CiteULike: Author Estrada

Common turbulent signature in sea surface temperature and chlorophyll maps

V Nieves — 2008-08-04T18:47:55-00:00

Geophysical Research Letters, Vol. 34 (1 December 2007), L23602.

A Distributional Approach to Asymptotics: Theory and Applications (Birkhäuser Advanced Texts / Basler Lehrbücher)

Ricardo Estrada — 2008-07-18T22:56:43-00:00

(08 February 2002)

Key features of this significantly expanded second edition: - addition of several new chapters and sections, including a presentation of time-domain asymptotics needed for the understanding of wavelet theory - extensive examples and problem sets - useful bibliography and index. This book is a modern introduction to asymptotic analysis intended not only for mathematicians, but for physicists, engineers, and graduate students as well. Written by two of the leading experts in the field, the text provides readers with a firm grasp of mathematical theory, and at the same time demonstrates applications in areas such as differential equations, quantum mechanics, noncommutative geometry, and number theory. "...The authors of this remarkable book are among the very few who have faced up to the challenge of explaining what an asymptotic expansion is, and of systematizing the handling of asymptotic series. The idea of using distributions is an original one, and we recommend that you read the book...[it] should be on your bookshelf if you are at all interested in knowing what an asymptotic series is." ¿ "The Bulletin of Mathematics Books" (Review of the 1st edition) "...The book is a valuable one, one that many applied mathematicians may want to buy. The authors are undeniably experts in their field...most of the material has appeared in no other book." ¿ "SIAM News" (Review of the 1st edition) Table of contents Preface 1. Basic Results in Asymptotics 2. Introduction to the Theory of Distributions 3. A Distributional Theory for Asymptotic Expansions 4. The Asymptotic Expansion of Multi-Dimensional Generalized Functions 5. The Asymptotic Expansion of Certain Series Considered by Ramamujan 6. The Cesaro Behavior of Distributions 7. Series of Dirac Delta Functions References Index

Three-Dimensional Analysis of a Concentrated Solar Flux

David Rosas — 2008-07-07T08:17:32-00:00

Journal of Solar Energy Engineering, Vol. 130, No. 1. (2008)

In order to improve the durability of receivers used in solar concentrating systems, it is necessary to minimize thermal stress during their operation. A possible way to do that is to design receivers in which the radiative flux density is homogeneous at the surface. For this reason, a detailed 3D study has been carried out for the distribution of concentrated solar radiation in the focal zone of a parabolic concentrator. A computer program has been developed to obtain isosurfaces of solar irradiance and achieve a homogeneous radiation flux on the receiver surface. The algorithm of the program proposes a methodology to obtain flux isosurfaces for a great variety of optical configurations. The effect of the optical errors on the mirror surface has been studied, as well as the effect of the shape of the mirror, e.g., round, square, or faceted. The numerical calculations were made using the convolution ray tracing technique.

Phytoplanktonic DOC and POC production in the Bransfield and Gerlache Straits as derived from kinetic experiments of 14C incorporation

Xosé Morán — 2008-06-25T13:08:48-00:00

Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 49, No. 4-5. (2002), pp. 769-786.

The production rates of DOC and POC by phytoplankton during the FRUELA 95 cruise were estimated by means of time-course experiments of 14C-bicarbonate incorporation. A three-compartment carbon exchange model was used to avoid the artifacts that may appear in end-point experiments due to heterotrophic removal of recently released DOC. The study area was classified into three regions with different ecological characteristics: Bransfield Strait, Gerlache Strait and the Gerlache-Bransfield Confluence (GB Confluence). Percent extracellular release (PER) for all stations ranged from 3% to 47%, with an average of 24%. In surface (5 m depth) waters, POC and DOC production rates were higher in Gerlache Strait than in the GB Confluence and Bransfield Strait. PER values followed an opposite trend, with an average of 26% in Bransfield Strait, 17% in the GB Confluence and 13% in Gerlache Strait. In Gerlache Strait, PER at 10 m depth was significantly higher than at the surface. With pooled data from all experiments, there was a positive relationship between DOC and POC production rates (log-log), but the slope significantly smaller than 1.0 indicated an inverse trend between PER and primary production rate. Phytoplanktonically produced DOC appeared to meet carbon requirements of heterotrophic prokaryotes in the whole area. A positive relationship between prokaryotic heterotrophic production and DOC production rate was found only in Bransfield Strait. These differences are discussed in relationship with the ecological characteristics of the different regions

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Anthony Philippakis — 2006-07-06T00:25:45-00:00

PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53.

