bluuebunny/crossref_metadata_2025 huggingface dataset:
Image and Memory
Authors: Cieplak Piotr A.
Published: April 2009

Eric Kabera is a Rwandan documentary and fiction filmmaker and producer. He collaborated on one of the first fictionalised films about the genocide, 100 Days (dir. Nick Hughes), and has participated in a variety of projects related to the process of memorialisation and commemoration of the events of 1994 and their aftermath. Kabera is also the founder of the Rwanda Cinema Centre and the Rwanda Film Festival, which aim to bring the moving image to the country's rural populations. This interview focuses on Kabera's documentary film The Keepers of Memory: Survivors' Accounts of the Rwandan Genocide (2005), which traces the individual trajectories of those affected by the genocide and gives them a platform to voice their experience. Special attention is paid to the relationship with physical surrounding, to image and to the internal and external experience of trauma and memory in their collective and individual forms. The theoretical assertions about memory recording are juxtaposed with pragmatic issues encountered by a filmmaker as practitioner. The interview was conducted on 30 March 2008 in Kigali, Rwanda.
Behavioral Inhibition and Its Relation to Anxiety and Depression Symptoms in Adolescents With Sickle Cell Disease: A Preliminary Study
Authors: Carpentier Melissa Y. , Elkin T. David , Starnes Sarah E.
Published: April 2009

Several investigations have found support for the role of behavioral inhibition in the etiology of childhood anxiety and depression disorders. However, nothing is known about how this relation extends to children with a chronic, life-threatening illness. The purpose of the current study was to examine behavioral inhibition and its relation to anxiety and depression symptoms among 30 adolescents with sickle cell disease (SCD). Adolescents with SCD and their primary caregivers completed instruments assessing demographic information, behavioral inhibition, and anxiety and depression symptoms. A majority of adolescents with SCD classified themselves as middle or low on behavioral inhibition. Adolescents with SCD who classified themselves as high on behavioral inhibition displayed higher levels of anxiety and depression than adolescents with SCD who classified themselves as low on behavioral inhibition; adolescents with SCD endorsing the middle behavioral inhibition category generally scored in between. These data extend previous work with healthy children and adolescents and suggest that early and continued assessment of behavioral inhibition may be important in preventing adverse psychological outcomes among a group that is already at risk for internalizing disorders.
Diagnostic Dilemma: Solitary Fibrous Tumor or Hemangiopericytoma of the Submandibular Region in a Patient with Multiple Odontogenic Keratocysts
Authors: Garg Deepti , Palaskar Sangeeta , Shetty Vishwa Prakash , Bhushan Anju , Bhatia Prateek , Sarin Jyoti
Published: April 2009

Solitary fibrous tumors (SFTs) are rare spindle cell neoplasms that originate from mesothelial-lined surfaces, mainly the pleura and peritoneum. SFT is a distinctive mesenchymal neoplasm of the pleura but can be found in extrapleural sites. The treatment of SFT is simple excision or wide local resection. This is the case study of a 14-year-old girl who presented with a large diffuse swelling in the left submandibular region, ultimately diagnosed with SFT and surgically excised.
Qualitative Analysis of the Role of Culture in Coping Themes of Latina and European American Mothers of Children With Cancer
Authors: Johns Alexis L. , Oland Alyssa A. , Katz Ernest R. , Sahler Olle Jane Z. , Askins Martha A. , Butler Robert W. , Dolgin Michael J.
Published: April 2009

It has been well established that mothers of children diagnosed with cancer experience high levels of distress. Latina mothers may be at risk for higher levels of distress related to language barriers, cultural factors, and economic, immigration, and acculturation stressors. Despite the increasing US Latino population, few studies have examined the role of culture within pediatric oncology, including how mothers cope with their child's cancer. This study used qualitative analysis of 24 sessions from 3 Latina and 3 European American mothers of children recently diagnosed with cancer. The session transcripts were divided into a total of 2328 thought segments that were then analyzed for themes using a collaborative iterative process. Analysis identified 9 shared coping themes that included, with some variations: gathering information, professional help-seeking, activities, problem solving, positive thinking, present orientation, reframing, avoidance, and religion. Three themes were culture specific: only European American mothers discussed compromise, whereas normalization and perspective taking were unique to the Latina mothers and suggest that the cultural value of simpatía influences coping. Clinical and research recommendations are discussed.
Aspects of Modeling Piezoelectric Active Thin-walled Structures
Authors: Marinković Dragan , Köppe Heinz , Gabbert Ulrich
Published: April 2009

The objective of this article is to reconsider some important aspects of modeling piezoelectric active thin-walled structures. Hence, it is dealt here with thin-walled laminated structures involving piezoelectric patches. A recently developed shell type finite element is used for the purpose. The first aspect is adequate modeling of electric field within the piezoelectric patches polarized in the thickness direction. The influence of higher order functions for the electric field on the accuracy of the model is discussed. The second aspect is related to modeling geometrical non-linearities in the behavior of the considered structures and their significance on the accuracy of the predicted behavior. Both aspects are considered with respect to static and dynamic cases.
The Team Climate Inventory (TCI)
Authors: Tseng Hsu-Min , Liu Feng-Chuan , West Michael Alun
Published: April 2009

