Dairy product production and lactose demand in New Zealand and Ireland under different simulated milk product-processing portfolios

peer-reviewedMaximising dairy industry profitability involves maximising product returns for a specific set of costs or minimising costs for a certain level of output. A strategy currently utilised by the New Zealand dairy industry to optimise the value of exports is to incorporate imported lactose along with local milk to maximise the production of whole milk powder (WMP) while complying with the Codex Alimentarius (Codex) standards, in addition to increasing the exported product for every litre of milk. This study investigated the impact of different product portfolio strategies on lactose requirements for the Irish and New Zealand dairy industries for current and predicted 2020 milk output projections. A mass balance processing sector model that accounts for all inputs, outputs and losses involved in dairy processing was used to simulate the processing of milk into WMP, skim milk powder (SMP), cheese, butter and fluid milk of different proportions. All scenarios investigated projected an increase in production and revenue from 2012 to 2020. Higher cheese production reduced industry lactose demand through whey processing, while scenarios reliant on an increase in the proportion of WMP were associated with increased lactose deficits.Livestock Improvement Corporation Pat Shannon Scholarshi

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

Synchronous communication in PLM environments using annotated CAD models

The connection of resources, data, and knowledge through communication technology plays a vital role in current collaborative design methodologies and Product Lifecycle Management (PLM) systems, as these elements act as channels for information and meaning. Despite significant advances in the area of PLM, most communication tools are used as separate services that are disconnected from existing development environments. Consequently, during a communication session, the specific elements being discussed are usually not linked to the context of the discussion, which may result in important information getting lost or becoming difficult to access. In this paper, we present a method to add synchronous communication functionality to a PLM system based on annotated information embedded in the CAD model. This approach provides users a communication channel that is built directly into the CAD interface and is valuable when individuals need to be contacted regarding the annotated aspects of a CAD model. We present the architecture of a new system and its integration with existing PLM systems, and describe the implementation details of an annotation-based video conferencing module for a commercial CAD application.This work was supported by the Spanish Ministry of Economy and Competitiveness and the FEDER Funds, through the ANNOTA project (Ref. TIN2013-46036-C3-1-R).Camba, JD.; Contero, M.; Salvador Herranz, GM.; Plumed, R. (2016). Synchronous communication in PLM environments using annotated CAD models. Journal of Systems Science and Systems Engineering. 25(2):142-158. https://doi.org/10.1007/s11518-016-5305-5S142158252Abrahamson, S., Wallace, D., Senin, N. & Sferro, P. (2000). Integrated design in a service marketplace. Computer-Aided Design, 32(2):97–107.Ahmed, S. (2005). Encouraging reuse of design knowledge: a method to index knowledge. Design Studies, 26:565–592.Alavi, M. & Tiwana, A (2002). Knowledge integration in virtual teams: the potential role of KMS. Journal of the American Society for Information Science and Technology, 53:1029–1037.Ameri, F. & Dutta, D. (2005). Product lifecycle management: closing the knowledge loops. Computer-Aided Design and Applications, 2(5):577–590.Anderson, A.H., Smallwood, L., MacDonald, R., Mullin, J., Fleming, A. & O'Malley, C. (2000). Video data and video links in mediated communication: what do users value? International Journal of Human-Computer Studies, 52(1):165–187.Arias, E., Eden, H., Fischer, G., Gorman, A. & Scharff, E. (2000). Transcending the individual human mind–creating shared understanding through collaborative design. ACM Transactions on Computer-Human Interaction (TOCHI) 7(1): 84–113.Barley, W.C., Leonardi, P.M., & Bailey, D.E. (2012). Engineering objects for collaboration: strategies of ambiguity and clarity