bluuebunny/crossref_metadata_2025 huggingface dataset:
S-Phase and M-Phase Timing Are under Independent Circadian Control in the Dinoflagellate Lingulodinium
Authors: Dagenais-Bellefeuille Steve , Bertomeu Thierry , Morse David
Published: October 2008

In many phytoplankton species, cell division (mitosis) usually occurs at defined times of day. This timing is also observed under constant conditions, indicating that it is regulated by a circadian clock rather than by a simple response to the light-dark cycle. For those algae with cell cycles longer than a day, the clock opens a window of opportunity for mitosis at a particular time of day through which cells in an appropriate phase of the cell cycle can pass. Although the timing of mitosis is generally studied due to ease of measurement, for some phytoplankton the timing of S-phase is also circadian. This thus raises the possibility that mitosis is not directly gated by the clock but occurs instead at a defined interval (a constant G2 length) following a circadian controlled S-phase. To determine if the clock exercises independent control over the timing of both S- and M-phase, we measured the timing of both S- and M-phase in cultures of the dinoflagellate Lingulodinium grown under a variety of different photoperiods. We interpret the phase angles of both rhythms, in particular those resulting in a change in the length of G2, as an indication that the clock independently regulates the timing of S-phase and mitosis.
Pigment-Dispersing Factor (PDF) Has Different Effects on Drosophila's Circadian Clocks in the Accessory Medulla and in the Dorsal Brain
Authors: Wülbeck Corinna , Grieshaber Eva , Helfrich-Förster Charlotte
Published: October 2008

The neuropeptide pigment-dispersing factor (PDF) is a key transmitter in the circadian clock of Drosophila melanogaster. Here we studied the rhythmic behavior of neural mutants with modified arborizations of the large PDF neurons. In sine oculis1 ( so1) mutants we found a higher density of PDF fibers in the fly's pacemaker center, the accessory medulla. These flies exhibited a significantly longer period (24.6 h) than control flies. When PDF levels were elevated to very high levels in the dorsal brain as true for somda mutants and small optic lobes;so1 double mutants ( sol1;so 1), a short-period component split off the long period in behavioral rhythmicity. The short period became shorter the higher the amount of PDF in this brain region and reached a value of ~21 h. The period alterations were clearly dependent on PDF, because so1;Pdf 01 and somda;Pdf 01 double mutants showed a single free-running component with a period similar to Pdf 01 mutants (~22.5 h) and significantly longer than the short period of somda mutants. These observations indicate that PDF feeds back on the clock neurons and changes their period. Obviously, PDF lengthens the period of some clock neurons and shortens that of others.
Maternal Photoperiodic History Affects Offspring Development in Syrian Hamsters
Authors: Beery Annaliese K. , Paul Matthew J. , Routman David M. , Zucker Irving
Published: October 2008

During the first 7 weeks of postnatal life, short day lengths inhibit the onset of puberty in many photoperiodic rodents, but not in Syrian hamsters. In this species, timing of puberty and fecundity are independent of the early postnatal photoperiod. Gestational day length affects postnatal reproductive development in several rodents; its role in Syrian hamsters has not been assessed. We tested the hypothesis that cumulative effects of pre- and postnatal short day lengths would restrain gonadal development in male Syrian hamsters. Males with prenatal short day exposure were generated by dams transferred to short day lengths 6 weeks, 3 weeks, and 0 weeks prior to mating. Additional groups were gestated in long day lengths and transferred to short days at birth, at 4 weeks of age, or not transferred (control hamsters). In pups of dams exposed to short day treatment throughout gestation, decreased testis growth was apparent by 3 weeks and persisted through 9 weeks of age, at which time maximum testis size was attained. A subset of males (14%), whose dams had been in short days for 3 to 6 weeks prior to mating displayed pronounced delays in testicular development, similar to those of other photoperiodic rodents. This treatment also increased the percentage of male offspring that underwent little or no gonadal regression postnatally (39%). By 19 weeks of age, males housed in short days completed spontaneous gonadal development. After prolonged long day treatment to break refractoriness, hamsters that initially were classified as nonregressors underwent testicular regression in response to a 2nd sequence of short day lengths. The combined action of prenatal and early postnatal short day lengths diminishes testicular growth of prepubertal Syrian hamsters no later than the 3rd week of postnatal life, albeit to a lesser extent than in other photoperiodic rodents.
Absence of Long-Wavelength Photic Potentiation of Murine Intrinsically Photosensitive Retinal Ganglion Cell Firing In Vitro
Authors: Mawad Kareem , Van Gelder Russell N.
Published: October 2008