Understanding the feasibility of applying the Team Climate Inventory (TCI) in non-Western cultures is essential for researchers attempting to understand the influence of culture on workers' perceived climate. This study describes the application of the TCI in such a setting using data from 203 administrators employed in a Taiwanese medical center. Reliability and factor analyses were performed to establish the feasibility and psychometric properties of the TCI Taiwan version. Reliabilities of both the four- and five-factor solutions exceeded .80. Factor analyses indicated a satisfactory four-factor structure, despite some variations in comparison with the U.K. version. The TCI Taiwan version is feasible and has acceptable psychometric properties. Further research is warranted regarding the degree to which disparities result from cultural differences and the specific nature of organizational systems in Chinese communities.
The Long History of Gaming in Military Training
Authors: Smith Roger
Published: April 2009

The dual-use of games in both military and entertainment applications has a long history. This has taken the form of sand tables, miniatures, board games, and computer games. The current tension between entertainment and military applications over games is just the return of similar concerns that have surrounded gaming tools and technologies in previous generations. Dynamic representations of the physical world are interesting and useful tools in a number of fields, to include the military, city planning, architecture, education, and entertainment. Modern computer games contain technologies and tools that allow many different communities to accomplish similar goals.
Teaching Lean Manufacturing With Simulations and Games: A Survey and Future Directions
Authors: Badurdeen Fazleena , Marksberry Philip , Hall Arlie , Gregory Bob
Published: April 2009

Problem-based learning focuses on small groups using authentic problems as a means to help participants obtain knowledge and problem-solving skills. This approach makes problem-based learning ideal for teaching lean manufacturing, which is driven by a culture of problem solving that values learning as one key output of manufacturing production. Thus, simulations that organize participants in teams for realistic manufacturing production problem solving are widespread as a way to use problem-based learning to teach lean manufacturing. But a critical assessment of existing simulations for lean manufacturing instruction has been lacking. Accordingly, a literature survey is conducted and existing simulations are classified according to their emphasis on lean tools or the overall lean system; the degree of their focus on soft skills, if any; and their area of application, whether academic or industry. Four gaps are found in existing simulation designs: lack of stress on soft skills, a mistaken focus on “linear lean,” misunderstanding of the key role of the facilitator, and lack of realism. Future directions for study and improvement in lean simulation design are suggested.
Simulation Design for Off-Line Training of Practical Lean Manufacturing Concepts for Visual Inspection
Authors: Tetteh Edem , McWilliams Douglas
Published: April 2009

Customer needs for high-quality goods and the risk of product-liability litigation against businesses have made companies look for a way to sustain quality assurance in their products and services. Lean manufacturing is the latest and most successful system being used by companies to turn their business around. Visual inspection plays an important role to ensure quality product in manufacturing and service industries. Simulation accompanied by training has been proven to be effective in implementing lean concepts in visual inspection systems by enhancing operator accuracy and reducing search time. This article describes the development and application of a training system in a simulated visual inspection environment using a computer-based program to mimic the actual industrial setting. The system is designed and used to simulate and evaluate lean metrics such as time, accuracy, pacing, and data collection needed to train visual inspectors off-line.
Retrospective evaluation of venous thromboembolism prophylaxis in the adult cancer population
Authors: Reeves David , Liu Chin Y
Published: April 2009

Study objectives. Hospitalized cancer patients are at an increased risk for venous thromboembolism (VTE) and it is recommended they receive pharmacologic prophylaxis unless otherwise contraindicated. The majority of data supporting this recommendation comes from sub-group analyses and extrapolation of data gathered in general medical/surgical patients. This study seeks to assess the safety and efficacy of VTE prophylaxis in cancer patients admitted to our institution.

Methods. Charts of patients 18—89 years of age receiving VTE prophylaxis with unfractionated heparin, low molecular weigh heparin, or fondaparinux while admitted to Karmanos Cancer Center between September and October 2007 were retrospectively reviewed. Risk factors for VTE were assessed and the efficacy/safety of the prophylactic agents was compared.

Results. One-hundred and eighty consecutive patients were identified. The average number of risk factors for developing VTE was 3—4 per hospital admission in addition to an active cancer diagnosis. Three VTEs occurred in the heparin group with two patients experiencing a VTE during their admission and one experiencing a VTE within 1 month after discharge. Four (2.6%) patients receiving heparin had a major bleeding event. Minor bleeding occurred in 14.3, 11.5, and 22.2% of patients receiving heparin, enoxaparin, and fondaparinux, respectively.

Conclusions. This retrospective study showed cancer patients are at increased risk for VTE, typically with 3—4 risk factors per admission. VTEs were uncommon; however, three patients receiving heparin experienced a VTE and four had a major bleeding event. Minor bleeding rates were similar among groups.
The role of the pharmacist in optimizing the use of erythropoietin stimulating agents
Authors: Nabhani Gebara Shereen , Moubayed Hiba
Published: April 2009

Purpose. With the emerging new warnings surrounding the use of erythropoiesis—stimulating agents (ESAs), the pharmacist’s role as health educator and risk communicator expands further to include patient scrutiny to check for eligibility and patient monitoring to check for response or toxicity. This review explores the benefits and risks linked to ESAs use, and the proposed role.

