-efficacy by means of marketing messages that emphasize their ability to face challenges and, consequently, increase their preferences, behavioral intentions and financial commitments toward a DTA product.
Conceptualising the management of packaging within new product development
Authors: Simms Christopher , Trott Paul
Published: November 2014

Purpose

– The purpose of this study is to: contribute to existing models of new product development (NPD) and provide new understanding of how a new product’s packaging is managed and integrated into the NPD process of fast-moving consumer goods (FMCG) firms and build on prior research, suggesting that firms lack a pipeline of new packaging innovations by uncovering the factors that influence this pipeline issue.

Design/methodology/approach

– A grounded theory methodology was adopted. Research was conducted through a total of 37 interviews with key informants in the UK FMCG industry, packaging industry and associated firms.

Findings

– Three distinct levels of packaging development were revealed: skin deep, body modification and format change. The emphasis within many firms is primarily on changes to packaging at the level of the label (skin deep) or aesthetic design (body modification), whilst technological and format changes are overlooked. The factors that contribute to the level at which development is undertaken are identified.

Research limitations/implications

– Existing literature has largely examined packaging at the level of skin-deep and body modification. The development of new packaging technology has been overlooked. This study’s propositions guide the way forward for further research.

Practical implications

– For firms, the development of new formats and genuine packaging innovation may be being overlooked. There is a need for them to re-examine their activities to ensure that they are addressing all three levels.

Originality/value

– This theory-building study has generated a new typology which, alongside the unique framework, reveals the factors influencing the level of emphasis within firms.
The role of convenience in a recreational shopping trip
Authors: Reimers Vaughan , Chao Fred
Published: November 2014

Purpose

– The purpose of this study is to determine the role of convenience in a recreational shopping trip. In an effort to address the shopping strip’s forfeiture of market share to the mall and the Internet, retail planners have utilised a variety of intervention strategies. One such strategy is to differentiate the strip by emphasising its hedonic attributes. An often overlooked alternative is to compete with both of these formats in a key area of competitive disadvantage – convenience. Whereas these two alternatives have traditionally been regarded as separate strategies, this study examines whether convenience actually serves as a source of satisfaction in a hedonic shopping context.

Design/methodology/approach

– A recreational shopping trip to a shopping strip (also referred to as Main Street or the High Street) in Melbourne, Australia, served as the context for this study. The study used a quantitative survey approach to collect its data and structural equation modelling to analyse it.

Findings

– Surprisingly, the hedonic attributes of a shopping strip do not influence trip satisfaction in the context of a recreational shopping strip. Contrary to a significant body of academic research, it is instead the time-saving and distance-minimising properties of a shopping strip, as well as its overall convenience, which determine satisfaction.

Originality/value

– The results have important implications for Town Centre Management schemes because they suggest that responsibility for providing a hedonic shopping experience rests with its individual retailers. Instead, the role of strip planners is to facilitate the other side of the value-equation by minimising the hassles involved in strip shopping. The results of this study also question the traditional belief that hedonic- and convenience-based rejuvenation strategies should be treated as two distinct strategies. Instead, convenience should be regarded as a prerequisite to a satisfying recreational shopping trip.
Discrete choice model for air-cargo mode selection
Authors: Mitra Subhro , M. Leon Steven
Published: November 2014

Purpose

– The purpose of this paper is to develop a better understanding of the factors that influence a shipper's decision to choose air cargo as a mode of shipment.

Design/methodology/approach

– A disaggregate multinomial discrete choice model is developed using freight shipment survey data to identify critical factors influencing air cargo mode choice. Disaggregate revealed preference data is obtained from surveying 347 manufacturers, freight forwarders, and other third-party service providers.

Findings

– The empirical model developed in this research shows that the rate of shipment, time of transit, cost-per-pound shipped, quantity shipped, perishability and delay rate of the mode are significant factors that influence mode choice.

Research limitations/implications

– The discrete choice model developed can be improved by taking into account logistics costs not considered in this research. Perhaps more in-depth surveys of the shippers and freight forwarders are needed. Additionally, improving the mode choice model by including stated preference data and subsequently incorporating service quality latent variables would be beneficial.