Melanopsin is an opsin-family photopigment required for photosensitivity of the intrinsically photosensitive retinal ganglion cells (ipRGCs), which subserve photic entrainment of circadian rhythms in mammals. The melanopsin photocycle is presently unknown but is independent of the enzymatic photocycle employed by rhodopsin and cone opsins. Recent experiments have demonstrated that red-light exposure potentiates circadian phase-shifting responses to blue-light stimuli, consistent with the hypothesis that melanopsin functions as a bistable photopigment. To further test this hypothesis, we analyzed ipRGC firing activity in response to 480-nm blue light with or without intervening long-wavelength 620-nm red-light stimulation, using in vitro multielectrode array recording of postnatal day 8 to 10 murine retina. Cell-firing responses to 480-nm light were highly reproducible. No significant potentiating or bleaching effect of intervening subthreshold 620-nm light on ipRGC firing to 480-nm light could be discerned. Further physiologic and biochemical analysis of the ipRGC photoreception is required to reconcile the presence of long-wavelength potentiation at the level of the SCN with its absence in light-induced ipRGC firing.
Sensitivity of the Human Circadian System to Short-Wavelength (420-nm) Light
Authors: Brainard George C. , Sliney David , Hanifin John P. , Glickman Gena , Byrne Brenda , Greeson Jeffrey M. , Jasser Samar , Gerner Edward , Rollag Mark D.
Published: October 2008

The circadian and neurobehavioral effects of light are primarily mediated by a retinal ganglion cell photoreceptor in the mammalian eye containing the photopigment melanopsin. Nine action spectrum studies using rodents, monkeys, and humans for these responses indicate peak sensitivities in the blue region of the visible spectrum ranging from 459 to 484 nm, with some disagreement in short-wavelength sensitivity of the spectrum. The aim of this work was to quantify the sensitivity of human volunteers to monochromatic 420-nm light for plasma melatonin suppression. Adult female ( n = 14) and male ( n = 12) subjects participated in 2 studies, each employing a within-subjects design. In a fluence-response study, subjects ( n = 8) were tested with 8 light irradiances at 420 nm ranging over a 4-log unit photon density range of 1010 to 1014 photons/cm 2/sec and 1 dark exposure control night. In the other study, subjects ( n = 18) completed an experiment comparing melatonin suppression with equal photon doses (1.21 × 1013 photons/cm2/sec) of 420 nm and 460 nm monochromatic light and a dark exposure control night. The first study demonstrated a clear fluence-response relationship between 420-nm light and melatonin suppression ( p < 0.001) with a half-saturation constant of 2.74 × 1011 photons/cm2/sec. The second study showed that 460-nm light is significantly stronger than 420-nm light for suppressing melatonin ( p < 0.04). Together, the results clarify the visible short-wavelength sensitivity of the human melatonin suppression action spectrum. This basic physiological finding may be useful for optimizing lighting for therapeutic and other applications.
Depression, Disability and Intermediate Pathways: A Review of Longitudinal Studies in Elders
Authors: Schillerstrom Jason E. , Royall Donald R. , Palmer Raymond F.
Published: October 2008

Cross-sectional studies demonstrate depression is associated with disability in elders. These studies also report that disability in depressed elders is associated with greater medical illness burden, cognitive impairment, and behavioral changes. Only longitudinal studies, however, can determine the impact of depression and its comorbidities on functional decline. This review summarizes the findings of 20 longitudinal studies examining the relationship between baseline or incident depression and functional decline. However, the mediational effects of potential risk factors identified by cross-sectional studies cannot be derived from the current literature. We propose a mediational effects model for future longitudinal studies, incorporating measures sensitive to both mood symptoms and the medical, cognitive, and behavioral comorbidities of depression to better understand the impact of each on functional decline and to focus future clinical interventions.
Persisting Burden Predicts Depressive Symptoms in Dementia Caregivers
Authors: Epstein-Lubow Gary , Davis Jennifer Duncan , Miller Ivan W. , Tremont Geoffrey
Published: October 2008

Dementia caregivers often report feeling burdened by caretaking responsibilities. Caregiver burden is correlated with caregiver depression, but the interrelationship between burden and depression requires further investigation. This study hypothesized that persisting elevated burden results in subsequent depressive symptoms. Participants were 33 dementia caregivers divided into two groups based on their Zarit Burden Interview score. The outcome variable was the total score on the Geriatric Depression Scale after 12 months. Caregivers who had persisting high burden showed significantly worse depression scores after 12 months compared to those caregivers without persisting high burden. Regression analysis controlling for baseline depression also demonstrated burden as a significant predictor of subsequent depression. These data suggest that longitudinal burden may be predictive of higher depressive symptoms; therefore, reducing burden could decrease depressive symptoms in dementia caregivers.
Reaction Times and Performance Variability in Normal Aging, Mild Cognitive Impairment, and Alzheimer's Disease
Authors: Gorus Ellen , De Raedt Rudi , Lambert Margareta , Lemper Jean-Claude , Mets Tony
Published: October 2008

