bluuebunny/crossref_metadata_2025 huggingface dataset:
Political Cultures of Opposition
Authors: Reed Jean-Pierre , Foran John
Published: January 2008

Using interview data from Nicaragua, we propose the concept of “political cultures of opposition” for bringing culture and agency into the study of revolutions, and linking the subjective elements of experience and emotion with the social structural ones of organizations and networks. We use evidence from the Nicaraguan uprising of the 1970s to show how a repressive political structure was experienced by ordinary citizens, who turned to two political cultures — liberation theology and Sandinismo. These cultural constructions enabled participants from diverse backgrounds to channel their experiences and emotions into revolutionary actions, most often with and alongside the Sandinistas.
The Impact of Contract Primary Care on Health Care Expenditures and Quality of Care
Authors: Liu Chuan-Fen , Chapko Michael K. , Perkins Mark W. , Fortney John , Maciejewski Matthew L.
Published: January 2008

The Department of Veterans Affairs (VA) established community-based outpatient clinics to improve veterans' access to primary care. This article compares VA use and expenditures among primary care users at 76 VA-staffed community clinics ( n = 17,060) and 32 non-VA contract community clinics receiving capitation ( n = 6,842) using VA administrative databases. It estimates utilization using negative binomial models and expenditures using generalized linear one-part or two-part models. Contract community clinic patients are less likely to use all types of outpatient services than VA-staffed community clinic patients but had similar quality of care. For patients seeking care, contract community clinic patients had similar specialty care expenditures but lower primary care, outpatient, and overall expenditures. Results suggest that capitated contract clinics did not shift costs to specialty care and appeared to be an economically efficient mechanism for improving veterans' access to primary care while meeting VA quality of care standards.
The petrography of weathering processes: facts and outlooks
Authors: Meunier A. , Sardini P. , Robinet J. C. , Prêt D.
Published: January 2008

Rock weathering has been investigated from atomic to global scales through the different but complementary approaches of mineralogy, petrography, geomorphology and geochemistry. The sequences of mineral reactions involved in the alteration process are now well known. They explain the global trend of weathering phenomena but do not account for the actual rock transformation dynamics. In particular, they ignore the intimate relation of the mineral reaction progress with the increase in connected porosity. At the hand specimen scale, heterogeneity is the rule: mineral reactions are controlled by local physicochemical conditions. Alteration processes depend largely on the rock microstructure properties. They proceed through nearly-closed, semi- and completely open microsystems which are interconnected by fractures or pores. Before being leached out by the solutions which flow in the large fractures (flux), the soluble elements migrate inside the connected porosity through chemical diffusion. The dissolution of the primary minerals is mediated through local gradients of chemical potential. With increasing alteration, the rock porosity increases, as does the length of the fluid passageways and their constrictivity and tortuosity. Consequently, the apparent diffusion coefficient for the most soluble elements decreases. The amplitude of the chemical potential gradients for the most soluble elements is reduced by the progressive coating of the reactive surfaces by clays and Fe oxyhydroxides. The residence time of these elements inside the weathered rock increases as alteration progresses; an effect enhanced by their temporary adsorption on the exchangeable sites of clays and Fe oxyhydroxides. Consequently, the weathering rate decreases with time. A possible new way to calculate weathering rates could be to measure the residence time of soluble elements inside the different microsystems during their migration towards the diluted solution which occurs in the large fractures.
Interactions in organic rectorite composite gel polymer electrolyte
Authors: Huang Y. , Ma X. Y. , Liang G. Z. , Yan H. X.
Published: January 2008

Rectorite (REC) was modified with dodecyl benzyl dimethyl ammonium chloride (1227) to form an organic-modified rectorite, termed OREC. The OREC was used as a filler additive to modify gel polymer electrolytes (GPEs) which consisted of polymethyl methacrylate (PMMA), propylene carbonate (PC) and LiClO4. Studies of ionic conductivity and viscosity of liquid electrolytes and pure PC, respectively, clearly showed that these properties are greatly influenced by temperature and the amount of OREC added; a consequence of the interactions between the components of CPEs. The Fourier transform infrared (FTIR) spectroscopy results indicated that there were two kinds of interaction: namely (1) a strong hydrogen bond between Si–OH and C=O of PC and (2) a weak interaction between Li+ and C=O. Inverse gas chromatography (IGC) research supported the FTIR interpretation, indicating that the two interactions exist and that the H bond is the stronger of the two. In CPEs, the polymer matrix of PMMA merely supports the active components and does not influence the interactions between them. The OREC greatly increased the crucial plasticizer maintenance property when the amount of clay added was optimum.
Pedogenic formation of smectites in a vertisol developed from granitic rock from Kaélé (Cameroon, Central Africa)
Authors: Nguetnkam J. P. , Kamga R. , Villiéras F. , Ekodeck G. E. , Yvon J.
Published: January 2008

