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Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS., (© 2018 The Authors. Published under the terms of the CC BY 4.0 license.)

ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b)., (open access.)

In the Mediterranean region, wildfires are a major disturbance, determined by ecosystem and forest species characteristics. Both the flammability and resistance to fire of a mixed forest may vary from those of the individual species. Two mixed Mediterranean woodlands, a Cupressus sempervirens and Quercus ilex stand in Italy; and a Juniperus thurifera and Quercus faginea stand in Spain were investigated. Laboratory flammability tests were conducted on live foliage, litter samples and on litter beds from individual and mixed species to evaluate: (i) the flammability traits of the mixtures of live foliage and litter samples; (ii) whether the flammability of the two-species mixtures are non-additive, i.e., differ from expected flammability based on arithmetic sum of the single effects of each components species in monospecific fuel; (iii) the ignition success and initial fire propagation in litter beds. Flammability tests were also conducted on bark samples to estimate the resistance of the tree species to fire. The ignitibility of live foliage was lower and the combustibility was higher in Cupressaceae than in Quercus . Non-additive effects were observed in some flammability components of live foliage and litter, especially in the mixtures of C. sempervirens and Q. ilex . Ignitability and combustibility were higher and lower than expected, respectively, and tended to be driven by Quercus ), while the consumability was lowered more than expected by both Cupressaceae . The ignition success in the litter beds was low, especially for the presence of Cupressaceae that increase the bulk density of the mixtures. Cupressaceae , which have a thinner bark, suffered more damage to the cambium after shorter exposure to the heat source than Quercus species. In all the species studied, time to reach lethal temperatures in the cambium was dependent on thickness rather than on flammability of the bark. The study findings revealed that tree species may influence flammability of mixed fuels disproportionately to their load. The studied species showed to exert a contrasted effect on flammability of the mixtures, increasing ignitability and decreasing combustibility and consumability well out of their proportion in the mixture. This may potentially influence fire dynamics in mixed forests.

Background: Restless legs syndrome (RLS) is a common complication of uremia that may improve after transplantation. Its frequency might not be as low as expected, as some uremic disturbances may continue even after a successful graft. Our aim was to investigate the prevalence and related conditions for RLS in renal transplant patients., Methods: We carried out a cross-sectional, observational study. A self-administered questionnaire following the International Restless Legs Syndrome Study Group diagnostic criteria was administered to 129 patients (82 men and 47 women) aged 57 ± 12.8 years followed up for at least 1 year, with stable renal function (Cr 1.5 ± 0.54 mg/dL). Patients with probable RLS according to the screening questionnaire underwent comprehensive neurological examination to exclude RLS mimics., Results: The frequency of RLS according to questionnaires was 29.5% (18 men/20 women). After neurological exam, RLS was confirmed in 19 patients providing an overall frequency of 14.8% (higher than the prevalence in the general population). A definitive diagnosis of RLS was established for 6 men (7.3%) and 13 women (27.7%), indicating a positive predictive value for the screening questionnaire of 65% for women and 33% for men. There were fewer patients under renin-angiotensin aldosterone system (RAAS) blocking treatment in the RLS group (21.1 vs. 47.3%). Women with RLS had poorer renal function (52 ± 17.5 vs. 42 ± 13.9 mL/min) and phosphate-reabsorption rate (75 ± 10.5 vs. 65 ± 9.2). There was no difference in age, comorbidities, anticalcineurin therapy, renal function, anemia and time since transplantation between transplant patients with and without RLS., Conclusion: The prevalence of RLS after transplantation remains high (14.8%). This condition is twice more prevalent for females. Contribution of RAAS, graft function and phosphate overload requires further investigation., (© 2018 S. Karger AG, Basel.)

This study aimed to evaluate the reliability of cone-beam computed tomography (CBCT) imaging of the maxillary structures and the postoperative dentoskeletal, nasal airway, periodontal, and facial soft tissue changes after surgically assisted rapid palatal expansion (SARPE). A systematic review of the literature on CBCT analysis of SARPE was performed. The PubMed, Embase, and Cochrane Library databases were searched. Nine articles were included, involving a total of 228 patients. The general trend was tooth-borne distraction with pterygomaxillary dysjunction. A systematic increase in all transverse dimensions at the dentoalveolar and dental levels, as well as a certain degree of tipping and extrusion of the anchorage teeth and tipping of the skeletal segments, was detected. Soft tissue findings reflected the underlying dentoalveolar changes. A decrease in the buccal alveolar bone thickness and alveolar crest level occurred. Results confirm that CBCT is an accurate and reliable method to assess anatomical changes after SARPE. Although this systematic review provides valuable preliminary information about the effects of SARPE, results should be interpreted with caution due to the low level of evidence of the publications, great heterogeneity among study groups regarding outcome variables and surgical-orthodontic protocols, and lack of long-term data., (Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.)

