bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of ResDE-DependentfnrTranscription inBacillus subtilis
Authors: Geng Hao , Zhu Yi , Mullen Karl , Zuber Cole S. , Nakano Michiko M.
Published: December 2006

The ResD-ResE signal transduction system is required for transcription of genes involved in aerobic and anaerobic respiration inBacillus subtilis. Phosphorylated ResD (ResD∼P) interacts with target DNA to activate transcription. A strong sequence similarity was detected in promoter regions of some ResD-controlled genes includingfnrandresA. Single-base substitutions in thefnrandresApromoters were performed to determine a ResD-binding sequence. DNase I footprinting analysis indicated that ResD∼P itself does not bind tofnr, but interaction of ResD∼P with the C-terminal domain of the α subunit (αCTD) of RNA polymerase (RNAP) facilitates cooperative binding of ResD∼P and RNAP, thereby increasingfnrtranscription initiation. Consistent with this result, amino acid substitutions in αCTD, such as Y263A, K267A, A269I, or N290A, sharply reducedfnrtranscription in vivo, and the K267A αCTD protein, unlike the wild-type protein, did not increase ResD∼P binding to thefnrpromoter. Amino acid residues of αCTD required for ResD-dependentfnrtranscription, with the exception of N290, which may interact with DNA, constitute a distinct surface, suggesting that these residues likely interact with ResD∼P.
Characterization of a Novel
d
-Lyxose Isomerase from
Cohnella laevoribosii
RI-39 sp. nov
Authors: Cho Eun-Ah , Lee Dong-Woo , Cha Yun-Hwan , Lee Sang-Jae , Jung Heung-Chae , Pan Jae-Gu , Pyun Yu-Ryang
Published: December 2006

A newly isolated bacterium,
Cohnella laevoribosii
RI-39, could grow in a defined medium with
l
-ribose as the sole carbon source. A 21-kDa protein isomerizing
l
-ribose to
l
-ribulose, as well as
d
-lyxose to
d
-xylulose, was purified to homogeneity from this bacterium. Based on the N-terminal and internal amino acid sequences of the purified enzyme obtained by N-terminal sequencing and quantitative time of flight mass spectrometry-mass spectrometry analyses, a 549-bp gene (
lyxA
) encoding
d
-lyxose (
l
-ribose) isomerase was cloned and expressed in
Escherichia coli
. The purified endogenous enzyme and the recombinant enzyme formed homodimers that were activated by Mn
2+
.
C. laevoribosii
d
-lyxose (
l
-ribose) isomerase (CLLI) exhibits maximal activity at pH 6.5 and 70°C in the presence of Mn
2+
for
d
-lyxose and
l
-ribose, and its isoelectric point (pI) is 4.2 (calculated pI, 4.9). The enzyme is specific for
d
-lyxose,
l
-ribose, and
d
-mannose, with apparent

K
m

values of 22.4 ± 1.5 mM, 121.7 ± 10.8 mM, and 34.0 ± 1.1 mM, respectively. The catalytic efficiencies (
k
cat
/

K
m

) of CLLI were 84.9 ± 5.8 mM
−1
s
−1
for
d
-lyxose (
V
max
, 5,434.8 U mg
−1
), 0.2 mM
−1
s
−1
for
l
-ribose (
V
max
, 75.5 ± 6.0 U mg
−1
), and 1.4 ± 0.1 mM
−1
s
−1
for
d
-mannose (
V
max
, 131.8 ± 7.4 U mg
−1
). The ability of
lyxA
to permit
E. coli
cells to grow on
d
-lyxose and
l
-ribose and homology searches of other sugar-related enzymes, as well as previously described sugar isomerases, suggest that CLLI is a novel type of rare sugar isomerase.
Mutations of the Act Promoter in
Myxococcus xanthus
Authors: Gronewold Thomas M. A. , Kaiser Dale
Published: December 2006

Mutations within the −12 and −24 elements provide evidence that the
act
promoter is recognized by sigma-54 RNA polymerase. Deletion of the −20 base pair, which lies between the two conserved elements of sigma-54 promoters, decreased expression by 90%. In addition, mutation of a potential enhancer sequence, around −120, led to an 80% reduction in
act
gene expression.
actB
, the second gene in the
act
operon, encodes a sigma-54 activator protein that is proposed to be an enhancer-binding protein for the
act
operon. All
act
genes,
actA
to
actE
, are expressed together and constitute an operon, because an in-frame deletion of
actB
decreased expression of
actA
and
actE
to the same extent. After an initially slow phase of
act
operon expression, which depends on FruA, there is a rapid phase. The rapid phase is shown to be due to the activation of the operon expression by ActB, which completes a positive feedback loop. That loop appears to be nested within a larger positive loop in which ActB is activated by the C signal via ActA, and the
act
operon activates transcription of the
csgA
gene. We propose that, as cells engage in more C signaling, positive feedback raises the number of C-signal molecules per cell and drives the process of fruiting body development forward.
YjjG, a dUMP Phosphatase, Is Critical for Thymine Utilization by
Escherichia coli
K-12
Authors: Weiss Bernard
Published: December 2006