Smectite formation in a vertisol developed from a granitic parent rock in the Kaélé region of Cameroon in a tropical, dry climate was studied by means of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), chemical analyses, cation exchange capacity (CEC) and low temperature gas adsorption. The soil profile comprises three horizons (from base to top): (1) a saprolite, (2) an intermediate horizon, and (3) an upper dark grey horizon. In the saprolite, the progressive alteration of feldspars gave rise to the exclusive neoformation of beidellite exhibiting a typical honeycomb fabric. This process resulted in Al, Fe, Ca, Mg, Ti and Mn enrichment, a depletion of Si and Na and a significant negative Eu anomaly. In the upper horizons, beidellite evolves and is transformed into montmorillonite and kaolinite, probably through a series of smectite-kaolinite mixed layers. This transformation, from the saprolite to the upper horizons, causes the observed decrease in the CEC and the increase in specific surface area and mesoporosity of the clay. The REE patterns of the bulk soil and clay fraction display similar behaviour, indicating that the three horizons, and hence the clay minerals, have a common source in the underlying granite. Mass-balance calculations show that the intense weathering of the granite leads to a mass reduction of ~80–90%.
Unique subset of natural killer cells develops from progenitors in lymph node
Authors: Veinotte Linnea L. , Halim Timotheus Y. F. , Takei Fumio
Published: January 2008

Natural killer (NK) cells have been thought to develop from committed progenitors in the bone marrow. However, a novel pathway of thymus-dependent NK-cell development that produces a unique subset of NK cells expressing CD127 has recently been reported. We now have identified 2 populations of NK progenitors, one in the thymus and the other in the lymph node (LN). Immature double-negative 2 (CD4−CD8−CD44+CD25+) thymocytes have potential to produce NK cells with rearranged T-cell receptor γ genes (Tcrγ+) in vitro. Tcrγ+ NK cells are rare in spleen but relatively abundant in the thymus and LN. Approximately 20% of LN NK cells are Tcrγ+, and they are found at similar levels in both CD127+ and CD127− subsets. Moreover, a subpopulation of LN cells resembling immature thymocytes differentiates into Tcrγ+ NK cells in vitro and also repopulates the NK compartment in lymphopenic mice. Athymic mice lack the LN NK progenitors expressing CD127 as well as Tcrγ+ NK cells. These results suggest that Tcrγ+ NK cells may be generated from unique progenitors in the thymus as well as in the LN.
The small GTPase Ral mediates SDF-1–induced migration of B cells and multiple myeloma cells
Authors: de Gorter David J. J. , Reijmers Rogier M. , Beuling Esther A. , Naber Hildegonda P. H. , Kuil Annemieke , Kersten Marie José , Pals Steven T. , Spaargaren Marcel
Published: January 2008

Chemokine-controlled migration plays a critical role in B-cell development, differentiation, and function, as well as in the pathogenesis of B-cell malignancies, including the plasma cell neoplasm multiple myeloma (MM). Here, we demonstrate that stimulation of B cells and MM cells with the chemokine stromal cell–derived factor-1 (SDF-1) induces strong migration and activation of the Ras-like GTPase Ral. Inhibition of Ral, by expression of the dominant negative RalN28 mutant or of RalBPΔGAP, a Ral effector mutant that sequesters active Ral, results in impaired SDF-1–induced migration of B cells and MM cells. Of the 2 Ral isoforms, RalA and RalB, RalB was found to mediate SDF-1–induced migration. We have recently shown that Btk, PLCγ2, and Lyn/Syk mediate SDF-1–controlled B-cell migration; however, SDF-1–induced Ral activation is not affected in B cells deficient in these proteins. In addition, treatment with pharmacological inhibitors against PI3K and PLC or expression of dominant-negative Ras did not impair SDF-1–induced Ral activation. Taken together, these results reveal a novel function for Ral, that is, regulation of SDF-1–induced migration of B cells and MM cells, thereby providing new insights into the control of B-cell homeostasis, trafficking, and function, as well as into the pathogenesis of MM.
Validation of protein models by a neural network approach
Authors: Mereghetti Paolo , Ganadu Maria Luisa , Papaleo Elena , Fantucci Piercarlo , De Gioia Luca
Published: January 2008

Background

The development and improvement of reliable computational methods designed to evaluate the quality of protein models is relevant in the context of protein structure refinement, which has been recently identified as one of the bottlenecks limiting the quality and usefulness of protein structure prediction.

