bluuebunny/crossref_metadata_2025 huggingface dataset:
Automating curation using a natural language processing pipeline
Authors: Alex Beatrice , Grover Claire , Haddow Barry , Kabadjov Mijail , Klein Ewan , Matthews Michael , Tobin Richard , Wang Xinglong
Published: September 2008

Background:

The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers. The approach to these tasks taken by the University of Edinburgh team was to adapt and extend the existing natural language processing (NLP) system that we have developed as part of a commercial curation assistant. Although this paper concentrates on using NLP to assist with curation, the system can be equally employed to extract types of information from the literature that is immediately relevant to biologists in general.

Results:

Our system was among the highest performing on the interaction subtasks, and competitive performance on the gene mention task was achieved with minimal development effort. For the gene normalization task, a string matching technique that can be quickly applied to new domains was shown to perform close to average.

Conclusion:

The technologies being developed were shown to be readily adapted to the BioCreative II tasks. Although high performance may be obtained on individual tasks such as gene mention recognition and normalization, and document classification, tasks in which a number of components must be combined, such as detection and normalization of interacting protein pairs, are still challenging for NLP systems.
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks
Authors: Abi-Haidar Alaa , Kaur Jasleen , Maguitman Ana , Radivojac Predrag , Rechtsteiner Andreas , Verspoor Karin , Wang Zhiping , Rocha Luis M
Published: September 2008

Background:

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (interaction article subtask [IAS]), discovery of protein pairs (interaction pair subtask [IPS]), and identification of text passages characterizing protein interaction (interaction sentences subtask [ISS]) in full-text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam detection techniques, as well as an uncertainty-based integration scheme. We also used a support vector machine and singular value decomposition on the same features for comparison purposes. Our approach to the full-text subtasks (protein pair and passage identification) includes a feature expansion method based on word proximity networks.

Results:

Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of measures of performance used in the challenge evaluation (accuracy, F-score, and area under the receiver operating characteristic curve). We also report on a web tool that we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full-text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages.

Conclusion:

Our approach to abstract classification shows that a simple linear model, using relatively few features, can generalize and uncover the conceptual nature of protein-protein interactions from the bibliome. Because the novel approach is based on a rather lightweight linear model, it can easily be ported and applied to similar problems. In full-text problems, the expansion of word features with word proximity networks is shown to be useful, although the need for some improvements is discussed.
Mining physical protein-protein interactions from the literature
Authors: Huang Minlie , Ding Shilin , Wang Hongning , Zhu Xiaoyan
Published: September 2008

Background:

Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information. The BioCreative (Critical Assessment of Information Extraction systems in Biology) challenge evaluation provided common standards and shared evaluation criteria to enable comparisons among different approaches.

Results:

During the benchmark evaluation of BioCreative 2006, all of our results ranked in the top three places. In the task of filtering articles irrelevant to physical protein interactions, our method contributes a precision of 75.07%, a recall of 81.07%, and an AUC (area under the receiver operating characteristic curve) of 0.847. In the task of identifying protein mentions and normalizing mentions to molecule identifiers, our method is competitive among runs submitted, with a precision of 34.83%, a recall of 24.10%, and an F1 score of28.5%. In extracting protein interaction pairs, our profile-based method was competitive on the SwissProt-only subset (precision = 36.95%, recall = 32.68%, and F1 score = 30.40%) and on the entire dataset (30.96%, 29.35%, and26.20%, respectively). From the biologist's point of view, however, these findings are far from satisfactory. The error analysis presented in this report provides insight into how performance could be improved: three-quarters of false negatives were due to protein normalization problems (532/698), and about one-quarter were due to problems with correctly extracting interactions for this system.

Conclusion:

We present a text-mining framework to extract physical protein-protein interactions from the literature. Three key issues are addressed, namely filtering irrelevant articles, identifying protein names and normalizing them to molecule identifiers, and extracting protein-protein interactions. Our system is among the top three performers in the benchmark evaluation of BioCreative 2006. The tool will be helpful for manual interaction curation and can greatly facilitate the process of extracting protein-protein interactions.
OntoGene in BioCreative II
Authors: Rinaldi Fabio , Kappeler Thomas , Kaljurand Kaarel , Schneider Gerold , Klenner Manfred , Clematide Simon , Hess Michael , von Allmen Jean-Marc , Parisot Pierre , Romacker Martin , Vachon Therese
Published: September 2008

Background:

Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment.