While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed “CodeFinder”) that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors) is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs) associated with a given gene set and quantify the enrichment for combinatorial subsets of transcription factor binding site motifs comprising the hypothesized TRM within these predicted CRMs. As a model system, we have examined a TRM experimentally demonstrated to drive the expression of two genes in a sub-population of cells in the developing Drosophila mesoderm, the somatic muscle founder cells. This TRM was previously hypothesized to be a general mode of regulation for genes expressed in this cell population. In contrast, the present analyses suggest that a modified form of this cis regulatory code applies to only a subset of founder cell genes, those whose gene expression responds to specific genetic perturbations in a similar manner to the gene on which the original model was based. We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells.

A review of recent MOSFET threshold voltage extraction methods

A Ortiz-Conde — 2008-06-16T15:21:33-00:00

Microelectronics Reliability, Vol. 42, No. 4-5. ( 2002), pp. 583-596.

Growth and stretch response of human exstrophy bladder smooth muscle cells: molecular evidence of normal intrinsic function

Anna Orsola — 2004-12-28T18:20:19-00:00

BJU International, Vol. 95, No. 1., 144.

Solving the Coagulation Equation by the Moments Method

Paul Estrada — 2008-05-22T17:09:13-00:00

(25 Apr 2008)

We demonstrate an approach to solving the coagulation equation that involves using a finite number of moments of the particle size distribution. This approach is particularly useful when only general properties of the distribution, and their time evolution, are needed. The numerical solution to the integro-differential Smoluchowski coagulation equation at every time step, for every particle size, and at every spatial location is computationally expensive, and serves as the primary bottleneck in running evolutionary models over long periods of time. The advantage of using the moments method comes in the computational time savings gained from only tracking the time rate of change of the moments, as opposed to tracking the entire mass histogram which can contain hundreds or thousands of bins depending on the desired accuracy. The collision kernels of the coagulation equation contain all the necessary information about particle relative velocities, cross-sections, and sticking coefficients. We show how arbitrary collision kernels may be treated. We discuss particle relative velocities in both turbulent and non-turbulent regimes. We present examples of this approach that utilize different collision kernels and find good agreement between the moment solutions and the moments as calculated from direct integration of the coagulation equation. As practical applications, we demonstrate how the moments method can be used to track the evolving opacity, and also indicate how one may incorporate porous particles.

Strong far-field coherent scattering of ultraviolet radiation by holococcolithophores

Quintero Torres — 2008-05-04T23:04:15-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 3. (2006)

By considering the structure of holococcoliths (calcite plates that cover holococcolithophores, a haploid phase of the coccolithophore life cycle) as a photonic structure, we apply a discrete dipolar approximation to study the light backscattering properties of these algae. We show that some holococcolith structures have the ability to scatter the ultraviolet radiation. This property may represent an advantage for holococcolithophores possessing it, by allowing them to live higher in the water column than other coccolithophores.

Early beneficial effect of matrix metalloproteinase inhibition on blood-brain barrier permeability as measured by magnetic resonance imaging countered by impaired long-term recovery after stroke in rat brain

RR Sood — 2008-04-09T17:52:08-00:00

J. Cereb. Blood Flow Metab., Vol. 28, No. 2. (2008), pp. 431-438.

Proteolytic disruption of the extracellular matrix with opening of the blood-brain barrier (BBB) because of matrix metalloproteinases (MMPs) occurs in reperfusion injury after stroke. Matrix metalloproteinase inhibition blocks the early disruption of the BBB, but the long-term consequences of short-term MMP inhibition are not known. Recently, a method to quantify BBB permeability by graphical methods was described, which provides a way to study both early disruption of the BBB and long-term effects on recovery in the same animal. We used a broad-spectrum MMP inhibitor, BB1101, to determine both the usefulness of the Magnetic resonance imaging (MRI) method for treatment studies and the long-term effects on recovery. Magnetic resonance imaging studies were performed in control (N=6) and drug-treated (N=8) groups on a dedicated 4.7-T MRI scanner. Adult Wistar-Kyoto underwent a 2-h middle cerebral artery occlusion followed by an MRI study after 3 h of reperfusion, which consisted of T2- and diffusion-weighted techniques. Additionally, a rapid T1 mapping protocol was also implemented to acquire one pre-gadolinium-diethylenetriaminepentaacetic acid baseline data set followed by postinjection data sets at 3-min intervals for 45 mins. The same animal was imaged again at 48 h for lesion size estimation. Data was postprocessed pixel-wise to generate apparent diffusion coefficient and permeability coefficient maps. Treatment with BB-1101 significantly reduced BBB permeability at 3 h, but failed to reduce lesion size at 48 h. Behavioral studies showed impairment in recovery in treated rats. Magnetic resonance imaging allowed for the monitoring of multiple parameters in the same animal. Our studies showed that BB-1101 was an excellent inhibitor of the BBB damage. However, results show that BB-1101 may be responsible for significant deterioration in neurologic status of treated animals. Although these preliminary results suggest that BB-1101 is useful in reducing early BBB leakage owing to reperfusion injury in stroke, further studies will be needed to determine whether the later detrimental effects can be eliminated by shorter time course of drug delivery. © 2008 ISCBFM All rights reserved.

Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells.

RM Adam — 2008-03-11T15:57:45-00:00

Physiol Genomics, Vol. 20, No. 1. (15 December 2004), pp. 36-44.

Application of mechanical stimuli has been shown to alter gene expression in bladder smooth muscle cells (SMC). To date, only a limited number of "stretch-responsive" genes in this cell type have been reported. We employed oligonucleotide arrays to identify stretch-sensitive genes in primary culture human bladder SMC subjected to repetitive mechanical stimulation for 4 h. Differential gene expression between stretched and nonstretched cells was assessed using Significance Analysis of Microarrays (SAM). Expression of 20 out of 11,731 expressed genes ( approximately 0.17%) was altered >2-fold following stretch, with 19 genes induced and one gene (FGF-9) repressed. Using real-time RT-PCR, we tested independently the responsiveness of 15 genes to stretch and to platelet-derived growth factor-BB (PDGF-BB), another hypertrophic stimulus for bladder SMC. In response to both stimuli, expression of 13 genes increased, 1 gene (FGF-9) decreased, and 1 gene was unchanged. Six transcripts (HB-EGF, BMP-2, COX-2, LIF, PAR-2, and FGF-9) were evaluated using an ex vivo rat model of bladder distension. HB-EGF, BMP-2, COX-2, LIF, and PAR-2 increased with bladder stretch ex vivo, whereas FGF-9 decreased, consistent with expression changes observed in vitro. In silico analysis of microarray data using the FIRED algorithm identified c-jun, AP-1, ATF-2, and neurofibromin-1 (NF-1) as potential transcriptional mediators of stretch signals. Furthermore, the promoters of 9 of 13 stretch-responsive genes contained AP-1 binding sites. These observations identify stretch as a highly selective regulator of gene expression in bladder SMC. Moreover, they suggest that mechanical and growth factor signals converge on common transcriptional regulators that include members of the AP-1 family.

Major histocompatibility complex and tumor necrosis factor-alpha polymorphisms in pigeon breeder's disease.

A Camarena — 2008-03-05T13:26:26-00:00

Am J Respir Crit Care Med, Vol. 163, No. 7. (June 2001), pp. 1528-1533.

Pigeon breeders disease (PBD) is caused by the exposure of a susceptible host to avian antigens. However, genetic factors determining individual predisposition are unknown. In this work, polymorphisms of the major histocompatibility complex (MHC) class II alleles and tumor necrosis factor alpha (TNF-alpha) promoter were evaluated in 44 patients with PBD, 99 healthy unrelated controls (HC), and 50 exposed but asymptomatic subjects (EAS). MHC typing was performed by PCR-specific sequence oligonucleotide analysis, and TNF-alpha polymorphism at -238 and -308 positions by amplification refractory mutation system-PCR. PBD patients showed a significant increase of the alleles HLA-DRB1*1305 (p < 0.001, OR = 15.4, 95% CI = 3.18-102.6 [HC], and OR = 17.05, 95% CI = 2.25-357.8 [EAS]) and HLA-DQB1*0501 (p < 0.05, OR = 2.93, 95% CI = 1.21-7.15 [HC], and OR = 2.96, 95% CI = 1.0-9.14 [EAS]). A decrease of HLA-DRB1*0802 was also noticed in patients when compared with both control groups (p < 0.05). Haplotype analysis revealed an increase of DRB1*1305-DQB1*0301 and a decrease of DRB1*0802-DQB1*0402. PBD patients had an increased frequency of TNF-2(-)(308) compared with both control groups (p < 0.05). Patients exhibiting the TNF-2(-)(308) allele were younger (33.9 +/- 14.6 versus 44.2 +/- 10.4 yr; p < 0.05), and displayed more lymphocytes in their bronchoalveolar lavages (88.0 +/- 12.1 versus 68.9 +/- 17.2; p < 0.05). These results suggest that genetic factors located within the MHC region contribute to the development of PBD.