This study evaluated whether reaction times (RT) and performance variability are potential markers for the early detection of Alzheimer's disease (AD). Cognitively healthy elderly (n = 218), persons with amnestic MCI (a-MCI) (n = 29) and patients with AD (n = 50) were examined with RT tasks with increasing complexity, subdividing RT into a decision and a movement component. Persons with cognitive deterioration demonstrated more intra-individual variability and more slowing than cognitively healthy elderly. The slowing in AD affects both the cognitive and the motor component, while performance variability mainly affects the cognitive component of the RT. Although in a-MCI not all differences reached statistical significance, primarily the cognitive component of the RT is affected in a-MCI. Intra-individual variability and RT of the complex tasks are the best predictors for a-MCI and AD status, respectively. We conclude that performance variability can be regarded as a useful preclinical marker for AD.
Management of Life-Threatening Hemorrhages and Unsafe Interventions in Nonhemophiliac Children by Recombinant Factor VIIa
Authors: Leblebisatan Göksel , Sasmaz Ilgen , Antmen Bulent , Yildizdas Dincer , Kilinc Yurdanur
Published: October 2008

The literature on the use of recombinant factor VIIa (rFVIIa), which was initially used in hemophiliac patients with inhibitors, for hemorrhages that cannot be managed with conventional methods or operations that cannot be performed safely is increasingly growing. This study presents a group of nonhemophiliac patients with hemorrhagic problems or hemorrhage risk for some interventions that were successfully resolved with the use of rFVIIa. The patient group was composed of 20 patients with different disorders resulting in similar results as hemorrhage or hemorrhage risk. Most of the patients were diagnosed with liver disorders primary or secondary to other diseases. The remaining cases were patients with leukemia, sepsis, intracranial hemorrhage, and burn. Some of the patients had multiple problems like a patient with liver disorder and intracranial hemorrhage or a leukemia patient with sepsis and disseminated intravascular coagulation. rFVIIa had been administered to the patients at dosages between 70 and 150 μg/kg up to 6 doses with 2-hour to 3-hour intervals. All the patients had benefited from the use of rFVIIa even though some of them died because of primary disease. This study shows that rFVIIa can be safely used in high-risk patients with a history of recurrent hemorrhage, for whom no improvement can be achieved in the hemostasis tests.
Protecting the Public Interest in Long-Term Concession Agreements for Transportation Infrastructure
Authors: Ortiz Iris N. , Buxbaum Jeffrey N.
Published: October 2008

Lack of cash has led virtually every U.S. state to explore innovative finance techniques that allow important improvement projects to move forward. Recent long-term concession agreements have inspired a debate over the merits and pitfalls of public—private partnerships (PPPs), particularly whether decision makers are considering and protecting the public interests. The concession approach has many advantages over traditional methods, but there are also many concerns. Very few people have a complete picture of the future implications of concessions. The public concerns include use of up-front payments, concession length, and noncompete clauses, among others. Many of these concerns are legacies from the past that have been rectified as both the public and private sectors have learned and adapted. This article summarizes public concerns related to concessions, describes how PPP procurements have evolved to respond to public reaction, and suggests key issues that need to be considered in the future.
New Veiling in Azerbaijan
Authors: Heyat Farideh
Published: October 2008

In the past few years, the growing presence of veiled women in Azerbaijan, particularly in the capital city, Baku, has been striking. This article traces the background to Islamism in Azerbaijan under the state dogma of atheism, and the post-Soviet changes that have facilitated a resurgence of religion in the country. It examines the motivations and the generational divide among women who have recently adopted veiling. Notions of `traditional' and `modern' are questioned here, pointing out the impact of identity politics and foreign Islamic forces on Azerbaijani society in today's increasingly globalized world. Furthermore, the article reveals the tensions and insecurities in the independent era that have reinforced the rise of Islamic ideology in the country and the contradictions involved in new veiling for Azeri women.
"What's the Footballer Doing Here?" Racialized Performativity, Reflexivity, and Identity
Authors: Carrington Ben
Published: October 2008

In this article I argue for the importance of ethnography and the efficacy of reflexive autobiography within sociological work in understanding the complexities of racial identity formation. I offer a rereading of some of my earlier research as a way to draw out some of the elisions embedded within that work. I suggest that understanding such moments of "silence," those passages where the ethnographic narrator disappears from view, are central and not marginal to any theorization of "race," culture, and identity. This is because such literary and symbolic suppressions point to both the ontological gaps within identity formation and subjectivity and the continuing shortfalls within our theorizing of those concepts. The article thus develops both an epistemological framework for a reflexive cultural studies/critical sociology of sport methodology that is sensitive to questions of racialization and an analysis of the conceptual problematics in thinking through the contingent nature and embodied performance of race. The article concludes by noting the limitations to the autobiographical turn and the use of reflexivity within ethnographic accounts such as those found within autoethnography. It is argued that although critical interpretive perspectives offer a needed correction to positivistic approaches founded on a naive objectivism, the production of subjectivity and the use of autobiography always need to be located within broader frameworks that map the historical forces and social formations that make (racial) identity possible.
Time to Try a Little Tenderness? The Detrimental Effects of Accountability When Coupled With Abusive Supervision
Authors: Breaux Denise M. , Perrewé Pamela L. , Hall Angela T. , Frink Dwight D. , Hochwarter Wayne A.
Published: October 2008