Exogenous thymine must be converted to thymidine to enable a
thyA
(thymidylate synthase) mutant to grow. The deoxyribose in the thymidine comes from dUMP, which must first be dephosphorylated. The nucleotidase YjjG is critical for this step. A
yjjG thyA
mutant cannot use thymine for growth on a glucose minimal medium.
Growth Phase Regulation of
Vibrio cholerae
RTX Toxin Export
Authors: Boardman Bethany Kay , Meehan Brian M. , Fullner Satchell Karla J.
Published: December 2006

Vibrio cholerae
, the causative agent of the severe diarrheal disease cholera, secretes several “accessory” toxins, including RTX toxin, which causes the cross-linking of the actin cytoskeleton. RTX toxin is exported to the extracellular milieu by an atypical type I secretion system (T1SS), and we previously noted that RTX-associated activity is detectable only in supernatant fluids from log phase cultures. Here, we investigate the mechanisms for regulating RTX toxin activity in supernatant fluids. We find that exported proteases are capable of destroying RTX activity and may therefore play a role in the growth phase regulation of toxin activity. We determined that the absence of RTX toxin in stationary-phase culture supernatant fluids is also due to a lack of toxin secretion and not attributable to solely proteolytic degradation. We ascertained that the T1SS apparatus is regulated at the transcriptional level by growth phase control that is independent of quorum sensing, unlike other virulence factors of
V. cholerae
. Additionally, in stationary-phase cultures, all RTX toxin activity is associated with bacterial membranes or outer membrane vesicles.
Interanimal variability in preexisting collaterals is a major factor determining outcome in experimental angiogenesis trials
Authors: Zbinden Stephan , Clavijo Leonardo C. , Kantor Birgit , Morsli Hakim , Cortes Guillermo A. , Andrews James A. , Jang Gil Jin , Burnett Mary Susan , Epstein Stephen E.
Published: December 2006

Despite numerous animal trials reporting that cell therapy promotes collateral flow, clinical trials have not convincingly shown benefit. Patient-related risk factors are often used to explain these discrepancies. However, during the course of our own angiogenesis studies using mice, we noted large anatomical variability in collateral vessels. The purpose of the present investigation was to define how important this factor might be in determining intervention outcomes. Hindlimb ischemia was induced in BALB/c mice by ligating the superficial femoral artery. After 24 h, animals were treated by injecting the adductor muscle with either control media or cultured mesenchymal stem cells (MSCs). Blood flow recovery was measured using laser-Doppler [laser-Doppler perfusion imaging (LDPI) ratio]. In a second experiment, mice were stratified 24 h after arterial ligation before treatment by using a simple clinical score of the ligated leg: 1, able to flex, mild discoloration; 2, no flexion, mild discoloration; 3, severe discoloration; and 4, any necrosis. Without stratification, blood flow recovery significantly increased in the MSC-treated group ( P < 0.05, n = 6 MSC group, n = 7 media group). In the experiment employing stratification, all differences between the groups disappeared ( n = 11 MSC group, n = 10 media group; P = 0.3). Furthermore, we found a striking inverse correlation between clinical score on day 1 and the LDPI ratio on day 28 ( P < 0.0001; n = 79). Anatomical confirmation of the disparity in preexisting collaterals was found in two different mouse strains using microscopic computed tomography. In conclusion, there is substantial interanimal variability in preexisting collateral flow, and this variability can importantly influence outcome. To overcome this, either animals must be stratified before treatment, the number of animals must be increased substantially, or, preferably, both.
Regulation of lymphatic capillary regeneration by interstitial flow in skin
Authors: Goldman Jeremy , Conley Kelly A. , Raehl Alisha , Bondy Dona M. , Pytowski Bronislaw , Swartz Melody A. , Rutkowski Joseph M. , Jaroch David B. , Ongstad Emily L.
Published: December 2006

Decreased interstitial flow (IF) in secondary lymphedema is coincident with poor physiological lymphatic regeneration. However, both the existence and direction of causality between IF and lymphangiogenesis remain unclear. This is primarily because the role of IF and its importance relative to the action of the prolymphangiogenic growth factor vascular endothelial growth factor (VEGF)-C (which signals primarily through its receptor VEGFR-3) are poorly understood. To clarify this, we explored the cooperative roles of VEGFR-3 and IF in a mouse model of lymphangiogenesis in regenerating skin. Specifically, a region of lymphangiogenesis was created by substituting a portion of mouse tail skin with a collagen gel within which lymphatic capillaries completely regenerate over a period of 60 days. The relative importance of IF and VEGF-C signaling were evaluated by either inhibiting VEGFR-3 signaling with antagonistic antibodies or by reducing IF. In some cases, VEGF-C signaling was then increased with exogenous protein. To clarify the role of IF, the distribution of endogenous matrix metalloproteinases (MMPs) and VEGF-C within the regenerating region was determined. It was found that inhibition of either VEGFR-3 or IF suppressed endogenous lymphangiogenesis. Reduction of IF was found to decrease lymphatic migration and transport of endogenous MMP and VEGF-C through the regenerating region. Therapeutic VEGF-C administration restored lymphangiogenesis following inhibition of VEGFR-3 but did not increase lymphangiogenesis following inhibition of IF. These results identify IF as an important regulator of the pro-lymphangiogenic action of VEGF-C.
Na channel expression and activity in the medullary collecting duct of rat kidney
Authors: Frindt Gustavo , Ergonul Zuhal , Palmer Lawrence G.
Published: January 2007