Results:

In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation.

Conclusion:

Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature.
Gene mention normalization and interaction extraction with context models and sentence motifs
Authors: Hakenberg Jörg , Plake Conrad , Royer Loic , Strobelt Hendrik , Leser Ulf , Schroeder Michael
Published: September 2008

Background:

The goal of text mining is to make the information conveyed in scientific publications accessible to structured search and automatic analysis. Two important subtasks of text mining are entity mention normalization - to identify biomedical objects in text - and extraction of qualified relationships between those objects. We describe a method for identifying genes and relationships between proteins.

Results:

We present solutions to gene mention normalization and extraction of protein-protein interactions. For the first task, we identify genes by using background knowledge on each gene, namely annotations related to function, location, disease, and so on. Our approach currently achieves an f-measure of 86.4% on the BioCreative II gene normalization data. For the extraction of protein-protein interactions, we pursue an approach that builds on classical sequence analysis: motifs derived from multiple sequence alignments. The method achieves an f-measure of 24.4% (micro-average) in the BioCreative II interaction pair subtask.

Conclusion:

For gene mention normalization, our approach outperforms strategies that utilize only the matching of genes names against dictionaries, without invoking further knowledge on each gene. Motifs derived from alignments of sentences are successful at identifying protein interactions in text; the approach we present in this report is fully automated and performs similarly to systems that require human intervention at one or more stages.

Availability:

Our methods for gene, protein, and species identification, and extraction of protein-protein are available as part of the BioCreative Meta Services (BCMS), see http://bcms.bioinfo.cnio.es/.
Overview of BioCreative II gene mention recognition
Authors: Smith Larry , Tanabe Lorraine K , Ando Rie Johnson nee , Kuo Cheng-Ju , Chung I-Fang , Hsu Chun-Nan , Lin Yu-Shi , Klinger Roman , Friedrich Christoph M , Ganchev Kuzman , Torii Manabu , Liu Hongfang , Haddow Barry , Struble Craig A , Povinelli Richard J , Vlachos Andreas , Baumgartner William A , Hunter Lawrence , Carpenter Bob , Tsai Richard Tzong-Han , Dai Hong-Jie , Liu Feng , Chen Yifei , Sun Chengjie , Katrenko Sophia , Adriaans Pieter , Blaschke Christian , Torres Rafael , Neves Mariana , Nakov Preslav , Divoli Anna , Maña-López Manuel , Mata Jacinto , Wilbur W John
Published: September 2008

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.
Overview of BioCreative II gene normalization
Authors: Morgan Alexander A , Lu Zhiyong , Wang Xinglong , Cohen Aaron M , Fluck Juliane , Ruch Patrick , Divoli Anna , Fundel Katrin , Leaman Robert , Hakenberg Jörg , Sun Chengjie , Liu Heng-hui , Torres Rafael , Krauthammer Michael , Lau William W , Liu Hongfang , Hsu Chun-Nan , Schuemie Martijn , Cohen K Bretonnel , Hirschman Lynette
Published: September 2008

Background:

The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%.

Results:

Twenty groups submitted one to three runs each, for a total of 54 runs. Three systems achieved F-measures (balanced precision and recall) between 0.80 and 0.81. Combining the system outputs using simple voting schemes and classifiers obtained improved results; the best composite system achieved an F-measure of 0.92 with 10-fold cross-validation. A 'maximum recall' system based on the pooled responses of all participants gave a recall of 0.97 (with precision 0.23), identifying 763 out of 785 identifiers.

Conclusion:

Major advances for the BioCreative II gene normalization task include broader participation (20 versus 8 teams) and a pooled system performance comparable to human experts, at over 90% agreement. These results show promise as tools to link the literature with biological databases.
Overview of the protein-protein interaction annotation extraction task of BioCreative II
Authors: Krallinger Martin , Leitner Florian , Rodriguez-Penagos Carlos , Valencia Alfonso
Published: September 2008

Background:

The biomedical literature is the primary information source for manual protein-protein interaction annotations. Text-mining systems have been implemented to extract binary protein interactions from articles, but a comprehensive comparison between the different techniques as well as with manual curation was missing.