Practical implications

– Identifying the sensitivity of the shippers to various factors influencing mode selection enables transportation planners make better demand forecast for each mode of transportation.

Originality/value

– This paper extends previous mode choice studies by analyzing mode selection between air cargo and other modes. Better forecasting is achieved by replacing the logit model with probit, heteroscedastic extreme value and mixed logit models.
Impact of international outsourcing on the value adding of industries
Authors: Hamed MoosaviRad Seyed , Kara Sami , Ibbotson Suphunnika
Published: November 2014

Purpose

– The value adding of each industry represents the value difference between the outputs and inputs of that industry. The purpose of this paper is to investigate the effect of international outsourcing on the value adding of industries.

Design/methodology/approach

– Input output analysis and linear programming are used as for the research methodology. Australian Motor Vehicle and Parts Manufacturing (AMVPM) industry as an outsourcer and its main suppliers were selected for ten alternative international outsourcing scenarios in a case study.

Findings

– In all international outsourcing scenarios except the baseline scenario, the reduction in the value adding of Australia would be approximately three times more than the value adding reduction of the AMVPM industry. Moreover, the international outsourcing ratio has negative relationships with the value adding of the Australian industries and positive relationship with the international industries. Finally, it was found that the degree of supplier's dependency on the orders of the outsourcer effects the percentage reduction of supplier's value adding.

Research limitations/implications

– The aggregated data and the uncertainties in the technical coefficients are the main limitations of this research. The social and environmental costs, other tangible and intangible costs, as well as benefits of international outsourcing need to be further analysed in future research.

Practical implications

– This study would help decision makers at the macro level to analyse and control the effect of international outsourcing on the value adding of their economies.

Originality/value

– This study expands the current research at the industry level of international outsourcing by quantifying the effect of international outsourcing upon the value adding of all respected industries.
Collaborative tracking and tracing: the value of a composite design
Authors: Mirzabeiki Vahid , Holmström Jan , Främling Kary
Published: November 2014

Purpose

– The purpose of this paper is to propose a collaborative tracking and tracing (T&T) system that enables supply chain actors to join and leave the system in run-time without disrupting the function of the system.

Design/methodology/approach

– A collaborative T&T system is introduced using a conceptual approach. Supporting empirical data are collected through a deductive case study of a Swedish automotive supply chain.

Findings

– A collaborative T&T system based on composite and observer design patterns is an appropriate solution for inter-organizational T&T.

Research limitations/implications

– This research contributes to the body of knowledge in the field of logistics T&T. The conceptually developed collaborative T&T system needs to be validated empirically.

Practical implications

– The collaborative T&T system developed conceptually here could be used as a model for the practical development of inter-organizational T&T systems.

Originality/value

– The introduction of a collaborative T&T system, adopting the theories of software engineering and product data management, represents an original contribution to the field of T&T in logistics and transportation.
Integrated planning in hybrid courier operations
Authors: Ninikas George , Athanasopoulos Theodore , Zeimpekis Vasileios , Minis Ioannis
Published: November 2014

Purpose

– The purpose of this paper is to present the design and evaluation of an integrated system that supports planners and dispatchers to deliver enhanced courier operations. In addition to regular deliveries and pickups, these operations include: first, mass deliveries to be served over a horizon of multiple days; and second, real-time dynamic requests (DRs) to be served within the same service period.

Design/methodology/approach

– To address the aforementioned challenges, the authors developed an architecture that enhances a typical fleet management system by integrating purpose designed methods. Specifically, the authors plan mass deliveries taking into account typical routes of everyday operations. For planning DRs in real time, the authors propose an efficient insertion heuristic.

Findings

– The results from testing the proposed optimization algorithms for planning mass deliveries and real-time DRs are encouraging, since the proposed algorithms outperform current practices. Testing in a practical courier environment, indicated that the enhanced planning system may improve significantly operational performance.