The expression and activity of epithelial Na+ channels (ENaC) in the medullary collecting duct of the rat kidney were examined using a combination of whole cell patch-clamp measurements of amiloride-sensitive currents ( INa) in split-open tubules and Western blot analysis of α-, β-, and γ-ENaC proteins. In the outer medullary collecting duct, amiloride-sensitive currents were undetectable in principal cells from control animals but were robust when rats were treated with aldosterone ( INa = 960 ± 160 pA/cell) or fed a low-Na diet ( INa = 440 ± 120 pA/cell). In both cases, the currents were similar to those measured in principal cells of the cortical collecting duct from the same animals. In the inner medullary collecting duct, currents were much lower, averaging 120 ± 20 pA/cell in aldosterone-treated rats. Immunoblots showed that all three ENaC subunits were expressed in the cortex, outer medulla, and inner medulla of the rat kidney. When rats were fed a low-Na diet for 1 wk, similar changes in α- and γ-ENaC occurred in all three regions of the kidney; the amounts of full-length as well as putative cleaved α-ENaC protein increased, and the fraction of γ-ENaC protein in the cleaved state increased at the expense of the full-length protein. The appearance of a presumably fully glycosylated form of β-ENaC in Na-depleted animals was observed mainly in the outer and inner medulla. These findings suggest that the capability of hormone-regulated, channel-mediated Na reabsorption by the nephron extends at least into the outer medullary collecting duct.
Nonsynonymous Coding Single-Nucleotide Polymorphisms Spanning the Genome in Relation to Glioblastoma Survival and Age at Diagnosis
Authors: Wrensch Margaret , McMillan Alex , Wiencke John , Wiemels Joe , Kelsey Karl , Patoka Joe , Jones Hywel , Carlton Victoria , Miike Rei , Sison Jennette , Moghadassi Michelle , Prados Michael
Published: January 2007

Purpose: Our aim was to discover possible inherited factors associated with glioblastoma age at diagnosis and survival. Although new genotyping technologies allow greatly expanded exploration of such factors, they pose many challenges.

Experimental Design: In this pilot study, we (a) genotyped 112 newly diagnosed glioblastoma patients ascertained through a population-based study (group 1) with the ParAllele assay panel of ∼10,000 nonsynonymous coding single-nucleotide polymorphisms (SNP), (b) used several statistical and bioinformatic techniques to identify 17 SNPs potentially related to either glioblastoma age at diagnosis or survival, and (c) genotyped 16 of these SNPs using conventional PCR methods in an independent group of 195 glioblastoma patients (group 2).

Results: In group 2, only one of the 16 SNPs, rs8057643 (located on 16p13.2), was significantly associated with glioblastoma age at diagnosis (nominal P = 0.0017; Bonferroni corrected P = 0.054). Median ages at diagnosis for those with 0, 1, or 2 T alleles were 66, 57, and 59 years in group 1 and 64, 57, and 55 years in group 2 (combined P = 0.001). Furthermore, Cox regression analyses of time to death with number of T alleles adjusted for gender and patient group yielded a hazard ratio of 0.82 (95% confidence interval, 0.68-0.98; P = 0.03).

Conclusions: Although limited by a relatively small sample size, this pilot study, using well-characterized, unambiguous disease characteristics, illustrates the necessity of independent replication owing to the likelihood of false positives. Several other challenges are discussed, including attempts to incorporate information on the potential functional importance of SNPs in genome-disease association studies.
Monitoring Response to Anticancer Therapy by Targeting Microbubbles to Tumor Vasculature
Authors: Korpanty Grzegorz , Carbon Juliet G. , Grayburn Paul A. , Fleming Jason B. , Brekken Rolf A.
Published: January 2007

Purpose: New strategies to detect tumor angiogenesis and monitor response of tumor vasculature to therapy are needed. Contrast ultrasound imaging using microbubbles targeted to tumor endothelium offers a noninvasive method for monitoring and quantifying vascular effects of antitumor therapy. We investigated the use of targeted microbubbles to follow vascular response of therapy in a mouse model of pancreatic adenocarcinoma.