Results:

We designed a community challenge, the BioCreative II protein-protein interaction (PPI) task, based on the main steps of a manual protein interaction annotation workflow. It was structured into four distinct subtasks related to: (a) detection of protein interaction-relevant articles; (b) extraction and normalization of protein interaction pairs; (c) retrieval of the interaction detection methods used; and (d) retrieval of actual text passages that provide evidence for protein interactions. A total of 26 teams submitted runs for at least one of the proposed subtasks. In the interaction article detection subtask, the top scoring team reached an F-score of 0.78. In the interaction pair extraction and mapping to SwissProt, a precision of 0.37 (with recall of 0.33) was obtained. For associating articles with an experimental interaction detection method, an F-score of 0.65 was achieved. As for the retrieval of the PPI passages best summarizing a given protein interaction in full-text articles, 19% of the submissions returned by one of the runs corresponded to curator-selected sentences. Curators extracted only the passages that best summarized a given interaction, implying that many of the automatically extracted ones could contain interaction information but did not correspond to the most informative sentences.

Conclusion:

The BioCreative II PPI task is the first attempt to compare the performance of text-mining tools specific for each of the basic steps of the PPI extraction pipeline. The challenges identified range from problems in full-text format conversion of articles to difficulties in detecting interactor protein pairs and then linking them to their database records. Some limitations were also encountered when using a single (and possibly incomplete) reference database for protein normalization or when limiting search for interactor proteins to co-occurrence within a single sentence, when a mention might span neighboring sentences. Finally, distinguishing between novel, experimentally verified interactions (annotation relevant) and previously known interactions adds additional complexity to these tasks.
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
Authors: Chatr-aryamontri Andrew , Kerrien Samuel , Khadake Jyoti , Orchard Sandra , Ceol Arnaud , Licata Luana , Castagnoli Luisa , Costa Stefano , Derow Cathy , Huntley Rachael , Aranda Bruno , Leroy Catherine , Thorneycroft Dave , Apweiler Rolf , Cesareni Gianni , Hermjakob Henning
Published: September 2008

Background

In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consuming and the coverage of published interaction data is therefore far from complete. The use of text-mining tools to identify relevant publications and to assist in the initial information extraction could help to improve the efficiency of the curation process and, as a consequence, the database coverage of data available in the literature. The 2006 BioCreative competition was aimed at evaluating text-mining procedures in comparison with manual annotation of protein-protein interactions.

Results

To aid the BioCreative protein-protein interaction task, IntAct and MINT (Molecular INTeraction) provided both the training and the test datasets. Data from both databases are comparable because they were curated according to the same standards. During the manual curation process, the major cause of data loss in mining the articles for information was ambiguity in the mapping of the gene names to stable UniProtKB database identifiers. It was also observed that most of the information about interactions was contained only within the full-text of the publication; hence, text mining of protein-protein interaction data will require the analysis of the full-text of the articles and cannot be restricted to the abstract.

Conclusion

The development of text-mining tools to extract protein-protein interaction information may increase the literature coverage achieved by manual curation. To support the text-mining community, databases will highlight those sentences within the articles that describe the interactions. These will supply data-miners with a high quality dataset for algorithm development. Furthermore, the dictionary of terms created by the BioCreative competitors could enrich the synonym list of the PSI-MI (Proteomics Standards Initiative-Molecular Interactions) controlled vocabulary, which is used by both databases to annotate their data content.
Introducing meta-services for biomedical information extraction
Authors: Leitner Florian , Krallinger Martin , Rodriguez-Penagos Carlos , Hakenberg Jörg , Plake Conrad , Kuo Cheng-Ju , Hsu Chun-Nan , Tsai Richard Tzong-Han , Hung Hsi-Chuan , Lau William W , Johnson Calvin A , Sætre Rune , Yoshida Kazuhiro , Chen Yan Hua , Kim Sun , Shin Soo-Yong , Zhang Byoung-Tak , Baumgartner William A , Hunter Lawrence , Haddow Barry , Matthews Michael , Wang Xinglong , Ruch Patrick , Ehrler Frédéric , Özgür Arzucan , Erkan Güneş , Radev Dragomir R , Krauthammer Michael , Luong ThaiBinh , Hoffmann Robert , Sander Chris , Valencia Alfonso
Published: September 2008

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.
Text mining for biology - the way forward: opinions from leading scientists
Authors: Altman Russ B , Bergman Casey M , Blake Judith , Blaschke Christian , Cohen Aaron , Gannon Frank , Grivell Les , Hahn Udo , Hersh William , Hirschman Lynette , Jensen Lars Juhl , Krallinger Martin , Mons Barend , O'Donoghue Seán I , Peitsch Manuel C , Rebholz-Schuhmann Dietrich , Shatkay Hagit , Valencia Alfonso
Published: September 2008