Background: Early branching or syllepsis has been positively correlated with high biomass yields in short-rotation coppice (SRC) poplar plantations, which could represent an important lignocellulosic feedstock for the production of second-generation bioenergy. In prior work, we generated hybrid poplars overexpressing the chestnut gene RELATED TO ABI3/VP1 1 ( CsRAV1 ), which featured c. 80% more sylleptic branches than non-modified trees in growth chambers. Given the high plasticity of syllepsis, we established a field trial to monitor the performance of these trees under outdoor conditions and a SRC management., Results: We examined two CsRAV1-overexpression poplar events for their ability to maintain syllepsis and their potential to enhance biomass production. Two poplar events with reduced expression of the CsRAV1 homologous poplar genes PtaRAV1 and PtaRAV2 were also included in the trial. Under our culture conditions, CsRAV1-overexpression poplars continued developing syllepsis over two cultivation cycles. Biomass production increased on completion of the first cycle for one of the overexpression events, showing unaltered structural, chemical, or combustion wood properties. On completion of the second cycle, aerial growth and biomass yields of both overexpression events were reduced as compared to the control., Conclusions: These findings support the potential application of CsRAV1-overexpression to increase syllepsis in commercial elite trees without changing their wood quality. However, the syllepsis triggered by the introduction of this genetic modification appeared not to be sufficient to sustain and enhance biomass production.

Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically.

MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined.

Several drug-metabolizing enzymes, preferentially expressed in the liver, have the potential to act as minor histocompatibility antigens. In the present study, we analyzed the impact of glutathione S-transferase T1 (GSTT1), glutathione S-transferase M1, glutathione S-transferase P1, and UDP glucuronosyl transferase 2B17 (UGT2B17) disparities on the outcome of 125 patients undergoing allogeneic hematopoietic stem cell transplantation. Grades 2 to 4 acute graft-versus-host disease (aGVHD) developed in 56.2% versus 73.3% of GSTT1-matched versus mismatched patients (P = .048). Remarkably, 8.6% GSTT1-matched patients developed grades 2 to 4 liver aGVHD, compared with 36.8% among GSTT1-mismatched recipients (P < .001). Regarding chronic graft-versus-host disease (cGVHD), 34.8% versus 70.7% matched versus mismatched patients developed overall cGVHD (P = .038) and 16.3% versus 48% developed hepatic cGVHD (P = .006). We also found a strong association between the UGT2B17 mismatch and the risk of severe aGVHD (P = .001), especially with gut involvement (P < .001). Most striking was the influence of the GSTT1 mismatch on nonrelapse mortality (26.8% versus 52.6%, P = .031) and overall survival (62% versus 36.9%, P = .045). In summary, UGT2B17 and GSTT1 mismatch are risk factors for the development of GVHD and the latter also influences on mortality and survival after allogeneic transplantation from HLA-identical donors., (Copyright © 2014 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.)

Parathyroid carcinoma is a very rare malignancy. It has been associated with hyperparathyroidism-jaw tumour syndrome, familial isolated primary hyperparathyroidism, and multiple endocrine neoplasia type 1 (MEN-1) and 2A (MEN-2A) syndromes. We report a 54-year-old man with a MEN-2A which presents with a nonfunctional metastatic parathyroid carcinoma and a pheochromocytoma in the absence of medullary thyroid carcinoma. Only a few cases of parathyroid carcinoma have been reported in the literature associated with this syndrome.

Primary cardiac tumors constitute an infrequent heart pathology with a generally good prognosis. We present the case of a 45-year-old woman without a relevant medical history and with recurrent transient ischemic attacks of unknown origin. After follow-up with neurologic examination and repeated echocardiograms, an elongated mobile mass image was seen in the left atrial appendage. Surgical treatment consisted of resecting the mass by left atrial appendage excision through left atriotomy, closing with running suture. Anatomopathologic examination revealed findings compatible with a hamartomatous-like malformation. Discharged 5 days after surgery, the patient has no symptoms and does not require any drugs 1 year later., (Copyright © 2013 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