Experimental Design: Microbubbles conjugated to monoclonal antibodies were used to image and quantify vascular effects of two different antitumor therapies in s.c. and orthotopic pancreatic tumors in mice. Tumor-bearing mice were treated with anti-vascular endothelial growth factor (VEGF) monoclonal antibodies and/or gemcitabine, and the localization of microbubbles to endoglin (CD105), VEGF receptor 2 (VEGFR2), or VEGF-activated blood vessels (the VEGF-VEGFR complex) was monitored by contrast ultrasound.

Results: Targeted microbubbles showed significant enhancement of tumor vasculature when compared with untargeted or control IgG–targeted microbubbles. Video intensity from targeted microbubbles correlated with the level of expression of the target (CD105, VEGFR2, or the VEGF-VEGFR complex) and with microvessel density in tumors under antiangiogenic or cytotoxic therapy.

Conclusions: We conclude that targeted microbubbles represent a novel and attractive tool for noninvasive, vascular-targeted molecular imaging of tumor angiogenesis and for monitoring vascular effects specific to antitumor therapy in vivo.
A study of the impact of the expectation of a holiday on an individual's sense of well-being
Authors: Gilbert David , Abdullah Junaida
Published: January 2007

This paper offers an investigation into what effect the expectation of holiday taking has on the sense of well-being of UK tourists. The well-being of the tourist is currently an under-researched area. This sphere of study is related to research which attempts to accountfor the perceived negative and positive affects regarding the state of affairs and the subjective judgments of an individual's lIfe domain.1 As such, a study incorporating applications of well-being assessment is an important addition to the study of tourism. This study investigates whether anticipation of a holiday affects or changes the well-being of the tourist. The research design includes a non-holiday control group in order to identify whether there is any significant diference between the well-being of a holiday-taking group and a group who are not going on a holiday. Thefindings indicated signficant diferences between the holiday-taking group and the non-holiday-taking group in terms of current effect, their global well-being (lfte as a whole) and in three specific life domains: family, economic situation and health. It appears that those who are waiting to go on a holiday are much happier with their life as a whole, experience less negative or unpleasantfeelings and thus enjoy an overall net positive effect or pleasantfeelings. The holiday-taking group are also happier with their family, economic situation and health domains compared to the non-holiday-taking group. However, the effect is not strong enough to affect all the specific life domain aspects, such as the realm of nation. The overallfinding is that the anticipation of afavourable event (holiday trip) has affected the respondents' subjective well-being equilibrium. It is argued that this is because the respondents' level of effect (hedonic) has changed positively, thereby increasing their well-being. This in turn makes themfeel much happier and hence experience more pleasantfeelings.
The impact of customer service on a resort community
Authors: Thomas David F.
Published: January 2007

The level of customer service provided by businesses in the resort community of Estes Park, Colorado, was investigated in this study. The problems and barriers in delivering quality customer service were determined through a collaborative process of data gathering that involved the use of surveys, group interviews and focus groups. The research confirmed that inconsistent customer service is a direct result of the lack of any customer service training programme, non-existent effort among the providers of tourism services, and low awareness of the impact of customer service as a key marketing and management tool in attracting new and repeat visitors. The research produced a model for developing a tourist-centred customer service campaign that incorporated community involvement in the design and execution of the research and resulting programmes.
Multiple upstream modules regulate zebrafish myf5expression
Authors: Chen Yau-Hung , Wang Yun-Hsin , Chang Min-Yen , Lin Cheng-Yung , Weng Chih-Wei , Westerfield Monte , Tsai Huai-Jen
Published: January 2007

Background

Myf5 is one member of the basic helix-loop-helix family of transcription factors, and it functions as a myogenic factor that is important for the specification and differentiation of muscle cells. The expression of myf5 is somite- and stage-dependent during embryogenesis through a delicate regulation. However, this complex regulatory mechanism of myf5 is not clearly understood.

Results

We isolated a 156-kb bacterial artificial chromosome clone that includes an upstream 80-kb region and a downstream 70-kb region of zebrafish myf5 and generated a transgenic line carrying this 156-kb segment fused to a green fluorescent protein (GFP) reporter gene. We find strong GFP expression in the most rostral somite and in the presomitic mesoderm during segmentation stages, similar to endogenous myf5 expression. Later, the GFP signals persist in caudal somites near the tail bud but are down-regulated in the older, rostral somites. During the pharyngula period, we detect GFP signals in pectoral fin buds, dorsal rostral myotomes, hypaxial myotomes, and inferior oblique and superior oblique muscles, a pattern that also corresponds well with endogenous myf5 transcripts. To characterize the specific upstream cis-elements that regulate this complex and dynamic expression pattern, we also generated several transgenic lines that harbor various lengths within the upstream 80-kb segment. We find that (1) the -80 kb/-9977 segment contains a fin and cranial muscle element and a notochord repressor; (2) the -9977/-6213 segment contains a strong repressive element that does not include the notochord-specific repressor; (3) the -6212/-2938 segment contains tissue-specific elements for bone and spinal cord; (4) the -2937/-291 segment contains an eye enhancer, and the -2937/-2457 segment is required for notochord and myocyte expression; and (5) the -290/-1 segment is responsible for basal transcription in somites and the presomitic mesoderm.