This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next steps are, and what role future BioCreative evaluations can play. The responses identify several broad themes, including the possibility of fusing literature and biological databases through text mining; the need for user interfaces tailored to different classes of users and supporting community-based annotation; the importance of scaling text mining technology and inserting it into larger workflows; and suggestions for additional challenge evaluations, new applications, and additional resources needed to make progress.
Concept recognition for extracting protein interaction relations from biomedical text
Authors: Baumgartner William A , Lu Zhiyong , Johnson Helen L , Caporaso J Gregory , Paquette Jesse , Lindemann Anna , White Elizabeth K , Medvedeva Olga , Cohen K Bretonnel , Hunter Lawrence
Published: September 2008

Background:

Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics. The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing.

Results:

Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential uses by the benchside biologist.

Conclusion:

Current information extraction technologies are approaching performance standards at which concept recognition can begin to deliver high quality data to the benchside biologist. Our system is available as part of the BioCreative Meta-Server project and on the internet http://bionlp.sourceforge.net.
Assessing the Influence of Field- and GIS-based Inquiry on Student Attitude and Conceptual Knowledge in an Undergraduate Ecology Lab
Authors: Simmons M. E. , Wu X. B. , Knight S. L. , Lopez R. R.
Published: September 2008

Combining field experience with use of information technology has the potential to create a problem-based learning environment that engages learners in authentic scientific inquiry. This study, conducted over a 2-yr period, determined differences in attitudes and conceptual knowledge between students in a field lab and students with combined field and geographic information systems (GIS) experience. All students used radio-telemetry equipment to locate fox squirrels, while one group of students was provided an additional data set in a GIS to visualize and quantify squirrel locations. Pre/postsurveys and tests revealed that attitudes improved in year 1 for both groups of students, but differences were minimal between groups. Attitudes generally declined in year 2 due to a change in the authenticity of the field experience; however, attitudes for students that used GIS declined less than those with field experience only. Conceptual knowledge also increased for both groups in both years. The field-based nature of this lab likely had a greater influence on student attitude and conceptual knowledge than did the use of GIS. Although significant differences were limited, GIS did not negatively impact student attitude or conceptual knowledge but potentially provided other benefits to learners.
Community-based Inquiry Improves Critical Thinking in General Education Biology
Authors: Quitadamo Ian J. , Faiola Celia L. , Johnson James E. , Kurtz Martha J.
Published: September 2008

National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking gains in the CBI group but decreases in a traditional group and a mixed CBI/traditional group. Prior critical-thinking skill, instructor, and ethnicity also significantly influenced critical-thinking gains, with nearly all ethnicities in the CBI group outperforming peers in both the mixed and traditional groups. Females, who showed decreased critical thinking in traditional courses relative to males, outperformed their male counterparts in CBI courses. Through the results of this study, it is hoped that faculty who value both research and critical thinking will consider using the CBI method.
Money, Sex, and Drugs: A Case Study to Teach the Genetics of Antibiotic Resistance
Authors: Cloud-Hansen Karen A. , Kuehner Jason N. , Tong Lillian , Miller Sarah , Handelsman Jo
Published: September 2008

The goal of the work reported here was to help students expand their understanding of antibiotic resistance, the Central Dogma, and evolution. We developed a unit entitled “Ciprofloxacin Resistance in Neisseria gonorrhoeae,” which was constructed according to the principles of scientific teaching by a team of graduate students, science faculty, and instructors. A variety of activities and assessments were used, including a case study, short lectures, and group problem-solving. Implementation of “Ciprofloxacin Resistance in Neisseria gonorrhoeae” in a college freshman seminar suggests these materials are useful in increasing understanding of complex biological topics and improving problem-solving abilities.
Online Protocol Annotation: A Method to Enhance Undergraduate Laboratory Research Skills
Authors: Ruble Julie E. , Lom Barbara
Published: September 2008