Summary. ESAs have been increasingly used for the treatment of chemotherapy—induced anemia because of its documented effect on decreasing transfusion dependency. However, their use has been associated with thromboembolic complications, tumor progression, and decreased overall survival. This review covers current recommendations and guidelines that surround ESAs use in the supportive care of cancer patients.

Conclusion. To minimize or prevent the complications associated with ESAs use, cancer patients should be adequately monitored and counseled. This highlights the importance of the pharmacist’s involvement to optimize patient care.
Blepharoptosis following oxaliplatin administration
Authors: Lau S. Cecilia , Shibata Stephen I
Published: April 2009

Oxaliplatin is a unique platinum derivative with anti-tumor activity in a number of malignancies, with neurotoxicity being a frequent side effect. Neurotoxicity can manifest in an acute phase and a chronic phase. The acute phase usually presents as dysesthesias of the hands and feet, jaw tightness, and pharyngolaryngo-dysesthesia, triggered and exacerbated by physical contact with cold temperatures. Although various other symptoms have been reported in the literature, little details are available. We report here, in detail, a case of blepharoptosis which appeared after repeated oxaliplatin infusions, and the disappearance of which seemed to be dependent on the infusion rate.
A Multidisciplinary Approach to Total Joint Replacement
Authors: Naville Julie , Volz Tina , Curry Joy
Published: April 2009

Baptist Hospital East is proud to be the leading joint replacement center in the Commonwealth of Kentucky. More joint replacement surgeries are performed at Baptist Hospital East than at any other hospital in the state. In addition, the hospital staff has designed a cutting edge total joint replacement program that assists patients from preadmission to postdischarge. Patients attend pre—joint replacement class to help prepare them for the surgery and for postsurgical recovery. After surgery, the staff promptly addresses the need for therapeutic services and pain management. Furthermore, measures to reduce postoperative complications have been implemented and have proven to be very successful. As a result of all of these measures, Baptist Hospital East total joint program has an infection rate below the national benchmark and an average length of stay of 3.7 days, with 70% of the patients returning directly to a home environment.
Extending Use of Direct Behavior Rating Beyond Student Assessment
Authors: Hagermoser Sanetti Lisa M. , Chafouleas Sandra M. , Christ Theodore J. , Gritter Katie L.
Published: April 2009

To make valid decisions about intervention effectiveness in a tiered intervention system, it is essential to formatively assess treatment integrity along with student outcomes. Despite significant advances in technologies for ongoing assessment of student outcomes, research regarding treatment integrity assessment has not shared the same progress in that most available methods lack adequate psychometric evidence and require significant resources. Direct behavior rating has been discussed and evaluated as a tool for assessing student behavior, yet the technology could be extended to result in an efficient treatment integrity assessment method with utility in a multi-tiered model of school-based intervention delivery. This article reviews options in treatment integrity assessment, with emphasis on how direct behavior rating technology might be incorporated within a multi-tiered model of intervention delivery. Implications for both practice and research are addressed.
Antecedents of Service Employees' Organizational Citizenship Behaviors in Full-Service Restaurants in Korea
Authors: Kim Wansoo , Ok Chihyung , Myong Jae Lee
Published: April 2009

In the aggregate, employees' organizational citizenship behaviors (OCBs) promote organizational performance in many ways and thereby gain significance as market competition gets fierce. The purpose of this study is to investigate how the leader-member exchange (LMX) relationships affect the service employee's OCBs. Following other research approaches, the structural equation model presented here hypothesizes the mediating roles of two forms of justice between LMX constructs and OCB constructs using the following constructs. The LMX forms are perceived contribution and affect, the justice constructs are interactional justice and distributive justice, and the OCB types are those directed toward supervisors and those directed at the organization. Based on an analysis of 293 responses collected from fifty-four full-service restaurants in a metropolitan city in South Korea, this study concludes that both forms of LMX significantly influence employees' perceptions of justice (that is, both interactional and distributive). Those perceptions, in turn, significantly affect the employees' tendency to engage in OCBs.
From structure topology to chemical composition. IX. Titanium silicates: revision of the crystal chemistry of lomonosovite and murmanite, Group-IV minerals
Authors: Cámara F. , Sokolova E. , Hawthorne F. C. , Abdu Y.
Published: April 2009

