bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the change in marker geometry during respiration motion: a preliminary study for dynamic-multi-leaf real-time tumor tracking
Authors: Yamazaki Rie , Nishioka Seiko , Date Hiroyuki , Shirato Hiroki , Koike Takao , Nishioka Takeshi 
Published: December 2012

Abstract

Background
The use of stereotactic body radiotherapy (SBRT) is rapidly increasing. Presently, the most accurate method uses fiducial markers implanted near the tumor. A shortcoming of this method is that the beams turn off during the majority of the respiratory cycle, resulting in a prolonged treatment time. Recent advances in collimation technology have enabled continuous irradiation to a moving tumor. However, the lung is a dynamic organ characterized by inhalation exhalation cycles, during which marker/tumor geometry may change (i.e., misalignment), resulting in under-dosing to the tumor.

Findings
Eight patients with lung cancer who were candidates for stereotactic radiotherapy were examined with 4D high-resolution CT. As a marker surrogate, virtual bronchoscopy using the pulmonary artery (VBPA) was conducted. To detect possible marker/tumor misalignment during the respiration cycle, the distance between the peripheral bronchus, where a marker could be implanted, and the center of gravity of a tumor were calculated for each respiratory phase. When the respiration cycle was divided into 10 phases, the median value was significantly larger for the 30%-70% respiratory phases compared to that for the 10% respiratory phase (P<0.05, Mann–Whitney U-test).

Conclusions
These results demonstrate that physiological aspect must be considered when continuous tumor tracking is applied to a moving tumor. To minimize an “additional” internal target volume (ITV) margin, a marker should be placed approximately 2.5 cm from the tumor.
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network
Authors: Qin Tingting , Tsoi Lam C , Sims Kellie J , Lu Xinghua , Zheng W Jim 
Published: December 2012

AbstractBackgroundDespite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network has been explored to meet this challenge, employing existing biological knowledge for network prediction is difficult. The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven Bayesian network learning; and to further use the trained model to predict cellular responses.ResultsWe applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition. The challenge results showed that our method accurately captured signal transduction of a network of protein kinases and phosphoproteins in that the predicted protein phosphorylation levels under all experimental conditions were highly correlated (R2= 0.93) with the observed results. Based on the evaluation of the DREAM4 organizer, our team was ranked as one of the top five best performers in predicting network structure and protein phosphorylation activity under test conditions.ConclusionsBayesian network can be used to simulate the propagation of signals in cellular systems. Incorporating the Ontology Fingerprint as prior biological knowledge allows us to efficiently infer concise signaling network structure and to accurately predict cellular responses.
The CXCR4-CXCL12 axis in Ewing sarcoma: promotion of tumor growth rather than metastatic disease
Authors: Berghuis Dagmar , Schilham Marco W , Santos Susy J , Savola Suvi , Knowles Helen J , Dirksen Uta , Schaefer Karl-Ludwig , Vakkila Jukka , Hogendoorn Pancras CW , Lankester Arjan C 
Published: December 2012

Abstract

Background
Chemokine receptor CXCR4, together with its ligand CXCL12, plays critical roles in cancer progression, including growth, metastasis and angiogenesis. Ewing sarcoma is a sarcoma with poor prognosis despite current therapies, particularly for patients with advanced-stage disease. Lungs and bone (marrow), organs of predilection for (primary/metastatic) Ewing sarcoma, represent predominant CXCL12 sources.

Methods
To gain insight into the role of the CXCR4-CXCL12 axis in Ewing sarcoma, CXCR4, CXCL12 and hypoxia-inducible factor-1α protein expression was studied in therapy-naïve and metastatic tumors by immunohistochemistry. CXCR4 function was assessed in vitro, by flow cytometry and proliferation/ cell viability assays, in the presence of recombinant CXCL12 and/or CXCR4-antagonist AMD3100 or under hypoxic conditions.