at knowledge boundaries. Human Communication Research, 38:280–308.Boujut, J.F. & Dugdale, J. (2006). Design of a 3D annotation tool for supporting evaluation activities in engineering design. Cooperative Systems Design, COOP 6:1–8.Camba, J., Contero, M., Johnson, M. & Company, P. (2014). Extended 3D annotations as a new mechanism to explicitly communicate geometric design intent and increase CAD model reusability. Computer-Aided Design, 57:61–73.Camba, J., Contero, M. & Salvador-Herranz, G. (2014). Speak with the annotator: promoting interaction in a knowledge-based CAD environment built on the extended annotation concept. Proceedings of the 2014 IEEE 18th International Conference on Computer Supported Cooperative Work in Design (CSCWD), 196–201.Chudoba, K.M., Wynn, E., Lu, M. & Watson-Manheim, M.B. (2005). How virtual are we? Measuring virtuality and understanding its impact in a global organization. Information Systems Journal, 15(4):279–306.Danesi, F., Gardan, N. & Gardan, Y. (2006). Collaborative Design: from Concept to Application. Geometric Modeling and Imaging—New Trends, 90–96.Durstewitz, M., Kiefner, B., Kueke, R., Putkonen, H., Repo, P. & Tuikka, T. (2002). Virtual collaboration environment for aircraft design. Proceedings of the IEEE 6th International Conference on Information Visualisation, 502–507.Fisher, D., Brush, A.J., Gleave, E. & Smith, M.A. (2006). Revisiting Whittaker and Sidner’s email overload ten years later. Proceedings of the 2006 20th Anniversary Conference on Computer Supported Cooperative Work. ACM, BanffFonseca, M.J., Henriques, E., Silva, N., Cardoso, T. & Jorge, J.A. (2006). A collaborative CAD conference tool to support mobile engineering. Rapid Product Development (RPD’06), Marinha Grande, Portugal.Frechette, S.P. (2011). Model based enterprise for manufacturing. Proceedings of the 44th CIRP International Conference on Manufacturing Systems.Fu, W.X., Bian, J. & Xu, Y.M. (2013). A video conferencing system for collaborative engineering design. Applied Mechanics and Materials, 344:246–252.Fuh, J.Y.H. & Li, W.D. (2005). Advances in collaborative CAD: the-state-of-the art. Computer-Aided Design, 37:571–581.Fussell, S.R., Kraut, R.E. & Siegel, J. (2000). Coordination of communication: effects of shared visual context on collaborative work. Proceedings of the 2000 ACM Conference on Computer Supported Cooperative Work, 21–30.Gajewska, H., Kistler, J., Manasse, M.S. & Redell, D. (1994). Argo: a system for distributed collaboration. Proceedings of the ACM Second International Conference on Multimedia, San Francisco, CA, USA. 433–440.Gantz, J., Reinsel, D., Chute, C., Schlichting, W., Mcarthur, J., Minton, S., Xheneti, I., Toncheva, A. & Manfrediz, A. (2007). The expanding digital universe: a forecast of worldwide information growth through 2010. IDC, Massachusetts.Gowan, Jr. J.A. & Downs, J.M. (1994). Video conferencing human-machine interface: a field study. Information and Management, 27(6):341–356.Gupta, A., Mattarelli, E., Seshasai, S. & Broschak, J. (2009). Use of collaborative technologies and knowledge sharing in co-located and distributed teams: towards the 24-h knowledge factory. The Journal of Strategic Information Systems, 18:147–161.Hickson, I. (2009). The Web Socket Protocol IETF, Standards Track.Hong, J., Toye, G. & Leifer, L.J. (1996). Engineering design notebook for sharing and reuse. Computers in Industry, 29:27–35.Isaacs, E.A. & Tang, J.C. (1994). What video can and cannot do for collaboration: a case study. Multimedia Systems, 2(2):63–73.Karsenty, L. (1999). Cooperative work and shared visual context: an empirical study of comprehension problems in side-by-side and remote help dialogues. Human Computer Interaction, 14(3): 283–315.Lahti, H., Seitamaa-Hakkarainen, P. & Hakkarainen, K. (2004). Collaboration patterns in computer supported collaborative designing. Design Studies, 25:351–371.Leenders, R.T.A., Van Engelen, J.M. & Kratzer, J. (2003). Virtuality, communication, and new product team creativity: a social network perspective. Journal of Engineering and Technology Management, 20(1):69–92.Levitt, R.E., Jin, Y. & Dym, C.L. (1991). Knowledge-based support for management of concurrent, multidisciplinary design. Artificial Intelligence for Engineering, Design, Analysis and Manufacturing, 5(2):77–95.Li, C., McMahon, C. & Newnes, L. (2009). Annotation in