bluuebunny/crossref_metadata_2025 huggingface dataset:
The politics of maps: Constructing national territories in Israel
Authors: Leuenberger Christine , Schnell Izhak
Published: September 2010

Within the last 2000 years the land demarcated by the Mediterranean Sea to the west and the Jordan Valley to the east has been one of the most disputed territories in history. World powers have redrawn its boundaries numerous times. Since the establishment of the state of Israel in 1948 within British Mandate Palestine, Palestinians and Israelis have disagreed over the national identity of the land that they both inhabit. The struggles have extended from the battlefields to the classrooms. In the process, different national and ethnic groups have used various sciences, ranging from archeology to history and geography, to prove territorial claims based on their historical presence in the region. But how have various Israeli social and political groups used maps to solidify claims over the territory? In this paper we bring together science studies and critical cartography in order to investigate cartographic representations as socially embedded practices and address how visual rhetoric intersects with knowledge claims in cartography. Before the 1967 war between Israel and its Arab neighbors, the Israeli government and the Jewish National Fund produced maps of Israel that established a Hebrew topography of the land. After 1967, Israel’s expanded territorial control made the demarcation of its borders ever more controversial. Consequently, various Israeli interest groups and political parties increasingly used various cartographic techniques to forge territorial spaces, demarcate disputed boundaries, and inscribe particular national, political, and ethnic identities onto the land.
Characteristics of ferrocement thin composite elements using various reinforcement meshes in flexure
Authors: Wafa Mahmoud A , Fukuzawa Kimio
Published: September 2010

This article focuses on the experimental investigation carried out on the characteristics of ferrocement thin composite elements using various reinforcement meshes in flexure. The parameters of this study include: the effect of the various kinds of reinforcement meshes (stainless steel meshes and E-fiberglass meshes); number of mesh layers and various mesh diameters with opening size as well as various kinds of mortar materials as matrix (cement grout mortar and polymer— cement grout mortar) on the first crack load; bending stiffness; ultimate flexural load; load—deflection behavior; crack characteristics; energy absorption capacity; and ductility index. The results clarify that the use of stainless steel meshes as reinforcement system in the ferrocement thin composite elements contributes significantly to the improvement of bending characteristics in terms of first crack load, bending stiffness, ultimate flexural load, energy absorption to failure, and numerous fine and well-distributed cracks with a smaller width than while using fiberglass meshes. The method outlined by ACI Building Code is used to compute ultimate moment capacities. The results obtained using this method are compared with the experimental results.
Organizational Assimilation: A Multidimensional Reconceptualization and Measure
Authors: Gailliard Bernadette M. , Myers Karen K. , Seibold David R.
Published: September 2010

The authors offer a multidimensional reconceptualization of organizational assimilation developed from a reexamination of the Organizational Assimilation Index (OAI). Using a sample of 656 employees in the United States, the OAI was extended to include a seventh factor and used to detect group differences between men and women, managers and nonmanagers, and members with lengthy and short organizational tenure. Evidence for construct validity was found in relationships between the OAI factors and related variables. Results demonstrate the utility of conceptualizing assimilation as a set of interrelated processes that fluctuate based on various characteristics of organizational membership. The authors discuss implications for assimilation research and offer directions for future scholarship in the area.
Sex and the anarchist unconscious: A brief history
Authors: Cohn Jesse
Published: September 2010

‘We need form, not formlessness!’ In Gustav Landauer’s plaintive cry echoes a century-old controversy among the most singular minds of an entire generation of anarchists — Otto Gross, Erich Mühsam, Margarethe Hardegger — over sexuality and the ‘new science’ of psychoanalysis. At stake in the dispute are questions that continue to haunt anarchist thought and practice in the 21st century: What ‘forms’ can and ought libertarian sexual culture take? What constitutes a libertarian politics of marriage and the family? Does psychoanalysis constitute a complement to the anarchist tradition, a crucial supplement to its logic, or a perilous substitute?
Radical refusals: On the anarchist politics of women choosing asexuality
Authors: Fahs Breanne
Published: September 2010

This article examines how women consciously choosing asexuality might inform both radical feminist politics and anarchic concepts of positive and negative liberty. By resituating some of the lesser-known narratives of the 1960s’ and 1970s’ radical feminist movement (e.g. Valerie Solanas’ SCUM Manifesto and Boston’s Cell 16 and No More Fun and Games), asexuality is shown to disrupt key intersections between sexuality and the state, particularly institutions that control reproduction, pleasure, and women’s bodies. Using interview data with Cell 16 members, content analysis of early radical feminist writings, and theoretical and historical analyses of separatism, the piece argues that, by removing themselves from sexuality, women can take a more anarchic stance against the entire institution of sex, thereby working toward more nihilistic, anti-reproduction, anti-family goals that severely disrupt commonly held assumptions about sex, gender, and power.
A life course perspective on fandom
Authors: Lee Harrington C. , Bielby Denise D.
Published: September 2010