Conclusion

We suggest that the cell lineage-specific expression of myf5 is delicately orchestrated by multiple modules within the distal upstream region. This study provides an insight to understand the molecular control of myf5 and myogenesis in the zebrafish.
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center
Authors: Saikatendu Kumar Singh , Zhang Xuejun , Kinch Lisa , Leybourne Matthew , Grishin Nick V , Zhang Hong
Published: December 2006

Background

The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function.

Results

The structure of SA1388 has been solved to 2.0Å resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site.

Conclusion

SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.
Cdc42 and ARP2/3-independent regulation of filopodia by an integral membrane lipid-phosphatase-related protein
Authors: Sigal Yury J. , Quintero Omar A. , Cheney Richard E. , Morris Andrew J.
Published: January 2007

Filopodia are dynamic cell surface protrusions that are required for proper cellular development and function. We report that the integral membrane protein lipid-phosphatase-related protein 1 (LPR1) localizes to and promotes the formation of actin-rich, dynamic filopodia, both along the cell periphery and the dorsal cell surface. Regulation of filopodia by LPR1 was not mediated by cdc42 or Rif, and is independent of the Arp2/3 complex. We found that LPR1 can induce filopodia formation in the absence of the Ena/Vasp family of proteins, suggesting that these molecules are not essential for the development of the protrusions. Mutagenesis experiments identified residues and regions of LPR1 that are important for the induction of filopodia. RNA interference experiments in an ovarian epithelial cancer cell line demonstrated a role for LPR1 in the maintenance of filopodia-like membrane protrusions. These observations, and our finding that LPR1 is a not an active lipid phosphatase, suggest that LPR1 may be a novel integral membrane protein link between the actin core and the surrounding lipid layer of a nascent filopodium.
Regions of Rationality: Maps for Bounded Agents
Authors: Hogarth Robin M. , Karelaia Natalia
Published: December 2006

An important problem in descriptive and prescriptive research in decision making is to identify “regions of rationality,” i.e., the areas for which heuristics are and are not effective. To map the contours of such regions, we derive probabilities that heuristics identify the best of m alternatives (m ≥ 2) characterized by k attributes or cues (k ≥ 1). The heuristics include a single variable (lexicographic), variations of elimination-by-aspects, equal weighting, hybrids of the preceding, and models exploiting dominance. We use 20 simulated and 4 empirical data sets for illustration. We further provide an overview by regressing heuristic performance on factors characterizing environments. Overall, “sensible” heuristics generally yield similar choices in many environments. However, selection of the appropriate heuristic can be important in some regions (e.g., if there is low intercorrelation among attributes or cues). Because our work assumes a hit-or-miss decision criterion, we conclude by outlining extensions for exploring the effects of different loss functions.
The Sensitivity of Probability Assessments to Time Units and Performer Characteristics
Authors: Yechiam Eldad , Budescu David V.
Published: December 2006

This paper examines the sensitivity of probability judgments pertaining to real-world events (e.g., the chance of getting a speeding ticket) to the events’ time horizon (e.g., 1, 2, or 8 weeks) and performer characteristics (e.g., 1, 2, and 8 drivers). Using the participants’ multiple responses to different time horizons and number of performers, we assessed the degree of deviance from the normative prescription and potential explanations for such deviance. In Study 1, two questionnaires were administered to a sample of 120 students. In the first questionnaire, in violation of the normative disjunctive model, most participants did not adjust probabilities sufficiently for various time horizons. This pattern cannot be attributed merely to regression to the mean with a fixed error term (Erev et al. 1994). In the second questionnaire, the same bias was replicated in scenarios featuring different numbers of individuals, indicating no time-specific contributing factors. In Study 2, a sample of 140 students responded to a computerized questionnaire in which the items preceding target questions were controlled. The direction of the deviance did not change as a function of previous items. The results are attributed to the “extension neglect” tendency (Kahneman 2003).
A Survey Study of Factors Influencing Risk-Taking Behavior in Real-World Decisions Under Uncertainty
Authors: Baucells Manel , Rata Cristina
Published: December 2006

With the goal of investigating decision making under uncertainty in real-world decisions, we conduct a survey requiring 261 subjects to describe a recent real-life decision and to answer questions about several dimensions of such decision, including reference-dependence, domain, the default alternative, and the type of consequences. We confirm a key prediction of prospect theory, namely, that perceiving the sure outcome as a loss increases risk-taking behavior. Such perception of losses also increases the attractiveness (perceived probabilities and estimated consequences) of the risky option. The results also confirm that the domain (professional versus private) of a decision is a factor influencing risk-taking behavior. Risk-taking behavior does not vary across the three groups considered (undergraduates, MBA students, and executives) and does not depend on the type of consequences (monetary or not). We confirm that reference-dependence, and not the default alternative, is the driver of risk-taking behavior.
From the Special Issue Editors… Special Issue on Psychology and Decision Analysis
Authors: Kleinmuntz Don N. , Wu George
Published: December 2006

