CiteULike: Author Haddad

Effects of landscape corridors on seed dispersal by birds.

DJ Levey — 2008-08-12T04:41:49-00:00

Science (New York, N.Y.), Vol. 309, No. 5731. (1 July 2005), pp. 146-148.

Habitat fragmentation threatens biodiversity by disrupting dispersal. The mechanisms and consequences of this disruption are controversial, primarily because most organisms are difficult to track. We examined the effect of habitat corridors on long-distance dispersal of seeds by birds, and tested whether small-scale (<20 meters) movements of birds could be scaled up to predict dispersal of seeds across hundreds of meters in eight experimentally fragmented landscapes. A simulation model accurately predicted the observed pattern of seed rain and revealed that corridors functioned through edge-following behavior of birds. Our study shows how models based on easily observed behaviors can be scaled up to predict landscape-level processes.

Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator.

OC Ezezika — 2008-07-23T16:56:34-00:00

Journal of molecular biology, Vol. 367, No. 3. (30 March 2007), pp. 616-629.

BenM, a bacterial transcriptional regulator, responds synergistically to two effectors, benzoate and cis,cis-muconate. CatM, a paralog with overlapping function, responds only to muconate. Structures of their effector-binding domains revealed two effector-binding sites in BenM. BenM and CatM are the first LysR-type regulators to be structurally characterized while bound with physiologically relevant exogenous inducers. The effector complexes were obtained by soaking crystals with stabilizing solutions containing high effector concentrations and minimal amounts of competing ions. This strategy, including data collection with fragments of fractured crystals, may be generally applicable to related proteins. In BenM and CatM, the binding of muconate to an interdomain pocket was facilitated by helix dipoles that provide charge stabilization. In BenM, benzoate also bound in an adjacent hydrophobic region where it alters the effect of muconate bound in the primary site. A charge relay system within the BenM protein appears to underlie synergistic transcriptional activation. According to this model, Glu162 is a pivotal residue that forms salt-bridges with different arginine residues depending on the occupancy of the secondary effector-binding site. Glu162 interacts with Arg160 in the absence of benzoate and with Arg146 when benzoate is bound. This latter interaction enhances the negative charge of muconate bound to the adjacent primary effector-binding site. The redistribution of the electrostatic potential draws two domains of the protein more closely towards muconate, with the movement mediated by the dipole moments of four alpha helices. Therefore, with both effectors, BenM achieves a unique conformation capable of high level transcriptional activation.

Nonlinear Dynamical Systems and Control: A Lyapunov-Based Approach

Wassim Haddad — 2008-07-20T16:14:09-00:00

(28 January 2008)

_Nonlinear Dynamical Systems and Control_ presents and develops an extensive treatment of stability analysis and control design of nonlinear dynamical systems, with an emphasis on Lyapunov-based methods. Dynamical system theory lies at the heart of mathematical sciences and engineering. The application of dynamical systems has crossed interdisciplinary boundaries from chemistry to biochemistry to chemical kinetics, from medicine to biology to population genetics, from economics to sociology to psychology, and from physics to mechanics to engineering. The increasingly complex nature of engineering systems requiring feedback control to obtain a desired system behavior also gives rise to dynamical systems. Wassim Haddad and VijaySekhar Chellaboina provide an exhaustive treatment of nonlinear systems theory and control using the highest standards of exposition and rigor. This graduate-level textbook goes well beyond standard treatments by developing Lyapunov stability theory, partial stability, boundedness, input-to-state stability, input-output stability, finite-time stability, semistability, stability of sets and periodic orbits, and stability theorems via vector Lyapunov functions. A complete and thorough treatment of dissipativity theory, absolute stability theory, stability of feedback systems, optimal control, disturbance rejection control, and robust control for nonlinear dynamical systems is also given. This book is an indispensable resource for applied mathematicians, dynamical systems theorists, control theorists, and engineers.

Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family

Ezezika — 2007-06-13T11:32:05-00:00

Acta Crystallographica Section F: Structural Biology and Crystallization Communications, Vol. 63, No. 5. (May 2007), pp. 361-368.

Epidermal sensing of oxygen is essential for systemic hypoxic response.

AT Boutin — 2008-07-16T06:45:03-00:00

Cell, Vol. 133, No. 2. (18 April 2008), pp. 223-234.

Skin plays an essential role, mediated in part by its remarkable vascular plasticity, in adaptation to environmental stimuli. Certain vertebrates, such as amphibians, respond to hypoxia in part through the skin; but it is unknown whether this tissue can influence mammalian systemic adaptation to low oxygen levels. We have found that epidermal deletion of the hypoxia-responsive transcription factor HIF-1alpha inhibits renal erythropoietin (EPO) synthesis in response to hypoxia. Conversely, mice with an epidermal deletion of the von Hippel-Lindau (VHL) factor, a negative regulator of HIF, have increased EPO synthesis and polycythemia. We show that nitric oxide release induced by the HIF pathway acts on cutaneous vascular flow to increase systemic erythropoietin expression. These results demonstrate that in mice the skin is a critical mediator of systemic responses to environmental oxygen.

Unusual 1H NMR chemical shifts support (His) Cepsilon 1---Hmiddle dotmiddle dotmiddle dotO==C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis

Elissa Ash — 2008-06-04T11:18:16-00:00

Proceedings of the National Academy of Sciences, Vol. 97, No. 19. (12 September 2000), pp. 10371-10376.

10.1073/pnas.97.19.10371

Central Vein Stenosis: A Nephrologist's Perspective

Agarwal — 2007-01-21T03:12:07-00:00

Seminars in Dialysis, Vol. 20, No. 1. (February 2007), pp. 53-62.