In this article we explore a life course perspective on fandom, with particular emphasis on fandom and adult development. While there is growing interest in issues of age and aging within fan studies and within media studies more broadly, there is a tendency in this literature to discuss aging and the life course atheoretically, ignoring a rich body of scholarship in gerontology, sociology, psychology and human development that examines how lives unfold over time. Our goal in this manuscript is to make explicit what is typically rendered implicit in fan studies by drawing directly on life course perspectives to enrich our understanding of long-term and later-life fandom, and to suggest ways that fan studies might more fully account for fandom over time. This article thus synthesizes two bodies of literature that rarely inform one another: fan studies and life course scholarship.
Hidden sights
Authors: Tegelberg Matthew
Published: September 2010

This article examines discourses of tourist location as articulated in the influential and highly successful travel guide Lonely Planet Cambodia . The aim is to direct attention to discourses and representations in guidebooks and their influential role in emerging tourist markets such as Cambodia by accomplishing two central tasks. First, an investigation of the discursive context within which Cambodia has been framed for more than a century reveals Lonely Planet Cambodia’s tendency to reproduce a problematic colonial discourse. Discourse analysis of examples from the guide demonstrates how this particular narrative continues to perpetuate a history of silencing local perspectives. These observations lead to a second line of argumentation. Despite Lonely Planet’s stated intention to promote a responsible and socially conscious mode of tourism, this agenda is contradicted by discursive practices that strategically avoid controversial issues. Instead, the guidebook relies on common tourist themes that are primarily concerned with producing an image of Cambodia that appeals to the Western traveller.
Othering, racial hierarchies and identity construction in Japanese television advertising
Authors: Prieler Michael
Published: September 2010

Although non-Japanese actors have appeared in Japanese television commercials for years, little systematic research has been conducted on them. Using a sample of 20,000 commercials, this article shows that the inclusion of ‘Others’ in TV commercials conforms to an artificial ‘racial hierarchy’ that mirrors Japanese society’s perception of racial groups. White people appear more often than all other groups combined, are represented through discernible stereotypes and advertise nearly all product categories. By contrast, blacks and non-Japanese Asians are associated with a narrower range. The former appear as musicians and athletes; the latter are either famous celebrities or associated with products from their countries of origin. These ‘Others’ are often stereotyped in ways that differentiate them from Japanese. Overall, this article provides insight into the attitudes of the Japanese toward ‘Others’, contributing both to the long-standing discourse of Japanese exceptionalism ( nihonjinron) and the understanding of Japanese society in a globalizing world.
Un/knowing and the practice of ethnography
Authors: Mimica Jadran
Published: September 2010

Framed by a critical take on the anthropological use of Western epistemological and cosmo-ontological notions, this article explores their applications to different cultural life-worlds that anthropologists explore and write about. I assess the inadequacy of this enterprise and offer a constructive corrective based on a positive and critical anthropological appreciation and appropriation of Western intellectual tradition. More specifically, this is carried out by means of the phenomenologically grounded considerations of the history of Western philosophy, theology and religiosity. My exercise is primarily motivated by my pursuit of the interpretation of the originality of the cosmo-ontological dimensions constitutive of New Guinea life-worlds, the region where I have done long-term field research. Accordingly, although I will primarily draw on ethnographies from New Guinea, relevant examples from other parts of the world are also used. As for the critical epistemological problematics of the article, it is relevant for anthropology’s universal and ongoing constructive self-elucidation and transformation.
Researching Reflexivity: Negotiating Identity and Ambiguity in a Cross-Cultural Research Project
Authors: Hill Peter S. , Lee Vanessa , Jennaway Megan
Published: September 2010

This article examines a multidisciplinary, ethnically diverse team of researchers and their relationship with the research in which they were engaged: a study of overseas trained doctors (OTDs) recruited to work in health services in Aboriginal and Torres Strait Islander communities across four Australian states. The reflexive analysis presented in this article is based on interviews of 13 of the 15 researchers engaged in that project, examining the ways in which the researchers construct their own identities in relation to the research and the commonalities and differences evident within and between clusters of researchers based on their own social and cultural backgrounds and migration histories. The analysis also identifies ways in which discourses emerging from this analysis influence further engagement with the research process itself and the findings of that research by making explicit the assumptions underlying qualitative observations and insights.
Increasing Response Rates and the Consequences in the Dutch Parliamentary Election Study 2006
Authors: Schmeets Hans
Published: September 2010