Research limitations/implications

– The proposed optimization algorithm for the dynamic aspect of this problem comprises a heuristic approach that reaches suboptimal solutions of high quality. The development of fast optimal algorithms for solving these very interesting and practical problems is a promising area for further research.

Practical implications

– The proposed integrated system addresses significant problems of hybrid courier operations in an integrated, balanced manner. The tests showed that the allocation of flexible orders within a three-day time horizon improved the cost per flexible order by 7.4 percent, while computerized routing improved the cost of initial (static) routing by 14 percent. Furthermore, the proposed method for managing DRs reduced the excess cost per served request by over 40 percent. Overall, the proposed integrated system improved the total routing costs by 16.5 percent on average compared to current practices.

Originality/value

– Both the planning problems and the related solution heuristics address original aspects of practical courier operations. Furthermore, the system integration and the proposed systematic planning contribute to the originality of the work.
Copyright, open access and library instruction
Authors: Fargo McKinnon Laura , S. Helge Kris
Published: November 2014

Purpose

– The purpose of this article is to provide a general review of the concepts of copyright and open access as they relate to library instruction. The authors provide instructional advice to librarians on these topics.

Design/methodology/approach

– The authors approach the topic from a descriptive and instructional stance. General research on the topics listed above was conducted and is presented as an overview.

Findings

– The authors discuss the basics of copyright law, Creative Commons licenses, open access resources and copyright considerations specific to using music in instruction.

Originality/value

– This article includes useful tips and resources for instructional librarians, such as where to find open access or Creative Commons content. It is of value to any librarian that utilizes other entities’ content in the course of instruction.
“Where do I find that?”: creating a central shared documentation system for publishing staff using Google tools at the University of Michigan Library
Authors: Norton Alix
Published: November 2014

Purpose

– This aim of this report is to summarize how Google Sites can be used as an open-source, intuitive, and robust solution for designing an intranet system for a unique library department. Michigan Publishing is a department within the University of Michigan (U-M) campus library system that also includes a revenue-based operation as the U-M Press. The need for a central documentation system has become apparent to organize and streamline policies and procedures in this unique library department. Google Sites was chosen as a solution to compile departmental documentation and serve as a collaborative space for the many units within Michigan Publishing.

Design/methodology/approach

– One librarian and one graduate student intern worked on this project for 5-10 hours a week over the course of three months. Michigan Publishing managers created an inventory showing all existing informational resources in the department, and were then interviewed about these resources. An initial “landing page” was created for this Google-based site, and more comprehensive content has since been migrated from existing informational resources to this central site.

Findings

– A specific Google Sites Staff Intranet for Michigan Publishing has been an integral solution for providing a one-stop, central area for current internal resources. It also fosters a sense of departmental identity and community, since there are many separate units within the department, each with a different focus and place within the larger library system. This site provides an online forum for collaboration, communication and policy codification.

Originality/value

– This report summarizes how Google Sites can be used as an open-source, intuitive, and robust solution for designing an intranet system for a unique library department.
Texturization of deoiled cake of sunflower, soybean and flaxseed into food grade meal and its utilization in preparation of cookies
Authors: Bhise Suresh , Kaur A. , Ahluwali Preeti , Thind S. S.
Published: November 2014

Purpose

– The purpose of the present study was to plan with the objectives to optimize and find out the best level of texturized protein from sunflower, soybean and flaxseed on the basis of quality and overall acceptability of the cookies.

Design/methodology/approach

– Defatted meal from sunflower, soybean and flaxseed was texturized using extruder. Texturized defatted meal of sunflower, soybean and flaxseed was blended at 10, 20, 30 and 40 per cent levels with wheat flour for making cookies using standard procedure.

Findings

– Functional properties such as water absorption index, foaming capacity and protein digestibility were increased, while water solubility index and fat absorption capacity decreased with increased levels of texturized defatted meal in wheat flour. Spread ratio, sensory, colour and overall acceptability of cookies were negatively affected when level of texturized flour increased as compared with the control. The force required for breaking cookies decreased with increased level of texturized defatted meal of sunflower, soybean and flaxseed incorporation. Cookies with 10 per cent texturized sunflower, soybean and flaxseed flour received the highest sensory scores. The result showed that texturized defatted meals serve as good substitute to wheat flour with increased protein content in cookies production and utilization.