Honey-Bees Mating Optimization (HBMO) Algorithm: A New Heuristic Approach for Water Resources Optimization

Omid Haddad — 2008-03-18T20:43:09-00:00

Water Resources Management, Vol. 20, No. 5. (22 October 2006), pp. 661-680.

Abstract Over the last decade, evolutionary and meta-heuristic algorithms have been extensively used as search and optimization tools in various problem domains, including science, commerce, and engineering. Their broad applicability, ease of use, and global perspective may be considered as the primary reason for their success. The honey-bees mating process may also be considered as a typical swarm-based approach to optimization, in which the search algorithm is inspired by the process of real honey-bees mating. In this paper, the honey-bees mating optimization algorithm (HBMO) is presented and tested with few benchmark examples consisting of highly non-linear constrained and/or unconstrained real-valued mathematical models. The performance of the algorithm is quite comparable with the results of the well-developed genetic algorithm. The HBMO algorithm is also applied to the operation of a single reservoir with 60 periods with the objective of minimizing the total square deviation from target demands. Results obtained are promising and compare well with the results of other well-known heuristic approaches.

NF-κB links innate immunity to the hypoxic response through transcriptional regulation of HIF-1α

Jordi Rius — 2008-04-24T18:13:59-00:00

Nature (23 April 2008)

PVFS: A Parallel Virtual File System for Linux Clusters

Ibrahim Haddad — 2008-05-03T17:43:32-00:00

Linux J. (2000)

A metric for odorant comparison

Rafi Haddad — 2008-04-30T10:23:32-00:00

Nat Meth, Vol. 5, No. 5. (May 2008), pp. 425-429.

Cellular transplantation: future therapeutic options.

R Allan — 2008-04-25T12:49:27-00:00

Current opinion in cardiology, Vol. 22, No. 2. (March 2007), pp. 104-110.

PURPOSE OF REVIEW: Cardiac transplantation is a complex undertaking and an imperfect solution to end-stage heart failure. Cellular transplantation has been proposed as an alternative solution; however, clinical trials at present are small and show variable results. The mechanisms behind stem cell therapy have not yet been elucidated. RECENT FINDINGS: Several large trials have been presented that address the question of bone marrow stem cells as therapy for acute myocardial infarction, and also the possible benefits of therapy with granulocyte colony-stimulating factor. Although some trials show a modest improvement in ejection fraction or reduction of infarct size, other trials show no change with treatment. Fewer clinical data are available on the treatment of chronic left ventricular systolic function. Many questions remain such as what cell type to use, dosing, the ideal timing for therapy, and the technique of cell delivery. Finally, further research continues on the cellular milieu, enhancement of cell engraftment, proliferation, and survival. SUMMARY: This review briefly examines the background for stem cell therapy, as well as the larger clinical trials of stem cell therapy for acute myocardial infarction and chronic left ventricular systolic dysfunction, and possible pharmacologic enhancement options.

Sleep apnea in chronic heart failure.

AH Anselm — 2008-04-10T07:27:54-00:00

Current opinion in cardiology, Vol. 23, No. 2. (March 2008), pp. 121-126.

PURPOSE OF REVIEW: As heart failure continues to carry significant morbidity and mortality it is crucial to pursue new lines of therapy. Addressing sleep apnea, which is highly prevalent in these patients, offers just such an avenue. We discuss how sleep apnea may contribute to the propagation of heart failure, and how understanding its effects and reversing these effects might benefit heart failure patients. RECENT FINDINGS: Continuous positive airway pressure ventilation, atrial pacing, and chronic resynchronization therapy have all been studied in sleep apnea. Some of these therapies have shown benefits in heart failure. This offers hope for improved outcomes, particularly with respect to mortality. Delineating how these therapies affect the heart's energetics and metabolism may also provide further understanding of the relationship between sleep apnea and heart failure. SUMMARY: As both obstructive and central sleep apnea are highly prevalent in heart failure, treating these patients with continuous positive airway pressure, atrial pacing, or chronic resynchronization therapy may offer morbidity and mortality benefits. Much remains to be understood about the relationship between sleep apnea and heart failure, and understanding the interaction between the two at both the myocardial and clinical level is crucial.

Switching characteristics of Cu[sub 2]O metal-insulator-metal resistive memory

A Chen — 2008-04-09T18:27:04-00:00

Applied Physics Letters, Vol. 91, No. 12. (2007)

View this record in Web of Science

DIVERSITY AND EVOLUTION OF PROTEIN TRANSLOCATION

Mechthild Pohlschroder — 2008-03-28T08:39:35-00:00

Annual Review of Microbiology, Vol. 59, No. 1. (2005), pp. 91-111.

Abstract Cells need to translocate proteins into and across hydrophobic membranes in order to interact with the extracellular environment. Although a subset of proteins are thought to spontaneously insert into lipid bilayers, translocation of most transported proteins requires additional cellular components. Such components catalyze efficient lateral transport into or across cellular membranes in prokaryotes and eukaryotes. These include, among others, the conserved YidC/Oxa1/Alb3 proteins as well as components of the Sec and the Tat pathways. Our current knowledge of the function and distribution of these components and their corresponding pathways in organisms of the three domains of life is reviewed. On the basis of this information, the evolution of protein translocation is discussed.