Assessment of the flammability of ornamental vegetation (particularly hedges) planted around houses is necessary in light of the increasing urbanization of the wildland-urban interfaces (WUIs) and the high fire occurrence in such areas. The structure and flammability of seven of the species most frequently planted as hedges in Provence (southeastern France) were studied at particle level. Spatial repartition of the different types of fuel particles within plants was assessed by means of the cube method. The leaf flammability was assessed using an epiradiator as a burning device, and measurements of foliar physical characteristics and gross heat of combustion (GHC) helped to explain the results of burning experiments. Co-inertia analysis revealed that species with thin leaves were quick to ignite (Pyracantha coccinea, Phyllostachys sp.) and species with high leaf GHC burned the longest (Pittosporum tobira, Nerium oleander). Species presenting high ignitability (Photinia fraseri, Phyllostachys sp. and Pyracantha coccinea) were characterized by high foliar surface area-to-volume ratio, and species presenting lower ignitability were characterized by high GHC (Pittosporum tobira, Nerium oleander, Cupressus sempervirens). Hierarchical cluster analysis of the flammability variables (ignition frequency, time-to-ignition and flaming duration) categorized the relative flammability of the seven species (including dead Cupressus sempervirens) in five clusters of species from poorly flammable (Pittosporum tobira) to extremely flammable (dead Cupressus sempervirens).This study provides useful information for reducing fire risk in WUIs in the study area.

Myelolipoma is a benign tumour consisting of mature fat with scattered foci of haematopoietic elements resembling bone marrow. Extra-adrenal myelolipomas are an infrequent pattern of presentation. We report the case of a 64-year-old woman who presented a heterogeneous 1.4×2.5×3 cm paravertebral thoracic mass detected by chest tomography during the study of a leukocytosis of unknown aetiology. The CT findings and pathology revealed the diagnosis of myelolipoma.

The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

In Precision Agriculture, images coming from camera-based sensors are commonly used for weed identification and crop line detection, either to apply specific treatments or for vehicle guidance purposes. Accuracy of identification and detection is an important issue to be addressed in image processing. There are two main types of parameters affecting the accuracy of the images, namely: (a) extrinsic, related to the sensor's positioning in the tractor; (b) intrinsic, related to the sensor specifications, such as CCD resolution, focal length or iris aperture, among others. Moreover, in agricultural applications, the uncontrolled illumination, existing in outdoor environments, is also an important factor affecting the image accuracy. This paper is exclusively focused on two main issues, always with the goal to achieve the highest image accuracy in Precision Agriculture applications, making the following two main contributions: (a) camera sensor arrangement, to adjust extrinsic parameters and (b) design of strategies for controlling the adverse illumination effects.

Primary sclerosing cholangitis is a chronic progressive disorder which involves the medium size and large ducts in the intrahepatic and extrahepatic biliary tree. The great majority of cases have underlying inflammatory bowel disease, mainly ulcerative colitis. A higher risk of colorectal cancer has been described among ulcerative colitis patients with primary sclerosing cholangitis. Here we report a case of a primary sclerosing cholangitis in a young male with a newly diagnosed ulcerative colitis presenting with colonic dysplasia. Surveillance for colorectal cancer should be strongly recommended in this group of patients., (Copyright © 2012. Published by Elsevier B.V.)

MAP17 is a small, 17-kDa, non-glycosylated membrane protein that is overexpressed in a percentage of carcinomas. In the present work, we have analyzed the role of MAP17 expression during mammary cancer progression. We have found that MAP17 is expressed in 60% human mammary tumors while it is not expressed in normal or benign neoplasias. MAP17 levels increased with breast tumor stage and were strongly correlated with mammary tumoral progression. A significant increase in the levels of reactive oxygen species (ROS) was observed in MAP17-expressing cells, as compared with parental cells. This increase was further paralleled by an increase in the tumorigenic capacity of carcinoma cells but not in immortal non-tumoral breast epithelial cells, which provides a selective advantage once tumorigenesis has begun. Expression of specific MAP17 shRNA in protein-expressing tumor cells reduced their tumorigenic capabilities, which suggests that this effect is dependent upon MAP17 protein expression. Our data show that ROS functions as a second messenger that enhances tumoral properties, which are inhibited in non-tumoral cells. We have found that p38α activation mediates this response. MAP17 triggers a ROS-dependent, senescence-like response that is abolished in the absence of p38a activation. Furthermore, in human breast tumors, MAP17 activation is correlated with a lack of phosphorylation of p38α. Therefore, MAP17 is overexpressed in late-stage breast tumors, in which oncogenic activity relies on p38 insensitivity to induce intracellular ROS.

