A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Pervasive decision support to predict football corners and goals by means of data mining

Football is considered nowadays one of the most popular sports. In the betting world, it has acquired an outstanding position, which moves millions of euros during the period of a single football match. The lack of profitability of football betting users has been stressed as a problem. This lack gave origin to this research proposal, which it is going to analyse the possibility of existing a way to support the users to increase their profits on their bets. Data mining models were induced with the purpose of supporting the gamblers to increase their profits in the medium/long term. Being conscience that the models can fail, the results achieved by four of the seven targets in the models are encouraging and suggest that the system can help to increase the profits. All defined targets have two possible classes to predict, for example, if there are more or less than 7.5 corners in a single game. The data mining models of the targets, more or less than 7.5 corners, 8.5 corners, 1.5 goals and 3.5 goals achieved the pre-defined thresholds. The models were implemented in a prototype, which it is a pervasive decision support system. This system was developed with the purpose to be an interface for any user, both for an expert user as to a user who has no knowledge in football games.

Mòdul per a la gestió d'una borsa de treball a un centre universitari

Aquest projecte consisteix en realitzar el disseny, la implementació i el desenvolupament d’una aplicació que permeti la gestió administrativa d’una oficina de borsa de treball per a un centre universitari. Per a poder realitzar aquesta tasca cal que ofereixi les eines necessàries per a poder introduir, mantenir i explotar les dades relacionades amb estudiants, empreses, convenis, ofertes i reconeixements, que són els elements bàsics que composen les tasques administratives de la borsa de treball. L’aplicació resultant ha de ser multiusuari, dissenyada segons el model client-servidor i s’ha d’integrar com un mòdul nou dins d’una altra aplicació ja existent.

Markers of atherosclerosis and of inflammation for prediction of coronary heart disease in older adults

BACKGROUND: Several markers of atherosclerosis and of inflammation have been shown to predict coronary heart disease (CHD) individually. However, the utility of markers of atherosclerosis and of inflammation on prediction of CHD over traditional risk factors has not been well established, especially in the elderly. METHODS: We studied 2202 men and women, aged 70-79, without baseline cardiovascular disease over 6-year follow-up to assess the risk of incident CHD associated with baseline noninvasive measures of atherosclerosis (ankle-arm index [AAI], aortic pulse wave velocity [aPWV]) and inflammatory markers (interleukin-6 [IL-6], C-reactive protein [CRP], tumor necrosis factor-a [TNF-a]). CHD events were studied as either nonfatal myocardial infarction or coronary death ("hard" events), and "hard" events plus hospitalization for angina, or the need for coronary-revascularization procedures (total CHD events). RESULTS: During the 6-year follow-up, 283 participants had CHD events (including 136 "hard" events). IL-6, TNF-a and AAI independently predicted CHD events above Framingham Risk Score (FRS) with hazard ratios [HR] for the highest as compared with the lowest quartile for IL-6 of 1.95 (95%CI: 1.38-2.75, p for trend<0.001), TNF-a of 1.45 (95%CI: 1.04-2.02, p for trend 0.03), of 1.66 (95%CI: 1.19-2.31) for AAI £0.9, as compared to AAI 1.01-1.30. CRP and aPWV were not independently associated with CHD events. Results were similar for "hard" CHD events. Addition of IL-6 and AAI to traditional cardiovascular risk factors yielded the greatest improvement in the prediction of CHD; C-index for "hard"/total CHD events increased from 0.62/0.62 for traditional risk factors to 0.64/0.64 for IL-6 addition, 0.65/0.63 for AAI, and 0.66/0.64 for IL-6 combined with AAI. Being in the highest quartile of IL-6 combined with an AAI £ 0.90 or >1.40 yielded an HR of 2.51 (1.50-4.19) and 4.55 (1.65-12.50) above FRS, respectively. With use of CHD risk categories, risk prediction at 5 years was more accurate in models that included IL-6, AAI or both, with 8.0, 8.3 and 12.1% correctly reclassified respectively. CONCLUSIONS: Among older adults, markers of atherosclerosis and of inflammation, particularly IL-6 and AAI, are independently associated with CHD. However, these markers only modestly improve cardiovascular risk prediction beyond traditional risk factors. Acknowledgments: This study was supported by Contracts NO1-AG-6-2101, NO1-AG-6- 2103, and NO1-AG-6-2106 of the National Institute on Aging. This research was supported in part by the Intramural Research Program of the NIH, National Institute on Aging.