EEG feature extraction for classification of sleep stages

E Estrada — 2008-03-05T13:07:54-00:00

Engineering in Medicine and Biology Society, 2004. IEMBS '04. 26th Annual International Conference of the IEEE, Vol. 1 (2004), pp. 196-199 Vol.1.

Automated sleep staging based on EEG signal analysis provides an important quantitative tool to assist neurologists and sleep specialists in the diagnosis and monitoring of sleep disorders as well as evaluation of treatment efficacy. A complete visual inspection of the EEG recordings acquired during nocturnal polysomnography is time consuming, expensive, and often subjective. Therefore, feature extraction is implemented as an essential preprocessing step to achieve significant data reduction and to determine informative measures for automatic sleep staging. However, the analysis of the EEG signal and extraction of sensitive measures from it has been a challenging task due to the complexity and variability of this signal. We present three different schemes to extract features from the EEG signal: relative spectral band energy, harmonic parameters, and Itakura distance. Spectral estimation is performed by using autoregressive (AR) modeling. We then compare the performance of these schemes with the view to select an optimal set of features for specific, sensitive, and accurate neuro-fuzzy classification of sleep stages.

Recognition of host immune activation by Pseudomonas aeruginosa.

L Wu — 2007-12-27T22:31:35-00:00

Science, Vol. 309, No. 5735. (29 July 2005), pp. 774-777.

It is generally reasoned that lethal infections caused by opportunistic pathogens develop permissively by invading a host that is both physiologically stressed and immunologically compromised. However, an alternative hypothesis might be that opportunistic pathogens actively sense alterations in host immune function and respond by enhancing their virulence phenotype. We demonstrate that interferon-gamma binds to an outer membrane protein in Pseudomonas aeruginosa, OprF, resulting in the expression of a quorum-sensing dependent virulence determinant, the PA-I lectin. These observations provide details of the mechanisms by which prokaryotic organisms are directly signaled by immune activation in their eukaryotic host.

BiP mutants that are unable to interact with endoplasmic reticulum DnaJ proteins provide insights into interdomain interactions in BiP

Walid Awad — 2008-02-13T09:24:06-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 4. (29 January 2008), pp. 1164-1169.

The heat shock protein (Hsp)70 family of molecular chaperones interacts with unfolded proteins through a C-terminal substrate-binding domain (SBD) that is controlled by nucleotide binding to the N-terminal domain. The ATPase cycle is regulated by cochaperones, including DnaJ proteins that accelerate ATP hydrolysis to stabilize the Hsp70substrate complex. We found that R197 in hamster BiP, which resides at the surface of the nucleotide-binding domain, is critical for both association with endoplasmic reticulum DnaJ proteins and interaction with the SBD. Decreasing the positive charge at this residue enhanced basal ATPase activity, destabilized interaction with the SBD, and reduced substrate release both in vitro and in vivo. Mutation of three glutamic acids in the SBD mimicked many of these effects. Our data provide insights into communications between the two domains and suggest a mechanism by which DnaJ proteins increase ATP hydrolysis. 10.1073/pnas.0702132105

Subgraph centrality in complex networks.

E Estrada — 2005-08-16T00:11:35-00:00

Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 71, No. 5 Pt 2. (May 2005)

We introduce a new centrality measure that characterizes the participation of each node in all subgraphs in a network. Smaller subgraphs are given more weight than larger ones, which makes this measure appropriate for characterizing network motifs. We show that the subgraph centrality [C(S)(i)] can be obtained mathematically from the spectra of the adjacency matrix of the network. This measure is better able to discriminate the nodes of a network than alternate measures such as degree, closeness, betweenness, and eigenvector centralities. We study eight real-world networks for which C(S)(i) displays useful and desirable properties, such as clear ranking of nodes and scale-free characteristics. Compared with the number of links per node, the ranking introduced by C(S)(i) (for the nodes in the protein interaction network of S. cereviciae) is more highly correlated with the lethality of individual proteins removed from the proteome.

Localized field reduction and rate limitation in visible light photon counters

A Bross — 2008-01-25T10:52:29-00:00

Applied Physics Letters, Vol. 85, No. 24. (2004), pp. 6025-6027.

From early requirements to user interface prototyping: a methodological approach

A Martinez — 2007-05-06T09:32:34-00:00

Automated Software Engineering, 2002. Proceedings. ASE 2002. 17th IEEE International Conference on (2002), pp. 257-260.