A well-constructed, step-by-step protocol is a critical starting point for teaching undergraduates new techniques, an important record of a lab's standard procedures, and a useful mechanism for sharing techniques between labs. Many research labs use websites to archive and share their protocols for these purposes. Here we describe our experiences developing and using a protocol website for the additional purpose of enhancing undergraduate research training. We created our lab's protocol website in a message board format that allows undergraduates to post comments on protocols describing the lessons they learned, questions that arose, and/or insights they gained while learning to execute specific research protocols. Encouraging and expecting students to comment on the protocols they are learning to execute is beneficial for both the student and for the lab in which they are training. For the student, annotations encourage active reflection on their execution of techniques and emphasize the important message that attending to and understanding details of a protocol is a critical factor in producing reliable data. For the lab, annotations capture valuable insights for future generations of researchers by describing missing details, hints, and common hurdles for newcomers.
David Wells
Authors: Hoopes Laura L. Mays
Published: September 2008

Note from the Editor

Educator Highlights for CBE—Life Sciences Education show how professors at different kinds of institutions educate students in life sciences with inspiration and panache. If you have a particularly creative teaching portfolio yourself, or if you wish to nominate an inspiring colleague to be profiled, please e-mail Laura Hoopes at lhoopes@pomona.edu.
Gregory Florant
Authors: Hoopes Laura L. Mays
Published: September 2008

Note from the Editor

Educator Highlights for CBE—Life Sciences Education show how professors at different kinds of institutions educate students in life sciences with inspiration and panache. If you have a particularly creative teaching portfolio yourself, or if you wish to nominate an inspiring colleague to be profiled, please e-mail Laura Hoopes at lhoopes@pomona.edu.
Practice Abstracts
Authors: Denton Brian T.
Published: September 2008

The goal of “Practice Abstracts” is to present interesting, topical, and novel applications of operations research methodology to a wide range of industrial applications. “Practice Abstracts” are intended to provide Interfaces readers with short (2–4 page) descriptions of the most relevant aspects of operations research-based projects, in a form that is accessible to academics and practitioners in other organizations. Contributions should be sent for evaluation to the editor of “Practice Abstracts,” Brian T. Denton, Edward P. Fitts Department of Industrial and Systems Engineering, North Carolina State University, 370 Daniels Hall, 111 Lampe Drive, Raleigh, North Carolina 27695-7906 (bdenton@ncsu.edu).
Disseminating Emergency Preparedness Planning Models as Automatically Generated Custom Spreadsheets
Authors: Herrmann Jeffrey W.
Published: September 2008

When public health officials requested OR models to help county health departments across the United States create plans for dispensing medications and vaccines during emergencies, we developed capacity planning and queueing network models. We then faced the challenge of distributing these models to people with minimal experience with OR techniques and no resources for acquiring and learning new software. To eliminate the most significant obstacles, we decided to use spreadsheets. We created a spreadsheet application that runs Visual Basic for Applications (VBA) macros to generate customized analytical models without the assistance of an OR professional; thus, users could evaluate a wide variety of plans. Developing spreadsheets for this type of application differs significantly from end-user modeling and typical spreadsheet applications. The software is available on our website for public health emergency preparedness planners to download.
Analyzing Supply Chains at HP Using Spreadsheet Models
Authors: Amaral Jason , Kuettner Dorothea
Published: September 2008

To satisfy shifting customer demand for an evolving product offering, every manufacturing company must reconfigure its supply chain network periodically. The network can be simple or complex. It may include suppliers, factories, final assembly locations, and distribution centers. Hewlett-Packard's (HP's) Strategic Planning and Modeling (SPaM) team has helped company executives to analyze numerous supply chain networks using spreadsheets (with and without Visual Basic for Applications (VBA)), spreadsheets with add-ins, custom-written software programs, and packaged software applications. Spreadsheets with and without VBA and add-ins are the most frequently used approach for analyzing supply chain networks. The team employs many advanced spreadsheet and VBA capabilities. It also minimizes unnecessary modeling complexity wherever possible. In this paper, we review why and how we use spreadsheets to analyze supply chains and discuss some of the ways of overcoming their limitations.
Spreadsheet Model Helps to Assign Medical Residents at the University of Vermont's College of Medicine
Authors: Ovchinnikov Anton , Milner Joseph
Published: September 2008