Precast Concrete Panel Thickness for Epoxy-Coated Prestressing Strands, Volume 2, HR-353, 1994

This final report for Phase 1 of the research on epoxy-coated, prestressing strands in precast prestressed concrete (PC) panels has been published in two volumes. Volume 1--Technical Report contains the problem description, literature review, and survey results; descriptions of the test specimens, experimental tests, and analytical models; discussions of the analytical and experimental results; summary, conclusions, and recommendations; list of references; and acknowledgments. Volume 2--Supplemental Report contains additional information in the form of appendix material for Volume 1 on the questionnaires, strand forces, geometry of the specimens, concrete crack patterns that formed in the strand transfer length and strand development length specimens, concrete strains in the strand transfer length specimens, and load-point deflections and strand-slip measurements for the strand development length specimens. Appendix A contains the questionnaires that were sent to the design agencies and precast concrete producers. A summary of the results to the questions on the surveys are given as the number of respondents who provided the same answers and as paraphrased comments from the respondents. Appendix B contains graphs of strand force versus time, strand force versus temperature, and strand force versus strand cutting sequence for the concrete castings. Appendix C contains figures that show the location of each specimen in the prestress bed, the geometrical configurations for the strand transfer length (T-type) specimens and strand development length (D-type) specimens, and the concrete cracks that developed in some of the T-type specimens when they were prestressed. Appendix D contains figures that show the concrete cracks that developed in the D-type specimens during the strand development length tests. For each of these tests, the sequence of the failure for the specimen is specified. Appendix E contains graphs of concrete strain versus distance from the end of the T-type specimens that were instrumented with internal embedment strain gages. Appendix F contains graphs of load versus load-point deflection and load versus strand-slip for the strand development length tests of the D-type specimens.

BioSWR - Semantic Web services Registry for Bioinformatics

Article About the Authors Metrics Comments Related Content Abstract Introduction Functionality Implementation Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/​under the LGPL license.

Mobiiliavusteisen rakennusprojektin seurantajärjestelmän suunnittelu ja toteutus

In the construction industry, the role of project management and monitoring is emphasized, because the responsibilities have been carefully planned and divided. A concrete element factory manufactures the units based on construction drawings, while a transport company is responsible of transporting the elements to the worksite. At the worksite, an installation team assembles the elements according to plans. Usually, there are several manufacturers and transport companies involved in the construction process and the distances between different parties can be rather long. Therefore, the role of information exchange is critical in order to control, for example, schedules and exceptions. From the viewpoint of project management, the whole process should be controlled and monitored in realtime - in such a way that the managers are able to analyze and report the data afterwards. In this master’s thesis, a mobile-aided construction project monitoring system is designed and implemented. The monitoring system consists of three main components: mobile phone application, server software and an interface application to Tekla Structures BIM-software. Precast construction components, projects and users are identified by using 2D-barcodes that are read with the camera of a mobile phone. An option would be to use RFID tags and readers. After successful identification, the precast component can be tagged with monitoring data, including state acknowledgments and error reports that are sent and saved to the server. Collected data can be viewed through the www-pages of the monitoring system. In addition, the data can be synchronized to the Tekla Structures-software that is running the 3D-model of the whole building. Synchronization maintains and enhances the traceability of monitoring data, as well as, helps to visualize the progression of the project.

The politics of weddings at Athens: an iconographic assessment

Despite recent scholarship that has suggested that most if not all Athenian vases were created primarily for the symposium, vases associated with weddings constitute a distinct range of Athenian products that were used at Athens in the period of the Peloponnesian War and its immediate aftermath (430-390 BCE). Just as the subject matter of sympotic vases suggested stories or other messages to the hetaireia among whom they were used, so the wedding vases may have conveyed messages to audiences at weddings. This paper is an assessment of these wedding vases with particular attention to function: how the images reflect the use of vases in wedding rituals (as containers and/or gifts); how the images themselves were understood and interpreted in the context of weddings; and the post-nuptial uses to which the vases were put. The first part is an iconographic overview of how the Athenian painters depicted weddings, with an emphasis on the display of pottery to onlookers and guests during the public parts of weddings, important events in the life of the polis. The second part focuses on a large group of late fifth century vases that depict personifications of civic virtues, normally in the retinue of Aphrodite (Pandemos). The images would reinforce social expectations, as they advertised the virtues that would create a happy marriage—Peitho, Harmonia (Harmony), and Eukleia (Good Repute)—and promise the benefits that might result from adherence to these values—Eudaimonia and Eutychia (Prosperity), Hygieia (Health), and Paidia (Play or Childrearing). Civic personifications could be interpreted on the private level—as personal virtues—and on the public level—as civic virtues— especially when they appeared on vases that functioned both in public and private, at weddings, which were public acknowledgments of private changes in the lives of individuals within the demos.