ID29 is an ESRF undulator beamline with a routinely accessible energy range of between 20.0 keV and 6.0 keV (λ = 0.62 Å to 2.07 Å) dedicated to the use of anomalous dispersion techniques in macromolecular crystallography. Since the beamline was first commissioned in 2001, ID29 has, in order to provide an improved service to both its academic and proprietary users, been the subject of almost continuous upgrade and refurbishment. It is now also the home to the ESRF Cryobench facility, ID29S. Here, the current status of the beamline is described and plans for its future are briefly outlined.

This paper proposes a new method, oriented to image real-time processing, for identifying crop rows in maize fields in the images. The vision system is designed to be installed onboard a mobile agricultural vehicle, that is, submitted to gyros, vibrations, and undesired movements. The images are captured under image perspective, being affected by the above undesired effects. The image processing consists of two main processes: image segmentation and crop row detection. The first one applies a threshold to separate green plants or pixels (crops and weeds) from the rest (soil, stones, and others). It is based on a fuzzy clustering process, which allows obtaining the threshold to be applied during the normal operation process. The crop row detection applies a method based on image perspective projection that searches for maximum accumulation of segmented green pixels along straight alignments. They determine the expected crop lines in the images. The method is robust enough to work under the above-mentioned undesired effects. It is favorably compared against the well-tested Hough transformation for line detection.

A reliable and reproducible method to automatically characterize the radiation sensitivity of macromolecular crystals at the ESRF beamlines has been developed. This new approach uses the slope of the linear dependence of the overall isotropic B-factor with absorbed dose as the damage metric. The method has been implemented through an automated procedure using the EDNA on-line data analysis framework and the MxCuBE data collection control interface. The outcome of the procedure can be directly used to design an optimal data collection strategy. The results of tests carried out on a number of model and real-life crystal systems are presented.

Prescribed burning is commonly used to prevent accumulation of biomass in fire-prone shrubland in NW Spain. However, there is a lack of knowledge about the efficacy of the technique in reducing fire hazard in these ecosystems. Fire hazard in burned shrubland areas will depend on the initial capacity of woody vegetation to recover and on the fine ground fuels existing after fire. To explore the effect that time since burning has on fire hazard, experimental tests were performed with two fuel complexes (fine ground fuels and regenerated shrubs) resulting from previous prescribed burnings conducted in a gorse shrubland (Ulex europaeus L.) one, three and five years earlier. A point-ignition source was used in burning experiments to assess ignition and initial propagation success separately for each fuel complex. The effect of wind speed was also studied for shrub fuels, and several flammability parameters were measured. Results showed that both ignition and initial propagation success of fine ground fuels mainly depended on fuel depth and were independent of time since burning, although flammability parameters indicated higher fire hazard three years after burning. In contrast, time since burning increased ignition and initial propagation success of regenerated shrub fuels, as well as the flammability parameters assessed, but wind speed had no significant effect. The combination of results of fire hazard for fine ground fuels and regenerated shrubs according to the variation in relative coverage of each fuel type after prescribed burning enabled an assessment of integrated fire hazard in treated areas. The present results suggest that prescribed burning is a very effective technique to reduce fire hazard in the study area, but that fire hazard will be significantly increased by the third year after burning. These results are valuable for fire prevention and fuel management planning in gorse shrubland areas., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

This paper presents a mapping method for wide row crop fields. The resulting map shows the crop rows and weeds present in the inter-row spacing. Because field videos are acquired with a camera mounted on top of an agricultural vehicle, a method for image sequence stabilization was needed and consequently designed and developed. The proposed stabilization method uses the centers of some crop rows in the image sequence as features to be tracked, which compensates for the lateral movement (sway) of the camera and leaves the pitch unchanged. A region of interest is selected using the tracked features, and an inverse perspective technique transforms the selected region into a bird's-eye view that is centered on the image and that enables map generation. The algorithm developed has been tested on several video sequences of different fields recorded at different times and under different lighting conditions, with good initial results. Indeed, lateral displacements of up to 66% of the inter-row spacing were suppressed through the stabilization process, and crop rows in the resulting maps appear straight.

We present a novel strategy for computing disparity maps from hemispherical stereo images obtained with fish-eye lenses in forest environments. At a first segmentation stage, the method identifies textures of interest to be either matched or discarded. This is achieved by applying a pattern recognition strategy based on the combination of two classifiers: Fuzzy Clustering and Bayesian. At a second stage, a stereovision matching process is performed based on the application of four stereovision matching constraints: epipolar, similarity, uniqueness and smoothness. The epipolar constraint guides the process. The similarity and uniqueness are mapped through a decision making strategy based on a weighted fuzzy similarity approach, obtaining a disparity map. This map is later filtered through the Hopfield Neural Network framework by considering the smoothness constraint. The combination of the segmentation and stereovision matching approaches makes the main contribution. The method is compared against the usage of simple features and combined similarity matching strategies.