This paper describes a spreadsheet model that MBA students enrolled in an MS course constructed to replace the manual method of assigning medical residents in radiology to on-call and emergency rotations at the University of Vermont's College of Medicine. Although it contains more than 10,000 variables, the model was easy to build and solve by practitioners who are “lightly educated” in OR/MS. Based on this group's work, we discuss an approach that end-user practitioners can take to create spreadsheet optimization models. We also provide several observations and argue that spreadsheet models can provide an alternative scheduling method for problems of a smaller scope. Despite the major advances in personnel-scheduling methodologies and software, manual scheduling is still the predominant method used for such smaller-scope problems.
A Spreadsheet Implementation of an Ammunition Requirements Planning Model for the Canadian Army
Authors: Hurley W. J. , Balez Mathieu
Published: September 2008

This paper describes our experience constructing a spreadsheet implementation of a dynamic ammunition requirements model for Canadian Army training. Each year, the Canadian Army offers a variety of training courses and expends approximately $40 million in ammunition costs to run these courses. It was budgeting over $60 million, and this created a number of organizational problems. The Canadian Army needed a planning tool to bring budgeted expenditures into line with actual expenditures. Our 14 MB spreadsheet implementation accomplished this objective, and the Canadian Army is very pleased with the result.
Spreadsheet Models for Inventory Target Setting at Procter & Gamble
Authors: Farasyn Ingrid , Perkoz Koray , Van de Velde Wim
Published: September 2008

Spreadsheet models have been instrumental in helping Procter & Gamble (P&G) to set inventory targets. The Global Analytics group of P&G's Business Analysis Solutions organization, an in-house modeling, decision-support, and consultancy group, created global inventory models. The models determine the best inventory levels and yield the required customer-service levels, subject to the characteristics and constraints of a particular supply chain. These spreadsheet models are easy to use and share. Therefore, they have become the standard tool for setting inventory targets at P&G; hundreds of supply chain planners worldwide now use them. They have contributed to inventory reductions of over $350 million and significant intangible benefits.
Optimal Trading of ETFs: Spreadsheet Prototypes and Applications to Client-Server Applications
Authors: Kumiega Andrew , Van Vliet Ben
Published: September 2008

This paper presents an application of an Excel spreadsheet-development methodology used by quantitative analysts and traders in financial markets. The spreadsheet used regression and Excel's Solver to determine the optimal investment of a firm's risk capital. The proprietary methodology used to develop real-time trading tools and its repetitive design structure allowed the firm to become a market-maker exchange traded fund (ETF) rapidly. By adhering to the methodology, the firm's documentation of user requirements, data inputs, calculations, and user interfaces, and a full prototype using Excel, made incremental growth possible and provided a solid foundation for conversion into coded software. Rapid development gave the firm the opportunity to derive revenue from market-making activities in new investment products; these would become a major source of revenue. This methodology, which the authors presented in 2001 at the International Conference on Software Quality in Pittsburgh, Pennsylvania, and its implementation led to the development of a complete trading-system development methodology.
Hypo International Strengthens Risk Management with a Large-Scale, Secure Spreadsheet-Management Framework
Authors: Jafry Yusuf , Marrison Christopher , Umkehrer-Neudeck Ulrike
Published: September 2008

We present the solution that Hypo Real Estate Bank International (Hypo) implemented to perform Monte Carlo simulations of its commercial real estate credit risk. The solution uses Risk Integrated's proprietary software, the Specialized Finance System, which is supported by another Risk Integrated technology, the Enterprise Spreadsheet Platform. The platform embeds individual master spreadsheets within a high-performance, server-based, computational-engine architecture; thus, it enables them to be accessed enterprise-wide. The major benefit of this approach is the near-elimination of spreadsheet risk in Hypo's banking system. The solution allows domain experts to have the flexible programming power that spreadsheets provide; however, it does not sacrifice the reliability and auditability expected from traditional business applications.
Lockheed Martin Space Systems Company Optimizes Infrastructure Project-Portfolio Selection
Authors: Gurgur Cigdem Z. , Morley Charles T.
Published: September 2008

Lockheed Martin Space Systems Company spends millions of dollars on the maintenance and modernization of its infrastructure each year. Projects often involve investments that cannot be justified purely in terms of net present value or other classical investment-evaluation methods. The options are also restricted because funds that are not spent within a given time frame must be relinquished. Furthermore, some projects may be delayed and the unplanned carryover of their costs moved into the next fiscal year; this causes the postponement or cancellation of other unrelated projects because of in-budget transfers. In this paper, we used multiattribute utility theory and chance-constrained programming to optimize the selection of infrastructure projects. Our solution ensured the selection of high-value projects to maximize the company's performance. These selections were subject to the constraints that a portfolio did not exceed the available budget and that the carryover of the unspent funds to the next fiscal year did not exceed predetermined limits. We used Microsoft Excel to ensure broad accessibility, transparency, user interaction, improved data collection and asset management, and ease-of-use by managers.
Applying Organisational Theory to Isolated, Confined and Extreme Settings
Authors: Sarris Aspa
Published: September 2008