A Study On The Flow Characteristics Influenced By Hydraulic Structure At A Channel Junction

Natural riversare consisting of various networks as junction andstreams. And sediment and erosion are occurred by specific stream condition. When flood season,large discharge flew in the river and river bed changed by high flow velocity. Especially junction area’s flow characteristics are very complex. The purpose of this study is to analyze the flow characteristics in channel junction, which are most influenced by large discharge like flooding and input water from tributary. We investigate the flow characteristics by using hydrodynamics and transport module in MIKE 3 FM. MIKE 3 FM model was helpful tool to analysis 3D hydrodynamics, erosion and sediment effect from channel bed. We analyze flow characteristics at channel junction. Also we consider hydraulic structures like a bridge pier which is influencing flow characteristics like a flow velocity, water level, erosion and scour depth in channel bed. In the model, we controlled discharge condition according to Froude Number and reflect various grain diameter size and flow ratio change in main stream and tributary. In the result, flow velocity, water level, erosion and sediment depth are analyzed. Additionally, we suggest a these result relationship with equations. This study will help the understand flow characteristics and influence of hydraulic structure in channel junction. Acknowledgments This research was supported by a grant (12-TI-C01) from Advanced Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.

Análise modal de uma estrutura do tipo viga utilizando materiais piezelétricos (PVDF) como sensores

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Erratum to: The effects of dynamic loading on the intervertebral disc

Erratum to: Eur Spine J DOI 10.1007/s00586-011-1827-1 In the original article ‘‘Acknowledgments’’ was missing. The Acknowledgment is given below: Acknowledgments This project was supported by the Swiss National Science Foundation (SNF # 310030-127586/1) and the Department for Orthopedic Research, Insel University Hospital, Bern, Switzerland.

A Smart TCP Acknowledgment Approach for Multihop Wireless Networks

Reliable data transfer is one of the most difficult tasks to be accomplished in multihop wireless networks. Traditional transport protocols like TCP face severe performance degradation over multihop networks given the noisy nature of wireless media as well as unstable connectivity conditions in place. The success of TCP in wired networks motivates its extension to wireless networks. A crucial challenge faced by TCP over these networks is how to operate smoothly with the 802.11 wireless MAC protocol which also implements a retransmission mechanism at link level in addition to short RTS/CTS control frames for avoiding collisions. These features render TCP acknowledgments (ACK) transmission quite costly. Data and ACK packets cause similar medium access overheads despite the much smaller size of the ACKs. In this paper, we further evaluate our dynamic adaptive strategy for reducing ACK-induced overhead and consequent collisions. Our approach resembles the sender side's congestion control. The receiver is self-adaptive by delaying more ACKs under nonconstrained channels and less otherwise. This improves not only throughput but also power consumption. Simulation evaluations exhibit significant improvement in several scenarios

Extended duration of torsional loading reduced the survival of the NP cells of the intervertebral disc

Introduction Previous studies on the influence of torsion and combined torsion-compression loading revealed a positive effect on the cell viability when a repetitive short-term torsion was applied at a physiological magnitude to intervertebral disc organ culture.1 However, after an extended period (8 hours) of combined torsion-compression loading, substantial cell death was detected in the nucleus pulposus (NP).2 In this follow-up study, we aimed to investigate the relationship, if any, between the duration of torsion applied to the intervertebral disc (IVD) and the level of NP cell viability. Materials and Methods Bovine caudal discs were harvested and cultured in a custom-built multiaxis dynamic loading bioreactor.2 Torsion (± 2 degrees) was applied to the samples at a frequency of 0.2 Hz. Torsion was applied for durations of 0, 1, 4, and 8 h/d, repeated over 7 days. After the last day of loading, disc tissue was dissected for analysis of cell viability and gene expression. Results Disc NP cell viability remained above 85% after torsional loading for 0, 1, or 4 h/d. Viability was statistical significantly reduced to below 70% when torsion was applied for 8 h/d (p = 0.03) (Table 1). The daily duration of torsional loading did not affect the AF cell viability (> 80% for all loading durations). The trend of collagen 2 gene upregulation and matrix metalloproteases 13 downregulation with an increasing duration of torsion was observed in both NP and AF (Fig. 1).Conclusion We have demonstrated that an extended duration of torsion could inhibit the survival of NP cells within the IVD in organ culture. Acknowledgments Funds from the Orthopedic Department of the Insel University Hospital of Bern and a private donation from Prof. Dr. Paul Heini, Spine Surgeon, Sonnenhof Clinic Bern were received to support this work. Disclosure of Interest None declared References References 1 Chan SC, Ferguson SJ, Wuertz K, Gantenbein-Ritter B. Biological response of the intervertebral disc to repetitive short-term cyclic torsion. Spine 2011;36(24):2021–2030 2 Chan SC, Walser J, Käppeli P, Shamsollahi MJ, Ferguson SJ, Gantenbein-Ritter B. Region specific response of intervertebral disc cells to complex dynamic loading: an organ culture study using a dynamic torsion-compression bioreactor. PLoS ONE 2013;8(8):e72489

Is fast track management after elective cranial surgery safe and can it replace routine early postoperative computed tomography?