The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.

Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.

Experimental evidence has revealed that several thymidylate synthase (TS) DNA polymorphisms modulate gene expression, which, in turn is known to be down-regulated by oestrogen receptor subtypes. Consequently, this process might be influenced by female hormones. Based on these data, we investigated whether patient's gender and TS polymorphism exert an interactive effect on the clinical evolution of patients with advanced colorectal cancer (CRC) subjected to 5 fluorouracil (5FU)-based adjuvant chemotherapy. A retrospective study was carried out on paraffin-embedded sections from 81 CRC patients. A variable tandem repeat (VNTR) of 28 bp, a G/C single nucleotide polymorphism (SNP), and a deletion of 6 bp (ins1494del 6 bp) were studied. Genotyping methods were polymerase chain reaction (PCR) for VNTR, and PCR followed by restriction length fragment polymorphism (PCR-RFLP) for SNP and ins1494del 6 bp. The effect of TS genotype and gender on overall and progression-free survival was assessed in univariate and multivariate (Cox regression model) tests. In male patients, the study of combined TS genotypes showed that G&6+/6+ was an adverse marker for overall (P=0.04; median: not reached) and progression-free survival (P=0.03; median: 12 months, 95% CI: 0-32.4). In the multivariate analysis, the concurrence of G&6+/6+ combination and male patients resulted in a 5.5-fold increased risk of relapse or disease progression (95% CI: 1-32.1; likelihood test P=0.004; interaction P=0.06). TS genotype did not affect survival among women. The present study supports that the effect of TS polymorphisms on the clinical evolution of advanced CRC patients is significantly influenced by gender.

In this paper we propose a new method for combining simple classifiers through the analogue Hopfield Neural Network (HNN) optimization paradigm for classifying natural textures in images. The base classifiers are the Fuzzy clustering (FC) and the parametric Bayesian estimator (BP). An initial unsupervised training phase determines the number of clusters and estimates the parameters for both FC and BP. Then a decision phase is carried out, where we build as many Hopfield Neural Networks as the available number of clusters. The number of nodes at each network is the number of pixels in the image which is to be classified. Each node at each network is initially loaded with a state value, which is the membership degree (provided by FC) that the node (pixel) belongs to the cluster associated to the network. Each state is later iteratively updated during the HNN optimization process taking into account the previous states and two types of external influences exerted by other nodes in its neighborhood. The external influences are mapped as consistencies. One is embedded in an energy term which considers the states of the node to be updated and the states of its neighbors. The other is mapped as the inter-connection weights between the nodes. From BP, we obtain the probabilities that the nodes (pixels) belong to a cluster (network). We define these weights as a relation between states and probabilities between the nodes in the neighborhood of the node which is being updated. This is the classifier combination, making the main finding of this paper. The proposed combined strategy based on the HNN outperforms the simple classifiers and also classical combination strategies.

The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick-Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.

ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.

The increasing technology of high-resolution image airborne sensors, including those on board Unmanned Aerial Vehicles, demands automatic solutions for processing, either on-line or off-line, the huge amountds of image data sensed during the flights. The classification of natural spectral signatures in images is one potential application. The actual tendency in classification is oriented towards the combination of simple classifiers. In this paper we propose a combined strategy based on the Deterministic Simulated Annealing (DSA) framework. The simple classifiers used are the well tested supervised parametric Bayesian estimator and the Fuzzy Clustering. The DSA is an optimization approach, which minimizes an energy function. The main contribution of DSA is its ability to avoid local minima during the optimization process thanks to the annealing scheme. It outperforms simple classifiers used for the combination and some combined strategies, including a scheme based on the fuzzy cognitive maps and an optimization approach based on the Hopfield neural network paradigm.

This paper describes a novel feature-based stereovision matching process based on a pair of omnidirectional images in forest stands acquired with a stereovision sensor equipped with fish-eye lenses. The stereo analysis problem consists of the following steps: image acquisition, camera modelling, feature extraction, image matching and depth determination. Once the depths of significant points on the trees are obtained, the growing stock volume can be estimated by considering the geometrical camera modelling, which is the final goal. The key steps are feature extraction and image matching. This paper is devoted solely to these two steps. At a first stage a segmentation process extracts the trunks, which are the regions used as features, where each feature is identified through a set of attributes of properties useful for matching. In the second step the features are matched based on the application of the following four well known matching constraints, epipolar, similarity, ordering and uniqueness. The combination of the segmentation and matching processes for this specific kind of sensors make the main contribution of the paper. The method is tested with satisfactory results and compared against the human expert criterion.