This article deals with specific measures to enhance response rates in the Dutch Parliamentary Election Study (DPES) conducted around the elections on November 22, 2006. It demonstrates that a specific fieldwork strategy, including new advance letters, incentives, interviewer training sessions, and a reapproach of noncontacts and refusals, resulted in a response rate of 72% (first wave) and 64% (second wave). Moreover, the distributions of party choice in the DPES fit perfectly with the official election results. However, the 93.1% reported turnout is substantially higher than the official 80.1% turnout figure. Five percent of the 13% gap in reported and official turnout in the DPES is assigned to stimulus effects and the remaining 8% to a mixture of nonresponse bias and social desirability effects.
Femoral Profunda Artery Aneurysm as an Unusual First Presentation of Behcet Disease
Authors: O'Leary Elizabeth A. , Sabahi Iraj , Ricotta John J. , Walitt Brian , Akbari Cameron M.
Published: September 2010

Behcet disease is a multisystem inflammatory disorder, rarely found in African Americans. Arterial involvement occurs in less than 8% of patients. Profunda femoral artery aneurysms (PFAAs) are extremely rare and often occur with synchronous aneurysms. We present a case of an African American man diagnosed with Behcet disease from his presentation with PFAA. He was also found to have a synchronous hypogastric artery aneurysm. The patient was immediately treated with corticosteroids and infliximab to control systemic and vascular inflammation, returning 1 month later for surgery. He had a repair of the left PFAA with a common femoral to profunda femoris artery bypass with reversed saphenous vein graft and aneurysmorrhaphy. When a patient presents with an aneurysm in an unusual location, it is important to evaluate for other aneurysms. A careful history and physical examination is also required to see if the aneurysm may be part of an underlying systemic syndrome.
Eversion Endarterectomy for External Iliac Artery Occlusive Disease
Authors: Donohoe C.L. , Dowdall J.F. , McDonnell C.O. , O'Malley M.K. , O'Donohoe M.K.
Published: September 2010

Introduction: The advent of effective endovascular techniques has revolutionized the treatment of iliac occlusive disease. Long-segment iliac occlusions remain technically difficult to treat, particularly in the presence of femoral disease. Iliac endarterectomy is an established procedure for the treatment of iliac occlusive disease, but it has been suggested that in the era of effective endovascular intervention, its role is limited. Methods: A review of all patients who had eversion endarterectomy of the external iliac artery from a single institution between 2000 and 2008. Results: Twenty-one patients (18 male) underwent eversion external iliac endarterectomy, 15 for external iliac and 6 for iliofemoral disease. Mean age was 64.7 years (range: 46-78 years) and the modal American Society of Anaesthesiologists (ASA) grade was 3. The indications were critical ischemia (n = 16) and disabling claudication (n = 5). Twelve had adjunctive procedures. The mean follow-up was 25.3 months (range: 1-59 months). There were no technical failures. Seventeen patients had significant improvement in symptoms and three had moderate improvement. The cumulative primary patency at 1 year was 81%. One patient had no improvement (because of infrainguinal occlusive disease), and subsequently required femoro-popliteal bypass. There was no systemic morbidity within 30 days. There was 1 in-hospital death from sudden cardiac arrest (47 days postoperatively). Six patients died during follow-up (from unrelated illness). Conclusion: Eversion external iliac endarterectomy is an effective means of treating iliofemoral occlusive disease with excellent short-term outcomes and a low complication rate in a cohort with high levels of comorbidity.
Cost-Effective Diagnostic Strategies in Patients With a High, Intermediate, or Low Clinical Probability of Pulmonary Embolism
Authors: Lee Jung-Ah , Zierler Brenda K. , Liu Chuan-Fen , Chapko Michael K.
Published: September 2010

Rapid quantitative D-dimer assays (DD), lower extremity venous duplex ultrasonography (US), and multislice computed tomographic (CT) angiography have been shown to have adequate sensitivities and specificities for diagnostic purpose. The purpose of this study was to evaluate cost-effectiveness of diagnostic strategies for pulmonary embolism (PE) in patients with a high, intermediate, or low clinical probability of PE. A formal cost-effectiveness analysis for the diagnosis of PE was performed. The main outcome measure for effectiveness was 3-month expected survival. The strategy of DD followed by CT was cost-effective and had the lowest cost per life saved for all patients suspected with PE. The conventional strategy including ventilation and perfusion lung scanning followed by pulmonary angiography (PA) or CT was not cost-effective. The leg US after CT was not also cost-effective. In clinical practice, the individual patient’s condition should be considered when choosing appropriate diagnostic tests.
Is Endovascular Stent-Graft Treatment of Primary Aortoesophageal Fistula Worthwhile?
Authors: Malas Mahmoud B. , Saha Surajit , Qazi Umair , Duncan Mark , Perler Bruce A. , Freischlag Julie A. , Veith Frank J.
Published: September 2010