Originality/value

– The study demonstrated that deoiled cake, a byproduct obtained from sunflower, soybean and flaxseed oil industry, offers great potential for supplementation of proteins in food products.
Nutritional quality evaluation of surimi and kamaboko obtained from mechanically separated chicken meat
Authors: Cortez-Vega William Renzo , Pizato Sandriane , Prentice Carlos
Published: November 2014

Purpose

– The purpose of this paper was to determine the nutritional quality of the surimi and kamaboko obtained from mechanically separated chicken meat and evaluate the bioavailability of essential amino acids found in these products.

Design/methodology/approach

– The mechanically separated chicken meat (MSCM) was characterized by the proximate composition, and the surimi and kamaboko were characterized byin vitrodigestibility, determination of chemical score of amino acids and apparent bioavailability.

Findings

– The MSCM contains 68.1 ± 0.5, 12.9 ± 0.24, 18.5 ± 0.28 and 0.6 ± 0.06 per cent moisture, protein, lipids and ash, respectively. The moisture of the MSCM (surimi) was 80.45 ± 0.15 per cent, and the protein was 10.04 ± 0.21 per cent. The highest digestibility was found for the kamaboko (92.27 per cent) which was heat-treated and the lowest was for surimi (90.82 per cent). Histidine is a limiting amino acid. In this study, the surimi showed 84.69 per cent and the kamaboko presented 81.31 per cent of the minimum requirement for adults. In relation to the apparent bioavailability, there was a decrease of surimi to kamaboko of 2.52 per cent of the limiting amino acid histidine. The surimi and the kamaboko presented 76.94 and 75 per cent of the minimum requirement for adults, respectively.

Originality/value

– The application of the surimi technology in the production of a surimi-like material from mechanically deboned chicken meat provides a new approach toward increasing its value and utilization, e.g. for the development of meat-based products and analogs, as alternative protein sources, the surimi and the kamaboko exhibited a high content of essential amino acids, indicating that the protein has a relatively high nutritional quality.
Knowledge transfer in Hero Motor Corp Ltd.
Authors: Rana Geeta , Kumar Goel Alok , Kumar Saini Ajay
Published: November 2014

Purpose

– This paper aims to examine the issues of knowledge transfer in international strategic alliance within Hero Moto Corp. Ltd., an Indian multinational company. International Strategic alliances have been increasing in numbers in the past decades and transfer of knowledge and its transfer in multinational companies is wider debate. The case explores the complex issues involved in cross-organization and cross-country transfer of knowledge. The company has forged a strategic alliance with the US-based Erik Buell Racing for accessing technology and design inputs.

Design/methodology/approach

– It presents a structured case study that examines a wide range of knowledge transfer issues of international strategic alliance.

Findings

– It reveals that a major influencing factor is the national culture of the parents and that of the host country which provides the context with in which alliances are operate. It is also explored the ways in which the multi-parentage of strategic alliances influences their Human Resource Management (HRM) policies and practices.

Originality/value

– It provides plenty of useful information on an issue that affects virtually every employee and organization.
Towards a framework for performing outsourcing capability
Authors: Pratap Sankalp
Published: November 2014

Purpose

– The aim of this paper is to go beyond the “What to outsource” and “To Outsource or Not” debate. Recognizing outsourcing as a fast growing reality that firms have to depend upon, the paper concerns itself with optimal management of outsourcing arrangements through the practice of “outsourcing capability”. It argues that outsourcing failure can be mitigated if organizations see outsourcing as an “ongoing activity” to be managed as opposed to treating it as a one-time opportunistic “act”.