The design of the control systems for sensor networks presents important challenges. Besides the traditional problems about how to process the sensor data to obtain the target information, engineers need to consider additional aspects such as the heterogeneity and high number of sensors, and the flexibility of these networks regarding topologies and the sensors in them. Although there are partial approaches for resolving these issues, their integration relies on ad hoc solutions requiring important development efforts. In order to provide an effective approach for this integration, this paper proposes an architecture based on the multi-agent system paradigm with a clear separation of concerns. The architecture considers sensors as devices used by an upper layer of manager agents. These agents are able to communicate and negotiate services to achieve the required functionality. Activities are organized according to roles related with the different aspects to integrate, mainly sensor management, data processing, communication and adaptation to changes in the available devices and their capabilities. This organization largely isolates and decouples the data management from the changing network, while encouraging reuse of solutions. The use of the architecture is facilitated by a specific modelling language developed through metamodelling. A case study concerning a generic distributed system for fire fighting illustrates the approach and the comparison with related work.

Senescence is a mechanism that limits cellular lifespan and constitutes a barrier against cellular immortalization. To identify new senescence regulatory genes that might play a role in tumorigenesis, we have designed and performed a large-scale antisense-based genetic screen in primary mouse embryo fibroblasts (MEFs). Out of this screen, we have identified five different genes through which loss of function partially bypasses senescence. These genes belong to very different biochemical families: csn2 (component of the Cop9 signalosome), aldose reductase (a metabolic enzyme) and brf1 (subunit of the RNA polymerase II complex), S-adenosyl homocysteine hydrolase and Bub1. Inactivation, at least partial, of these genes confers resistance to both p53- and p16INK4a-induced proliferation arrest. Furthermore, such inactivation inhibits p53 but not E2F1 transcriptional activity and impairs DNA-damage-induced transcription of p21. Since the aim of the screen was to identify new regulators of tumorigenesis, we have tested their inactivation in human tumors. We have found, either by northern blot or quantitative reverse transcriptase-PCR analysis, that the expression of three genes, Csn2, Aldose reductase and Brf1, is lost at different ratios in tumors of different origins. These genes are located at common positions of loss of heterogeneity (15q21.2, 7q35 and 14q32.33); therefore,we have measured genomic losses of these specific genes in different tumors. We have found that Csn2 and Brf1 also show genomic losses of one allele in different tumors. Our data suggest that the three genes identified in the genome-wide loss-of-function genetic screen are putative tumor suppressors located at 15q21.2; 7q35 and 14q32.33.

Background: Down syndrome (DS) is a frequent cause of intellectual disability. With the increasing life expectancy of these patients, concerns have been raised about the risk of osteoporosis. In fact, several investigators have reported a reduced bone mass in DS. However, the results may be confounded by comorbid diseases, and differences in lifestyle habits and body size. Therefore, we planned to determine anthropometric and lifestyle factors influencing bone mineral density (BMD) in young adults with DS., Methods: Thirty-nine patients with DS (mean age 26 years) and 78 controls were studied. Areal BMD was measured by dual x-ray densitometry (DXA); volumetric BMD at the lumbar spine and femoral neck was estimated with published formulae., Results: DS patients had lower areal BMD than controls at all regions (spine, hip and total body). Height and projected bone area were also lower. There were no differences between both groups regarding estimated volumetric BMD at the femoral neck. However, spine volumetric BMD was also lower in DS than controls. In multivariate analysis, DS, male sex, little physical activity and low sunlight exposure were associated with lower spine volumetric BMD; on the other hand, fat mass and sunlight exposure were associated with femoral neck volumetric BMD., Conclusion: This study shows that patients with DS had a reduced areal BMD, but it is in part a consequence of the reduced body size, particularly at the femoral neck. Physical activity and sunlight exposure are associated to volumetric BMD and should be stimulated in order to maintain an adequate bone mass in these patients.