Aortoesophageal fistula (AEF) as a result of prolonged nasogastric intubation is rare and certainly fatal, without prompt surgical intervention. We report the case of a 41-year-old man with morbid obesity who was admitted after suffering 55% of total body surface area burns. After several skin graft operations over the course of 12 weeks, he was rushed into surgery because of the acute onset of severe upper gastrointestinal bleeding. Exploratory laparotomy and esophagogastroduodenoscopy (EGD) suggested an AEF, which was then quickly confirmed by a diagnostic angiogram. An endovascular aortic stent graft repair was performed that successfully stopped the bleeding. We include a review of the literature pertaining to cases of AEF treated by endovascular surgery, which appears to be a promising alternative to open surgery in the unfit patient.
POEMFIELDs and the Materiality of the Computational Screen
Authors: Patterson Zabet
Published: September 2010

This article explores how the POEMFIELD series of computer animations, created by Stan VanDerBeek and Kenneth Knowlton between 1964—70, consciously mines a terrain between visibility and invisibility, drawing numbers and letters into cascades of representation simultaneously pictorial, linguistic and schematic. Skating the border of legibility, the animations exhibit a double vision of text and image, code and picture and, in so doing, work to figure a larger, epistemic question of computational visibility ‘at the close of the mechanical age’. The subtitle of the MoMA 1968 exhibition — ‘The Machine’ — marked the emergence of a computational model in which mechanical animation would no longer be visible to the human eye. The resulting crisis of visibility takes on a particular importance in light of the model of the ‘graphical user interface’ being explored at that time. In the POEMFIELD series, VanDerBeek and Knowlton attempt to convey both the complexity and the promise of this emerging paradigm of layered pictoriality, language and code.
Natalizumab in pediatric multiple sclerosis patients
Authors: Yeh E. Ann , Weinstock-Guttman Bianca
Published: September 2010

Pediatric multiple sclerosis (MS) comprises 2-5% of all cases of MS. Although first-line disease-modifying therapy (DMT) including interferons and glatiramer acetate appear to be well tolerated in this population, recent work has suggested that a growing number of children suffer from disease which is resistant to treatment with these therapies. Natalizumab is a therapy which, although associated with a 1 : 1000 risk for progressive multifocal leukoencephalopathy (PML), has been shown to be well tolerated in the adult population and may lead to disease remission in adults with highly active disease. Reports of use of this therapy in the pediatric population with highly active disease have been published. This paper reviews current experience with the use of natalizumab in the pediatric MS population, with attention to potential risks and possible long-term outcomes in this population.
An update on the treatment of Sydenham’s chorea: the evidence for established and evolving interventions
Authors: Walker Kathleen G. , Wilmshurst Jo M.
Published: September 2010

Over 320 years after Thomas Sydenham described the condition labelled Sydenham’s chorea, it remains poorly understood. The disorder is an antineuronal antibody-mediated neuropsychiatric disorder caused by a poststreptococcal, autoimmune condition affecting control of movement, mood, behaviour and potentially the heart. The treatment remains empirical, and is less than optimal. There are few large clinically controlled trials. Recommendations for optimal management remain inconsistent and are hampered by the side effects from pharmacotherapy. Care for patients should be targeted at primary treatment (penicillin and bed rest), secondary palliation (symptomatic medication) and supportive (social) care. Small studies have demonstrated trends to support the use of immunoglobulins and steroids as therapeutic interventions for children affected by Sydenham’s chorea.
Giant Choledochal Cyst as a Differential Diagnosis for Hepatic Cyst
Authors: Ferreira de Souza Luis Ronan Marquez , Pascoal Gianne , Marques Cappellari Pietro Franchon , Saldanha Cardoso Mateus , Franco Lacerda Croider , Crema Eduardo
Published: September 2010

Choledochal cysts are rare congenital anomalies of the biliary tract characterized by dilation of the biliary tree. Most cases are diagnosed during the first decade of life, whereas only 20% are diagnosed in adulthood. They present as a classic trio: abdominal pain, jaundice, and a tangible mass. The mass is identified in just one-third of the cases. This case presents a patient with the trio, with a painful palpable mass of 15 cm in the epigastrium and right hypochondrium. Sonography and computed tomography were performed initially and suggested that this was a case of a hepatic cyst. However, magnetic resonance cholangiography was decisive in diagnosing this as a case of giant choledochal cyst (Todani I), which was confirmed by anatomopathology.
Persistent Extrahepatic Right Umbilical Vein
Authors: Javer Noorie
Published: September 2010