Results
Whereas CXCR4 was predominantly expressed by tumor cells, CXCL12 was observed in both tumor and stromal areas. Survival analysis revealed an (expression level-dependent) negative impact of CXCR4 expression (p < 0.04). A role for the CXCR4-CXCL12 axis in Ewing sarcoma growth was suggested by our observations that i) CXCR4 expression correlated positively with tumor volume at diagnosis (p = 0.013), ii) CXCL12 was present within the microenvironment of virtually all cases, iii) CXCL12 induced proliferation of CXCR4-positive Ewing sarcoma cell lines, which could be abrogated by AMD3100. CXCR4 expression was not correlated with occurrence of metastatic disease. Also, therapy-naïve tumors demonstrated higher CXCR4 expression as compared to metastases (p = 0.027). Evaluation of in vivo hypoxia-inducible factor-1α expression and culture of cells under hypoxic conditions revealed no role for hypoxia in CXCR4 expression.

Conclusions
Together, our results imply a crucial role for the CXCR4-CXCL12 axis in auto- and/or paracrine growth stimulation. Integration of CXCR4-targeting strategies into first- and/or second-line treatment regimens may represent a promising treatment option for Ewing sarcoma.
Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly
Authors: Baschek Johanna E , R Klein Heinrich C , Schwarz Ulrich S 
Published: December 2012

Abstract

Background
In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly).

Results
In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results.

Conclusions
Our analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science.
Dynamics of dendritic cell-derived vesicles: high-resolution flow cytometric analysis of extracellular vesicle quantity and quality
Authors: Nolte-‘t Hoen Esther N M , van der Vlist Els J , de Boer-Brouwer Mieke , Arkesteijn Ger J A , Stoorvogel Willem , Wauben Marca H M 
Published: December 2012

Abstract
Application of a described high-resolution flow cytometrybased analysis of individual extracellular vesicles, to study the dynamics of dendritic cell-derived vesicle secretion and composition.
Nano-sized membrane vesicles are secreted by many cell types. These vesicles can serve as carriers of cellular information. DC-derived vesicles can be targeted to other immune cells and modify their function. Accurate analysis of quantitative and qualitative changes in EV production by DC upon different activation stimuli is needed to further reveal the immune regulatory properties of DC-derived EVs. However, methods for reliable quantification of individual EVs and for analysis of the heterogeneity of EV populations are limited. With our recently developed high-resolution flow cytometry-based method, we can perform a high-throughput, multiparameter, and quantitative analysis of individual EVs. With the use of this novel technique, we show that despite previous assumptions, stimulation with bacterial LPS increases EV release by DC. Furthermore, we demonstrate heterogeneity in DC-derived EVs regarding their buoyant density and MHC class II content. Finally, we show that cognate interaction between LPS-stimulated DC and CD4+ T cells affects both the quantity and quality of LPS DC-derived EVs present in the culture supernatant. These data indicate that flow cytometry-based analysis of individual EVs is a valuable, novel tool to study the dynamics of EV secretion and composition, offering great opportunities to unveil the function of immune cell-derived EVs.
Blessures des frontières
Authors: Setti Nadia 
Published: December 2012

Supported by Judith Butler’s work, and also by the theme of ambivalence and nonsense as defined by Homi Bhabha, this article initiates thoughts on agency in the historic, literary and cultural context of postcolonial narrations around the reconfiguration of borders in an era of
globalization. This analysis of the works of Malika Mokeddem, Nina Bouraoui, Hélène Cixous, Maryse Condé and Marie NDiaye concentrates on the way in which the texts’ main female characters are all presented as trespassers – human beings struggling to exist,
to speak, to give an account of themselves, and who are breaking away from the standards and displacing borders. A strong feeling of ‘inseparation’ emanates from what divides through unity, from the border as a wound uniting and separating both narrations and people. This
includes wounds of sexual difference, of the sexual body. Traces of wounds consecutive to crossing borders can be found in these wounded narrations where memories attempt to express themselves, often through the necessity of delaying the accounts through repetitions which in themselves
act as means of working through the trauma.
REVIEWS
Authors: Banerji Sushmita , Bhattacharya Nandini , Mahadevan Sudhir , Schulz Suzanne L. 
Published: December 2012