Research on person–environment fit theory has largely developed within the context of people and organisations in urban settings. There has been little research of this kind within organisations in isolated and confined contexts. The purpose of this article was to examine the implications of person–environment fit theory within the context of the complementary fit and supplementary fit paradigm (Muchinsky & Monahan, 1987), for people working in isolated and remote organisational settings. Using a sample of Antarctic personnel, this study examined the extent to which psychological need fulfilment and subjective fit with Antarctic station culture were equally important in predicting individual attitudes, including satisfaction with being an expedition member, intent to return and willingness to recommend the Antarctic to others. Results showed that gender and subjective fit with Antarctic station culture predicted satisfaction with station membership. Results also showed that subjective fit predicted willingness to recommend the Antarctic as a good place to work, while psychological need fulfilment was not a predictor of any of the outcome variables examined. Results suggest that outcomes such as intention to return (or to stay) may be less relevant in such settings because of the unique and temporary nature of the experience and the work. Results also attest to the need for further development of organisational theories, including person–environment fit theory, using data collected from organisations in isolated, confined and extreme environmental contexts.
Twin-to-Twin Transfusion Syndrome
Authors: Faye-Petersen Ona M. , Crombleholme Timothy M.
Published: September 2008

Twin-to-twin transfusion syndrome (TTTS) may be acute or chronic, but chronic TTTS complicates 10% to 20% of monochorionic twin gestations and has an 80% to 100% mortality rate if severe and left untreated. Both types are due to the presence of placental anastomoses between the two twins, but the mechanisms involved in the development of chronic TTTS are particularly complex and incompletely understood. Many of the apparent pathogenic mechanisms have implications for the appearances and cardiovascular and physiologic disturbances of neonates born following this intrauterine condition and their response to treatment. We present an update in the pathogenesis of TTTS that includes an overview of the placental features, fetal adaptive and maladaptive responses, and molecular mechanisms involved in the development of TTTS.
Twin-to-Twin Transfusion Syndrome
Authors: Faye-Petersen Ona M. , Crombleholme Timothy M.
Published: September 2008

Most anomalies seen in fetuses and neonates who have chronic twin-to-twin transfusion syndrome (TTTS) represent sequelae of cardiovascular dysfunction or vascular disruption. The placental examination can provide critical information to the neonatologist caring for infants who have a history of TTTS, especially in instances wherein the twins are not necessarily growth-discordant but have cardiovascular or renal dysfunction or neuropathologic findings. In this review, we present an updated discussion of the fetal and neonatal pathologies and adverse sequelae associated with TTTS and advances in antenatal diagnosis and clinical interventions for monochorionic gestations complicated by TTTS. We also present highlights of the placental examination so the neonatologist can inspect the placenta at the time of delivery and possibly gain insights that may affect patient care.
Twin-to-Twin Transfusion
Authors: Faye-Petersen Ona M. , Crombleholme Timothy M.
Published: September 2008

The high morbidity and mortality rates of twin-to-twin transfusion syndrome (TTTS) generally are related to sequelae of cardiovascular dysfunction or vascular disruption. Neurologic sequelae associated with TTTS are emerging concerns for survivors. A variety of clinical interventions, including amnioreduction, microseptostomy of the inter-twin membrane, and fetoscopic laser photocoagulation of placental anastomoses, have been used alone or in sequence to reduce the rates of mortality and morbidity. Because many of these specialized interventional procedures are performed at select centers in the United States, women may be treated at considerable distance from their primary obstetric care institutions and later return to deliver at their local facilities. Neonatologists may be unfamiliar with the relative efficacies and outcomes of the interventional procedures. In this review, we present a focused summary of the neurodevelopmental outcomes associated with these antenatal treatments.
Pulse Oximetry Screening at 4 Hours of Age to Detect Critical Congenital Heart Defects
Authors: Sendelbach Dorothy M. , Jackson Gregory L. , Lai Susanna S. , Fixler David E. , Stehel Elizabeth K. , Engle William D.
Published: September 2008

OBJECTIVE. The purpose of this prospective study was to assess the feasibility and reliability of pulse oximetry screening to detect critical congenital heart defects in a newborn nursery.