Persistent right umbilical vein (PRUV) is a vascular pathology in which the left umbilical vein becomes occluded while the right umbilical vein persists and remains open. When observing fetal anatomy during a routine 18-week scan, it is important to notice the direction of the vasculature for possible fetal anomalies such as PRUV. In this case, a full detailed sonogram of the fetus was conducted and an extrahepatic PRUV was observed using 2D imaging and further confirmed using color Doppler to identify the type of PRUV. Following the identification of the PRUV, the fetus was thoroughly assessed for the possibility of other associated anomalies. Clearly, when an anomaly is observed, it is crucial to assess the fetus for associated congenital variances to identify risk and potential outcome.
Ewing Sarcoma Family of Tumors
Authors: Puchalski Amy
Published: September 2010

The diagnosis and management of Ewing sarcoma is laborious and requires the correlation of multiple imaging modalities. This is an aggressive, malignant tumor of bone and soft tissue. Ewing sarcoma rarely affects individuals older than 20 years of age. Clinical symptoms are variable and nonspecific. Biopsy is the only definitive diagnosis. Multimodality medical imaging plays a great role in visualizing the tumor, documenting metastatic spread, tumor staging, associated complications, and response to therapy. Standard treatment of Ewing sarcoma is a multimodal therapeutic regimen, including chemotherapy, surgery, and radiation. Prognosis depends on tumor location, presence of metastases, and tumor size.
Comparison of carbonitriding and nitrocarburising on size and shape distortion of plain carbon SAE 1010 steel
Authors: Campagna V , Bowers R , Northwood D O , Sun X C , Bauerle P
Published: September 2010

Carbonitriding is a widely accepted method of heat treatment used by North American manufacturers for plain carbon steel. While the process imparts a hard, wear resistant case, it is also associated with both size and shape distortion, which can be problematic for components in tight fitting assemblies. This research compares the effects of the carbonitriding and nitrocarburising processes on SAE 1010 steel with respect to residual stress and distortion. Results indicate that the two processes develop residual compressive stresses and are associated with both size and shape distortion. Although the magnitude of the compressive stresses in nitrocarburised steels is lower, this process was noted to give rise to overall smaller dimensional changes than the carbonitriding process. The findings from this study are applied to a manufacturing application involving the surface treatment of a thin shelled automotive component in a light loading application.
During EPO or anemia challenge, erythroid progenitor cells transit through a selectively expandable proerythroblast pool
Authors: Dev Arvind , Fang Jing , Sathyanarayana Pradeep , Pradeep Anamika , Emerson Christine , Wojchowski Don M.
Published: September 2010

Investigations of bone marrow (BM) erythroblast development are important for clinical concerns but are hindered by progenitor cell and tissue availability. We therefore sought to more specifically define dynamics, and key regulators, of the formation of developing BM erythroid cell cohorts. A unique Kit−CD71highTer119− “stage E2” proerythroblast pool first is described, which (unlike its Kit+ “stage E1” progenitors, or maturing Ter119+ “stage E3” progeny) proved to selectively expand ∼ 7-fold on erythropoietin challenge. During short-term BM transplantation, stage E2 proerythroblasts additionally proved to be a predominantly expanded progenitor pool within spleen. This E1→E2→E3 erythroid series reproducibly formed ex vivo, enabling further characterizations. Expansion, in part, involved E1 cell hyperproliferation together with rapid E2 conversion plus E2 stage restricted BCL2 expression. Possible erythropoietin/erythropoietin receptor proerythroblast stage specific events were further investigated in mice expressing minimal erythropoietin receptor alleles. For a hypomorphic erythropoietin receptor-HM allele, major defects in erythroblast development occurred selectively at stage E2. In addition, stage E2 cells proved to interact productively with primary BM stromal cells in ways that enhanced both survival and late-stage development. Overall, findings reveal a novel transitional proerythroblast compartment that deploys unique expansion devices.
Prospective assessment of thrombin generation test for dose monitoring of bypassing therapy in hemophilia patients with inhibitors undergoing elective surgery
Authors: Dargaud Yesim , Lienhart Anne , Negrier Claude
Published: September 2010

Clinical response to bypassing agents (BPAs) may vary between patients. Surgery is a particular situation, requiring effective hemostasis during the procedure and for several days postoperatively to obtain satisfactory wound healing. However, the optimal dose of BPA in different surgical situations has not been clearly established. We report here a prospective assessment of thrombin generation test (TGT) in monitoring the effectiveness of BPA during 10 elective invasive procedures performed in 6 patients with severe hemophilia and high-titer inhibitors. A standardized 3-step protocol was used in all cases to individually tailor BPA. Thrombin-generating capacity of patients increased after in vitro and ex vivo addition of BPA in a dose-dependent manner. Our results also showed a correlation between in vivo clinical response to BPA and thrombin-generating capacity. These data suggest that TGT may represent a surrogate marker for monitoring bypassing therapies in surgical situations.
Leukemia-initiating cells in human T-lymphoblastic leukemia exhibit glucocorticoid resistance
Authors: Chiu Priscilla P. L. , Jiang Hong , Dick John E.
Published: September 2010