The deleterious health and behavioral consequences of reporting to an abusive supervisor have been documented in past research. Furthermore, recent corporate scandals have led to increased pressure to hold employees accountable for their behaviors and decisions at work. This study examines the interactive effects of abusive supervision on experienced relationships between accountability and work outcomes (job tension, job satisfaction, and emotional exhaustion), with a sample of 366 employees across a myriad of contexts and conditions for answerability. Specifically, it was hypothesized that high levels of perceived abuse would interact with accountability such that job satisfaction declines and tension and exhaustion escalate because of the control-depleting properties of abuse. Study results were supportive of these proposed relationships. Key contributions and limitations of the study, as well as directions for future research, are discussed.
A Grounded Theory of High-Quality Leadership Programs
Authors: Eich Darin
Published: October 2008

Drawing on the experiences and perspectives of multiple stakeholders closely associated with diverse types of successful student leadership programs, the purpose of this study was to identify the attributes of leadership programs—including the specific actions associated with these attributes—that contribute significantly to undergraduate student leadership development. A total of 62 interviews was conducted with individuals across the four programs in the sample. The researcher employed the constant comparative method to construct a grounded theory model. The theory of high-quality leadership programs developed in this study is grounded in those programmatic attributes that, when enacted, contribute significantly to enhancing student learning and leadership development. The data analysis revealed 16 attributes of high-quality leadership programs organized into three clusters: (a) participants engaged in building and sustaining a learning community; (b) student-centered experiential learning experiences; and (c) research-grounded continuous program development.
Building a Climate for Innovation Through Transformational Leadership and Organizational Culture
Authors: Sarros James C. , Cooper Brian K. , Santora Joseph C.
Published: October 2008

Research has called for organizations to be more flexible, adaptive, entrepreneurial, and innovative in meeting the changing demands of today's environment. Appropriate leadership to effect such change is required; however, there has been little empirical analysis of the theoretical relationships among the key components that make up such change strategy, including transformational leadership, organizational culture, and organizational innovation. This study examines these linkages in terms of their relationships with climate for organizational innovation in Australian private sector organizations. Structural equation modeling based on responses to a survey of 1,158 managers explores the relationship between transformational leadership and climate for organizational innovation and the extent to which a competitive, performance-oriented organizational culture mediates this relationship. Strategies for building innovative organizations are discussed.
SHD1 is a novel cytokine-inducible, negative feedback regulator of STAT5-dependent transcription
Authors: Nakajima Hideaki , Tamura Toshiki , Ito Miyuki , Shibata Fumi , Kuroda Kana , Fukuchi Yumi , Watanabe Naohide , Kitamura Toshio , Ikeda Yasuo , Handa Makoto
Published: October 2008

STAT5 is a critical mediator of a variety of cytokine signaling whose transcriptional activity is regulated by associating with various proteins. During a search for STAT5-interacting proteins, we identified SHD1, a mammalian homologue of yeast gene Sac3, as a potential interacter. SHD1 was localized in the nucleus, and induced by cytokines that activate STAT5, such as erythropoietin, interleukin-2 (IL-2), or IL-3. SHD1 interacted specifically with STAT5A and STAT5B, and interestingly, it specifically repressed STAT5-dependent transcription in vitro without affecting the stability or phosphorylation of STAT5 protein. Gene disruption study revealed that T, B, or bone marrow cells from mice lacking SHD1 were hyperresponsive to T-cell–receptor engagement, or stimulation with various STAT5-activating cytokines. These results suggest that SHD1 is a novel cytokine-inducible negative feedback regulator of STAT5.
The GPIIb/IIIa (integrin αIIbβ3) odyssey: a technology-driven saga of a receptor with twists, turns, and even a bend
Authors: Coller Barry S. , Shattil Sanford J.
Published: October 2008

Starting 90 years ago with a clinical description by Glanzmann of a bleeding disorder associated with a defect in platelet function, technologic advances helped investigators identify the defect as a mutation(s) in the integrin family receptor, αIIbβ3, which has the capacity to bind fibrinogen (and other ligands) and support platelet-platelet interactions (aggregation). The receptor's activation state was found to be under exquisite control, with activators, inhibitors, and elaborate inside-out signaling mechanisms controlling its conformation. Structural biology has produced high-resolution images defining the ligand binding site at the atomic level. Research on αIIbβ3 has been bidirectional, with basic insights resulting in improved Glanzmann thrombasthenia carrier detection and prenatal diagnosis, assays to identify single nucleotide polymorphisms responsible for alloimmune neonatal thrombocytopenia, and the development of αIIbβ3 antagonists, the first rationally designed antiplatelet agents, to prevent and treat thrombotic cardiovascular disease. The future looks equally bright, with the potential for improved drugs and the application of gene therapy and stem cell biology to address the genetic abnormalities. The αIIbβ3 saga serves as a paradigm of rigorous science growing out of careful clinical observations of a rare disorder yielding both important new scientific information and improved diagnosis, therapy, and prevention of other disorders.
A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukemia reveals genomic deletion, copy number neutral loss of heterozygosity, and association with specific cytogenetic subgroups
Authors: Sulong Sarina , Moorman Anthony V. , Irving Julie A. E. , Strefford Jonathan C. , Konn Zoe J. , Case Marian C. , Minto Lynne , Barber Kerry E. , Parker Helen , Wright Sarah L. , Stewart Adam R. M. , Bailey Simon , Bown Nick P. , Hall Andrew G. , Harrison Christine J.
Published: October 2008