Results

In this contribution, we present a computational method (Artificial Intelligence Decoys Evaluator: AIDE) which is able to consistently discriminate between correct and incorrect protein models. In particular, the method is based on neural networks that use as input 15 structural parameters, which include energy, solvent accessible surface, hydrophobic contacts and secondary structure content. The results obtained with AIDE on a set of decoy structures were evaluated using statistical indicators such as Pearson correlation coefficients, Z
nat
, fraction enrichment, as well as ROC plots. It turned out that AIDE performances are comparable and often complementary to available state-of-the-art learning-based methods.

Conclusion

In light of the results obtained with AIDE, as well as its comparison with available learning-based methods, it can be concluded that AIDE can be successfully used to evaluate the quality of protein structures. The use of AIDE in combination with other evaluation tools is expected to further enhance protein refinement efforts.
Evaluation of two methods for computational HLA haplotypes inference using a real dataset
Authors: Bettencourt Bruno F , Santos Margarida R , Fialho Raquel N , Couto Ana R , Peixoto Maria J , Pinheiro João P , Spínola Hélder , Mora Marian G , Santos Cristina , Brehm António , Bruges-Armas Jácome
Published: January 2008

Background

HLA haplotype analysis has been used in population genetics and in the investigation of disease-susceptibility locus, due to its high polymorphism. Several methods for inferring haplotype genotypic data have been proposed, but it is unclear how accurate each of the methods is or which method is superior. The accuracy of two of the leading methods of computational haplotype inference – Expectation-Maximization algorithm based (implemented in Arlequin V3.0) and Bayesian algorithm based (implemented in PHASE V2.1.1) – was compared using a set of 122 HLA haplotypes (A-B-Cw-DQB1-DRB1) determined through direct counting. The accuracy was measured with the Mean Squared Error (MSE), Similarity Index (IF) and Haplotype Identification Index (IH).

Results

None of the methods inferred all of the known haplotypes and some differences were observed in the accuracy of the two methods in terms of both haplotype determination and haplotype frequencies estimation. Working with haplotypes composed by low polymorphic sites, present in more than one individual, increased the confidence in the assignment of haplotypes and in the estimation of the haplotype frequencies generated by both programs.

Conclusion

The PHASE v2.1.1 implemented method had the best overall performance both in haplotype construction and frequency calculation, although the differences between the two methods were insubstantial. To our knowledge this was the first work aiming to test statistical methods using real haplotypic data from the HLA region.
Cheiradone: a vascular endothelial cell growth factor receptor antagonist
Authors: Hussain Sajjad , Slevin Mark , Mesaik Mohammad A , Choudhary Mohammad I , Elosta Abdul H , Matou Sabine , Ahmed Nessar , West David , Gaffney John
Published: January 2008

Background

Angiogenesis, the growth of new blood vessels from the pre-existing vasculature is associated with physiological (for example wound healing) and pathological conditions (tumour development). Vascular endothelial growth factor (VEGF), fibroblast growth factor-2 (FGF-2) and epidermal growth factor (EGF) are the major angiogenic regulators. We have identified a natural product (cheiradone) isolated from a Euphorbia species which inhibited in vivo and in vitro VEGF- stimulated angiogenesis but had no effect on FGF-2 or EGF activity. Two primary cultures, bovine aortic and human dermal endothelial cells were used in in vitro (proliferation, wound healing, invasion in Matrigel and tube formation) and in vivo (the chick chorioallantoic membrane) models of angiogenesis in the presence of growth factors and cheiradone. In all cases, the concentration of cheiradone which caused 50% inhibition (IC50) was determined. The effect of cheiradone on the binding of growth factors to their receptors was also investigated.

Results

Cheiradone inhibited all stages of VEGF-induced angiogenesis with IC50 values in the range 5.20–7.50 μM but did not inhibit FGF-2 or EGF-induced angiogenesis. It also inhibited VEGF binding to VEGF receptor-1 and 2 with IC50 values of 2.9 and 0.61 μM respectively.

Conclusion

Cheiradone inhibited VEGF-induced angiogenesis by binding to VEGF receptors -1 and -2 and may be a useful investigative tool to study the specific contribution of VEGF to angiogenesis and may have therapeutic potential.
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes
Authors: Carter Ben , Wu Guanghui , Woodward Martin J , Anjum Muna F
Published: January 2008

Background

Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity.

Results

The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data.

Conclusion

After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.
Metabolic and morphological alterations induced by proteolysis-inducing factor from Walker tumour-bearing rats in C2C12myotubes
Authors: Yano Claudia L , Ventrucci Gislaine , Field William N , Tisdale Michael J , Gomes-Marcondes Maria Cristina C
Published: January 2008

Background

Patients with advanced cancer suffer from cachexia, which is characterised by a marked weight loss, and is invariably associated with the presence of tumoral and humoral factors which are mainly responsible for the depletion of fat stores and muscular tissue.