T-cell acute lymphoblastic leukemia (T-ALL) is associated with a significant risk of disease relapse, but the biological basis for relapse is poorly understood. Here, we identify leukemiainitiating cells (L-ICs) on the basis of functional assays and prospective isolation and report a role for L-ICs in T-ALL disease and relapse. Long-term proliferation in response to NOTCH1 activating signals in OP9-DL1 coculture system or capacity to initiate leukemia in xenografts by the CD7+CD1a− subset of primary T-ALL samples was superior to other subsets, refining the identity of T-ALL L-ICs. T-ALL engraftment was improved in nonobese diabetic/severe combined immunodeficiency (NOD/scid)IL2Rγnull (NSG) mice compared with NOD/scid with anti-CD122 treatment (NS122), but both showed changes in leukemia immunophenotype. Clonal analysis of xenografts using the TCRG locus revealed the presence of subclones of T-ALL L-ICs, some of which possess a selective growth advantage and correlated with the capacity of CD7+CD1a+ xenograft cells to engraft secondary NSG mice. Treatment of high-risk T-ALL xenografts eliminated CD1a+ T-ALL cells, but CD1a− cells were resistant and their number was increased. Our results establish that primary CD1a− T-ALL cells are functionally distinct from CD1a+ cells and that the CD7+CD1a− subset is enriched for L-IC activity that may be involved in mediating disease relapse after therapy.
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome
Authors: Asbury Thomas M , Mitman Matt , Tang Jijun , Zheng W Jim
Published: September 2010

Background

New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

Results

We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration.

Conclusions

Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome.
Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
Authors: Wong Emily HM , Smith David K , Rabadan Raul , Peiris Malik , Poon Leo LM
Published: September 2010

Background

The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.

Results

Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus.

Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes.

Conclusions

Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.
Multi-targeted priming for genome-wide gene expression assays
Authors: Adomas Aleksandra B , Lopez-Giraldez Francesc , Clark Travis A , Wang Zheng , Townsend Jeffrey P
Published: September 2010

Background

Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays.

Results

We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of Saccharomyces cerevisiae and Neurospora crassa while avoiding priming ribosomal RNA or transfer RNA. Examining the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression.

Conclusions

Our results provide the most complete and detailed expression profiles of the yeast nitrogen starvation response and N. crassa early sexual development to date. Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome.
Cyst formation in the PKD2 (1-703) transgenic rat precedes deregulation of proliferation-related pathways
Authors: Koupepidou Panayiota , Felekkis Kyriacos N , Kränzlin Bettina , Sticht Carsten , Gretz Norbert , Deltas Constantinos
Published: September 2010

Background

Polycystic Kidney Disease is characterized by the formation of large fluid-filled cysts that eventually destroy the renal parenchyma leading to end-stage renal failure. Although remarkable progress has been made in understanding the pathologic mechanism of the disease, the precise orchestration of the early events leading to cyst formation is still unclear. Abnormal cellular proliferation was traditionally considered to be one of the primary irregularities leading to cyst initiation and growth. Consequently, many therapeutic interventions have focused on targeting this abnormal proliferation, and some have even progressed to clinical trials. However, the role of proliferation in cyst development was primarily examined at stages where cysts are already visible in the kidneys and therefore at later stages of disease development.

Methods

In this study we focused on the cystic phenotype since birth in an attempt to clarify the temporal contribution of cellular proliferation in cyst development. Using a PKD2 transgenic rat model (PKD2 (1-703)) of different ages (0-60 days after birth) we performed gene expression profiling and phenotype analysis by measuring various kidney parameters.

Results

Phenotype analysis demonstrated that renal cysts appear immediately after birth in the PKD2 transgenic rat model (PKD2 (1-703)). On the other hand, abnormal proliferation occurs at later stages of the disease as identified by gene expression profiling. Interestingly, other pathways appear to be deregulated at early stages of the disease in this PKD model. Specifically, gene expression analysis demonstrated that at day 0 the RAS system is involved. This is altered at day 6, when Wnt signaling and focal adhesion pathways are affected. However, at and after 24 days, proliferation, apoptosis, altered ECM signaling and many other factors become involved.