Decision analysis and the psychology of judgment and decision making are two distinct fields linked by common foundations and overlapping communities of researchers. Progress in psychological science is important to decision analysis because it provides insights about when decision analysis is likely to be needed as well as the practical problems we may encounter in implementing analytic processes in real world settings. This special issue includes four contributions to the psychology of decision making that are relevant to prescriptive decision analysis. The first article proposes a theoretical account of when choice heuristics are likely to perform well (or not) relative to normative benchmarks. The second contribution examines how decision makers aggregate multiple sources of information. The third article reports a survey study of real-world risk-taking behavior, and the fourth article investigates the sensitivity of probability assessments to time horizons.
Exact Algorithms for a Loading Problem with Bounded Clique Width
Authors: Moonen Linda S. , Spieksma Frits C. R.
Published: December 2006

In this paper we discuss a special pallet-loading problem, which we encountered at a manufacturing company. In graph-theoretical terms, the problem is equivalent to partitioning a permutation graph into bounded-size cliques. We formulate the problem as an integer program, and present two exact algorithms for solving it. The first algorithm is a branch-and-price algorithm based on the integer-programming formulation; the second one is an algorithm based on the concept of bounded clique width. The latter algorithm was motivated by the structure present in the real-world instances. Test results are given, both for real-world instances and randomly generated instances. As far as we are aware, this is the first implementation of an algorithm based on bounded clique width.
A Memetic Heuristic for the Generalized Quadratic Assignment Problem
Authors: Cordeau Jean-François , Gaudioso Manlio , Laporte Gilbert , Moccia Luigi
Published: December 2006

In the generalized quadratic assignment problem (GQAP) we are given n weighted facilities, m capacitated sites, a traffic intensity matrix between facilities, a distance matrix between sites, unit traffic costs, and assignment costs of facilities to sites. The aim is to determine an assignment of facilities to sites so that the sum of assignment and traffic costs is minimized and the total weight of all facilities assigned to the same site does not exceed the site capacity. The GQAP is a generalization of the quadratic assignment problem (QAP) in which n = m and exactly one facility must be assigned to each site. The problem has applications in container yard management and in the assignment of equipment to manufacturing sites. This article describes a memetic heuristic for the GQAP, as well as an integer linear programming formulation that can be solved by CPLEX for small instances. For larger instances, feasible solutions can be obtained by a truncated branch-and-bound procedure. Computational experiments show that on small instances the proposed heuristic always yields an optimal solution; on larger instances it always outperforms the truncated branch-and-bound algorithm.
Improving Customer Service Operations at Amazon.com
Authors: Keblis Matthew F. , Chen Maomao
Published: December 2006

The success of the Internet retailer Amazon.com depends on its providing high-quality customer service. Amazon.com’s customer service operations consist of internally and externally managed contact centers. Amazon.com must size its contact centers appropriately, deciding about hiring and training at internally managed centers, and the volume of voice calls and e-mail messages to allocate to external service providers. We developed an approach based on mathematical programming that Amazon.com uses in planning capacity, reducing the average cost of handling a customer contact, and increasing the service level provided customers.
Operations Research Models and the Management of Agricultural and Forestry Resources: A Review and Comparison
Authors: Weintraub Andrés , Romero Carlos
Published: December 2006

Operations research (OR) has helped people to understand and manage agricultural and forestry resources during the last 40 years. We analyzed its use to assess the past performance of OR models in this field and to highlight current problems and future directions of research and applications. Thus, in the agriculture part, we concentrate on planning problems at the farm and regional-sector level, environmental implications, risk and uncertainty issues, multiple criteria, and the formulation of livestock rations and feeding stuffs. In the forestry part, we concentrate on planning problems at the strategic, tactical, and operational levels, implementation issues, environmental implications, as well as the treatment of uncertainty and multiple objectives. Finally we made a comparison between the two areas in terms of problem types, problem-solving approaches, and reported applications.
Responding to Bioterrorist Smallpox in San Antonio
Authors: Miller George , Randolph Stephen , Patterson Jan E.
Published: December 2006

We used discrete-event simulation to help the San Antonio public health and acute medical care communities to plan their response to a bioterrorist attack. The analysis, based on a scenario positing an attack with aerosolized smallpox, indicated the resources and strategies needed for an effective response. We found that a mixture of public-health measures designed to stop the spread of the disease would form a more robust and effective response than any single measure. However, unless the attack is very small, the public-health system is unlikely to be able to prevent a surge in demand for acute care that will require community-wide coordination of resources, a definitive patient-triage policy, and temporary treatment practices. The San Antonio communities are integrating our recommendations into their plans.
How Effective Is Security Screening of Airline Passengers?
Authors: Martonosi Susan E. , Barnett Arnold
Published: December 2006