Methods

In this work, we used cytotoxicity and enzymatic assays and morphological analysis to examine the effects of a proteolysis-inducing factor (PIF)-like molecule purified from ascitic fluid of Walker tumour-bearing rats (WF), which has been suggested to be responsible for muscle atrophy, on cultured C2C12 muscle cells.

Results

WF decreased the viability of C2C12 myotubes, especially at concentrations of 20–25 μg.mL-1. There was an increase in the content of the pro-oxidant malondialdehyde, and a decrease in antioxidant enzyme activity. Myotubes protein synthesis decreased and protein degradation increased together with an enhanced in the chymotrypsin-like enzyme activity, a measure of functional proteasome activity, after treatment with WF. Morphological alterations such as cell retraction and the presence of numerous cells in suspension were observed, particularly at high WF concentrations.

Conclusion

These results indicate that WF has similar effects to those of proteolysis-inducing factor, but is less potent than the latter. Further studies are required to determine the precise role of WF in this experimental model.
Topical rapamycin inhibits tuberous sclerosis tumor growth in a nude mouse model
Authors: Rauktys Aubrey , Lee Nancy , Lee Laifong , Dabora Sandra L
Published: January 2008

Background

Skin manifestations of Tuberous Sclerosis Complex (TSC) cause significant morbidity. The molecular mechanism underlying TSC is understood and there is evidence that systemic treatment with rapamycin or other mTOR inhibitors may be a useful approach to targeted therapy for the kidney and brain manifestations. Here we investigate topical rapamycin in a mouse model for TSC-related tumors.

Methods

0.4% and 0.8% rapamycin ointments were applied to nude mice bearing subcutaneous, TSC-related tumors. Topical treatments were compared with injected rapamycin and topical vehicle. Rapamycin levels in blood and tumors were measured to assess systemic drug levels in all cohorts.

Results

Treatment with topical rapamycin improved survival and reduced tumor growth. Topical rapamycin treatment resulted in systemic drug levels within the known therapeutic range and was not as effective as injected rapamycin.

Conclusion

Topical rapamycin inhibits TSC-related tumor growth. These findings could lead to a novel treatment approach for facial angiofibromas and other TSC skin lesions.
Generation of functional scFv intrabody to abate the expression of CD147 surface molecule of 293A cells
Authors: Tragoolpua Khajornsak , Intasai Nutjeera , Kasinrerk Watchara , Mai Sabine , Yuan Yuan , Tayapiwatana Chatchai
Published: January 2008

Background

Expression of intracellular antibodies (intrabodies) has become a broadly applicable technology for generation of phenotypic knockoutsin vivo. The method uses surface depletion of cellular membrane proteins to examine their biological function. In this study, we used this strategy to block the transport of cell surface molecule CD147 to the cell membrane. Phage display technology was introduced to generate the functional antibody fragment to CD147, and we subsequently constructed a CD147-specific scFv that was expressed intracellularly and retained in the endoplasmic reticulum by adenoviral gene transfer.

Results

The recombinant antibody fragments, Fab and scFv, of the murine monoclonal antibody (clone M6-1B9) reacted specifically to CD147 by indirect enzyme-linked immunosorbent assays (ELISA) using a recombinant CD147-BCCP as a target. This indicated that the Fab- and scFv-M6-1B9 displaying on phage surfaces were correctly folded and functionally active. We subsequently constructed a CD147-specific scFv, scFv-M6-1B9-intrabody, in 293A cells. The expression of CD147 on 293A cell surface was monitored at 36 h after transduction by flow cytometry and demonstrated remarkable reduction. Colocalization of scFv-M6-1B9 intrabody with CD147 in the ER network was depicted using a 3D deconvolution microscopy system.

Conclusion

The results suggest that our approach can generate antibody fragments suitable for decreasing the expression of CD147 on 293A cells. This study represents a step toward understanding the role of the cell surface protein, CD147.
Clinical Ethics Consultation: Examining how American and Japanese experts analyze an Alzheimer's case
Authors: Nagao Noriko , Aulisio Mark P , Nukaga Yoshio , Fujita Misao , Kosugi Shinji , Youngner Stuart , Akabayashi Akira
Published: January 2008

Background

Few comparative studies of clinical ethics consultation practices have been reported. The objective of this study was to explore how American and Japanese experts analyze an Alzheimer's case regarding ethics consultation.

Methods

We presented the case to physicians and ethicists from the US and Japan (one expert from each field from both countries; total = 4) and obtained their responses through a questionnaire and in-depth interviews.

Results

Establishing a consensus was a common goal among American and Japanese participants. In attempting to achieve consensus, the most significant similarity between Japanese and American ethics consultants was that they both appeared to adopt an "ethics facilitation" approach. Differences were found in recommendation and assessment between the American and Japanese participants. In selecting a surrogate, the American participants chose to contact the grandson before designating the daughter-in-law as the surrogate decision-maker. Conversely the Japanese experts assumed that the daughter-in-law was the surrogate.