The Nonlinear Dirac Equation in Bose-Einstein Condensates: Foundation and Symmetries

LH Haddad — 2008-03-27T08:51:31-00:00

(20 Mar 2008)

We show that Bose-Einstein condensates in a honeycomb optical lattice are described by a nonlinear Dirac equation in the long wavelength, mean field limit. Unlike nonlinear Dirac equations posited by particle theorists, which are designed to preserve the principle of relativity, i.e., Poincaré covariance, the nonlinear Dirac equation for Bose-Einstein condensates breaks this symmetry. We present a rigorous derivation of the nonlinear Dirac equation from first principles. We provide a thorough discussion of all symmetries broken and maintained.

Transcription factor FOXO3a controls the persistence of memory CD4+ T cells during HIV infection

Julien van Grevenynghe — 2008-03-07T16:12:29-00:00

Nature Medicine, Vol. 14, No. 3. (02 March 2008), pp. 266-274.

GaInP/GaAs dual junction solar cells on Ge/Si epitaxial templates

Melissa Archer — 2008-03-12T01:38:04-00:00

Applied Physics Letters, Vol. 92, No. 10. (2008)

Predicting the potential distribution of the alien invasive American bullfrog ( Lithobates catesbeianus ) in Brazil

João Giovanelli — 2008-02-29T13:32:43-00:00

Biological Invasions

Abstract The non-native invasive anuran Lithobates catesbeianus is presently distributed in Brazil, especially in the Atlantic Rainforest biodiversity hotspot. Here, we use a maximum entropy ecological niche modeling algorithm (i) to model the North American native geographic distribution of this species and (ii) to project that model onto the whole of Brazil. After applying a threshold value that balances commission and omission errors, the projection results suggested high probabilities of occurrence mostly in southern and southeastern Brazil. We also present the first report on the species known distribution in Brazil, showing good agreement with model predictions. If the predictive map is interpreted as depicting invasiveness potential of L. catesbeianus, strategies to prevent further invasion in Brazil should be focused especially in the Atlantic Rainforest biodiversity hotspot.

Corridors affect plants, animals, and their interactions in fragmented landscapes

Joshua Tewksbury — 2006-11-22T16:21:44-00:00

PNAS, Vol. 99, No. 20. (1 October 2002), pp. 12923-12926.

Among the most popular strategies for maintaining populations of both plants and animals in fragmented landscapes is to connect isolated patches with thin strips of habitat, called corridors. Corridors are thought to increase the exchange of individuals between habitat patches, promoting genetic exchange and reducing population fluctuations. Empirical studies addressing the effects of corridors have either been small in scale or have ignored confounding effects of increased habitat area created by the presence of a corridor. These methodological difficulties, coupled with a paucity of studies examining the effects of corridors on plants and plant-animal interactions, have sparked debate over the purported value of corridors in conservation planning. We report results of a large-scale experiment that directly address this debate. In eight large-scale experimental landscapes that control for patch area and test alternative mechanisms of corridor function, we demonstrate that corridors not only increase the exchange of animals between patches, but also facilitate two key plant-animal interactions: pollination and seed dispersal. Our results show that the beneficial effects of corridors extend beyond the area they add, and suggest that increased plant and animal movement through corridors will have positive impacts on plant populations and community interactions in fragmented landscapes. 10.1073/pnas.202242699

Continuous and Hybrid Distributed Control for Multiagent Coordination: Consensus, Flocking, and Cyclic Pursuit

Qing Hui — 2008-02-28T00:33:39-00:00

American Control Conference, 2007. ACC '07 (2007), pp. 2576-2581.

In this paper, we develop a unified framework for addressing consensus, flocking, and cyclic pursuit problems for multiagent dynamical systems. Specifically, we present continuous and hybrid distributed and decentralized controller architectures for multiagent coordination. The proposed controller architectures are predicated on system thermodynamic notions resulting in thermodynamically consistent continuous and hybrid controller architectures involving the exchange of information between agents that guarantee that the closed-loop dynamical network is consistent with basic thermodynamic principles. A unique feature of the proposed framework is that several of the proposed controller architectures are hybrid, and hence, the overall closed-loop dynamics under any of these controller algorithms achieving consensus, flocking, or cyclic pursuit possesses discontinuous flows since the controller algorithms combine logical switchings with continuous dynamics, leading to impulsive differential equations.

Women Bargaining to Seek Healthcare: Norms, Domestic Practices, and Implications in Rural Burkina Faso

Beatrice Nikiema — 2008-02-27T10:29:52-00:00

World Development, Vol. 36, No. 4. (April 2008), pp. 608-624.

Summary Based on a qualitative study contrasting a gender-relationally restrictive socio-cultural setting with a rather liberal one, we explain how social norms shape resource negotiation for women seeking modern healthcare. A system of "protection and dependency" covers them in principle for obviously serious illness, as far as household resources permit. In both settings, however, women must have "well behaved" and justify less-obvious needs in an unequal bargaining process with ambivalent recourse opportunities. Consequently, women may suffer delays in or exclusion from healthcare. Moreover, their self-esteem may lower and the domestic power imbalance may increase. The results suggest sectoral and sector-crosscutting solutions.

Spectral Efficiency of Cognitive Radio Systems

Majed Haddad — 2008-02-20T10:42:22-00:00

Global Telecommunications Conference, 2007. GLOBECOM '07. IEEE (2007), pp. 4165-4169.

Randomized clinical trial of post-operative radiotherapy versus concomitant carboplatin and radiotherapy for head and neck cancers with lymph node involvement.