Inactivation of the tumor suppressor gene, CDKN2A, can occur by deletion, methylation, or mutation. We assessed the principal mode of inactivation in childhood acute lymphoblastic leukemia (ALL) and frequency in biologically relevant subgroups. Mutation or methylation was rare, whereas genomic deletion occurred in 21% of B-cell precursor ALL and 50% of T-ALL patients. Single nucleotide polymorphism arrays revealed copy number neutral (CNN) loss of heterozygosity (LOH) in 8% of patients. Array-based comparative genomic hybridization demonstrated that the mean size of deletions was 14.8 Mb and biallelic deletions composed a large and small deletion (mean sizes, 23.3 Mb and 1.4 Mb). Among 86 patients, only 2 small deletions were below the resolution of detection by fluorescence in situ hybridization. Patients with high hyperdiploidy, ETV6-RUNX1, or 11q23/MLL rearrangements had low rates of deletion (11%, 15%, 13%), whereas patients with t(9;22), t(1;19), TLX3, or TLX1 rearrangements had higher frequencies (61%, 42%, 78%, and 89%). In conclusion, CDKN2A deletion is a significant secondary abnormality in childhood ALL strongly correlated with phenotype and genotype. The variation in the incidence of CDKN2A deletions by cytogenetic subgroup may explain its inconsistent association with outcome. CNN LOH without apparent CDKN2A inactivation suggests the presence of other relevant genes in this region.
A method for analyzing censored survival phenotype with gene expression data
Authors: Wu Tongtong , Sun Wei , Yuan Shinsheng , Chen Chun-Houh , Li Ker-Chau
Published: October 2008

Background

Survival time is an important clinical trait for many disease studies. Previous works have shown certain relationship between patients' gene expression profiles and survival time. However, due to the censoring effects of survival time and the high dimensionality of gene expression data, effective and unbiased selection of a gene expression signature to predict survival probabilities requires further study.

Method

We propose a method for an integrated study of survival time and gene expression. This method can be summarized as a two-step procedure: in the first step, a moderate number of genes are pre-selected using correlation or liquid association (LA). Imputation and transformation methods are employed for the correlation/LA calculation. In the second step, the dimension of the predictors is further reduced using the modified sliced inverse regression for censored data (censorSIR).

Results

The new method is tested via both simulated and real data. For the real data application, we employed a set of 295 breast cancer patients and found a linear combination of 22 gene expression profiles that are significantly correlated with patients' survival rate.

Conclusion

By an appropriate combination of feature selection and dimension reduction, we find a method of identifying gene expression signatures which is effective for survival prediction.
Improved generation of rat gene knockouts by target-selected mutagenesis in mismatch repair-deficient animals
Authors: van Boxtel Ruben , Toonen Pim W , Verheul Mark , van Roekel Henk S , Nijman Isaac J , Guryev Victor , Cuppen Edwin
Published: October 2008

Background

The laboratory rat (Rattus norvegicus) is one of the preferred model organisms in physiological and pharmacological research, although the availability of specific genetic models, especially gene knockouts, is limited. N-ethyl-N-nitrosourea (ENU)-driven target-selected mutagenesis is currently the most successful method in rats, although it is still very laborious and expensive.

Results

As ENU-induced DNA damage is normally recognized by the mismatch repair (MMR) system, we hypothesized that the effectiveness of the target-selected mutagenesis approach could be improved by using a MMR-deficient genetic background. Indeed, Msh6 knockout rats were found to be more sensitive to ENU treatment and the germ line mutation rate was boosted more than two-fold to 1 mutation per 585 kb. In addition, the molecular mutation spectrum was found to be changed in favor of generating knockout-type alleles by ~20%, resulting in an overall increase in efficiency of ~2.5 fold. The improved effectiveness was demonstrated by high throughput mutation discovery in 70 Mb of sequence in a set of only 310 mutant F1 rats. This resulted in the identification of 89 mutations of which four introduced a premature stopcodon and 64 resulted in amino acid changes.

Conclusion

Taken together, we show that the use of a MMR-deficient background considerably improves ENU-driven target-selected mutagenesis in the rat, thereby reducing animal use as well as screening costs. The use of a mismatch repair-deficient genetic background for improving mutagenesis and target-selected knockout efficiency is in principle applicable to any organism of interest.
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
Authors: Yu Jingkai , Pacifico Svetlana , Liu Guozhen , Finley Russell L
Published: October 2008

Background

Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster.