The crystal structures of lomonosovite, ideally Na10Ti4(Si2O7)2(PO4)2 O4, a = 5.4170(7) Å, b = 7.1190(9) Å, c = 14.487(2) Å, a = 99.957(3)°, β = 96.711(3)°, γ = 90.360(3)°, V= 546.28(4) Å3, Dcalc. = 3.175 g cm“3, and murmanite, ideally Na4Ti4(Si2O7)2O4(H2O)4, a = 5.3875(6) Å, b = 7.0579(7) Å, c = 12.176(1) Å, a = 93.511(2)°, 0 = 107.943(4)°, y = 90.093(2)°, V = 439.55(2) Å3, Dcalc. = 2.956 g.cm∼3, from the Lovozero alkaline massif, Kola Peninsula, Russia, have been refined in the space group P1̄ (Z = 1) to R values of 2.64 and 4.47%, respectively, using 4572 and 2222 observed |F°≥ 4σF| reflections collected with a single-crystal Bruker AXS SMART APEX diffractometer with a CCD detector and Mo-Kα. radiation. Electron microprobe analysis gave empirical formulae for lomonosovite (Na9.50Mn0.16Ca0.11)Σ9.77(Ti4+2.83Nb0.51Mn0.272+Zr0.11Mg0.11Fe2+0.10Fe3+0.06Ta0.01)Σ4.00(Si2.02O7)2(P0.98O4)2(O3.50F0.50)Σ4, Z = 1, calculated on the basis of 22(O+F) a.p.f.u., with H2O determined from structure refinement and Fe3+/(Fe2++Fe3+) ratios obtained by Mössbauer spectroscopy. The crystal structures of lomonosovite and murmanite are a combination of a titanium silicate (TS) block and an intermediate (I) block. The TS block consists of HOH sheets (H-heteropolyhedral, O-octahedral), and is characterized by a planar cell based on translation vectors, t1 and t2, with t1\ ∼5.5 and t2 ∼7 Å and ttA t2 close to 90°. The TS block exhibits linkage and stereochemistry typical for Group IV (Ti = 4 a.p.f.u.) of the Ti disilicate minerals: two H sheets connect to the O sheet such that two (Si2O7) groups link to Ti polyhedra of the O sheet adjacent along tx. In murmanite and lomonosovite, the invariant part of the TS block is of composition Na4Ti4(Si2O7)2O4. There is no evidence of vacancy-dominant cation sites or (OH) groups in the O sheet of lomonosovite or murmanite. In lomonosovite, the I block is a framework of Na polyhedra and P tetrahedra which gives 2[Na3 (PO)4] p.f.u. In murmanite, there are four (H2O) groups in the intermediate space between TS blocks. In lomonosovite, TS and I blocks alternate along c. In murmanite, TS blocks are connected via hydrogen bonding. The H atoms were located and details of the hydrogen bonding are discussed.
SCF induces γ-globin gene expression by regulating downstream transcription factor COUP-TFII
Authors: Aerbajinai Wulin , Zhu Jianqiong , Kumkhaek Chutima , Chin Kyung , Rodgers Griffin P.
Published: April 2009

Increased fetal hemoglobin expression in adulthood is associated with acute stress erythropoiesis. However, the mechanisms underlying γ-globin induction during the rapid expansion of adult erythroid progenitor cells have not been fully elucidated. Here, we examined COUP-TFII as a potential repressor of γ-globin gene after stem cell factor (SCF) stimulation in cultured human adult erythroid progenitor cells. We found that COUP-TFII expression is suppressed by SCF through phosphorylation of serine/threonine phosphatase (PP2A) and correlated well with fetal hemoglobin induction. Furthermore, down-regulation of COUP-TFII expression with small interfering RNA (siRNA) significantly increases the γ-globin expression during the erythroid maturation. Moreover, SCF-increased expression of NF-YA associated with redox regulator Ref-1 and cellular reducing condition enhances the effect of SCF on γ-globin expression. Activation of Erk1/2 plays a critical role in SCF modulation of downstream transcriptional factor COUP-TFII, which is involved in the regulation of γ-globin gene induction. Our data show that SCF stimulates Erk1/2 MAPK signaling pathway, which regulates the downstream repressor COUP-TFII by inhibiting serine/threonine phosphatase 2A activity, and that decreased COUP-TFII expression resulted in γ-globin reactivation in adult erythropoiesis. These observations provide insight into the molecular pathways that regulate γ-globin augmentation during stress erythropoiesis.
The importance of Src homology 2 domain-containing leukocyte phosphoprotein of 76 kilodaltons sterile-α motif domain in thymic selection and T-cell activation
Authors: Shen Shudan , Lau Jasmine , Zhu Minghua , Zou Jianwei , Fuller Deirdre , Li Qi-jing , Zhang Weiguo
Published: April 2009

The Src homology 2 domain–containing leukocyte phosphoprotein of 76 kilodaltons (SLP-76) is a cytosolic adaptor protein essential for thymocyte development and T-cell activation. It contains a sterile-α motif (SAM) domain, 3 phosphotyrosine motifs, a proline-rich region, and a Src homology 2 domain. Whereas the other domains have been extensively studied, the role of the SAM domain in SLP-76 function is not known. To understand the function of this domain, we generated SLP-76 knockin mice with the SAM domain deleted. Analysis of these mice showed that thymocyte development was partially blocked at the double-positive to single-positive transition. Positive and negative thymic selection was also impaired. In addition, we analyzed T-cell receptor (TCR)–mediated signaling in T cells from these mutant mice. TCR-mediated inositol 1,4,5-triphosphate production, calcium flux, and extracellular signal-regulated kinase activation were decreased, leading to defective interleukin-2 production and proliferation. Moreover, despite normal association between Gads and SLP-76, TCR-mediated formation of SLP-76 microclusters was impaired by the deletion of the SAM domain. Altogether, our data demonstrated that the SAM domain is indispensable for optimal SLP-76 signaling.
MicroRNA profiling identifies miR-34a and miR-21 and their target genes JAG1 and WNT1 in the coordinate regulation of dendritic cell differentiation
Authors: Hashimi Sara T. , Fulcher Jennifer A. , Chang Margaret H. , Gov Lanny , Wang Shuo , Lee Benhur
Published: April 2009