Séverine Racadot — 2008-01-29T18:46:11-00:00

Radiother Oncol (24 January 2008)

BACKGROUND AND PURPOSE: Post-operative radiotherapy is indicated for the treatment of head and neck cancers. In vitro, chemotherapy potentiates the cytotoxic effects of radiation. We report the results of a randomized trial testing post-operative radiotherapy alone versus concomitant carboplatin and radiotherapy for head and neck cancers with lymph node involvement. MATERIALS AND METHODS: The study involved patients undergoing curative-intent surgery for head and neck cancers with histological evidence of lymph node involvement. Patients were randomly assigned to receive radiotherapy alone (54-72Gy, 30-40 fractions, 6-8 weeks) or identical treatment plus concomitant Carboplatin (50mg/m(2) administered by IV infusion twice weekly). RESULTS: Between February 1994 and June 2002, 144 patients were included. With a median follow-up of 106 months (95% confidence interval (CI) [92-119]), the 2-year rate of loco-regional control was 73% (95% CI: 0.61-0.84) in the combined treatment group and 68% (95% CI: 0.57-0.80) in the radiotherapy group (p=0.26). Overall survival did not differ significantly between groups (hazard ratio for death, 1.05; 95% CI: 0.69-1.60; p=0.81). CONCLUSIONS: Twice-weekly administration of carboplatin concomitant to post-operative radiotherapy did not improve local control or overall survival rates in this population of patients with node-positive head and neck cancers.

Are Articles in "Top" Management Journals Necessarily of Higher Quality?

Gangaram Singh — 2008-01-29T10:58:26-00:00

Journal of Management Inquiry, Vol. 16, No. 4. (1 December 2007), pp. 319-331.

This study investigates the appropriateness of using publication of an article in a top (specifically, top five) management journal as a proxy for its quality. Social Science Citation Index citation counts were collected over 7-year event windows for articles published in 34 management journals in 1993 and 1996. Overall, the authors found that articles published in the five journals most often considered to be the top ones in management tend to be cited more often than ones published in the other journals. Far more important, however, across three different criteria for placing articles into top versus non-top categories, there were substantial classification errors from using journal ranking as a proxy for quality. This finding suggests that both administrators and the management discipline will be well served by efforts to evaluate each article on its own merits rather than abdicate this responsibility by using journal ranking as a proxy for quality. 10.1177/1056492607305894

[Abdominal compartment syndrome after cardiac surgery]

S Madi-Jebara — 2007-12-21T11:43:46-00:00

Ann Fr Anesth Reanim, Vol. 26, No. 9. (September 2007), pp. 799-801.

We report the case of a 60-year-old woman who underwent mitral valve replacement and tricuspid valve repair. Following surgery she developed rapid onset of ascitis and secondary abdominal compartmental syndrome with low cardiac output and oliguria. Following drainage of the ascitis, the abdominal pressure dropped with a spectacular improvement of both the cardiac ant the urine output.

Habitat Split and the Global Decline of Amphibians

Carlos Becker — 2007-12-14T12:37:46-00:00

Science, Vol. 318, No. 5857. (14 December 2007), pp. 1775-1777.

The worldwide decline in amphibians has been attributed to several causes, especially habitat loss and disease. We identified a further factor, namely "habitat split"defined as human-induced disconnection between habitats used by different life history stages of a specieswhich forces forest-associated amphibians with aquatic larvae to make risky breeding migrations between suitable aquatic and terrestrial habitats. In the Brazilian Atlantic Forest, we found that habitat split negatively affects the richness of species with aquatic larvae but not the richness of species with terrestrial development (the latter can complete their life cycle inside forest remnants). This mechanism helps to explain why species with aquatic larvae have the highest incidence of population decline. These findings reinforce the need for the conservation and restoration of riparian vegetation. 10.1126/science.1149374

Recursive Petri nets

Serge Haddad — 2007-11-15T22:09:40-00:00

Acta Informatica, Vol. 44, No. 7. (10 December 2007), pp. 463-508.

Abstract In order to design and analyse complex systems, modelers need formal models with two contradictory requirements: a high expressivity and the decidability of behavioural property checking. Here we present and develop the theory of such a model, the recursive Petri nets. First, we show that the mechanisms supported by recursive Petri nets enable to model patterns of discrete event systems related to the dynamic structure of processes. Furthermore, we prove that these patterns cannot be modelled by ordinary Petri nets. Then we study the decidability of some problems: reachability, finiteness and bisimulation. At last, we develop the concept of linear invariants for this kind of nets and we design efficient computations specifically tailored to take advantage of their structure.

Reaching Agreement in Hierarchical Groups

Nguilla Kooh — 2007-10-18T08:59:01-00:00

(August 1999)

We present a mechanism based on Chandra and Toueg unreliable failure detectors model. This mechanism can be used as building block for distributed systems running on Internet and requiring a nonblocking agreement between their components. The protocol we propose tolerates both local participants and groups of participants' failures in a large-scale and asynchronous environment prone to failures. 1

Intensity-Based Statistical Scorer for Tandem Mass Spectrometry

M Havilio — 2007-10-15T18:37:42-00:00

Anal. Chem., Vol. 75, No. 3. (1 February 2003), pp. 435-444.

Abstract: We describe a new statistical scorer for tandem mass spectrometry. The scorer is based on the probability that fragments with given chemical properties create measured intensity levels in the experimental spectrum. The scorer's parameters are computed using a fully automated procedure. Benchmarking the new scorer on a large set of experimental spectra, we show that it performs significantly better than the widely used cross-correlation scoring algorithm of Eng et al. (Eng, J. K.; McKormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.).