PRODUCING BOLLYWOOD: INSIDE THE CONTEMPORARY HINDI FILM INDUSTRY, TEJASWINI GANTI (2012) Durham, London: Duke University Press, Paperback, ISBN-13: 978-0822352136, $23.47, 440 pp.
GLOBAL ICONS: APERTURES TO THE POPULAR, BISHNUPRIYA GHOSH (2011) Durham: Duke University Press,
383 pp. Paperback: $25.95, ISBN: 978-0-8223-5016-3. Cloth: $94.95, ISBN: 978-0-8223-5004-0
CENSORSHIP AND SEXUALITY IN BOMBAY CINEMA, MONIKA MEHTA (2011) Austin: University of Texas Press, 348 pp., $40.20, ISBN: 978-0292726925
INDIAN MEDIA, ADRIAN ATHIQUE (2012)
Cambridge, UK: Polity Press, 244 pp., $24.95, ISBN: 978-0745653334
HINDI ACTION CINEMA: INDUSTRIES, NARRATIVES, BODIES, VALENTINA VITALI (2010) Bloomington, IN: Indiana University Press (reprint of Oxford University Press, 2008, 25 b&w illus.), ISBN 978-0-253-22222-0, p/bk $24.95.
Socioeconomic Status and In-Hospital Pediatric Mortality
Authors: Colvin Jeffrey D. , Zaniletti Isabella , Fieldston Evan S. , Gottlieb Laura M. , Raphael Jean L. , Hall Matthew , Cowden John D. , Shah Samir S. 
Published: December 2012

OBJECTIVE:Socioeconomic status (SES) is inversely related to pediatric mortality in the community. However, it is unknown if this association exists for in-hospital pediatric mortality. Our objective was to determine the association of SES with in-hospital pediatric mortality among children’s hospitals and to compare observed mortality with expected mortality generated from national all-hospital inpatient data.METHODS:This is a retrospective cohort study from 2009 to 2010 of all 1 053 101 hospitalizations at 42 tertiary care, freestanding children’s hospitals. The main exposure was SES, determined by the median annual household income for the patient’s ZIP code. The main outcome measure was death during the admission. Primary outcomes of interest were stratified by income and diagnosis-based service lines. Observed-to-expected mortality ratios were created, and trends across quartiles of SES were examined.RESULTS:Death occurred in 8950 (0.84%) of the hospitalizations. Overall, mortality rates were associated with SES (P &lt; .0001) and followed an inverse linear association (P &lt; .0001). Similarly, observed-to-expected mortality was associated with SES in an inverse association (P = .014). However, mortality overall was less than expected for all income quartiles (P &lt; .05). The association of SES and mortality varied by service line; only 3 service lines (cardiac, gastrointestinal, and neonatal) demonstrated an inverse association between SES and observed-to-expected mortality.CONCLUSIONS:Within children’s hospitals, SES is inversely associated with in-hospital mortality, but is lower than expected for even the lowest SES quartile. The association between SES and mortality varies by service line. Multifaceted interventions initiated in the inpatient setting could potentially ameliorate SES disparities in in-hospital pediatric mortality.
Diabetes and Risk of Fracture-Related Hospitalization
Authors: Schneider Andrea L.C. , Williams Emma K. , Brancati Frederick L. , Blecker Saul , Coresh Josef , Selvin Elizabeth 
Published: December 2012

OBJECTIVE
To examine the association between diabetes, glycemic control, and risk of fracture-related hospitalization in the Atherosclerosis Risk in Communities (ARIC) Study.