MicroRNAs (miRNAs, miRs) modulate a multitude of cellular events. Here, we identify functional miRNA-protein networks that regulate human monocyte-derived dendritic cell (MDDC) differentiation. miRNA profiling revealed stage-specific differential expression of 20 miRNAs during days 1, 3, and 5 of MDDC differentiation. To identify and prioritize miRNA-protein networks for functional validation, we developed a target ranking algorithm that incorporates many features of miRNA regulatory networks. This system prioritized miR-21, miR-34a, and their cognate targets WNT1 and JAG1 for functional validation. Inhibition of both miR-21 and miR-34a stalled MDDC differentiation, as quantified by DC-SIGN/CD14 expression ratios, showing cooperative involvement of these miRNAs in MDDC differentiation. We confirmed that the 3′ untranslated regions of WNT1 and JAG1 were functional targets of these miRNAs and provide evidence that these targets were translationally suppressed. Significantly, exogenously added Wnt-1 and Jagged-1 also stalled MDDC differentiation, suggesting that miRNA-mediated inhibition of endogenous WNT1 and JAG1 expression was important for proper MDDC differentiation. Finally, inhibition of miR-21 and miR-34a, or addition of Wnt-1 and Jagged-1, led to a decrease in endocytic capacity, a key function of immature DCs. Thus, our novel approach identified and validated some miRNA-protein networks involved in phenotypic and functional MDDC differentiation.
The leukemic stem cell niche: current concepts and therapeutic opportunities
Authors: Lane Steven W. , Scadden David T. , Gilliland D. Gary
Published: April 2009

The genetic events that contribute to the pathogenesis of acute myeloid leukemia are among the best characterized of all human malignancies. However, with notable exceptions such as acute promyelocytic leukemia, significant improvements in outcome based on these insights have not been forthcoming. Acute myeloid leukemia is a paradigm of cancer stem (or leukemia initiating) cells with hierarchy analogous to that seen in hematopoiesis. Normal hematopoiesis requires complex bidirectional interactions between the bone marrow microenvironment (or niche) and hematopoietic stem cells (HSCs). These interactions are critical for the maintenance of normal HSC quiescence and perturbations can influence HSC self-renewal. Leukemia stem cells (LSCs), which also possess limitless self-renewal, may hijack these homeostatic mechanisms, take refuge within the sanctuary of the niche during chemotherapy, and consequently contribute to eventual disease relapse. We will discuss the emerging evidence supporting the importance of the bone marrow microenvironment in LSC survival and consider the physiologic interactions of HSCs and the niche that inform our understanding of microenvironment support of LSCs. Finally, we will discuss approaches for the rational development of therapies that target the microenvironment.
Identification of crassin acetate as a new immunosuppressant triggering heme oxygenase-1 expression in dendritic cells
Authors: Matsushima Hironori , Tanaka Hiroaki , Mizumoto Norikatsu , Takashima Akira
Published: April 2009

By screening 720 natural compounds in a standard 2-way allogeneic mixed leukocyte reaction assay, we identified a potent immunosuppressive capacity of crassin acetate (CRA), a coral-derived cembrane diterpenoid. CRA efficiently inhibited allogeneic mixed leukocyte reaction as well as antigen-specific activation of CD4 T cells by bone marrow–derived dendritic cells (DCs). With regard to cellular targets, CRA suppressed not only mitogen-triggered T-cell activation, but also lipopolysaccharide-induced DC maturation, indicating dual functionality. Treatment with CRA at nontoxic doses induced heme oxygenase-1 (HO-1) mRNA/protein expression and HO-1 enzymatic activity in DCs, suggesting a unique mechanism of action. In fact, lipopolysaccharide-induced DC maturation was also inhibited by structurally unrelated compounds known to induce HO-1 expression or carbon monoxide (CO) release. Allergic contact hypersensitivity response to oxazolone and oxazolone-induced Langerhans cell migration from epidermis were both prevented almost completely by systemic administration of CRA. Not only do our results support the recent concept that HO-1/CO system negatively regulates immune responses, they also form both conceptual and technical frameworks for a more systematic, large-scale drug discovery effort to identify HO-1/CO-targeted immunosuppressants with dual target specificity.
Survey-based naming conventions for use in OBO Foundry ontology development
Authors: Schober Daniel , Smith Barry , Lewis Suzanna E , Kusnierczyk Waclaw , Lomax Jane , Mungall Chris , Taylor Chris F , Rocca-Serra Philippe , Sansone Susanna-Assunta
Published: April 2009

Background

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion.