Conclusion

Our findings suggest that consensus building through an "ethics facilitation" approach may be a commonality to the practice of ethics consultation in the US and Japan, while differences emerged in terms of recommendations, surrogate assessment, and assessing treatments. Further research is needed to appreciate differences not only among different nations including, but not limited to, countries in Europe, Asia and the Americas, but also within each country.
A new evaluation method for +Gz tolerance with loratadine by using a near-infrared spectroscopy
Authors: Onozawa Akihiko , Kikukawa Azusa , Miyamoto Yoshinori
Published: January 2008

Background

Loratadine (Claritin®), an over the counter antihistamine in U.S. and UK, is acceptable for use without adverse side effects by aircrew with mild or moderate allergic or other situations requiring an antihistamine. Although +Gz (head to foot direction) tolerance testing for aircrew with loratadine has not been documented in the published literature, it is commonly accepted that loratadine dose not effect +Gz tolerance. The purpose of this study was to offer and validate a new evaluation method for +Gz tolerance testing with loratadine by using a near-infrared spectroscopy (NIRS).

Methods

A double-blind, placebo-controlled, randomized, crossover protocol was used to administer 10 mg of loratadine or placebo in nine healthy subjects. The subjects didn't wear anti-G suit. The +Gz exposure profiles consisted of, in series, a gradual onset ran (0.1 G·sec-1) to the subject's visual end-point (peripheral light loss) or loss of consciousness (GLOC), and rapid onset run (1.0 G·sec-1) to the subject's same end-point. In this study, G-level tolerance was defined as the +Gz level at visual end-point and/or at GLOC. As a subject's G-duration tolerance, we measured the total time (seconds) during rapid onset run. Otherwise, to confirm the effect of loratadine on +Gz tolerance, we measured the cerebral NIRS variables (hemoglobin concentration changes and tissue oxygenation index) as a new quantitative method for +Gz tolerance during a centrifuge experiments.

Results

No significant differences were observed in +Gz tolerance (+Gz level, duration time and NIRS variables) between subjects taking loratadine and placebo.

Conclusion

Our results demonstrate that loratadine has no detectable effect on +Gz tolerance by using a new method with cerebral NIRS variables and the traditional method with +Gz level and duration time. This study represents the first use of a quantitative parameter such as cerebral NIRS variables to assess the effects of a drug on acceleration tolerance.
Reliability and relative validity of a child nutrition questionnaire to simultaneously assess dietary patterns associated with positive energy balance and food behaviours, attitudes, knowledge and environments associated with healthy eating
Authors: Wilson Annabelle M , Magarey Anthea M , Mastersson Nadia
Published: January 2008

Background

Food behaviours, attitudes, environments and knowledge are relevant to professionals in childhood obesity prevention, as are dietary patterns which promote positive energy balance. There is a lack of valid and reliable tools to measure these parameters. The aim of this study was to determine the reliability and relative validity of a child nutrition questionnaire assessing all of these parameters, used in the evaluation of a community-based childhood obesity prevention project.

Methods

The development of the 14-item questionnaire was informed by the aims of the obesity prevention project. A sub-sample of children aged 10–12 years from primary schools involved in the intervention was recruited at the project's baseline data collection (Test 1). Questionnaires were readministered (Test 2) following which students completed a 7-day food diary designed to reflect the questionnaire. Twelve scores were derived to assess consumption of fruit, vegetables, water, noncore foods and sweetened beverages plus food knowledge, behaviours, attitudes and environments. Reliability was assessed using (a) the intra class correlation coefficient (ICC) and 95% confidence intervals to compare scores from Tests 1 and 2 (test-retest reliability) and (b) Cronbach's alpha (internal consistency). Validity was assessed with Spearman correlations, bias and limits of agreement between scores from Test 1 and the 7-day diaries. The Wilcoxon signed rank test checked for significant differences between mean scores.

Results

One hundred and forty one students consented to the study. Test 2 (n = 134) occurred between eight and 36 days after Test 1. For 10/12 scores ICCs ranged from 0.47–0.66 (p < 0.001) while for two scores ICCs were < 0.4 (p < 0.05). Spearman correlations ranged from 0.34–0.48 (p < 0.01) and Cronbach's alpha 0.50–0.80. Three scores were modified based on this analysis. The Wilcoxon signed rank test found no evidence of a difference between means (p > 0.05) for 10/12 (test-retest reliability) and 3/7 (validity) scores.