RESEARCH DESIGN AND METHODS
Fracture-related hospitalization was defined using International Classification of Diseases, 9th revision, codes (733.1–733.19, 733.93–733.98, or 800–829). We calculated the incidence rate of fracture-related hospitalization by age and used Cox proportional hazards models to investigate the association of diabetes with risk of fracture after adjustment for demographic, lifestyle, and behavioral risk factors.

RESULTS
There were 1,078 incident fracture-related hospitalizations among 15,140 participants during a median of 20 years of follow-up. The overall incidence rate was 4.0 per 1,000 person-years (95% confidence interval [CI], 3.8–4.3). Diagnosed diabetes was significantly and independently associated with an increased risk of fracture (adjusted hazard ratio [HR], 1.74; 95% CI, 1.42–2.14). There also was a significantly increased risk of fracture among persons with diagnosed diabetes who were treated with insulin (HR, 1.87; 95% CI, 1.15–3.05) and among persons with diagnosed diabetes with hemoglobin A1c (HbA1c) ≥8% (1.63; 1.09–2.44) compared with those with HbA1c &lt;8%. Undiagnosed diabetes was not significantly associated with risk of fracture (HR, 1.12; 95% CI, 0.82–1.53).

CONCLUSIONS
This study supports recommendations from the American Diabetes Association for assessment of fracture risk and implementation of prevention strategies in persons with type 2 diabetes, particularly those persons with poor glucose control.
Modèle « de la poubelle » et dynamique du business model
Authors: Lefebvre Vincent , Radu-Lefebvre Miruna , Lamy Erwan 
Published: December 2012

Résumé Pour élaborer leur modèle d’affaires, les porteurs de projet en situation d’accompagnement sélectionnent certains choix et en écartent d’autres. Sur la base de quels critères ? À quel moment et pour quelles raisons décident-ils ultérieurement d’intégrer certaines options écartées de prime abord ? Pour le comprendre, les auteurs de l’article ont réalisé en 2009 et 2010 une série d’entretiens semi-directifs avec un accompagnateur et trois entrepreneurs dans le cadre de l’Incubateur d’Advancia.
L'éducation artistique et les émotions démocratiques
Authors: Desbarats Carole 
Published: December 2012

Résumé L’ouverture des élèves à l’art est un serpent de mer des réformes éducatives. Mais il ne faut pas aborder la question de l’éducation artistique sous le seul angle de l’« apprentissage ». Il s’agit en effet de créer des rencontres, par la pratique ou la confrontation aux œuvres, pour faire naître les « émotions démocratiques » dont parle Martha Nussbaum, et qui sont aussi de l’ordre de la pensée.
Evaluation of Retinal Nerve Fiber Layer Thickness in Patients With Anisometropic and Strabismic Amblyopia Using Optical Coherence Tomography
Authors: Ersan Ismail , Zengin Nazmi , Bozkurt Banu , Özkagnici Ahmet 
Published: December 2012

Purpose:
To evaluate the retinal nerve fiber layer (RNFL) thickness of eyes with amblyopia using optical coherence tomography (OCT).

Methods:
RNFL thickness measurements obtained by time-domain OCT of amblyopic eyes of patients with strabismus (35 patients) and patients with anisometropia (30 patients) were compared with their fellow eyes and age- and gender-matched healthy eyes (40 participants). RNFL thickness values of the groups were also compared and the correlation between RNFL thickness and refraction was evaluated.

Results:

In the strabismic and anisometropic groups, there were no statistically significant differences in average RNFL thickness between amblyopic eyes and their fellow eyes (
P
> .05). Temporal RNFL quadrant in the hypermetropic anisometropic group, and superior RNFL quadrant in the myopic anisometropic group were significantly thinner in amblyopic eyes compared to their fellow eyes (
P
< .05). RNFL thickness did not differ between strabismic amblyopic, anisometropic amblyopic, and control eyes (
P
> .05). In the anisometropic group, a significant correlation was found between mean RNFL thickness and refraction (
P
< .05).