Results

We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies.

Conclusion

Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.
Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins
Authors: Odronitz Florian , Becker Sebastian , Kollmar Martin
Published: April 2009

Background

Motor proteins have extensively been studied in the past and consist of large superfamilies. They are involved in diverse processes like cell division, cellular transport, neuronal transport processes, or muscle contraction, to name a few. Vertebrates contain up to 60 myosins and about the same number of kinesins that are spread over more than a dozen distinct classes.

Results

Here, we present the comparative genomic analysis of the motor protein repertoire of 21 completely sequenced arthropod species using the owl limpet Lottia gigantea as outgroup. Arthropods contain up to 17 myosins grouped into 13 classes. The myosins are in almost all cases clear paralogs, and thus the evolution of the arthropod myosin inventory is mainly determined by gene losses. Arthropod species contain up to 29 kinesins spread over 13 classes. In contrast to the myosins, the evolution of the arthropod kinesin inventory is not only determined by gene losses but also by many subtaxon-specific and species-specific gene duplications. All arthropods contain each of the subunits of the cytoplasmic dynein/dynactin complex. Except for the dynein light chains and the p150 dynactin subunit they contain single gene copies of the other subunits. Especially the roadblock light chain repertoire is very species-specific.

Conclusion

All 21 completely sequenced arthropods, including the twelve sequenced Drosophila species, contain a species-specific set of motor proteins. The phylogenetic analysis of all genes as well as the protein repertoire placed Daphnia pulex closest to the root of the Arthropoda. The louse Pediculus humanus corporis is the closest relative to Daphnia followed by the group of the honeybee Apis mellifera and the jewel wasp Nasonia vitripenni s. After this group the rust-red flour beetle Tribolium castaneum and the silkworm Bombyx mori diverged very closely from the lineage leading to the Drosophila species.
Gene set internal coherence in the context of functional profiling
Authors: Montaner David , Minguez Pablo , Al-Shahrour Fátima , Dopazo Joaquín
Published: April 2009

Background

Functional profiling methods have been extensively used in the context of high-throughput experiments and, in particular, in microarray data analysis. Such methods use available biological information to define different types of functional gene modules (e.g. gene ontology -GO-, KEGG pathways, etc.) whose representation in a pre-defined list of genes is further studied. In the most popular type of microarray experimental designs (e.g. up- or down-regulated genes, clusters of co-expressing genes, etc.) or in other genomic experiments (e.g. Chip-on-chip, epigenomics, etc.) these lists are composed by genes with a high degree of co-expression. Therefore, an implicit assumption in the application of functional profiling methods within this context is that the genes corresponding to the modules tested are effectively defining sets of co-expressing genes. Nevertheless not all the functional modules are biologically coherent entities in terms of co-expression, which will eventually hinder its detection with conventional methods of functional enrichment.

Results

Using a large collection of microarray data we have carried out a detailed survey of internal correlation in GO terms and KEGG pathways, providing a coherence index to be used for measuring functional module co-regulation. An unexpected low level of internal correlation was found among the modules studied. Only around 30% of the modules defined by GO terms and 57% of the modules defined by KEGG pathways display an internal correlation higher than the expected by chance.

This information on the internal correlation of the genes within the functional modules can be used in the context of a logistic regression model in a simple way to improve their detection in gene expression experiments.

Conclusion

For the first time, an exhaustive study on the internal co-expression of the most popular functional categories has been carried out. Interestingly, the real level of coexpression within many of them is lower than expected (or even inexistent), which will preclude its detection by means of most conventional functional profiling methods. If the gene-to-function correlation information is used in functional profiling methods, the results obtained improve the ones obtained by conventional enrichment methods.
M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island
Authors: Panchaud Alexandre , Guy Lionel , Collyn François , Haenni Marisa , Nakata Masanobu , Podbielski Andreas , Moreillon Philippe , Roten Claude-Alain H
Published: April 2009

Background

The increasing number of completely sequenced bacterial genomes allows comparing their architecture and genetic makeup. Such new information highlights the crucial role of lateral genetic exchanges in bacterial evolution and speciation.

Results

Here we analyzed the twelve sequenced genomes of Streptococcus pyogenes by a naïve approach that examines the preferential nucleotide usage along the chromosome, namely the usage of G versus C (GC-skew) and T versus A (TA-skew). The cumulative GC-skew plot presented an inverted V-shape composed of two symmetrical linear segments, where the minimum and maximum corresponded to the origin and terminus of DNA replication. In contrast, the cumulative TA-skew presented a V-shape, which segments were interrupted by several steep slopes regions (SSRs), indicative of a different nucleotide composition bias. Each S. pyogenes genome contained up to nine individual SSRs, encompassing all described strain-specific prophages. In addition, each genome contained a similar unique non-phage SSR, the core of which consisted of 31 highly homologous genes. This core includes the M-protein, other mga-related factors and other virulence genes, totaling ten intrinsic virulence genes. In addition to a high content in virulence-related genes and to a peculiar nucleotide bias, this SSR, which is 47 kb-long in a M1GAS strain, harbors direct repeats and a tRNA gene, suggesting a mobile element. Moreover, its complete absence in a M-protein negative group A Streptococcus natural isolate demonstrates that it could be spontaneously lost, but in vitro deletion experiments indicates that its excision occurred at very low rate. The stability of this SSR, combined to its presence in all sequenced S. pyogenes sequenced genome, suggests that it results from an ancient acquisition.