The objective of this paper is to define a software production process which represents the correspondence between the primitive elements of a business model (represented in the framework i*) and the user interface of the software system. The representation of the user interface is compliant with the Unified Model Language (UML). We use a use case model as an intermediary between the business requirements and the application software. By doing this, we go a step further in the process of properly embedding early requirements engineering into the software production process, because organizational users can validate their requirements as early as possible. This is done through the validation of the user interfaces which are generated as a software representation of these requirements. These interfaces can also be reused for further refinement as a useful starting point in the software development process.

Disrupting -Amyloid Aggregation for Alzheimer Disease Treatment

LD Estrada — 2008-01-07T11:43:37-00:00

pp. 115-126.

Alzheimer's disease is a devastating degenerative disorder for which there is no cure or effective treatment. Although the etiology of Alzheimer's disease is not fully understood, compelling evidence indicates that deposition of aggregates composed by a misfolded form of the amyloid beta peptide (Aβ) is the central event in the disease pathogenesis. Therefore, an attractive therapeutic strategy is to prevent or reverse Aβ misfolding and aggregation. Diverse strategies have been described to identify inhibitors of this process, including screening of libraries of small molecules chemical compounds, rational design of synthetic peptides, assessment of natural Aβ-binding proteins and stimulation of the immune system by vaccination. In this article we describe these different approaches, their principles and their potential strengths and weaknesses. Overall the available data suggest that the development of drugs to interfere with Aβ misfolding and aggregation is a feasible target that hold great promise for the treatment of Alzheimer's disease.

Learning and earning: relational scales of children's work

Jennings — 2006-09-23T21:32:29-00:00

Area, Vol. 38, No. 3. (September 2006), pp. 231-239.

Quantitative evaluation of a novel image segmentation algorithm

FJ Estrada — 2008-01-02T05:20:01-00:00

Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference on, Vol. 2 (2005), pp. 1132-1139 vol. 2.

We present a quantitative evaluation of SE-MinCut, a novel segmentation algorithm based on spectral embedding and minimum cut. We use human segmentations from the Berkeley segmentation database as ground truth and propose suitable measures to evaluate segmentation quality. With these measures we generate precision/recall curves for SE-MinCut and three of the leading segmentation algorithms: mean-shift, normalized Cuts, and the local variation algorithm. These curves characterize the performance of each algorithm over a range of input parameters. We compare the precision/recall curves for the four algorithms and show segmented images that support the conclusions obtained from the quantitative evaluation.

Matrix metalloproteinase-mediated disruption of tight junction proteins in cerebral vessels is reversed by synthetic matrix metalloproteinase inhibitor in focal ischemia in rat.

Y Yang — 2007-11-24T09:34:49-00:00

J Cereb Blood Flow Metab, Vol. 27, No. 4. (April 2007), pp. 697-709.

Matrix metalloproteinases (MMPs) disrupt the blood-brain barrier (BBB) during reperfusion. Occludin and claudins are recently described tight junction proteins (TJPs) that form the BBB. We hypothesized that the opening of the BBB was because of the degradation of TJPs by the MMPs. Spontaneously hypertensive rats had a 90 mins middle cerebral artery occlusion with reperfusion for 2, 3, or 24 h. Matrix metalloproteinases were measured by immunohistochemistry and in situ and gel zymography. Real-time polymerase chain reaction (PCR) measured mRNAs of MMP-2 and -9, furin, membrane-type MMP (MT1-MMP), occludin, and claudin-5. There was opening of the BBB in the piriform cortex after 3 h of reperfusion, and an MMP inhibitor, BB-1101 (30 mg/kg), prevented the opening. At 3 h, in situ zymograms showed gelatinase activity. Zymography and PCR showed greater increases in MMP-2 than in MMP-9. There were increased mRNA and immunohistochemistry for MT1-MMP and furin, which activate MMP-2. Claudin-5 and occludin mRNA expression decreased at 2 h in both hemispheres with fragments of both proteins seen on Western blot by 3 h on the ischemic side; treatment with BB-1101 reversed the degradation of the TJPs. Immunohistochemistry at 3 h showed fragmented TJPs within the endothelial cell clefts. By 24 h, in situ zymography showed gelatinase activity and gel zymography showed elevated levels of MMP-9. Disrupted TJPs previously seen in endothelial cells appeared in the surrounding astrocytes. Our results provide direct evidence that MMPs open the BBB by degrading TJPs and that an MMP inhibitor prevents degradation of the TJPs by MMPs.