Space and time organization in a shock-induced separated boundary layer

P Dupont — 2007-10-08T14:35:00-00:00

J. Fluid Mech., Vol. 559 (2006), pp. 255-277.

The interaction of an oblique shock wave impinging on a turbulent boundary layer at Mach number 2.3 is experimentally investigated for a wide range of shock intensities. Characteristic time and length scales of the unsteady reflected shock and inside the downstream interaction region are obtained and compared with already existing results obtained in compression ramp experiments as well as in subsonic detached flows. Dimensionless characteristic frequencies are highlighted to characterize low-frequency shock unsteadiness as well as the different large scales which develop inside the initial part of the interaction. The possibility of describing the spatial development of the large scales inside the interaction zone using a mixing-layer scheme including compressibility effects is tested for a wide range of Mach numbers, shock intensities and geometrical configurations. Moreover, strong evidence of a statistical link between low-frequency shock movements and the downstream interaction is given. Finally, the downstream evolution of the structures shed into the boundary layer is characterized and shows features specific of our configuration. \\copyright 2006 Cambridge University Press.

Evaluation of web usage mining approaches for user's next request prediction

Mathias Géry — 2007-10-02T15:01:27-00:00

(2003), pp. 74-81.

Islam, Gender, and Social Change

Yvonne Haddad — 2007-09-19T14:22:12-00:00

(31 October 1997)

For several decades, the Muslim world has experienced a religious resurgence. The reassertion of Islam in personal and political life has taken many forms, from greater attention to religious practice to the emergence of Islamic organizations, movements, and institutions. One of the most controversial and emotionally charged aspects of this revival has been its effect on women in Muslim societies. The essays collected in this book place this issue in its historical context and offer case studies of Muslim societies from North Africa to Southeast Asia. These fascinating studies shed light on the impact of the Islamic resurgence on gender issues in Iran, Egypt, Jordan, Pakistan, Oman, Bahrain, the Philippines, and Kuwait. Taken together, the essays reveal the wide variety that exists among Muslim societies and believers, and the complexity of the issues under consideration. They show that new things are happening for women across the Islamic world, and are in many cases being initiated by women themselves. The volume as a whole militates against the stereotype of Muslim women as repressed, passive, and without initiative, while acknowledging the very real obstacles to women's initiatives in most of these societies.

Predicting odor pleasantness from odorant structure: pleasantness as a reflection of the physical world.

RM Khan — 2007-09-17T12:27:23-00:00

J Neurosci, Vol. 27, No. 37. (12 September 2007), pp. 10015-10023.

Although it is agreed that physicochemical features of molecules determine their perceived odor, the rules governing this relationship remain unknown. A significant obstacle to such understanding is the high dimensionality of features describing both percepts and molecules. We applied a statistical method to reduce dimensionality in both odor percepts and physicochemical descriptors for a large set of molecules. We found that the primary axis of perception was odor pleasantness, and critically, that the primary axis of physicochemical properties reflected the primary axis of olfactory perception. This allowed us to predict the pleasantness of novel molecules by their physicochemical properties alone. Olfactory perception is strongly shaped by experience and learning. However, our findings suggest that olfactory pleasantness is also partially innate, corresponding to a natural axis of maximal discriminability among biologically relevant molecules.

Is It Possible to Recognize Pulmonary Infarction on Multisection CT Images?

Marie-Pierre Revel — 2007-09-15T01:03:58-00:00

Radiology, Vol. 244, No. 3. (1 September 2007), pp. 875-882.

Purpose: To retrospectively determine sensitivity and specificity of four findings for distinguishing pulmonary infarction from other causes of peripheral pulmonary consolidations on multidetector computed tomographic (CT) images, with other CT and clinical findings as reference. Materials and Methods: Institutional review board approved the study and waived informed consent. Three independent radiologists blindly analyzed selected multisection CT images of 50 pulmonary infarctionsnot showing direct arterial signs of pulmonary embolismand 100 peripheral consolidations of other origins. Readers analyzed four findings: triangular shape, vessel sign (defined as presence of an enlarged vessel at the apex of consolidation), central lucencies, and air bronchograms. Interobserver agreement; frequency on CT images with and without infarct; and sensitivity, specificity, and positive likelihood ratio (LR) for diagnosis of pulmonary infarction were assessed for each finding. Results: One hundred fifty peripheral consolidations were analyzed in 134 (75 men, 59 women) patients (mean age, 55.9 years +/- 17.4 [standard deviation] vs 54.7 +/- 19.9; P = .71). Interobserver agreement was good for central lucencies and air bronchograms and poor to moderate for the other two findings (kappa < 0.61). Compared with CT images without infarct, CT images with infarct had a higher frequency of vessel sign (32% [16 of 50] vs 11% [11 of 100], P = .029) and central lucencies (46% [23 of 50] vs 2% [two of 100], P < .001) and a lower frequency of air bronchograms (8% [four of 50] vs 40% [40 of 100], P = .003). Frequency of triangular shape was similar in both groups (52% [26 of 50] vs 40% [40 of 100], P = .17). Positive LR was 23.0 for central lucencies, 2.9 for vessel sign, 1.3 for triangular shape, and 0.2 for air bronchograms. Presence of central lucencies had 98% specificity and 46% sensitivity for pulmonary infarction. When the vessel sign and negative air bronchogram were combined with central lucencies, specificity increased to 99% but sensitivity decreased to 14%. Conclusion: Central lucencies in peripheral consolidations are highly suggestive of pulmonary infarction. (C) RSNA, 2007 10.1148/radiol.2443060846

Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR.

Fadia Haddad — 2007-05-05T17:17:44-00:00

BMC Biotechnology, Vol. 7 (04 May 2007), 21.