product lifecycle management: a review of approaches. Proceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, DETC2009. Vol. 2. New York: ASME, 797–806.Li, W.D., Lu, W.F., Fuh, J.Y. & Wong, Y.S. (2005). Collaborative computer-aided design-research and development status. Computer-Aided Design, 37(9):931–940.Londono, F., Cleetus, K.J., Nichols, D.M., Iyer, S., Karandikar, H.M., Reddy, S.M., Potnis, S.M., Massey, B., Reddy, A. & Ganti, V. (1992). Coordinating a virtual team. CERC-TR-RN-92-005, Concurrent Engineering Research Centre, West Virginia University, West Virginia.Lubell, J., Chen, K., Horst, J., Frechette, S., & Huang, P. (2012). Model based enterprise/technical data package summit report. NIST Technical Note, 1753.May, A. & Carter, C. (2001). A case study of virtual team working in the European automotive industry. International Journal of Industrial Ergonomics, 27(3):171–186.Olson, J.S., Olson, G.M. & Meader, D.K. (1995). What mix of video and audio is useful for small groups doing remote real-time design work? Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. ACM Press, Addison-Wesley Publishing Co.Ping-Hung, H., Mishra, C.S. & Gobeli, D.H. (2003). The return on R&D versus capital expenditures in pharmaceutical and chemical industries. IEEE Transactions on Engineering Management, 50:141–150.Sharma, A. (2005). Collaborative product innovation: integrating elements of CPI via PLM framework. Computer-Aided Design, 37(13):1425–1434.Shum, S.J.B., Selvin, A.M., Sierhuis, M., Conklin, J., Haley, C.B. & Nuseibeh, B. (2006). Hypermedia support for argumentation-based rationale: 15 Years on from Gibis and Qoc. Rationale Management in Software Engineering, 111–132.Siltanen, P. & Valli, S. (2013). Web-based 3D Mediated Communication in Manufacturing Industry. Concurrent Engineering Approaches for Sustainable Product Development in a Multidisciplinary Environment, 1181–1192. Springer London.Stark, J. (2011). Product Lifecycle Management. 1–16. Springer London.Tavcar, J., Potocnik, U. & Duhovnik, J. (2013). PLM used as a backbone for concurrent engineering in supply chain. Concurrent Engineering Approaches for Sustainable Product Development in a Multi-Disciplinary Environment, 681–692.Tay, F.E.H. & Ming, C. (2001). A shared multi-media design environment for concurrent engineering over the internet. Concurrent Engineering, 9(1):55–63.Tay, F.E.H. & Roy, A. (2003). CyberCAD: a collaborative approach in 3D-CAD technology in a multimedia-supported environment. Computers in Industry, 52(2):127–145.Toussaint, J. & Cheng, K. (2002). Design agility and manufacturing responsiveness on the web. Integrated Manufacturing Systems, 13(5):328–339.Tsoi, K.N. & Rahman, S.M. (1996). Media-on-demand multimedia electronic mail: a tool for collaboration on the web. Proceedings of the 5th IEEE International Symposium on High Performance Distributed Computing.Upton, D.M. & Mcafee, A. (1999). The Real Virtual Factory. Harvard Business School Press, 69–89.Vila, C., Estruch, A., Siller, H.R., Abellán, J.V. & Romero, F. (2007). Workflow methodology for collaborative design and manufacturing. Cooperative Design, Visualization, and Engineering 42–49, Springer Berlin Heidelberg.Wasiak, J., Hicks, B., Newnes, L., Dong, A., & Burrow, L. (2010). Understanding engineering email: the development of a taxonomy for identifying and classifying engineering work. Research in Engineering Design, 21(1):43–64.Wasko, M.M. & Faraj, S. (2005). Why should I share? Examining social capital and knowledge contribution in electronic networks of practice. MIS Quarterly: Management Information Systems, 29:35–57.Yang, Q.Z., Zhang, Y., Miao, C.Y. & Shen, Z.Q. (2008). Semantic annotation of digital engineering resources for multidisciplinary design collaboration. ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, 617–624. American Society of Mechanical Engineers.You, C.F. & Chao, S.N. (2006). Multilayer architecture in collaborative environment. Concurrent Engineering Research and Applications, 14(4):273–281.Yuan, Y.C., Fulk, J., Monge, P.R. & Contractor, N. (2010). Expertise directory development, shared task interdependence, and strength of communication network ties as multilevel predictors of expertise exchange in transactive memory work groups. Communication Research, 37: 20–47

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements