Encoding dynamics for multiscale community detection: Markov time sweeping for the map equation.

The detection of community structure in networks is intimately related to finding a concise description of the network in terms of its modules. This notion has been recently exploited by the map equation formalism [Rosvall and Bergstrom, Proc. Natl.

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals.

Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules.

Combinatorial stresses kill pathogenic Candida species.

Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses.

Endothelin ET(B) receptors are involved in the relaxation to the pig urinary bladder neck.

Aims: The involvement of endothelin receptors in the contraction of the lower urinary tract smooth muscle is well established. There is scarce information, however, about endothelin receptors mediating relaxation of the bladder outlet region. The current study investigates the possible existence of endothelin ET(B) receptors involved in the relaxation of pig bladder neck.

Sensory experience modifies spontaneous state dynamics in a large-scale barrel cortical model.

Experimental evidence suggests that spontaneous neuronal activity may shape and be shaped by sensory experience. However, we lack information on how sensory experience modulates the underlying synaptic dynamics and how such modulation influences the response of the network to future events. Here we study whether spike-timing-dependent plasticity (STDP) can mediate sensory-induced modifications in the spontaneous dynamics of a new large-scale model of layers II, III and IV of the rodent barrel cortex.

Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit.

In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the 'right' split into communities.

Mechanisms involved in testosterone-induced relaxation to the pig urinary bladder neck.

Objectives: Testosterone replacement therapy improves bladder capacity in urinary tract dysfunction. There is no information, however, about the role of this steroid hormone on the muscle tension of the bladder outflow region. The current study investigated the mechanisms underlying the testosterone-induced action in the pig bladder neck.

Parathyroid carcinoma in multiple endocrine neoplasia type 1. Case report and review of the literature.

Parathyroid carcinoma is an infrequent cause of primary hyperparathyroidism. Although hyperparathyroidism in multiple endocrine neoplasia 1 (MEN1) syndrome is the most common manifestation, parathyroid carcinoma is rare. We report a male patient who was diagnosed at 44 years of age with parathyroid carcinoma in the context of MEN1 syndrome coincident with a malignant gastrinoma and non-functioning adrenal adenomas.

Squeeze-and-breathe evolutionary Monte Carlo optimization with local search acceleration and its application to parameter fitting.

Estimating parameters from data is a key stage of the modelling process, particularly in biological systems where many parameters need to be estimated from sparse and noisy datasets. Over the years, a variety of heuristics have been proposed to solve this complex optimization problem, with good results in some cases yet with limitations in the biological setting. In this work, we develop an algorithm for model parameter fitting that combines ideas from evolutionary algorithms, sequential Monte Carlo and direct search optimization.

Verbal and visual memory performance and hippocampal volumes, measured by 3-Tesla magnetic resonance imaging, in patients with Cushing's syndrome.

Context: Cushing's syndrome (CS) affects cognition and memory.

Objective: Our objective was to evaluate memory and hippocampal volumes (HV) on 3-tesla magnetic resonance imaging (3T MRI) in CS patients and controls.

Patients And Methods: Thirty-three CS patients (11 active, 22 cured) and 34 controls matched for age, sex, and education underwent Rey Auditory Verbal Learning Test and Rey-Osterrieth Complex Figure memory tests.

Case report. Primary mucosa-associated lymphoid tissue lymphoma as a pleural mass.

Primary pleural lymphoma is a rare entity that has been described in association with human immunodeficiency virus (HIV) infection or pyothorax. It occurs in only 7% of primary lymphoma cases. We report the case of a 52-year-old male with no history of HIV infection or pyothorax who was diagnosed of obstructive sleep apnoea syndrome (OSAS) and underwent a routine chest X-ray to screen for any organic cause of the symptoms.

Mechanisms involved in endothelin-1-induced contraction of the pig urinary bladder neck.

Aims: There is no information about the signaling pathways involved in the endothelin-1 (ET-1)-induced contraction of bladder neck. The current study investigates the mechanisms involved in the ET-1-elicited contraction in the pig bladder neck.

Methods: Bladder neck strips were mounted in organ baths containing physiological saline solution at 37°C and gassed with 95% O(2) and 5% CO(2) , for isometric force recording to endothelin receptor agonists, noradrenaline (NA), and electrical field stimulation.

Flow graphs: interweaving dynamics and structure.

The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential because different dynamical processes may be affected very differently by network topology. A full characterization of such systems thus requires a formalization that encompasses both aspects simultaneously, rather than relying only on the topological adjacency matrix.

Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin-myosin light chain interaction.

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models.

Contribution of BK channels to action potential repolarisation at minimal cytosolic Ca2+ concentration in chromaffin cells.

BK channels modulate cell firing in excitable cells in a voltage-dependent manner regulated by fluctuations in free cytosolic Ca(2+) during action potentials. Indeed, Ca(2+)-independent BK channel activity has ordinarily been considered not relevant for the physiological behaviour of excitable cells. We employed the patch-clamp technique and selective BK channel blockers to record K(+) currents from bovine chromaffin cells at minimal intracellular (about 10 nM) and extracellular (free Ca(2+)) Ca(2+) concentrations.

Transient dynamics around unstable periodic orbits in the generalized repressilator model.

We study the temporal dynamics of the generalized repressilator, a network of coupled repressing genes arranged in a directed ring topology, and give analytical conditions for the emergence of a finite sequence of unstable periodic orbits that lead to reachable long-lived oscillating transients. Such transients dominate the finite time horizon dynamics that is relevant in confined, noisy environments such as bacterial cells (see our previous work [Strelkowa and Barahona, J. R.

[Intracranial hypotension syndrome: a review of the magnetic resonance findings].

Introduction: Intracranial hypotension syndrome (IHS) is a syndrome with a variable aetiology and clinical presentation that is, in most cases, caused by leakage of cerebrospinal fluid (CSF) through the thecal sac. Orthostatic headache associated to the typical magnetic resonance imaging (MRI) findings, secondary to depletion of CSF, is the key to a correct diagnosis.

Aims: To show the imaging findings that, within a suitable clinical context, allow this condition to be identified and diagnosed.

Complex thyroid nodules with nondiagnostic fine needle aspiration cytology: histopathologic outcomes and comparison of the cytologic variants (cystic vs. acellular).

Management of complex thyroid nodules (CTN) is a common dilemma due to their high prevalence and frequent nondiagnostic fine needle aspiration cytology (FNAC). In order to know the rate of malignancy, we reviewed our experience about histopathologic diagnosis of CTN with nondiagnostic FNAC, and we analyzed if cytological variants of nondiagnostic FNAC indicated different histopathologic outcomes. We conducted a review of 927 consecutive aspirations performed between 2003 and 2008.

Mechanisms involved in the nitric oxide independent inhibitory neurotransmission to the pig urinary bladder neck.

Aims: The current study investigates the mechanisms involved in nitric oxide (NO)-independent, nonadrenergic, noncholinergic (NANC) inhibitory neurotransmission to the pig urinary bladder neck.

Methods: Urothelium-denuded strips were mounted in organ baths containing physiological saline solution (PSS) at 37°C for isometric force recordings. The relaxations to electrical field stimulation (EFS) were carried out on strips treated with guanethidine, atropine and N(G) -nitro-L-arginine, to block noradrenergic neurotransmission, muscarinic receptors and NO synthase, respectively, and precontracted with phenylephrine.

Diagnosis of cure in Cushing's syndrome: lessons from long-term follow-up.

It is generally assumed that endocrine 'cure' of hypercortisolism after successful treatment for Cushing's syndrome (CS) is associated with reversal of increased morbidity and mortality, typical of the active disease. However, recent data do not support this idea; increased cardiovascular risk is still present 5 years after endocrine cure, and health-related quality of life (HRQoL), although improved when compared to the active phase of hypercortisolism, is still impaired when compared to normal population. Abnormal body composition typical of hypercortisolism (i.

Stability of graph communities across time scales.

The complexity of biological, social, and engineering networks makes it desirable to find natural partitions into clusters (or communities) that can provide insight into the structure of the overall system and even act as simplified functional descriptions. Although methods for community detection abound, there is a lack of consensus on how to quantify and rank the quality of partitions. We introduce here the stability of a partition, a measure of its quality as a community structure based on the clustered autocovariance of a dynamic Markov process taking place on the network.

Body composition after endogenous (Cushing's syndrome) and exogenous (rheumatoid arthritis) exposure to glucocorticoids.

Exposure to chronic glucocorticoid (GC) excess determines changes in body composition. The aim of the study was to compare body composition in women exposed to endogenous hypercortisolism (Cushing's syndrome, CS), exogenous glucocorticoid treatment (rheumatoid arthritis, RA) and controls. Fifty-one CS women, 26 RA women treated with low-dose prednisone (5 mg/day or 10 mg/2 days), and 78 female controls were included.

Crowding-induced anisotropic transport modulates reaction kinetics in nanoscale porous media.

We quantify the emergence of persistent anisotropy in the diffusion of spherical tracer particles through a nanoscale porous medium composed of a uniform distribution of purely symmetric crowding particles. We focus on the interior of a biological cell as an example of such a medium and find that diffusion is highly directional for distances comparable to the size of some organelles. We use a geometrical procedure that avoids the standard orientational averaging to quantify the anisotropy of diffusive paths and show that the point source distributions are predominantly of prolate ellipsoidal shape as a result of local volume exclusion.