Serum lipid response to the graduated enrichment of a Step I diet with almonds: a randomized feeding trial.

J Sabaté — 2007-07-05T21:07:43-00:00

Am J Clin Nutr, Vol. 77, No. 6. (June 2003), pp. 1379-1384.

BACKGROUND: Frequent consumption of nuts may lower the risk of cardiovascular disease by favorably altering serum lipid and lipoprotein concentrations. OBJECTIVE: We compared the effects of 2 amounts of almond intake with those of a National Cholesterol Education Program Step I diet on serum lipids, lipoproteins, apolipoproteins, and glucose in healthy and mildly hypercholesterolemic adults. DESIGN: In a randomized crossover design, 25 healthy subjects (14 men, 11 women) with a mean (+/- SD) age of 41 +/- 13 y were fed 3 isoenergetic diets for 4 wk each after being fed a 2-wk run-in diet (containing 34% of energy from fat). The experimental diets included a Step I diet, a low-almond diet, and a high-almond diet, in which almonds contributed 0%, 10%, and 20% of total energy, respectively. RESULTS: Inverse relations were observed between the percentage of energy in the diet from almonds and the subject's total cholesterol (P value for trend < 0.001), LDL-cholesterol (P < 0.001), and apolipoprotein B (P < 0.001) concentrations and the ratios of LDL to HDL cholesterol (P < 0.001) and of apolipoprotein B to apolipoprotein A (P < 0.001). Compared with the Step I diet, the high-almond diet reduced total cholesterol (0.24 mmol/L or 4.4%; P = 0.001), LDL cholesterol (0.26 mmol/L or 7.0%; P < 0.001), and apolipoprotein B (6.6 mg/dL or 6.6%; P < 0.001); increased HDL cholesterol (0.02 mmol/L or 1.7%; P = 0.08); and decreased the ratio of LDL to HDL cholesterol (8.8%; P < 0.001). CONCLUSIONS: Isoenergetic incorporation of approximately 68 g of almonds (20% of energy) into an 8368-kJ (2000-kcal) Step I diet markedly improved the serum lipid profile of healthy and mildly hypercholesterolemic adults. Total and LDL-cholesterol concentrations declined with progressively higher intakes of almonds, which suggests a dose-response relation.

A machine learning approach to the analysis of time-frequency maps, and its application to neural dynamics

Fran&\#231;ois Vialatte — 2007-06-13T13:26:11-00:00

Neural Netw., Vol. 20, No. 2. (March 2007), pp. 194-209.

Behavior of oral squamous cell carcinoma in subjects with prior lichen planus

Amanda Munoz — 2007-06-04T10:40:58-00:00

Otolaryngology - Head and Neck Surgery, Vol. 136, No. 3. (March 2007), pp. 401-404.

Objective To characterize the clinical behavior of oral squamous cell carcinomas (OSCCA) arising in patients with pre-existing oral lichen planus (OLP).Study design and setting Retrospective case-control study. Disease-free interval, time to first recurrence, subsequent therapy, and overall survival were calculated and compared between cases and controls matched for age, gender, primary site, and tumor stage.Results In 10 identified subjects with OLP/OSCCA, mean time from OLP diagnosis to OSCCA was 5.5 years. Three subjects suffered a local recurrence and two developed a second primary OSCCA. Mean actuarial survival for OLP patients was 119 months vs 42 months for the control patients, though this difference was not significant (P = 0.201, log-rank).Conclusions OLP/SCCA subjects may exhibit better actuarial survival than SCCA patients despite a somewhat higher rate of local recurrence and second primary SCCA. Further study is required to characterize the behavior of OSCCA arising in pre-existing OLP.

Adaptive median filters: new algorithms and results

H Hwang — 2007-06-01T21:11:30-00:00

Image Processing, IEEE Transactions on, Vol. 4, No. 4. (1995), pp. 499-502.

Based on two types of image models corrupted by impulse noise, we propose two new algorithms for adaptive median filters. They have variable window size for removal of impulses while preserving sharpness. The first one, called the ranked-order based adaptive median filter (RAMF), is based on a test for the presence of impulses in the center pixel itself followed by a test for the presence of residual impulses in the median filter output. The second one, called the impulse size based adaptive median filter (SAMF), is based on the detection of the size of the impulse noise. It is shown that the RAMF is superior to the nonlinear mean L<sub>p</sub> filter in removing positive and negative impulses while simultaneously preserving sharpness; the SAMF is superior to Lin's (1988) adaptive scheme because it is simpler with better performance in removing the high density impulsive noise as well as nonimpulsive noise and in preserving the fine details. Simulations on standard images confirm that these algorithms are superior to standard median filters

A single HPLC-PAD-APCI/MS method for the quantitative comparison of phenolic compounds found in leaf, stem, root and fruit extracts of Vaccinium angustifolium.

CS Harris — 2007-05-28T17:01:40-00:00

Phytochem Anal, Vol. 18, No. 2. (March 2007), pp. 161-169.

A method was developed for the analysis of Vaccinium angustifolium Ait. (Lowbush blueberry), which is a widely used natural health product, particularly for the treatment of diabetic symptoms. While the anthocyanin content of the fruit has been well characterized, the chemistry of the vegetative parts used in supportive therapy for diabetes has been largely ignored. Using a metabolomics-based approach for compound identification with an emphasis on phenolic metabolites, a single HPLC-PAD-APCI/ MS method was developed for the separation and quantitation of the major metabolites found in the 95% ethanol extracts of leaf, stem, root and fruit. The leaf extract contained high concentrations of chlorogenic acid (approximately 100 microg/mg extract) and a variety of quercetin glycosides that were also detected in the fruit and stem extracts. Flavan-3-ol monomers (+)-catechin and (-)-epicatechin were found in all plant parts but their procyanidin dimers were exclusively identified in the stem and root. The accuracy and precision of the presented method were corroborated by low intra- and inter-day variations in quantitative results in all plant part extracts. Further validation of the extraction and analytical protocols focused on identified compounds with reputed anti-diabetic activity, revealing recoveries greater than 80% and detection limits of 0.12-2.73 microg/mL.