Conclusion

This child nutrition questionnaire is a valid and reliable tool to simultaneously assess dietary patterns associated with positive energy balance, and food behaviours, attitudes and environments in Australian school children aged 10–12 years. Thus it can be used to monitor secular changes in these parameters and measure the effectiveness of this and other obesity prevention projects with similar aims.
Learning from positive examples when the negative class is undetermined- microRNA gene identification
Authors: Yousef Malik , Jung Segun , Showe Louise C , Showe Michael K
Published: January 2008

Background

The application of machine learning to classification problems that depend only on positive examples is gaining attention in the computational biology community. We and others have described the use of two-class machine learning to identify novel miRNAs. These methods require the generation of an artificial negative class. However, designation of the negative class can be problematic and if it is not properly done can affect the performance of the classifier dramatically and/or yield a biased estimate of performance. We present a study using one-class machine learning for microRNA (miRNA) discovery and compare one-class to two-class approaches using naïve Bayes and Support Vector Machines. These results are compared to published two-class miRNA prediction approaches. We also examine the ability of the one-class and two-class techniques to identify miRNAs in newly sequenced species.

Results

Of all methods tested, we found that 2-class naive Bayes and Support Vector Machines gave the best accuracy using our selected features and optimally chosen negative examples. One class methods showed average accuracies of 70–80% versus 90% for the two 2-class methods on the same feature sets. However, some one-class methods outperform some recently published two-class approaches with different selected features. Using the EBV genome as and external validation of the method we found one-class machine learning to work as well as or better than a two-class approach in identifying true miRNAs as well as predicting new miRNAs.

Conclusion

One and two class methods can both give useful classification accuracies when the negative class is well characterized. The advantage of one class methods is that it eliminates guessing at the optimal features for the negative class when they are not well defined. In these cases one-class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.

Availability

The OneClassmiRNA program is available at: [1]
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
Authors: Ivan Andra , Halfon Marc S , Sinha Saurabh
Published: January 2008

We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal.
Sensitivity of Static Traffic User Equilibria with Perturbations in Arc Cost Function and Travel Demand
Authors: Lu Shu
Published: January 2008

This paper deals with sensitivity analysis of static traffic user equilibrium problems. We apply some recently developed sensitivity analysis techniques for generalized equations to analyze the behavior of the equilibrium arc flow of such a problem when both the arc cost function and the travel demand vary. Our methods permit calculation of semiderivatives under general conditions and of derivatives under more restrictive conditions; we calculate the semiderivatives by solving a linear traffic user equilibrium problem and the derivatives by matrix multiplication together with the solution of a linear equation the dimension of which is at most the number of arcs. Three numerical examples show how to use these results in practice.
Vehicle Routing for Urban Snow Plowing Operations
Authors: Perrier Nathalie , Langevin André , Amaya Ciro-Alberto
Published: January 2008

Winter road maintenance planning involves a variety of decisions related to the routing of vehicles for spreading chemicals and abrasives, plowing roadways and sidewalks, loading snow into trucks, and transporting snow to disposal sites. In this paper, we present a model and two heuristic solution approaches based on mathematical optimization for the routing of vehicles for snow plowing operations in urban areas. Given a district and a single depot where a number of plows are based, the problem is to determine a set of routes, each performed by a single vehicle that starts and ends at the district's depot, such that all road segments are serviced while satisfying a set of operational constraints and minimizing a time objective. The formulation models general precedence relation constraints with no assumption on class connectivity, different service and deadhead speed possibilities, separate pass requirements for multilane road segments, class upgrading possibilities, and vehicle road segment dependencies. Several extensions, such as turn restrictions, load balancing constraints, and tandem service requirements, which are required in a real-life application, are also discussed. Two objectives are considered: A hierarchical objective and a makespan objective. The resulting model is based on a multicommodity network flow structure to impose the connectivity of the route performed by each vehicle. The two solution strategies were tested on data from the City of Dieppe, New Brunswick, Canada.
A Theoretical Comparison of Feasibility Cuts for the Integrated Aircraft-Routing and Crew-Pairing Problem
Authors: Mercier Anne
Published: January 2008

The integrated aircraft-routing and crew-pairing problem consists in determining a minimum-cost set of aircraft routes and crew pairings such that each flight leg is covered by one aircraft and one crew, and some side constraints are satisfied. Linking constraints impose minimum connection times for crews that depend on aircraft connections. The main solution approach for this problem consists in solving a constrained crew-pairing problem iteratively, adding feasibility cuts until a solution is found where the connection set used by the crew pairings is feasible for the aircraft-routing problem. The feasibility cuts can be generated by a Benders decomposition approach in which aircraft routing is handled by the subproblem, or they can be selected from a predefined family. We perform a theoretical comparison of the different types of feasibility cuts. We also propose a simple procedure to strengthen these cuts. Computational experiments performed on test instances provided by two major airlines are presented to support the theoretical results.
Identifying Transit Driver Preferences for Work Shift Structures: An Econometric Analysis
Authors: Miranda Felipe , Muñoz Juan Carlos , Ortúzar Juan de Dios
Published: January 2008

The combination of a strict labor legislation with daily and weekly time-dependent demand patterns has meant that transit companies tend to suffer significant inefficiencies; indeed, as more drivers than the minimum required are hired, providing services at off-peak periods, many tend to be inactive during these periods. To attack this problem, two strategies have been proposed. The first is using flexible shifts that may change daily according to a predefined contract. The other is using split shifts in which drivers' working hours are split in two to serve both the morning and afternoon peak periods. However, evidence of driver acceptance of these strategies is lacking.