With a simple mathematical model, we explored the antiterrorist effectiveness of airport passenger prescreening systems. Supporters of these systems often emphasize the need to identify the most suspicious passengers, but they ignore the point that such identification does little good unless dangerous items can actually be detected. Critics often focus on terrorists’ ability to probe the system and thereby thwart it, but ignore the possibility that the very act of probing can deter attempts at sabotage that would have succeeded. Using the model to make some preliminary assessments about security policy, we find that an improved baseline level of screening for all passengers might lower the likelihood of attack more than would improved profiling of high-risk passengers.
Responding to Emergencies: Lessons Learned and the Need for Analysis
Authors: Larson Richard C. , Metzger Michael D. , Cahn Michael F.
Published: December 2006

Large-scale emergency incidents, such as acts of terrorism, human-caused accidents, and acts of nature, often overwhelm local first-responder resources. A historical review of five recent major emergencies—the Oklahoma City bombing (1995), the crash of United Airlines Flight 232 (1989), the sarin attack in the Tokyo subway (1995), Hurricane Floyd (1999), and Hurricane Charlie (2004)—shows the need for additional research to develop decision-oriented, operations research models to improve preparation for and response to major emergencies. Local emergency managers need decision guidance regarding evacuation directives, management of near-the-scene logistics, triage on the scene and at hospitals, use of volunteers and off-duty personnel, reducing telephone traffic congestion, and integration of response with second- and third-level responders from other jurisdictions. Especially promising is the potential use of data mining and statistical inference to glean more real-time information from 911 calls that may be reporting a coordinated attack at multiple locations.
Global Optimization of Emergency Evacuation Assignments
Authors: Han Lee D. , Yuan Fang , Chin Shih-Miao , Hwang Holing
Published: December 2006

Conventional emergency evacuation plans often assign evacuees to fixed routes or destinations based mainly on geographic proximity. Such approaches can be inefficient if the roads are congested, blocked, or otherwise dangerous because of the emergency. By not constraining evacuees to prespecified destinations, a one-destination evacuation approach provides flexibility in the optimization process. We present a framework for the simultaneous optimization of evacuation-traffic distribution and assignment. Based on the one-destination evacuation concept, we can obtain the optimal destination and route assignment by solving a one-destination traffic-assignment problem on a modified network representation. In a county-wide, large-scale evacuation case study, the one-destination model yields substantial improvement over the conventional approach, with the overall evacuation time reduced by more than 60 percent. More importantly, emergency planners can easily implement this framework by instructing evacuees to go to destinations that the one-destination optimization process selects.
A Marketing-Decision-Support Model for Evaluating and Selecting Concepts for New Products
Authors: Gensch Dennis
Published: December 2006

For a major manufacturer of heating and cooling systems for large buildings, under increasing pressure to produce new product components, I developed a marketing-decision-support model of its process for selecting and developing new products that was comprehensive, objective, and dynamic. This approach is particularly suited for firms that feel the timing (introduction date) of new products significantly affects their sales potential. The firm has relied on this model and its expansions for over 25 years. Marketing-decision-support systems generally utilize a technical structure for dealing with a complex real-world problem. The technical structure is generally provided by a skilled modeler, the reality by experienced line managers dealing with the problem area. This interaction is a critical element in determining the success of real-world marketing-decision-support projects. The modeler must make sure the line managers feel intellectual ownership of the support system.
Sales-Force Decision Models: Insights from 25 Years of Implementation
Authors: Sinha Prabhakant , Zoltners Andris A.
Published: December 2006

Over 25 years, we have developed many sales-force and modeling insights through over 2,000 projects with several hundred selling organizations in over 50 countries. Content insights are useful in making sales-force decisions. Examples are that profitability is flat for a wide range of sales-force sizes; phased sales-force growth is rarely optimal; focused strategies dominate scattered strategies; most sales territories (55 percent) are too large or too small; and no compensation plan satisfies everyone. Implementation insights concern model building, use, and implementation, for example, a model's economic value can come from such sources as reduced uncertainty, accuracy, increased speed, objectivity, and stakeholder involvement; theory and practice have different and complementary perspectives; experience and wisdom are sometimes better than models; and models provide insights, while people make decisions.
Rebuilding the Coal Model in the Energy Information Administration's National Energy Modeling System
Authors: Hobbs Melinda , Mellish Michael , Murphy Frederic H. , Newcombe Richard , Sanders Reginald , Whitman Peter
Published: December 2006

The Energy Information Administration uses the National Energy Modeling System (NEMS) to forecast prices and quantities in energy markets. The coal model that the Energy Information Administration first used in NEMS contributed to convergence problems in NEMS because of its design. Furthermore, because the coal model could not be modified efficiently to incorporate the new sulfur dioxide market created by the Clean Air Act Amendments of 1990, we had to build a new model. Building the new model also allowed us to incorporate improved knowledge about coal resources and other aspects of coal markets, further improving the quality of the forecasts.
U S WEST Implements a Cogent Analytical Model for Optimal Vehicle Replacement
Authors: Dietz Dennis C. , Katz Paul A.
Published: December 2006