Aims: Patient management following elective cranial surgery varies between different neurosurgical institutions. Early routine postoperative cranial computed tomography (CT) is often performed while keeping patients sedated and ventilated for several hours. We hypothesize that fast track management without routine CT scanning, i.e., early extubation within one hour allowing neurological monitoring, is safe and does not increase the rate of return to OR compared with published data. Methods: We prospectively screened 1118 patients with cranial procedures performed at our department over a period of two years. 420 patients with elective brain surgery older than 18 years with no history of prior cranial surgery were included. Routine neurosurgical practice as it is performed at our department was not altered for this observational study. Fast track management was aimed for all cases, extubated and awake patients were further monitored. CT scanning within 48 hours after surgery was not performed except for unexpected neurological deterioration. This study was registered at ClinicalTrials.gov (NCT01987648). Results: 420 elective craniotomies were performed for 310 supra- and 110 infratentorial lesions. 398 patients (94.8%) were able to be extubated within 1 hour, 21 (5%) within 6 hours, and 1 patient (0.2%) was extubated 9 hours after surgery. Emergency CT within 48 hours was performed for 36 patients (8.6%, 26 supra- and 10 infratentorial cases) due to unexpected neurological worsening. Of these 36 patients 5 had to return to the OR (hemorrhage in 3, swelling in 2 cases). Return to OR rate of all included cases was 1.2%. This rate compares favorably with 1-4% as quoted in the current literature. No patient returned to the OR without prior CT imaging. Of 398 patients extubated within one hour 2 (0.5%) returned to the OR. Patients who couldn’t be extubated within the first hour had a higher risk of returning to the OR (3 of 22, i.e., 14%). Overall 30-day mortality was 0.2% (1 patient). Conclusions: Early extubation and CT imaging performed only for patients with unexpected neurological worsening after elective craniotomy procedures is safe and does not increase patient mortality or the return to OR rate. With this fast track approach early postoperative cranial CT for detection of postoperative complications in the absence of an unexpected neurological finding is not justified. Acknowledgments The authors thank Nicole Söll, study nurse, Department of Neurosurgery, Bern University Hospital, Switzerland for crucial support in data collection and managing the database.

Bovine coccygeal intervertebral discs contain multipotent Tie2+ cells which can differentiate into osteogenic and adipogenic lineages

Question: The intervertebral disc (IVD) has a limited regenerative potential and low back pain represents a leading cause of disability [1]. IVD repair strategies require an appropriate cell source that is able to regenerate the damaged tissue such as progenitor stem cells. Recently, progenitor cells that are positive for the angiopoietin re- ceptor (Tie2) in the nucleus pulposus were identified [2]. Here we isolated primary cells from bovine IVD and sorted bovine nucleus pulposus progenitor cells (NPPC) for the marker Tie2. Furthermorewe tested whether Tie2 expressing cells can differentiate into os- teogenic and adipogenic lineages in vitro. Methods: NP cells were obtained from 1 year old bovine tails by sequential digestion with pronase for 1 h and collagenase over- night. Sorted Tie2- and Tie2+ cells were cultured in osteogenic and adipogenic medium for 3 weeks. The formed cell layers from both subpopulations were stained for calcium deposition and fat droplets. Colony forming units were prepared for both cell sus- pensions in methylcellulose-based medium and formed colonies ([10 cells) were analyzed macroscopically after 8 days. Results: After 3 weeks of culture, sorted Tie2+ cells were able to differentiate into osteocytes and adipocytes as characterized by cal- cium deposition and fat droplet formation. By contrast, Tie2- cells generated a weak staining for calcium and no fat droplets were ob- tained (Fig. 1). Sorted Tie2- and Tie2+ subpopulations of cells both formed colonies, however with different morphologies. The colonies formed from Tie2+ cells were spheroid in shape whereas those from Tie2- cells were spread and fibroblastic. Conclusion: Our data showed that Tie2+ cells of the nucleus pul- posus cells are progenitor-like cells that are able to differentiate into osteogenic and adipogenic lineages. Sorting of NPPC for Tie2 may represent a promising strategy with the potential to be used in the clinics for treatment of intervertebral disc damage. References 1. Freemont AJ (2009) The cellular pathobiology of the degenerate intervertebral disc and discogenic back pain. Rheumatology (Oxford) 48:5–10 2. Sakai D, Nakamura Y, Nakai T et al (2012) Exhaustion of nucleus pulposus progenitor cells with ageing and degeneration of the intervertebral disc. Nat Commun 3:1264 Acknowledgments: This project was funded by two projects of the Swiss National Science Foundation grant number #IZK0Z3_154384 and #310030_153411.