This paper presents a methodology to identify which characteristics of a shift are important for drivers (considering their socioeconomic characteristics) and to quantify their impact. Such information would allow transit operators to offer better working shifts to their drivers, with mutual benefits. The approach includes estimation of a mixed logit model based on stated preference data for choice of working shift; the context definition, shift attributes, and in general the experimental design were quite involved. A sample of 436 drivers working at two important operators in Santiago were interviewed. Our modelling results show considerable heterogeneity in drivers' preferences and also show that a significant number of them would be prepared to participate in flexible shifts. Our method allows operators to determine the economic incentives they should attach to such shifts for them to be accepted by the required fraction of their drivers.
Optimizing Timetable Synchronization for Rail Mass Transit
Authors: Wong Rachel C. W. , Yuen Tony W. Y. , Fung Kwok Wah , Leung Janny M. Y.
Published: January 2008

In most urban public transit rail systems, passengers may need to make several interchanges between different lines to reach their destination. The design of coordinated timetables that enable smooth interchanges with minimal delay for all passengers is a very difficult task. This paper presents a mixed-integer-programming optimization model for this schedule synchronization problem for nonperiodic timetables that minimizes the interchange waiting times of all passengers. A novelty in our formulation is the use of binary variables that enable the correct representation of the waiting times to the “next available” train at the interchange stations.

By adjusting trains' run times and station dwell times during their trips and their dispatch times, turnaround times at the terminals, and headways at the stations, our model can construct high-quality timetables that minimize transfer waiting times. We also discuss an optimization-based heuristic for the model. We have tested our algorithm for the Mass Transit Railway (MTR) system in Hong Kong, which runs six railway lines with many cross-platform interchange stations. Preliminary numerical results indicate that our approach improves the synchronization significantly compared with the current practice of using fixed headways and trip times. We also explore the trade-offs among different operational parameters and flexibility and their impact on overall passenger waiting times.
Probabilistic Traveling Salesman Problem with Deadlines
Authors: Campbell Ann M. , Thomas Barrett W.
Published: January 2008

Time-constrained deliveries are one of the fastest growing segments of the delivery business, and yet there is surprisingly little literature that addresses time constraints in the context of stochastic customer presence. We begin to fill that void by introducing the probabilistic traveling salesman problem with deadlines (PTSPD). The PTSPD is an extension of the well-known probabilistic traveling salesman problem (PTSP) in which, in addition to stochastic presence, customers must also be visited before a known deadline. We present two recourse models and a chance constrained model for the PTSPD. Special cases are discussed for each model, and computational experiments are used to illustrate under what conditions stochastic and deterministic models lead to different solutions.
An Optimization-Based Heuristic for the Split Delivery Vehicle Routing Problem
Authors: Archetti Claudia , Speranza M. Grazia , Savelsbergh Martin W. P.
Published: January 2008

The split delivery vehicle routing problem is concerned with serving the demand of a set of customers with a fleet of capacitated vehicles at minimum cost. Contrary to what is assumed in the classical vehicle routing problem, a customer can be served by more than one vehicle, if convenient. We present a solution approach that integrates heuristic search with optimization by using an integer program to explore promising parts of the search space identified by a tabu search heuristic. Computational results show that the method improves the solution of the tabu search in all but one instance of a large test set.
Pickup and Delivery with Split Loads
Authors: Nowak Maciek , Ergun Özlem , White Chelsea C.
Published: January 2008

Splitting loads such that the delivery of certain loads is completed in multiple trips rather than one trip results in opportunities for a reduction in cost and the number of vehicles used. Several studies have shown the benefit of split deliveries for the vehicle routing problem, in which a vehicle operating out of a depot makes a series of deliveries on each route. In this paper, we quantify the benefit of using split loads for the pickup and delivery problem. A heuristic to solve the pickup and delivery problem with split loads is developed and applied to a set of random large-scale problem instances, revealing the potential benefit of split loads. This benefit is reduced when the heuristic is applied to a real-world trucking industry problem because of several problem instance characteristics. The benefit of split loads is found to be most closely tied to three characteristics: load size, cost associated with a pickup or delivery, and the frequency with which loads have origins or destinations in common. Prior to a discussion of these results, we define the pickup and delivery problem with split loads and prove that for a set of given origins and destinations the most benefit can occur with load sizes just above one half of vehicle capacity.
Parental Attachments and Psychological Distress Among African American College Students
Authors: Love Keisha McGhee
Published: January 2008