Conclusion:
Amblyopia is not associated with a decrease in RNFL thickness in strabismic or anisometropic amblyopia. In the anisometropic group, the inter-eye differences in RNFL thickness parameters seemed to be related to the refraction differences between the amblyopic eyes and their fellow eyes.

[J Pediatr Ophthalmol Strabismus 2013;50:113–117.]
Increased Myeloid-Derived Suppressor Cells in Gastric Cancer Correlate with Cancer Stage and Plasma S100A8/A9 Proinflammatory Proteins
Authors: Wang Linda , Chang Esther W. Y. , Wong Siew Cheng , Ong Siew-Min , Chong Debra Q. Y. , Ling Khoon Lin 
Published: December 2012

Abstract
Immune dysfunction may contribute to tumor progression in gastric cancer (GC) patients. One mechanism of immune dysfunction is the suppression of T cell activation and impairment of the efficacy of cancer immunotherapy by myeloid-derived suppressor cells (MDSCs). We assessed the phenotype and immunosuppressive function of MDSCs in GC patients. We further investigated the role of S100A8/A9 in GC and the relationship between S100A8/A9 and MDSC function. Lastly, the effect of MDSCs on survival rates and its potential as a prognostic factor in GC patients were investigated. MDSCs from PBMCs of GC patients were identified by comparing the expression of specific surface markers with PBMCs from healthy individuals. The ability of MDSCs to suppress T lymphocyte response and the effect of S100A8/A9 and RAGE blocking were tested in vitro by (autologous) MLR. GC patients had significantly more MDSCs than healthy individuals. These MDSCs suppressed both T lymphocyte proliferation and IFN-γ production and had high arginase-I expression. Levels of S100A8/A9 in plasma were higher in GC patients compared with healthy individuals, and they correlated with MDSC levels in the blood. Blocking of S100A8/A9 itself and the S100A8/A9 receptor RAGE on MDSCs from GC patients abrogated T cell effector function. We found that high levels of MDSCs correlated with more advanced cancer stage and with reduced survival (p = 0.006). S100A8/A9 has been identified as a potential target to modulate antitumor immunity by reversing MDSC-mediated immunosuppression.
Acetabular Version on Magnetic Resonance Imaging: Analysis of Two Different Measuring Techniques
Authors: Muhamad Abd R. , Freitas Joana M. , Bomar James D. , Hosalkar Harish 
Published: December 2012

Background Both increased anteversion and retroversion of the acetabulum can lead to clinical problems. Although computed tomography (CT) is the gold standard in acetabular version imaging, magnetic resonance imaging (MRI) is becoming increasingly popular. We conducted this retrospective study to answer the following questions: 1) can the bony landmarks necessary to outline and measure acetabular version on MRI be consistently and reproducibly identified; 2) are soft-tissue (labral) landmarks comparable to bony landmarks for the measurement of acetabular version? Methods Twenty-nine MRI torsional profile examinations were studied. A total of 232 readings (116 each for right and left sided acetabulae) were involved. Acetabular anteversion angle (AAA) was measured using two different methods (i.e. bony acetabulum landmarks and labrum), by two investigators, at two separate times. Results Mean age was 13 years, 8 months with a range of 14 years. There were 12 male patients and 17 female. It was possible to consistently identify bony and labral landmarks in all MR images. AAA measurements using both methods were consistent and reproducible. When comparing the two methods to each other we found them to be in excellent agreement with an ICC of 0.943 (95% confidence interval, 0.927 to 0.956), 37% of all readings were in perfect agreement and 97% were within 5 degrees. The mean difference in measurement between methods was 1.34 degrees. Conclusion Measurement of acetabular version using MRI remains consistent independent of the method used (bone versus labrum). MRI can provide adequate information for calculating acetabular version.