Description

DroID, the Drosophila Interactions Database, is a comprehensive interactions database designed specifically for Drosophila. DroID houses published physical protein interactions, genetic interactions, and computationally predicted interactions, including interologs based on data for other model organisms and humans. All interactions are annotated with original experimental data and source information. DroID can be searched and filtered based on interaction information or a comprehensive set of gene attributes from Flybase. DroID also contains gene expression and expression correlation data that can be searched and used to filter datasets, for example, to focus a study on sub-networks of co-expressed genes. To address the inherent noise in interaction data, DroID employs an updatable confidence scoring system that assigns a score to each physical interaction based on the likelihood that it represents a biologically significant link.

Conclusion

DroID is the most comprehensive interactions database available for Drosophila. To facilitate downstream analyses, interactions are annotated with original experimental information, gene expression data, and confidence scores. All data in DroID are freely available and can be searched, explored, and downloaded through three different interfaces, including a text based web site, a Java applet with dynamic graphing capabilities (IM Browser), and a Cytoscape plug-in. DroID is available at http://www.droidb.org.
High-resolution array CGH clarifies events occurring on 8p in carcinogenesis
Authors: Cooke Susanna L , Pole Jessica CM , Chin Suet-Feung , Ellis Ian O , Caldas Carlos , Edwards Paul AW
Published: October 2008

Background

Rearrangement of the short arm of chromosome 8 (8p) is very common in epithelial cancers such as breast cancer. Usually there is an unbalanced translocation breakpoint in 8p12 (29.7 Mb – 38.5 Mb) with loss of distal 8p, sometimes with proximal amplification of 8p11-12. Rearrangements in 8p11-12 have been investigated using high-resolution array CGH, but the first 30 Mb of 8p are less well characterised, although this region contains several proposed tumour suppressor genes.

Methods

We analysed the whole of 8p by array CGH at tiling-path BAC resolution in 32 breast and six pancreatic cancer cell lines. Regions of recurrent rearrangement distal to 8p12 were further characterised, using regional fosmid arrays. FISH, and quantitative RT-PCR on over 60 breast tumours validated the existence of similar events in primary material.

Results

We confirmed that 8p is usually lost up to at least 30 Mb, but a few lines showed focal loss or copy number steps within this region. Three regions showed rearrangements common to at least two cases: two regions of recurrent loss and one region of amplification. Loss within 8p23.3 (0 Mb – 2.2 Mb) was found in six cell lines. Of the genes always affected, ARHGEF10 showed a point mutation of the remaining normal copies in the DU4475 cell line. Deletions within 12.7 Mb – 19.1 Mb in 8p22, in two cases, affected TUSC3. A novel amplicon was found within 8p21.3 (19.1 Mb – 23.4 Mb) in two lines and one of 98 tumours.

Conclusion

The pattern of rearrangements seen on 8p may be a consequence of the high density of potential targets on this chromosome arm, and ARHGEF10 may be a new candidate tumour suppressor gene.
Kinematically equivalent velocity distributions
Authors: Stovas Alexey
Published: October 2008

For a layered medium, the seismic velocity model can be vertically heterogeneous within the layers. The traveltime parameters estimated from each reflection must be converted into layer traveltime parameters by using the layer-stripping method. The layer traveltime parameters must be inverted into layer velocity model parameters. Interpretation or inversion of layer traveltime parameters depends on the chosen velocity model within the layer. Different or kinematically equivalent velocity distributions can result in the same traveltime parameters. The inversion problem for traveltime parameters is strongly nonunique even if they are estimated accurately. To evaluate the accuracy of a velocity model, one can choose the phase for the two-way propagator. The discrepancy in this phase factor between the kinematically equivalent velocity models depends on the number of traveltime parameters estimated and increases with spatial frequency. By estimating two traveltime parameters, we approximately preserve the average velocity, regardless of the complexity of the vertically heterogeneous model. By estimating three traveltime parameters, we approximately preserve the average velocity gradient.
Data-driven tomographic velocity analysis in tilted transversely isotropic media: A 3D case history from the Canadian Foothills
Authors: Charles Sylvestre , Mitchell David R. , Holt Rob A. , Lin Jiwu , Mathewson John
Published: October 2008

We evaluated how velocity and anisotropy model-building strategies affect seismic imaging in the Canadian Foothills Thrust Belt by comparing the results of a model-driven approach with those of a data-driven approach. Two independently run Kirchhoff prestack depth-imaging projects were initiated using different static corrections for near-surface weathering layers and using different velocity and anisotropy model-building strategies. We observed that an isotropic data-driven reflection tomography velocity model-building approach resulted in a significantly better stack image than did a highly interpretive anisotropic model-driven velocity model-building approach. By carefully introducing anisotropy into the former, data-driven approach, we achieved significant improvements in positioning, including more accurate depth ties between the seismic image and well tops and better definition of structural geometries. The differences in the imaging observed at the various stages of this case history illustrate the sensitivity of the final depth images to the treatment of the near-surface velocity field, the macrointerval velocity model-building technique, and the choices of [Formula: see text] and [Formula: see text], which are the Thomsen anisotropy parameters for tilted transverse isotropy. The data-driven approach successfully challenged the historical idea that we must perform a geologic interpretation of the seismic data to derive an accurate depth velocity model in a complex geologic setting.
Anisotropic local tomography
Authors: Koren Zvi , Ravve Igor , Gonzalez Gladys , Kosloff Dan
Published: October 2008