Although activated macrophages destroy cancer cells more effectively than normal cells, the ability to escape activated macrophages is a characteristic of tumor cells. One of the mechanisms responsible for the specific killing of tumor cells by macrophages is the production of the cytokine tumor necrosis factor (TNF) alpha. Therefore, resistance to TNF may provide such cancer cells a selective advantage against host elimination. With the aim of identifying genes with these properties we undertook a large scale genetic screen to identify genes able to bypass TNF-induced G1 arrest. We identified MAP17, a small 17 kDa nonglycosylated membrane protein that localizes to the plasma membrane and the Golgi apparatus. Ectopic expression of MAP17 in tumor cells prevents TNF-induced G1 arrest by impairing p21waf1 induction. However, expression of MAP17 does not inhibit TNF-induced apoptosis in Me180-sensitive tumor cells. The inhibition of TNF is specific since MAP17 does not alter the response to other cytokines such as IFNgamma. As described in the Xenopus oocyte system, MAP17 increases the uptake of mannose in some cells, but this effect is not responsible for TNF bypass. We have also analyzed the expression of MAP17 mRNA in a panel of cell lines. MAP17 is expressed in 30% of cell lines of different origin. However, MAP17 mRNA expression did not correlate with TNF resistance. Our data indicates that although MAP17 expression might bypass TNF-induced growth arrest, it is not the only determinant of this response., ((c) 2007 Wiley-Liss, Inc.)

It is not clear whether invasive breast carcinomas with medullary features (IBCMFs, atypical medullary carcinomas) constitute a specific phenotype of breast cancer that is of biologic significance. Because medullary features are common in BRCA1-associated carcinomas and these tumors frequently show a basal-like phenotype, we examined whether IBCMFs expressed basal/myoepithelial markers and had a basal-like phenotype. We studied the immunohistochemical expression of 15 markers in tissue microarrays containing samples from 35 IBCMFs and 39 grade 3 invasive ductal carcinomas (IDCG3s) of no special type. In addition, we analyzed EGFR, C-MYC, and CCNE gene amplification by fluorescence in situ hybridization, because the expression of these genes is known to be associated with the basal-like phenotype. We defined the basal-like phenotype according to the criteria of Nielsen et al as being those tumors that were ER/HER2-negative and cytokeratin (CK) 5/6- and/or epidermal growth factor receptor-positive. IBCMFs were more frequently hormone receptor- and HER2-negative, but had greater expression of proliferation markers and p53. In addition, IBCMFs more frequently expressed basal/myoepithelial markers, such as CK5/6 and P-cadherin. A basal-like phenotype was found in 62.9% of IBCMFs but in only 18.9% of IDCG3s. No differences in gene amplification were found between IBCMFs and IDCG3s, although C-MYC amplification was more common in tumors without a basal-like phenotype. The identification of IBCMF as an independent group of tumors could be of clinical significance, given the high incidence of cases with a basal-like phenotype, which is a group of tumors with different prognosis and chemotherapy response from those of IDCG3s of no special type.

An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.

A standard sample holder and vial for cryocooled macromolecular crystals has been defined for use with robotic sample changers. This SPINE standard sample holder is a modified version, with added features and specifications, of sample holders in common use. In particular, the SPINE standard meets the precision required for automatic sample exchange and includes a cap that is identified by a two-dimensional datamatrix code as well as an optional vial. At the ESRF, the sample holder standard is in use with the EMBL/ESRF/BM14 robotic sample changer (SC3) which is installed on eight beamlines. The SC3 can hold up to 50 crystals stored in five baskets. A datamatrix reader in the SC3 ensures safe management of the sample flow and facilitates fully automatic screening and characterization of samples. Tools for handling and transporting 50 samples in a dry shipping dewar have been developed. In addition to the SC3, the SPINE sample holder is currently compatible with a number of other robotic sample changers.

The demand for access to macromolecular crystallography synchrotron beam time continues to increase. To meet this demand the ESRF has constructed a dual station beamline using a canted undulator system as the X-ray source. The first phase of the beamline to be constructed is ID23-1, a tunable MAD-capable station with a mini-focus X-ray beam. The beamline makes use of well characterized optical elements: a channel-cut monochromator with a high-precision toroidal mirror to focus the X-ray beam. The beamline has been conceived with the aim of providing high levels of automation to create an industrial-like environment for protein crystallography. A new software suite has been developed to permit reliable easy operation for the beamline users and beamline staff. High levels of diagnostics are built in to allow rapid trouble-shooting. These developments are now being exported to the ESRF macromolecular crystallography beamline complex and have been made in a modular fashion to facilitate transportability to other synchrotrons.

Oncogenic activation in primary murine fibroblasts initiates a senescence-like cell cycle arrest that depends on the p53 tumor suppressor pathway. Conditional p53 activation efficiently induced a reversible cell cycle arrest but was unable to induce features of senescence. In contrast, coexpression of oncogenic ras with p53 produced an irreversible cell cycle arrest that displayed features of cellular senescence. Introduction of a conditional murine p53 allele (p53val135) into double p53/p21-null mouse embryonic fibroblasts showed that p21waf1 was not required for this effect, since p53-/-;p21-/- double-null cells undergo terminal growth arrest with features of senescence following coexpression of oncogenic Ras and p53. Our results indicate that oncogenic activation of the Ras pathway in murine fibroblasts converts p53 into a senescence inducer through a p21waf1-independent mechanism., (Copyright 2004 Wiley-Liss, Inc.)