We developed and implemented a model-based replacement process for a diverse fleet of vehicles at U S WEST, a major telecommunications company (since June 2000, Qwest Communications International). The model considers relevant age-dependent factors, including annual maintenance cost, opportunity cost of downtime, depreciation, and salvage value. It assigns a replacement score to each candidate vehicle based on age, type, estimated replacement cost, and estimated maintenance cost in the next year of operation. The model then rank-orders the vehicles by score and identifies them for replacement subject to a budget constraint on fleet capital expenditure. Through implementation of the model-based process, the company expects an annual benefit of more than $13 million.
The Kellogg Company Optimizes Production, Inventory, and Distribution
Authors: Brown Gerald , Keegan Joseph , Vigus Brian , Wood Kevin
Published: December 2006

For over a decade, the Kellogg Company has used its planning system (KPS), a large-scale, multiperiod linear program, to guide production and distribution decisions for its cereal and convenience foods business. An operational version of KPS, at a weekly level of detail, helps determine where products are produced and how finished products and in-process products are shipped between plants and distribution centers. A tactical version of KPS, at a monthly level of detail, helps to establish plant budgets and make capacity-expansion and consolidation decisions. Operational KPS reduced production, inventory, and distribution costs by an estimated $4.5 million in 1995. Tactical KPS recently guided a consolidation of production capacity with a projected savings of $35 to $40 million per year.
Preparing Our Students to Be Newsvendors
Authors: Pfeifer Phillip E. , Bodily Samuel E. , Carraway Robert L. , Clyman Dana R. , Frey Sherwood C.
Published: December 2006

Teachers of management science in schools of business use a variety of criteria in deciding what to teach and how to teach it. An important criterion that is often ignored is how our students will—as opposed to could or even should—actually address decision-making situations they encounter after taking our courses. One such situation that is commonly addressed in management science courses is the newsvendor problem. Applying the criterion of how students are expected to act when facing a newsvendor problem or any other of the situations commonly addressed in management science courses is an important factor to consider when designing managerially relevant courses.
Program Does Not Equal Program: Constraint Programming and Its Relationship to Mathematical Programming
Authors: Lustig Irvin J. , Puget Jean-François
Published: December 2006

Arising from research in the computer science community, constraint programming is a fairly new technique for solving optimization problems. For those familiar with mathematical programming, a number of language barriers make it difficult to understand the concepts of constraint programming. In this short tutorial on constraint programming, we explain how it relates to familiar mathematical programming concepts and how constraint programming and mathematical programming technologies are complementary. We assume a minimal background in linear and integer programming.
Practice Abstract
Authors: Keefer Donald L. , Armacost Andrew P. , Barnhart Cynthia , Ware Keith A. , Wilson Alysia M. , DuPuy Wynand C.
Published: December 2006

Practice Abstracts carries short reports of specific current or recent OR/MS projects. Often these reports are based on existing documents, such as internal reports or company newsletters. We hope that these abstracts will be accessible, interesting, and valuable to practitioners in other organizations. Contributions should be sent for evaluation to the editor of “Practice Abstracts,” Donald L. Keefer, Department of Supply Chain Management, Arizona State University, Box 874706, Tempe, Arizona 85287-4706 [don.keefer@asu.edu].
The Ethical OR/MS Professional
Authors: Howard Ronald A.
Published: December 2006

A profession, since it affects the lives of others, must have ethics. Actions can be classified as prudential, legal, and ethical. Ethical theories are action based or consequence based; ethics can be positive, requiring action, or negative, proscribing action. Some people may have hierarchies establishing precedence among ethical rules. While harming and stealing are vital ethical concerns, most ethical issues in personal or professional life involve truth telling. Telling the whole truth requires going beyond not lying to a proactive concern with avoiding any deception. Keeping secrets is ethically sensitive because it changes your relationship with those who might benefit from knowing them. Issues of truth telling arise in business, academia, and in the lives of OR/MS professionals. Ethical dilemmas are best avoided by joining only those organizations whose ethical codes are consistent with your own, by refusing to participate in ethically objectionable activities, and by treating everyone as you would treat those you care about.
An Elementary Introduction to Auctions
Authors: Rothkopf Michael H. , Park Sunju
Published: December 2006

An auction designer faces many questions. Among the questions are what precisely is to be sold, who may bid, will there be multiple rounds of bidding, what kinds of payments will be made and which are biddable, how will the bids be compared, how will it be decided if a transaction occurs, how will the price be set, how will sales of multiple items be handled, and what information will be revealed and when. Different academic disciplines have contributed to answering these questions. In addition to OR/MS, these include engineering, economics, sociology, and computer science.