METHODS. The study was performed in a large urban hospital with an exclusively inborn population. Stable neonates who had a gestational age of ≥35 weeks and birth weight of ≥2100 g and in whom a critical congenital heart defect was not suspected were admitted to the newborn nursery. When the 4-hour pulse oximetry reading was <96%, pulse oximetry was repeated at discharge, and when the pulse oximetry reading remained at persistently <96%, echocardiography was performed.

RESULTS. Of 15299 admissions to newborn nursery during the 12-month study period, 15233 (99.6%) neonates were screened with 4-hour pulse oximetry. Pulse oximetry readings were ≥96% for 14374 (94.4%) neonates; 77 were subsequently evaluated before discharge for cardiac defects on the basis of clinical examination. Seventy-six were normal, and 1 had tetralogy of Fallot with discontinuous pulmonary arteries. Pulse oximetry readings at 4 hours were <96% in 859 (5.6%); 768 were rescreened at discharge, and 767 neonates had a pulse oximetry reading at ≥96%. One neonate had persistently low pulse oximetry at discharge; echocardiography was normal. Although 3 neonates with a critical congenital heart defect had a 4-hour pulse oximetry reading of <96%, all developed signs and/or symptoms of a cardiac defect and received a diagnosis on the basis of clinical findings, not screening results.

CONCLUSIONS. All neonates with a critical congenital heart defect were detected clinically, and no cases of critical congenital heart defect were detected by pulse oximetry screening. These results indicate that pulse oximetry screening does not improve detection of critical congenital heart defects above and beyond clinical observation and assessment. Our findings do not support a recommendation for routine pulse oximetry screening in seemingly healthy neonates.
Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal ITS and Chloroplast DNA Sequence Data
Authors: Havill Nathan P. , Campbell Christopher S. , Vining Thomas F. , LePage Ben , Bayer Randall J. , Donoghue Michael J.
Published: September 2008

Hemlock, Tsuga (Pinaceae), has a disjunct distribution in North America and Asia. To examine the biogeographic history of Tsuga, phylogenetic relationships among multiple accessions of all nine species were inferred using chloroplast DNA sequences and multiple cloned sequences
of the nuclear ribosomal ITS region. Analysis of chloroplast and ITS sequences resolve a clade that includes the two western North American species, T. heterophylla and T. mertensiana, and a clade of Asian species within which one of the eastern North American species, T.
caroliniana, is nested. The other eastern North American species, T. canadensis, is sister to the Asian clade. Tsuga chinensis from Taiwan did not group with T. chinensis from mainland China, and T. sieboldii from Ullung Island did not group with T. sieboldii
from Japan suggesting that the taxonomic status of these distinct populations should be reevaluated. The Himalayan species, T. dumosa, was in conflicting positions in the chloroplast and ITS trees, suggesting that it may be of hybrid origin. Likelihood-based biogeographic inference
with divergence time estimates infers an Eocene basal crown group diversification and an initial widespread circumpolar distribution with subsequent vicariance and extinction events leading to the current disjunct distribution.
A Morphometric Study of Species Boundaries of the Wild Potato Solanum Series Piurana (Solanaceae) and Putatively Related Species from Seven Other Series in Solanum Sect. Petota
Authors: Ames Mercedes , Salas Alberto , Spooner David M.
Published: September 2008

There are about 190 wild potato (Solanum L. section Petota Dumort.) species distributed from the southwestern United States to central Argentina and adjacent Chile and Uruguay. The morphological similarity of many of its constituent species has led to widely conflicting
taxonomic treatments. Solanum series Piurana Hawkes is one of 21 series recognized in section Petota in the latest comprehensive taxonomic treatment by Hawkes in 1990. They are distributed from southern Colombia, south through Ecuador to central Peru. The limits of the
series and validity of its constituent species are unresolved. We provide the first comprehensive morphological phenetic study of the series, to include putatively related species in ser. Conicibaccata, Cuneoalata, Ingifolia, Megistacroloba, Simplicissima, Tuberosa, and
Yungasensa, through an examination 188 living germplasm accessions of 33 species, planted in replicated plots in a field station in Andean Peru. Only four morphologically well-defined groups were supported. Continuing work is exploring molecular support for these species in these eight
series.