Design/methodology/approach

– Based on the review of existing literature and drawing upon recent instances of outsourcing successes and failures, the paper develops a conceptual framework which divides various organizational processes into four different classes. It delineates the varied aspects of “outsourcing capability” that a firm would need to use to manage these varied class of processes as and when they are outsourced.

Findings

– There is no “one-size-fits-all” approach to managing outsourced processes. Different processes require emphasis on different aspect of outsourcing capability if outsourcing is to deliver the envisaged benefits.

Originality/value

– The traditional focus in outsourcing literature has been on the core/non-core process with the recommendation to keep core processes in-house and outsource the non-core processes. This distinction can be transitory and hence detrimental in the era of hyper-competition. I argue that firms should instead focus on developing and refining aspects of “outsourcing capability” relevant to the varied class of processes that they wish/need to outsource.
Characterization of protein kinase PsSRPKL, a novel pathogenicity factor in the wheat stripe rust fungus
Authors: Cheng Yulin , Wang Xiaojie , Yao Juanni , Voegele Ralf T. , Zhang Yanru , Wang Wumei , Huang Lili , Kang Zhensheng
Published: November 2014

As in other eukaryotes, protein kinases (PKs) are generally evolutionarily conserved and play major regulatory roles in plant pathogenic fungi. Many PKs have been proven to be important for pathogenesis in model fungal plant pathogens, but little is currently known about their roles in the pathogenesis of cereal rust fungi, devastating pathogens in agriculture worldwide. Here, we report on an in planta highly induced PK gene PsSRPKL from the wheat stripe rust fungus Puccinia striiformis f. sp. tritici (Pst), one of the most important cereal rust fungi. PsSRPKL belongs to a group of PKs that are evolutionarily specific to cereal rust fungi. It shows a high level of intraspecies polymorphism in the kinase domains and directed green fluorescent protein chimers to plant nuclei. Overexpression of PsSRPKL in fission yeast induces aberrant cell morphology and a decreased resistance to environmental stresses. Most importantly, PsSRPKL is proven to be an important pathogenicity factor responsible for fungal growth and responses to environmental stresses, therefore contributing significantly to Pst virulence in wheat. We hypothesize that cereal rust fungi have developed specific PKs as pathogenicity factors for adaptation to their host species during evolution. Thus, our findings provide significant insights into pathogenicity and virulence evolution in cereal rust fungi.
A de novo transcriptomic analysis to reveal functional genes in Apolygus lucorum
Authors: Cao De‐Pan , Liu Yang , Wei Jin‐Jin , Li Jian‐Hong , Wang Gui‐Rong
Published: November 2014

The widespread planting of genetically engineered cotton producing the Cry1Ac toxin has led to significantly reduced pesticide applications since 1997. However, consequently, the number of green mirid bugs (GMB), Apolygus lucorum (Meyer‐Dür) has increased. So far the GMB, instead of the cotton bollworm Helicoverpa armigera (Hübner), has become the major pest in the transgenic Bt cotton field and has influenced cotton yield. Disproportionately, only a few studies on GMB at molecular level have been reported. Libraries from both third instar nymphs and adults were sequenced using Illumina technology, producing more than 106 million short reads and assembled into 63 029 unigenes of mean length 597 nt and N50 813 nt, ranging from 300 nt to 9771 nt. BLASTx analysis against Nr, Swissprot, GO and COG was performed to annotate these unigenes. As a result, 26 478 unigenes (42.01%) matched to known proteins and 107 immune‐related, 320 digestive‐related and 53 metamorphosis‐related genes were detected in these annotated unigenes. Additionally, we profiled gene expression using mapping based differentially expressed genes (DEGs) strategy between the two developmental stages: nymph and adult. The results demonstrated that thousands of genes were significantly differentially expressed at different developmental stages. The transcriptome and gene expression data provided comprehensive and global gene resources of GMB. This transcriptome would improve our understanding of the molecular mechanisms of various underlying biological characteristics, including development, digestion and immunity in GMB. Therefore, these findings could help elucidate the intrinsic factors of the GMB resurgence, offering novel pest management targets for future transgenic cotton breeding.