Local tomography is interactive, ray-based, residual-interval-parameter analysis for updating background anisotropic velocity parameters. The method operates directly on image gathers generated by anisotropic curved-ray Kirchhoff time migration. A locally 1D, spatially varying, vertical transversely isotropic model is assumed. The background anisotropy parameters are the instantaneous (interval) vertical compression velocity [Formula: see text] and the two Thomsen anisotropy parameters, [Formula: see text] and [Formula: see text]. The interval velocity [Formula: see text] is updated from short-offset reflection events, and [Formula: see text] is updated from available long-offset data. The medium parameters are updated from the top down both vertically and by layers, one parameter at a time. The picked residual-anisotropy parameters correspond to the residual-moveout (RMO) curves that best fit the migrated reflection events. The method is based on splitting the contribution to the computed RMO at a given point into two parts: from overburden residual parameters and from the actual picked residual parameter. This approach allows for direct residual-interval-parameter analysis to be applied in the same way we perform the commonly used residual-effective-parameter analysis. The local tomography enables a controlled interactive estimation of the long-wavelength anisotropy parameters. The reliable anisotropy parameters estimated by the local approach are used as a background (guiding) model for a global tomography. This makes it possible to successfully apply a global constrained inversion that is performed simultaneously for all parameters of all output intervals using detailed RMO information.
Nonlinear 3D tomographic least-squares inversion of residual moveout in Kirchhoff prestack-depth-migration common-image gathers
Authors: Adler Frank , Baina Reda , Soudani Mohamed Amine , Cardon Pierre , Richard Jean-Baptiste
Published: October 2008

Velocity-model estimation with seismic reflection tomography is a nonlinear inverse problem. We present a new method for solving the nonlinear tomographic inverse problem using 3D prestack-depth-migrated reflections as the input data, i.e., our method requires that prestack depth migration (PSDM) be performed before tomography. The method is applicable to any type of seismic data acquisition that permits seismic imaging with Kirchhoff PSDM. A fundamental concept of the method is that we dissociate the possibly incorrect initial migration velocity model from the tomographic velocity model. We take the initial migration velocity model and the residual moveout in the associated PSDM common-image gathers as the reference data. This allows us to consider the migrated depth of the initial PSDM as the invariant observation for the tomographic inverse problem. We can therefore formulate the inverse problem within the general framework of inverse theory as a nonlinear least-squares data fitting between observed and modeled migrated depth. The modeled migrated depth is calculated by ray tracing in the tomographic model, followed by a finite-offset map migration in the initial migration model. The inverse problem is solved iteratively with a Gauss-Newton algorithm. We applied the method to a North Sea data set to build an anisotropic layer velocity model.
Recent applications of turning-ray tomography
Authors: Zhu Xianhuai , Valasek Paul , Roy Baishali , Shaw Simon , Howell Jack , Whitney Steve , Whitmore Norman Daniel , Anno Phil
Published: October 2008

Recent applications of 2D and 3D turning-ray tomography show that near-surface velocities are important for structural imaging and reservoir characterization. For structural imaging, we used turning-ray tomography to estimate the near-surface velocities for static corrections followed by prestack time migration and the near-surface velocities for prestack depth migration. Two-dimensional acoustic finite-difference modeling illustrates that wave-equation prestack depth migration is very sensitive to the near-surface velocities. Field data demonstrate that turning-ray tomography followed by prestack time migration helps to produce superior images in complex geologic settings. When the near-surface velocity model is integrated into a background velocity model for prestack depth migration, we find that wave propagation is very sensitive to the velocities immediately below the topography. For shallow-reservoir characterization, we developed and applied azimuthal turning-ray tomography to investigate observed apparent azimuthal-traveltime variations, using a wide-azimuth land seismic survey from a heavy-oil field at Surmont, Canada. We found that the apparent azimuthal velocity variations are not necessarily related to azimuthal anisotropy, or horizontal transverse isotropy (HTI), induced by the stress field or fractures. Near-surface heterogeneity and the acquisition footprint also could result in apparent azimuthal variations.
Interval velocity analysis in the dip-angle domain
Authors: Reshef Moshe
Published: October 2008