Emerging drugs in lung transplantation

Mankidy — 2007-03-18T23:17:55-00:00

Expert Opinion on Emerging Drugs, Vol. 12, No. 1. (March 2007), pp. 61-73.

The refugee: The individual between sovereigns

E Haddad — 2007-04-02T21:28:40-00:00

Global Soc., Vol. 17, No. 3. (2003), pp. 297-322.

Starting with a look at the concept of sovereignty, therefore, I ask how the refugee fits into an international society made up of separate sovereign states. It will be seen that as the state became nationalised, so the refugee became vital as the "other" necessary for national citizens to successfully forge their identity. With the rise of national identity as the new indicator of allegiance, the refugee became the imagined outsider who allowed the concept of the nation-state to take hold. By showing how the refugee is defined in statist terms I highlight her portrayal as an exception to the otherwise "normal", sedentary nation-state-territory trinity. I then look at changes in how the international community has addressed and responded to the problem. In the years leading up to World War II, attempts to solve the refugee problem were thought to be found inside states, consistent with a positive view of sovereignty. Post-1945 approaches to the refugee problem have shifted the emphasis to ideas of negative sovereignty, with the solution said to be in relations between rather than within states.

Precision measurements of the absolute photoionization cross sections of He

JAR Samson — 2007-03-20T17:55:34-00:00

Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 27, No. 5. (1994), pp. 887-898.

Precision photoionization cross sections for He have been measured from threshold to 120 eV with an accuracy ranging from 1 to 2\%. In addition, a critical review of the published data has been made and recommended photoionization cross sections from the ionization threshold to 8 keV are presented with an estimated uncertainty of +or-10\% above 500 eV. The effect of coherent (Rayleigh) and incoherent (Compton) scattering is discussed.

CT assessment of anastomotic bowel leak.

N Power — 2007-02-19T10:54:23-00:00

Clin Radiol, Vol. 62, No. 1. (January 2007), pp. 37-42.

AIM: To evaluate the predictors of clinically important gastrointestinal anastomotic leaks using multidetector computed tomography (CT). SUBJECTS AND METHODS: Ninety-nine patients, 73 with clinical suspicion of anastomotic bowel leak and 26 non-bowel surgery controls underwent CT to investigate postoperative sepsis. Fifty patients had undergone large bowel and 23 small bowel anastomoses. The time interval from surgery was 3-30 days (mean 10+/-5.9 SD) for the anastomotic group and 3-40 days (mean 14+/-11 SD) for the control group (p=0.3). Two radiologists blinded to the final results reviewed the CT examinations in consensus and recorded the presence of peri-anastomotic air, fluid or combination of the two; distant loculated fluid or combination of fluid and air; free air or fluid; and intestinal contrast leak. Final diagnosis of clinically important anastomotic leak (CIAL) was confirmed at surgery or by chart review of predetermined clinical and laboratory criteria. RESULTS: The prevalence of CIAL in the group undergoing CT was 31.5% (23/73). The CT examinations with documented leak were performed 5-28 (mean; 11.4+/-6 SD) days after surgery. Nine patients required repeat operation, 10 percutaneous abscess drainage, two percutaneous drainage followed by surgery, and two prolonged antibiotic treatment and total parenteral nutrition (TPN). Of the CT features examined, only peri-anastomotic loculated fluid containing air was more frequently seen in the CIAL group as opposed to the no leak group (p=0.04). There was no intestinal contrast leakage in this cohort. Free air was present up to 9 days and loculated air up to 26 days without CIAL. CONCLUSION: Most postoperative CT features overlap between patients with and without CIAL. The only feature seen statistically more frequently with CIAL is peri-anastomotic loculated fluid containing air.

The Effects of Continuous Positive Airway Pressure on Myocardial Energetics in Patients With Heart Failure and Obstructive Sleep Apnea

Keiichiro Yoshinaga — 2007-01-30T23:36:29-00:00

J Am Coll Cardiol, Vol. 49, No. 4. (30 January 2007), pp. 450-458.

OBJECTIVES: We sought to examine the short-term and longer term (6-week) effects of continuous positive airway pressure (CPAP) on myocardial energetics. BACKGROUND: Obstructive sleep apnea (OSA) and heart failure (HF) are both states of increased afterload and metabolic demand. Treatment with CPAP may initially reduce stroke volume but subsequently improves left ventricular function. However, it is not clear whether CPAP therapy favorably affects myocardial energetics and hence improves cardiac efficiency. METHODS: Twelve patients with HF were divided into two groups: 7 patients with OSA were treated with CPAP (group I), and 5 patients without OSA served as a control group (group II). Oxidative metabolism was measured using the mono-exponential fit of the myocardial [11C] acetate positron emission tomography time-activity curve (k-mono). Myocardial efficiency was derived using the work metabolic index (WMI = [heart rate x stroke volume index x systolic blood pressure]/k-mono) measured at baseline, during short-term CPAP, and after 6 +/- 3 weeks of CPAP. RESULTS: In group I, short-term CPAP tended to reduce SVI (p = 0.063) and reduced oxidative metabolism (p = 0.031). Work metabolic index did not change. However, longer term CPAP improved left ventricular ejection fraction (38.4 +/- 3.3% to 43.4 +/- 4.8%, p = 0.031), tended to reduce oxidative metabolism (0.047 +/- 0.012 to 0.040 +/- 0.008 min-1, p = 0.078), and improved WMI (7.13 +/- 2.82 x 106 to 8.17 +/- 3.06 x 106 mm Hgmiddle dotml/m2, p = 0.031). In group II (control), these parameters did not change. CONCLUSIONS: In this cohort of patients with HF and OSA, short-term CPAP decreased oxidative metabolism and tended to decrease SVI, but did not alter cardiac efficiency. Longer term CPAP improved cardiac efficiency, indicating an energy-sparing effect. These effects may contribute to the benefits of CPAP therapy. 10.1016/j.jacc.2006.08.059