Conclusion

Thus, this non-phagic SSR is compatible with a pathogenicity island, acquired before S. pyogenes speciation. Its potential excision might bear relevance for vaccine development, because vaccines targeting M-protein might select for M-protein-negative variants that still carry other virulence determinants.
Tumor-directed gene therapy in mice using a composite nonviral gene delivery system consisting of the piggyBac transposon and polyethylenimine
Authors: Kang Yu , Zhang Xiaoyan , Jiang Wei , Wu Chaoqun , Chen Chunmei , Zheng Yufang , Gu Jianren , Xu Congjian
Published: April 2009

Background

Compared with viral vectors, nonviral vectors are less immunogenic, more stable, safer and easier to replication for application in cancer gene therapy. However, nonviral gene delivery system has not been extensively used because of the low transfection efficiency and the short transgene expression, especially in vivo. It is desirable to develop a nonviral gene delivery system that can support stable genomic integration and persistent gene expression in vivo. Here, we used a composite nonviral gene delivery system consisting of the piggyBac (PB) transposon and polyethylenimine (PEI) for long-term transgene expression in mouse ovarian tumors.

Methods

A recombinant plasmid PB [Act-RFP, HSV-tk] encoding both the herpes simplex thymidine kinase (HSV-tk) and the monomeric red fluorescent protein (mRFP1) under PB transposon elements was constructed. This plasmid and the PBase plasmid were injected into ovarian cancer tumor xenografts in mice by in vivo PEI system. The antitumor effects of HSV-tk/ganciclovir (GCV) system were observed after intraperitoneal injection of GCV. Histological analysis and TUNEL assay were performed on the cryostat sections of the tumor tissue.

Results

Plasmid construction was confirmed by PCR analysis combined with restrictive enzyme digestion. mRFP1 expression could be visualized three weeks after the last transfection of pPB/TK under fluorescence microscopy. After GCV admission, the tumor volume of PB/TK group was significantly reduced and the tumor inhibitory rate was 81.96% contrasted against the 43.07% in the TK group. Histological analysis showed that there were extensive necrosis and lymphocytes infiltration in the tumor tissue of the PB/TK group but limited in the tissue of control group. TUNEL assays suggested that the transfected cells were undergoing apoptosis after GCV admission in vivo.

Conclusion

Our results show that the nonviral gene delivery system coupling PB transposon with PEI can be used as an efficient tool for gene therapy in ovarian cancer.
Bipolar disorder and dopamine dysfunction: an indirect approach focusing on tardive movement syndromes in a naturalistic setting
Authors: van Rossum Inge , Tenback Diederik , van Os Jim
Published: April 2009

Background

It has been suggested that dopamine dysfunction may play a role in bipolar disorder (BD). An indirect approach to examine this issue was developed, focusing on associations between dopamine proxy measures observed in BD (dopamine-related clinical traits using tardive movement syndromes as dopamine proxy measure of reference).

Methods

3459 eligible bipolar patients were enrolled in an observational study. Incidence rates of tardive movement syndromes (tardive dyskinesia and tardive dystonia; TDD) were examined. A priori hypothesized associations between incident TDD and other dopamine proxies (e.g. prolactin-related adverse effects, bipolar symptoms) were tested over a 2 year follow-up period.

Results

The incidence rate of tardive syndromes was 4.1 %. Incident TDD was independently associated not only with use of antipsychotics, but also with more severe bipolar symptoms, other extrapyramidal symptoms and prolactin-related adverse effects of medication.

Conclusion

Apart from the well-known association with antipsychotics, development of TDD was associated with various other dopamine proxy measures, indirectly supporting the notion of generalised dopamine dysregulation in BD.
Knowledge and attitude on maternal health care among rural-to-urban migrant women in Shanghai, China
Authors: Zhao Qi , Kulane Asli , Gao Yi , Xu Biao
Published: April 2009

Background

In China, with the urbanization, women migrated from rural to big cities presented much higher maternal mortality rates than local residents. Health knowledge is one of the key factors enabling women to be aware of their rights and health status in order to seek appropriate health services. This study aims to assess the knowledge and attitude on maternal health care and the contributing factors to being knowledgeable among rural-to-urban migrant women in Shanghai.

Methods

A cross-sectional study was conducted in a district center hospital in Shanghai where migrants gathered. Totally 475 rural-to-urban migrant pregnant women were interviewed and completed the self-administered questionnaire after obtaining informed consent.