Although activated macrophages destroy cancer cells more effectively than normal cells, the facility to escape activated macrophages is a characteristic of tumor cells. One of the mechanisms responsible for the specific killing of tumor cells by macrophages is the production of the cytokine tumor necrosis factor alpha (TNF). Therefore, resistance to TNF may provide such cancer cells a selective advantage against host elimination. In the present work we explore the possibility that cyclin D1 overrides the cytostatic effect of TNF. We show that TNF induces p21(waf1) protein in malignant melanoma A375 cells and its binding to CDK2/4 and 6 proteins, and thereby inhibiting the activity of these complexes. This inhibition leads the cells to a G1 arrest. Overexpression of cyclin D1 in these cells makes them insensitive to TNF treatment with the recovery of CDK activity, however, is unable to overcome the inhibitory action of etoposide blocking the cells on G2/M. The bypass of TNF-induced G1 arrest seems to be related to the increase in the stability of cyclin D bound CDK complexes, increasing the total amount of CDK2/4 and 6 complexes and leading to a functional down titration of the p21(waf1) molecules. In these conditions the TNF-induced increase of p21(waf1) is not sufficient to inhibit the high amount of cyclin D-bound complexes. This hypothesis is supported by the fact that a reduction in the levels of p21(waf1) protein, induced by the expression of a mRNA antisense against p21(waf1), is also able to bypass of TNF-induced arrest. Our results confirm that p21(waf1) has an essential role in TNF-induced arrest and that the deregulation of cyclin D1 may be one of the mechanisms to escape physiological signals to restrict tumoral growth., (Copyright 2003 Wiley-Liss, Inc.)

The natural antioxidant ergothioneine (2-mercaptohistidine trimethylbetaine) is a fungal metabolite and found in most plant and animal tissues. The effect of ergothioneine on diabetic embryopathy in rats was assessed. Supplementation of diabetic pregnant rats with L-ergothioneine (1.147 mg/kg body weight) daily for the first 11.5 days of pregnancy reduced the rate of embryo malformations, to values similar to the non-diabetic animals. The ergothioneine had no effect on the plasma glucose levels, both in diabetic and control animals. We conclude that the inhibition of the glucose-mediated free radical dependent embryo malformation by ergothioneine is an important antioxidant prophylactic mechanism, which when combined with vitamin E could benefit the management of diabetic embryopathy.

A new meta-analysis of research on hostility and physical health was conducted that includes 15 studies used in previous meta-analytic reviews and 30 new independent studies. Overall, the results suggest that hostility is an independent risk factor for coronary heart disease (CHD). For structured interview indicators of potential for hostility, the weighted mean r was .18. After controlling for other risk factors for CHD, the widely used Cook-Medley Hostility Scale and other cognitive-experiential measures were most predictive of all-cause mortality (weighted mean r = .16) and, to a lesser extent, CHD (weighted mean r = .08). Similar to other areas of research, the increased use of high-risk studies in recent years produced an increase in null findings.

Objective: To find the origin of pharmacological prescriptions written in the primary care ambit, the effect of training on the prescribers and the influence of the organisational structure of the centres where they work on the quality of the drugs prescribed., Design: Observational study of a crossover type., Setting: Two health centres and two consulting-rooms in Areas 11 and 12, Valencia., Measurements and Main Results: The sample calculated corresponded to 664 prescriptions per centre. The origin of the prescription differed, depending on the model, so that in the consulting-rooms the origin of 55% of prescriptions was specialist care, whereas in the health centres this percentage went down to 31%. There were significant differences (p < 0.0001) in the quality of prescription in different organisational structures, but there were no significant differences among professionals with different training., Conclusions: A high percentage of pharmacological prescriptions have their origin in specialist care. Prescription quality is conditioned basically by the organisational model and is appreciably better in health centres.

L-thioproline (thiazolidine-4-carboxylic acid, L-Tp) reduces DNA synthesis in cultured HeLa cells by about 50% when added to synchronized cultures at the beginning of G1 phase. This inhibition is not observed when the drug is added at mid-S, in G2 or in M. L-Tp almost annuls the burst in 22Na uptake occurring at the beginning of G1 and is as potent an inhibitor as amiloride. It is also able to delay the apparition of the early S-specific cAMP peak and to elevate its intracellular concentration. These results indicate that L-Tp could decrease tumor cell growth by acting at the G1-S boundary.