Inoperable pulmonary aspergilloma: percutaneous CT-guided injection with glycerin and amphotericin B paste in 15 cases.

JM Giron — 2007-01-22T04:59:44-00:00

Radiology, Vol. 188, No. 3. (September 1993), pp. 825-827.

Fifteen patients with active inoperable pulmonary aspergilloma underwent percutaneous injection of a special therapeutic paste of glycerin and amphotericin B. This paste was warmed just prior to injection, and filling of the lesional cavity was achieved in one session if it was possible to obtain anaerobic conditions for destruction of the aspergilloma. Injection was performed with computed tomographic guidance with use of an 18-gauge flexible needle and with administration of anti-coughing analgesia. Follow-up was continued for 7 months on average. Filling of the lesion cavities required three sessions on average because of cough or bronchospasm. In 12 cases the aspergilloma regressed within 3 months and results at serology became negative. In three cases, there was no change in the cavity, but hemoptysis did not recur. Results in this series confirm the feasibility and efficacy of this palliative treatment.

Corridors Increase Plant Species Richness at Large Scales

Ellen Damschen — 2007-01-18T22:53:18-00:00

Science, Vol. 313, No. 5791. (1 September 2006), pp. 1284-1286.

Habitat fragmentation is one of the largest threats to biodiversity. Landscape corridors, which are hypothesized to reduce the negative consequences of fragmentation, have become common features of ecological management plans worldwide. Despite their popularity, there is little evidence documenting the effectiveness of corridors in preserving biodiversity at large scales. Using a large-scale replicated experiment, we showed that habitat patches connected by corridors retain more native plant species than do isolated patches, that this difference increases over time, and that corridors do not promote invasion by exotic species. Our results support the use of corridors in biodiversity conservation. 10.1126/science.1130098

Restriction landmark genomic scanning of mouse liver tumors for gene amplification: overexpression of cyclin A2.

R Haddad — 2006-12-18T01:51:00-00:00

Biochem Biophys Res Commun, Vol. 274, No. 1. (21 July 2000), pp. 188-196.

SV40 T/t antigen-induced liver tumors from transgenic mice were analyzed by Restriction Landmark Genomic Scanning (RLGS). Using NotI as the restriction landmark, RLGS targets CpG islands found in gene-rich regions of the genome. Since many RLGS landmarks are mapped, the candidate gene approach can be used to help determine which genes are altered in tumors. RLGS analysis revealed one tumor-specific amplification mapping close to CcnA2 (cyclin A2) and Fgf2 (fibroblast growth factor 2). Southern analysis confirmed that both oncogenes are amplified in this tumor and in a second, independent liver tumor. Whereas Fgf2 RNA is undetectable in tumors, CcnA2 RNA and cyclin A2 protein was overexpressed in 25 and 50% of tumors, respectively. Combining RLGS with the candidate gene approach indicates that cyclin A2 amplification and overexpression is a likely selected event in transgenic mouse liver tumors. Our results also indicate that our mouse model for liver tumorigenesis in mice accurately recapitulates events observed in human hepatocellular carcinoma.

Antidepressant discontinuation syndrome: consensus panel recommendations for clinical management and additional research.

AF Schatzberg — 2006-12-07T05:57:42-00:00

J Clin Psychiatry, Vol. 67 Suppl 4 (2006), pp. 27-30.

OBJECTIVE: Currently, no evidence-based guidelines exist for the management of serotonin reuptake inhibitor (SRI) discontinuation syndrome. This article summarizes recommendations with respect to future research as well as clinical management recommendations for SRI discontinuation syndrome. PARTICIPANTS: In April 2004, a panel of physicians convened in New York City to discuss recommendations for clinical management of and additional research on SRI discontinuation syndrome. EVIDENCE: Previous guidance for management of SRI discontinuation syndrome was proposed in 1997 in a consensus meeting also chaired by Alan F. Schatzberg. A literature search of the PubMed database was conducted to identify articles on SRI discontinuation syndrome that have been published since 1997. CONSENSUS PROCESS: The 2004 panel reviewed important preclinical and clinical studies, discussed prospective investigation of this syndrome in clinical trials, and suggested the establishment of a research network to collect data in naturalistic settings. The panel also reviewed the management recommendations published in 1997 and subsequently updated the recommendations, taking into account the latest clinical data as well as the personal experience of its members with patients. CONCLUSIONS: Additional preclinical and clinical studies are necessary to further elucidate the underlying biological mechanisms of SRI discontinuation syndrome and to identify the patient populations and agents that are most affected by this phenomenon. Management strategies include gradual tapering of doses and should emphasize clinical monitoring and patient education.