An Integrated in Silico Analysis of Drug-Binding to Human Serum Albumin

E Estrada — 2007-10-29T13:30:47-00:00

J. Chem. Inf. Model., Vol. 46, No. 6. (27 November 2006), pp. 2709-2724.

Abstract: Approaches such as quantitative structure-activity relationships (QSAR) and molecular modeling are integrated with the study of complex networks to understand drug binding to human serum albumin (HSA). A robust QSAR model using the topological substructural molecular descriptors/design (TOPS-MODE) approach has been derived and shows good predictability and interpretability in terms of structural contribution to drug binding to HSA. A perfect agreement exists between the group/fragment contributions found by TOPS-MODE and the specific interactions of drugs with HSA. These results indicate a preponderant contribution of hydrophobic regions of drugs to the specific binding to drug-binding sites 1 and 2 in HSA and specific roles of polar groups which anchor drugs to HSA binding sites. The occurrence of fragments contributing to drug binding to HSA can be represented by complex networks. The fragment-to-fragment complex network displays "small-world" and "scale-free" characteristics and in this way is similar to other complex networks including biological, social, and technological networks. A small number of fragments appear very frequently in most drugs. These molecular "empathic" fragments are good candidates for guiding future drug discovery research.

A web server for automatic analysis and extraction of relevant biological knowledge.

Juan Cedano — 2007-08-18T04:36:57-00:00

Comput Biol Med (24 May 2007)

Motivation: This application aims at assisting researchers with the extraction of significant medical and biological knowledge from data sets with complex relationships among their variables. Results: Non-hypothesis-driven approaches like Principal Curves of Oriented Points (PCOP) are a very suitable method for this objective. PCOP allows for obtaining of a representative pattern from a huge quantity of data of independent variables in a very flexible and direct way. A web server has been designed to automatically realize 'non-linear pattern' analysis, 'hidden-variable-dependent' clustering, and new samples 'local-dispersion-dependent' classification from the data involving new statistical techniques using the PCOP calculus. The tools facilitate the managing, comparison and visualization of results in a user-friendly graphical interface. Availability: http://ibb.uab.es/revresearch.

Outcomes and perioperative hyperglycemia in patients with or without diabetes mellitus undergoing coronary artery bypass grafting.

CA Estrada — 2007-08-17T20:08:25-00:00

Ann Thorac Surg, Vol. 75, No. 5. (May 2003), pp. 1392-1399.

BACKGROUND: The association between perioperative hyperglycemia and outcomes in patients with and without diabetes mellitus undergoing coronary artery bypass grafting is not well defined. We measured the association between perioperative hyperglycemia and outcomes among patients undergoing coronary artery bypass grafting. METHODS: We report a historic cohort study of 1574 patients who had undergone coronary artery bypass grafting between 1998 and 1999, 545 (34.6%) with diabetes. Perioperative blood glucose level was defined as the average of all blood glucose tests obtained on the day of and the day after surgery. Outcomes were 30-day mortality, infection rates (sternum, harvest site, sepsis, pneumonia, urinary tract), and resource utilization. RESULTS: After adjusting for diabetes status and calculated preoperative mortality or mediastinitis risk scores, each 50 mg/dL (2.78 mmol/L) blood glucose increase was not statistically associated with higher mortality (odds ratio 1.37; 95% confidence interval, 0.98 to 1.92; p = 0.07), or higher infection rate (odds ratio 1.23, 95% confidence interval 0.94 to 1.60; p = 0.14). Each 50 mg/dL blood glucose increase was associated with longer postoperative days by 0.76 days (95% confidence interval 0.36 to 1.17 days; p < 0.001), increased hospitalization charges by 2824 dollars (95% confidence interval 1599 dollars to 4049 dollars; p < 0.001), and increased hospitalization cost by 1769 dollars (95% confidence interval 928 dollars to 2610 dollars; p < 0.001). In the unadjusted analysis, infections occurred more frequently in patients with diabetes (6.6% vs 4.1%, p = 0.03). CONCLUSIONS: Perioperative hyperglycemia is associated with increased resource utilization in patients undergoing coronary artery bypass grafting with and without diabetes.

Treatment of dialysis catheter-related Staphylococcus aureus bacteremia with an antibiotic lock: a quality improvement report.

ID Maya — 2007-08-08T06:56:04-00:00

Am J Kidney Dis, Vol. 50, No. 2. (August 2007), pp. 289-295.