Conclusions

Our data suggest that cystogenesis precedes deregulation of proliferation-related pathways, suggesting that proliferation abnormalities may contribute in cyst growth rather than cyst formation.
Side effects of chaperone gene co-expression in recombinant protein production
Authors: Martínez-Alonso Mónica , García-Fruitós Elena , Ferrer-Miralles Neus , Rinas Ursula , Villaverde Antonio
Published: September 2010

Insufficient availability of molecular chaperones is observed as a major bottleneck for proper protein folding in recombinant protein production. Therefore, co-production of selected sets of cell chaperones along with foreign polypeptides is a common approach to increase the yield of properly folded, recombinant proteins in bacterial cell factories. However, unbalanced amounts of folding modulators handling folding-reluctant protein species might instead trigger undesired proteolytic activities, detrimental regarding recombinant protein stability, quality and yield. This minireview summarizes the most recent observations of chaperone-linked negative side effects, mostly focusing on DnaK and GroEL sets, when using these proteins as folding assistant agents. These events are discussed in the context of the complexity of the cell quality network and the consequent intricacy of the physiological responses triggered by protein misfolding.
Penta-O-galloyl-β-D-glucose induces G1arrest and DNA replicative S-phase arrest independently of P21 cyclin-dependent kinase inhibitor 1A, P27 cyclin-dependent kinase inhibitor 1B and P53 in human breast cancer cells and is orally active against triple-negative xenograft growth
Authors: Chai Yubo , Lee Hyo-Jeong , Shaik Ahmad Ali , Nkhata Katai , Xing Chengguo , Zhang Jinhui , Jeong Soo-Jin , Kim Sung-Hoon , Lü Junxuan
Published: September 2010

Introduction

Natural herbal compounds with novel actions different from existing breast cancer (BCa) treatment modalities are attractive for improving therapeutic efficacy and safety. We have recently shown that penta-1,2,3,4,6-O-galloyl-β-D-glucose (PGG) induced S-phase arrest in prostate cancer (PCa) cells through inhibiting DNA replicative synthesis and G1 arrest, in addition to inducing cell death at higher levels of exposure. We and others have shown that PGG through intraperitoneal (i.p.) injection exerts a strong in vivo growth suppression of human PCa xenograft models in athymic nude mice. This study aims to test the hypothesis that the novel targeting actions of PGG are applicable to BCa cells, especially those lacking proven drugable targets.

Methods

Mono-layer cell culture models of p53-wild type estrogen receptor (ER)-dependent MCF-7 BCa cells and p53-mutant ER-/progesterone receptor (PR)- and Her2-regular (triple-negative) MDA-MB-231 BCa were exposed to PGG for a comprehensive investigation of cellular consequences and molecular targets/mediators. To test the in vivo efficacy, female athymic mice inoculated with MDA-MB-231 xenograft were treated with 20 mg PGG/kg body weight by daily gavage starting 4 days after cancer cell inoculation.

Results

Exposure to PGG induced S-phase arrest in both cell lines as indicated by the lack of 5-bromo2'-deoxy-uridine (BrdU) incorporation into S-phase cells as well as G1 arrest. Higher levels of PGG induced more caspase-mediated apoptosis in MCF-7, in strong association with induction of P53 Ser15 phosphorylation, than in MDA-MB-231 cells. The cell cycle arrests were achieved without an induction of cyclin dependent kinase (CDK) inhibitory proteins P21Cip1 and P27Kip1. PGG treatment led to decreased cyclin D1 in both cell lines and over-expressing cyclin D1 attenuated G1 arrest and hastened S arrest. In serum-starvation synchronized MCF-7 cells, down-regulation of cyclin D1 was associated with de-phosphorylation of retinoblastoma (Rb) protein by PGG shortly before G1-S transition. In vivo, oral administration of PGG led to a greater than 60% inhibition of MDA-MB231 xenograft growth without adverse effect on host body weight.

Conclusions

Our in vitro and in vivo data support PGG as a potential drug candidate for breast cancer with novel targeting actions, especially for a triple negative BCa xenograft model.
Reevaluation of Quantitative ESR Spin Trapping Analysis of Hydroxyl Radical by Applying Sonolysis of Water as a Model System
Authors: Nakamura Keisuke , Kanno Taro , Ikai Hiroyo , Sato Emiko , Mokudai Takayuki , Niwano Yoshimi , Ozawa Toshihiko , Kohno Masahiro
Published: September 2010