African American college students attending predominately White institutions often encounter stressors that their Caucasian peers do not experience. Because of these unique stressors, African American students are more prone to experience psychological distress. Identifying factors that counteract psychological distress among these students is vital to increasing their sense of well being. This study examined parental attachments as a buffer against psychological distress among African American college students. Results demonstrated that maternal figures who were overprotective and controlling perpetuated psychological distress, whereas paternal figures who were warm and caring served as a buffer against psychological distress. Implications for mental health providers and college student personnel are discussed.
"It Takes a Village to Raise a Child": The Role of Social Capital in Promoting Academic Success for African American Men at a Black College
Authors: Palmer Robert , Gasman Marybeth
Published: January 2008

Historically Black colleges and universities (HBCUs) were created to provide educational opportunities for African Americans when other higher education venues restricted their participation. HBCUs are credited with nurturing and producing leaders who embraced W. E. B. Du Bois's concept of the "Talented Tenth," and exhibiting fortitude in advancing social equality for all. Over the years, as legalized segregation was overturned and efforts were made to expand opportunities for African Americans, some have questioned the continuing need for HBCUs. A study of 11 African American men attending a public, urban HBCU, indicated that the university's rich supply of social capital (a direct consequence of its mission and history) makes it a unique fixture in the landscape of higher education, one whose special features have not been replicated by historically White institutions.
Help-Seeking for Stressful Events Among Chinese College Students in Taiwan: Roles of Gender, Prior History of Counseling, and Help-Seeking Attitudes
Authors: Chang Hsiaowen
Published: January 2008

The present study examined the help-seeking behavior that Chinese college students used to cope with stressful events and the roles that gender, previous counseling experience, and help-seeking attitudes played in predicting informal and formal help-seeking behavior. Nine hundred ninety-five first-year Chinese college students at a private university in Taiwan completed the survey. The results revealed that most Chinese students sought help from informal helpers as compared to from professional helpers for academic/career, interpersonal, and personal/emotional problems. Logistic regression analyses revealed that although gender was significantly correlated with help-seeking attitudes, it was only predictive of informal help-seeking for interpersonal problems. Previous counseling experience was positively correlated with formal help-seeking regardless of the types of problems, whereas help-seeking attitudes were positively correlated with informal and formal help-seeking for personal/emotional problems.
Factors Supporting Cambodian American Students' Successful Adjustment Into the University
Authors: Chhuon Vichet , Hudley Cynthia
Published: January 2008

The current article examines the experiences of successful Cambodian American students as a unique ethnic group to understand their patterns of social and academic college integration. Cambodian American students' sense of academic belonging related closely to perceptions of personal connections. Our data suggest that integration into the campus environment and maintaining contact with the prior community are both important for Cambodian American students' successful adjustment. These data offer direction for college administrators, student affairs staff, and faculty in supporting the retention and academic success of Cambodian American college students.
University Students' Experiences of Nonmarital Breakups: A Grounded Theory
Authors: Hebert Sarah , Popadiuk Natalee
Published: January 2008

Prior nonmarital breakup research has been focused on negative outcomes, rarely examining the personal growth aspects of this experience. In this study, we used a qualitative grounded theory methodology to explore the changes that university students reported experiencing as a result of a heterosexual nonmarital breakup and how those changes arose. From the participant accounts, we constructed a grounded theoretical model that conceptualizes and explains change and personal growth following nonmarital breakups. In this model, we assert that students may experience stress-related growth after a breakup and we provide a framework for explaining these changes. Implications for counseling are discussed.
The Enlightenment in Paradise: Bougainville, Tahiti, and the Duty of Desire
Authors: Martin Andrew
Published: January 2008

Bougainville has been read both as rampant mythologist and objective anthropologist. I argue that these conflicting accounts of the Enlightenment explorer correspond to two contradictory discourses concerning the Tahitian woman in Voyage autour du monde (1771). Discourse 1, the origin of the "New Cythera" theory, is integrationist and describes all Tahitians as sexually switched-on pleasure-seekers and women as variations on Venus and Eve. Discourse 2, more analytic, differentiates men from women more markedly and suggests that the spontaneous feminine hedonism of Discourse 1 is contrived and choreographed. Out of the crossover of real and hyperreal, a paradox is created: the duty of desire. This is projected in a third proleptic or prophetic layer of discourse, part of a pervasive triangle of thought that anticipates three key scenes: pornographic, psychoanalytic, and revolutionary.