BACKGROUND: Dialysis catheter-related bacteremia is often treated successfully by instilling an antibiotic-heparin solution into the catheter lumen (an antibiotic lock) in conjunction with systemic antibiotic therapy without removal of the catheter. The efficacy of this therapy is uncertain in Staphylococcus aureus bacteremia. DESIGN: Quality improvement report. SETTING & PARTICIPANTS: 113 catheter-dependent hemodialysis outpatients with S aureus catheter-related bacteremia treated with a standardized antibiotic lock protocol. Data for all patients with catheter-related bacteremia are recorded in a prospective database. QUALITY IMPROVEMENT PLAN: In conjunction with systemic antibiotic therapy (vancomycin for methicillin-resistant S aureus or cefazolin for methicillin-sensitive S aureus), an antibiotic lock was instilled into each catheter lumen after each dialysis session for 3 weeks. MEASURES: Treatment failure is defined as persistent fever after 48 hours of antibiotic therapy or recurrent S aureus bacteremia within 90 days. Clinical cure is defined as resolution of fever and no recurrence of bacteremia. Major infection-related complications within 6 months were documented. RESULTS: The catheter could not be salvaged in 67 patients (59%) because of persistent fever in 40 patients and recurrent bacteremia in 27 patients. A clinical cure was achieved in 46 patients (41%). A serious complication of catheter-related bacteremia occurred in 9.7% of all patients (11 of 113 patients). Serious complications were observed in 25% of patients (10 of 40 patients) with persistent fever, but only 1.4% of all other patients (1 of 73 patients; P < 0.0001). LIMITATIONS: This was a single-center study. Serum antibiotic levels were not measured. CONCLUSIONS: Routine antibiotic lock therapy is not appropriate for patients with S aureus catheter-related bacteremia. Serious complications occur primarily in patients with persistent fever.

The higher-order matching polynomial of a graph

Oswaldo Araujo — 2007-07-13T18:08:02-00:00

Int. J. Math. Math. Sci., No. 10. (2005), pp. 1565-1576.

Complex Networks as Hypergraphs

Ernesto Estrada — 2006-09-23T14:07:47-00:00

(19 May 2005)

The representation of complex systems as networks is inappropriate for the study of certain problems. We show several examples of social, biological, ecological and technological systems where the use of complex networks gives very limited information about the structure of the system. We propose to use hypergraphs to represent these systems by introducing the concept of the complex hyper-network. We define several structural measures for complex hyper-networks. These measures characterize hyper-network structures on the basis of node participation in different hyper-edges (groups) and sub-hypergraphs. We also define two clustering coefficients, one characterizing the transitivity in the hyper-network through the proportion of hyper-triangles to paths of length two and the other characterizing the formation of triples of mutually adjacent groups in the hyper-network. All of these characteristics are studied in two different hyper-networks; a scientific collaboration hyper-network and an ecological competence hyper-network.

Topological structural classes of complex networks.

E Estrada — 2007-03-19T02:03:05-00:00

Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 75, No. 1 Pt 2. (January 2007)

We use theoretical principles to study how complex networks are topologically organized at large scale. Using spectral graph theory we predict the existence of four different topological structural classes of networks. These classes correspond, respectively, to highly homogenous networks lacking structural bottlenecks, networks organized into highly interconnected modules with low inter-community connectivity, networks with a highly connected central core surrounded by a sparser periphery, and networks displaying a combination of highly connected groups (quasicliques) and groups of nodes partitioned into disjoint subsets (quasibipartites). Here we show by means of the spectral scaling method that these classes really exist in real-world ecological, biological, informational, technological, and social networks. We show that neither of three network growth mechanisms-random with uniform distribution, preferential attachment, and random with the same degree sequence as real network-is able to reproduce the four structural classes of complex networks. These models reproduce two of the network classes as a function of the average degree but completely fail in reproducing the other two classes of networks.

Point scattering: A new geometric invariant with applications from (Nano)clusters to biomolecules

Ernesto Estrada — 2007-01-31T19:57:31-00:00

Journal of Computational Chemistry, Vol. 28, No. 4. (2007), pp. 767-777.