Results

The mean score of knowledge on maternal health care was 8.28 out of 12. However, only 36.6% women had attended the required 5 antenatal checks, and 58.3% of the subjects thought financial constrains being the main reason for not attending antenatal care. It was found that higher level of education (OR = 3.3, 95%CI: 1.8–3.8), husbands' Shanghai residence (OR = 4.0, 95%CI: 1.3–12.1) and better family income (OR = 3.3, 95%CI: 1.4–8.2) were associated with better knowledge.

Conclusions

Rural-to-urban migrant women's unawareness of maternal health service, together with their vulnerable living status, influences their utilization of maternal health care. Tailored maternal health education and accessible services are in demands for this population.
Rasch scaling procedures for informing development of a valid Fetal Surveillance Education Program multiple-choice assessment
Authors: Zoanetti Nathan , Griffin Patrick , Beaves Mark , Wallace Euan M
Published: April 2009

Background

It is widely recognised that deficiencies in fetal surveillance practice continue to contribute significantly to the burden of adverse outcomes. This has prompted the development of evidence-based clinical practice guidelines by the Royal Australian and New Zealand College of Obstetricians and Gynaecologists and an associated Fetal Surveillance Education Program to deliver the associated learning. This article describes initial steps in the validation of a corresponding multiple-choice assessment of the relevant educational outcomes through a combination of item response modelling and expert judgement.

Methods

The Rasch item response model was employed for item and test analysis and to empirically derive the substantive interpretation of the assessment variable. This interpretation was then compared to the hierarchy of competencies specified a priori by a team of eight subject-matter experts. Classical Test Theory analyses were also conducted.

Results

A high level of agreement between the hypothesised and derived variable provided evidence of construct validity. Item and test indices from Rasch analysis and Classical Test Theory analysis suggested that the current test form was of moderate quality. However, the analyses made clear the required steps for establishing a valid assessment of sufficient psychometric quality. These steps included: increasing the number of items from 40 to 50 in the first instance, reviewing ineffective items, targeting new items to specific content and difficulty gaps, and formalising the assessment blueprint in light of empirical information relating item structure to item difficulty.

Conclusion

The application of the Rasch model for criterion-referenced assessment validation with an expert stakeholder group is herein described. Recommendations for subsequent item and test construction are also outlined in this article.
Host immune responses to chlamydial inclusion membrane proteins B and C in Chlamydia trachomatis infected women with or without fertility disorders
Authors: Gupta Rishein , Srivastava Pragya , Vardhan Harsh , Salhan Sudha , Mittal Aruna
Published: April 2009

Background

With an increase in the number of putative inclusion membrane proteins (incs) in chlamydial genomes, there is a need for understanding their contribution in host-pathogen interactions. Thus in this study we determined the host mucosal and peripheral immune responses to incs (IncB and IncC) of Chlamydia trachomatis (CT).

Methods

Female patients (n = 296) attending the gynaecology out patient department of Safdarjung hospital, New Delhi were enrolled for the study and were clinically characterized into two groups; CT-positive fertile women (n = 38) and CT-positive women with fertility disorders (n = 29). Uninfected healthy fertile women were enrolled as controls (n = 31). Gene specific PCRs were used for detection of incB and incC genes in endocervical samples of CT-positive patients. ELISA and Western blot assay were used for detection of IgA and IgG antibodies to IncB and IncC in cervical washes and sera. Effect of IncB and IncC stimulation of cervical cells and PBMCs on cellular proliferation and cytotoxity was determined using MTT assay and Lactate dehydrogenase (LDH)-cytotoxicity assay respectively. Modulation of cytokines (Interleukin (IL)-1 Beta, IL-4, IL-5, IL-6, IL-10, Interferon-gamma, IL-12, Tumor Necrosis Factor-alpha and Granulocyte macrophage colony-stimulating factor (GM-CSF)) in cervical cells and PBMCs upon stimulation with IncB and IncC was determined by real-time reverse-transcriptase (RT)-PCR and ELISA. Further, CD4 positive T cells were purified from cervical cells and peripheral blood mononuclear cells (PBMCs) and secreted cytokines (Interferon-gamma and IL-4) were evaluated by ELISPOT and real-time RT-PCR.

Results

Using MTT assay, significantly high proliferative responses (P < 0.05) were observed in inc-stimulated cervical cells and PBMCs from CT-positive fertile women compared to CT-positive women with fertility disorders and controls. Interferon-gamma, IL-12 and GM-CSF were found to be elevated in inc-stimulated cervical cells and PBMCs of CT-positive fertile women compared to CT-positive women with fertility disorders and controls (P < 0.05). In contrast, IL-1 Beta, IL-4, IL-5, IL-6 and IL-10 levels were found to be higher in CT-positive women with fertility disorders compared to CT-positive fertile women and controls (P < 0.05). Interferon-gamma secreting cells and mRNA expression in inc-stimulated cervical and peripheral CD4 positive T cells were significantly higher (P < 0.05) in CT positive fertile women compared to CT-positive women with fertility disorders.

Conclusion

Our data overall suggests that CT incs, IncB and IncC modulate host immune responses and may have a role in protection/pathogenesis of genital chlamydial infection in women.