When interval velocity analysis is conducted over complex geologic regions, scattering-angle gathers may cause significant inaccuracies. These inaccuracies are related to the loss of structural dip information when generating common-image gathers (CIGs). In this study, the idea of performing interval velocity analysis in the dip-angle domain was examined and demonstrated with synthetic and real data examples. The effects of migration velocity errors and their identification in this domain were analyzed in detail. Carrying the analysis directly on dip-angle gathers is practically impossible. The ability to perform a standard analysis based on flattening the events in the CIGs is achieved by replacing the dip-angle measure with an equivalent offset measure. This equivalent offset provides higher sensitivity to velocity errors and may improve the accuracy of the resultant velocity model.
Velocity model building by 3D frequency-domain, full-waveform inversion of wide-aperture seismic data
Authors: Ben-Hadj-Ali Hafedh , Operto Stéphane , Virieux Jean
Published: October 2008

We assessed 3D frequency-domain (FD) acoustic full-waveform inversion (FWI) data as a tool to develop high-resolution velocity models from low-frequency global-offset data. The inverse problem was posed as a classic least-squares optimization problem solved with a steepest-descent method. Inversion was applied to a few discrete frequencies, allowing management of a limited subset of the 3D data volume. The forward problem was solved with a finite-difference frequency-domain method based on a massively parallel direct solver, allowing efficient multiple-shot simulations. The inversion code was fully parallelized for distributed-memory platforms, taking advantage of a domain decomposition of the modeled wavefields performed by the direct solver. After validation on simple synthetic tests, FWI was applied to two targets (channel and thrust system) of the 3D SEG/EAGE overthrust model, corresponding to 3D domains of [Formula: see text] and [Formula: see text], respectively. The maximum inverted frequencies are 15 and [Formula: see text] for the two applications. A maximum of 30 dual-core biprocessor nodes with [Formula: see text] of shared memory per node were used for the second target. The main structures were imaged successfully at a resolution scale consistent with the inverted frequencies. Our study confirms the feasibility of 3D frequency-domain FWI of global-offset data on large distributed-memory platforms to develop high-resolution velocity models. These high-velocity models may provide accurate macromodels for wave-equation prestack depth migration.
Wave tracing: Ray tracing for the propagation of band-limited signals: Part 2 — Applications
Authors: Washbourne John K. , Bube Kenneth P. , Carillo Pedro , Addington Carl
Published: October 2008

Modeling seismic propagation is critically important to our work; unfortunately, we often must trade simulation accuracy for reduced computational expense. We present a new seismic-modeling method that is as simple and computationally efficient as Snell’s law ray tracing but provides propagation paths and arrival times more consistent with finite-bandwidth data. We refer to this modeling method as wave tracing and apply it to nonlinear traveltime tomography and depth imaging. By replacing Snell’s law ray tracing with wave tracing, we get better ray coverage, more robust and faster ray bending (fewer iterations), and a much more robust and faster algorithm for nonlinear tomography (fewer iterations, too). A very significant benefit is increased stability and robustness of tomographic inversion with respect to small changes in model parameterization and regularization. A related benefit is the increased stability of depth images with respect to small changes in velocity, which can increase confidence in interpretation. The velocity models that result from wave tracing match picked arrival times in band-limited data better and generate improved depth images. These advantages of wave tracing relative to conventional Snell’s law ray tracing have been tested on both synthetic and real data examples for crosswell seismic geometry.
Advances in velocity model-building technology for subsalt imaging
Authors: Wang Bin , Kim Young , Mason Chuck , Zeng Xiansong
Published: October 2008

Seismic imaging of hydrocarbon accumulations below salt is a formidable challenge because complexly shaped salt bodies severely distort wavefronts or scatter seismic energy. We have highlighted some recent advances in building a velocity model for subsalt imaging. There are three main stages: suprasalt velocity determination, salt-model definition, and subsalt velocity update. Volumetric high-resolution tomography that incorporates high-velocity contrast boundaries is used to derive a good sediment velocity model before building a salt model. To facilitate integration of interpretation and depth processing, beam-based interactive imaging is used to refine the salt geometry. For subsalt velocity update, either subsalt tomography or subsalt scan-based techniques can be used, depending on the quality of subsalt reflections. There are concepts and techniques for attaining subsalt images suitable for hydrocarbon exploration beneath complexly shaped salt bodies.
Geologically constrained seismic imaging — Workflow
Authors: Foss Stig-Kyrre , Rhodes Mark , Dalstrøm Bjørn , Gram Christian , Welbon Alastair
Published: October 2008

We present the geologically constrained workflow for velocity-model building as a case study from offshore Brazil. The workflow involves basin reconstruction, gravity modeling, and seismic interpretation in addition to standard prestack depth migration (PSDM) model-building tools. Building a salt model based on seismic evidence can be highly nonunique. In a geologically constrained seismic-processing workflow, the main aim is to use geologic understanding with geophysical models and datasets to improve an input velocity realization for the PSDM loop, thereby improving image quality. All of these methods are inherently uncertain, and a final model is based on a range of subjective choices. Thus a final result that agrees with all sciences still can be completely wrong. However, an understanding of these choices enables a unique way of testing and constraining the number of antimodels: velocity models that fit the observations but are different from the final result. This can reduce time spent and uncertainty in geologic evaluation.