A new geometric invariant is defined from ?first principles? for a point ensemble, which can represent clusters, molecules, crystals, and biomolecules. The scattering of a point ensemble is defined in terms of the Euclidean distance matrix and a vector measuring the weighted departure of the points from the cluster centre. Using the Rayleigh-Ritz theorem this function is maximized obtaining the point scattering of the ensemble. The point scattering shows several properties which are useful for studying clusters, molecules, crystals, and biomolecules. We examined different natural clusters of hard spheres such as colloidal particles and fullerenes, as well as protein-peptide complexes and the effect of temperature on protein structure. In all cases point scattering differentiates point ensembles with different structures, which are not distinguished by other geometric invariants, such as the second moment of mass distribution, surface areas, and volumes. Point scattering also shows better correlation with thermodynamic parameters of binding and describes the interior cavities of hollowed ensembles better than the other geometric measures. © 2007 Wiley Periodicals, Inc. J Comput Chem 28: 767-777, 2007

Food webs robustness to biodiversity loss: The roles of connectance, expansibility and degree distribution

Ernesto Estrada — 2007-01-10T13:13:49-00:00

Journal of Theoretical Biology, Vol. 244, No. 2. (21 January 2007), pp. 296-307.

We analyse the robustness of food webs against species loss by considering the influence of several structural factors of the networks, such as connectance, degree distribution and expansibility. The last concept refers to the absence of structural bottlenecks in the food web, whose removal separate the network into large isolate clusters. In theory networks with identical connectance can display different expansibility characteristics. Using the spectral scaling method we studied 17 food networks and classified them as good expansion (GE) and not-GE networks. The combination of GE properties and degree distribution of species permitted the classification of food webs into six different classes. These classes characterize the differences in robustness of food webs to species loss. While the webs having uniform degree distributions and displaying GE properties are the most robust to species loss, the presence of bottlenecks and skewed distribution of the number of links per species make food webs very vulnerable to primary removal of species.

An Empirical Evaluation of the i* Framework in a Model-Based Software Generation Environment

Hugo Estrada — 2006-10-20T17:24:31-00:00

Lecture Notes in Computer Science : Advanced Information Systems Engineering (2006), pp. 513-527.

New fluorescent protein reporters for use with the <I>drosophila</I> gal4 expression system and for vital detection of balancer chromosomes

Marc Halfon — 2006-06-14T20:51:24-00:00

genesis, Vol. 34, No. 1-2. (2002), pp. 135-138.

No abstract.

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Anthony Philippakis — 2006-05-26T17:50:44-00:00

Application of a novel graph-theoretic folding degree index to the study of steroid-DB3 antibody binding affinity.

E Estrada — 2005-08-16T00:16:27-00:00

Comput Biol Chem, Vol. 27, No. 3. (July 2003), pp. 305-313.

A novel folding degree index, together with other macromolecular descriptors, is used to study steroid-DB3 antibody interactions. This index is based on graph spectral moments of a matrix representing the dihedral angles of a protein backbone. The causes influencing the different order of binding affinity of steroids to DB3 antibody are identified. It is shown that the changes in the chain compactness of the DB3 antibody with respect to its center of mass (radius of gyration) is compensated by a change in the folding degree index in the contrary sense. In fact, the increment in compactness of chain L and the lower increment in the folding degree index of chain H are able to explain the variations in affinity for DB3 of the steroids studied. Consequently, the highest binding affinities are reached by increasing the compactness of chain L in DB3 at the same time that producing the smallest increment in the folding degree of chain H. This study shows the possibilities of application for the graph-theoretic folding degree index in studying drug-protein interactions.

Characterization of the amino acid contribution to the folding degree of proteins.

E Estrada — 2005-08-16T00:16:14-00:00

Proteins, Vol. 54, No. 4. (1 March 2004), pp. 727-737.

The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach.

A protein folding degree measure and its dependence on crystal packing, protein size, secondary structure, and domain structural class.

E Estrada — 2005-08-16T00:15:45-00:00

J Chem Inf Comput Sci, Vol. 44, No. 4. (g 2004), pp. 1238-1250.

Comparing two or more protein structures with respect to their degree of folding is common practice in structural biology despite the fact that there is no scale for a folding degree. Here we introduce a formal definition of a folding degree, capable of quantitative characterization. This enables ordering among protein chains based on their degree of folding. The folding degree of a data set of 152 representative nonhomologous proteins is then studied. We demonstrate that the variation in the folding degree seen for this data set is not due to crystallization artifacts or experimental conditions, such as resolution, refinement protocol, pH, or temperature. A good linear relationship is observed between the folding degree and the percentages of secondary structures in the protein. The folding degree is able to account for the small changes produced in the structure due to crystal packing and temperature. Automating the classification of proteins into their respective structural domain classes, namely mainly-alpha, mainly-beta, and alpha-beta, is also possible.