Electron spin resonance (ESR) spin trapping using 5,5-dimethyl-1-pyrroline N-oxide (DMPO) is commonly applied for quantitative analysis of hydroxyl radical. For better understanding of the analysis, we investigated kinetics related to formation and decay of hydroxyl radical spin adduct of DMPO compared with that of 3,3,5,5-tetramethyl-1-pyrroline N-oxide (M4PO) and 5-(diphenylphosphinoyl)-5-methyl-1-pyrroline N-oxide (DPPMPO). In our study where hydroxyl radical was generated by sonolysis of water, we found that (1) DMPO-OH formation was saturated even though hydroxyl radical was generated continuously and (2) the concentration of DMPO-OH decreased in inverse proportion to time after cessation of ultrasound irradiation, suggesting that the decay is a second-order reaction. Similar results were obtained in an experiment of DMPO-OH generated by photolysis of H2O2. Other than DMPO, M4PO, and DPPMPO also trapped hydroxyl radical but the spin trap efficiency was less than that of DMPO. Furthermore, M4PO-OH and DPPMPO-OH decayed more quickly than DMPO-OH. From this, we conclude that DMPO is more suitable for quantification of hydroxyl radical than M4PO and DPPMPO but results from the quantitative analysis must be interpreted with consideration of the kinetics related to formation and decay of DMPO-OH, especially in quantification of large amount of hydroxyl radical generation.
Synthesis, Characterization, and Catalytic Properties of Hollow γ-Fe2O3 Spheres toward Liquid-Phase Oxidation Using Hydrogen Peroxide
Authors: Mori Kohsuke , Tanimura Isamu , Yamashita Hiromi
Published: September 2010

Hollow γ-Fe2O3 nanospheres were synthesized using carboxylated polystyrene spheres as a core template by thermal treatment followed by calcination. The obtained material was characterized by FT-IR, N2 adsorption–desorption, TEM, XRD, and Fe K-edge XAFS measurements. The size of the hollow γ-Fe2O3 nanospheres were about 400–500 nm, which was assembled from primary particles with a size of approximately 10–20 nm. The phase transition of the composed particles from magnetite (Fe3O4) to maghemite (γ-Fe2O3) was identified after calcination in the presence of O2 at relatively low temperature. The hollow γ-Fe2O3 acted as an efficient heterogeneous catalyst for the liquid-phase selective oxidation of 1-phenylethanol using hydrogen peroxide (H2O2) as an oxidant. It exhibited enhanced catalytic activity compared to its bulk counterpart and also showed higher selectivity than nanosized γ-Fe2O3. Recovery of the hollow γ-Fe2O3 nanospheres from the reaction mixture could be attained by applying an external permanent magnet, and the spent catalyst could be recycled without any appreciable loss of its inherent catalytic ability.
Serum Pattern Profiling for Analyzing Different Types of Stress by Protein Chip Technology: A Preliminary Study
Authors: Liu Hui , Hou Diandong , Wu Da , Yin Hong , Wu Xiaoyi
Published: September 2010

ProteinChip is a widely accepted tool for exploring serum pattern profile to evaluate the risk of somatic diseases from different stressors. In this study, by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-ToF), the serum proteomes from mice under restraint and thermal stresses were profiled in detail and compared with the control group. Around 150 characteristic peaks were detected in all three groups, with m/z ranging from 1500 to 50,000, with most peaks being within the 2000 m/z to 20,000 m/z range. Compared with the control group, three significant protein peaks with m/z values of 2780, 3303 and 3450 appeared specifically in the restrained stress group and four other peaks with m/z values of 7500, 7811, 29,950 and 38,565 in the thermal stress group. Unexpectedly, no universal positive stress peaks were detected. These preliminary results clearly suggested that there might not be a common mechanism shared by various psychophysiological disorders under different stressors. By fast serum proteomics profiling, SELDI-ToF may be a convenient tool for evaluating the risk of stress-induced illness.
Comparative Analyses of Different Surfactants on Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Peptide Analysis
Authors: Mandal Santi M. , Dey Satyahari , Mandal Mahitosh , Maria-Neto Simone , Franco Octavio L.
Published: September 2010

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been extensively used for proteomics and peptidomics analysis. Nevertheless, these analyses, when focused on low molecular mass proteins, show some limitation due to background interference from surfactant ions. Surfactants are routinely used as a solubilizing or denaturing agents for proteins and peptides. In this report, an evaluation and further comparison of the effects of an ionic surfactant, sodium dodecyl sulfate (SDS), and a non-ionic surfactant, tergitol, on MALDI-MS analyses of the amphipathic peptides, angiotensin and bradykinin, were carried out. At concentrations ⩾ 10 mmol L−1, SDS deteriorates the MALDI spectral quality by reducing the signal and intensity of the analyte ions. In particular, it affects the hydrophobic peptide where the signal of surfactant-interfering ions suppresses the analyte ion signal. Whereas, the non-ionic surfactant, tergitol, improves the MALDI-MS analysis of peptide mixtures or hydrophobic peptides by reducing interference from the surfactant itself in positive ion mode analysis. Three-dimensional molecular modeling of two different peptides in complex to tergitol NP-40 and SDS were conducted in order to explain the molecular effects of both agents. In summary, while SDS must be removed from the sample solution to avoid interference of ions from SDS and suppression of analyte ion signal, tergitol at low concentrations may be used as an additive with sample solution for MALDI-MS analysis of peptides. Finally, molecular modeling analyses associated with docking were used in order to explain experimental biochemical data.