Transcriptome Analysis of Renal Ischemia/Reperfusion Injury and Its Modulation by Ischemic Pre-Conditioning or Hemin Treatment

Ischemia/reperfusion injury (IRI) is a leading cause of acute renal failure. The definition of the molecular mechanisms involved in renal IRI and counter protection promoted by ischemic pre-conditioning (IPC) or Hemin treatment is an important milestone that needs to be accomplished in this research area. We examined, through an oligonucleotide microarray protocol, the renal differential transcriptome profiles of mice submitted to IRI, IPC and Hemin treatment. After identifying the profiles of differentially expressed genes observed for each comparison, we carried out functional enrichment analysis to reveal transcripts putatively involved in potential relevant biological processes and signaling pathways. The most relevant processes found in these comparisons were stress, apoptosis, cell differentiation, angiogenesis, focal adhesion, ECM-receptor interaction, ion transport, angiogenesis, mitosis and cell cycle, inflammatory response, olfactory transduction and regulation of actin cytoskeleton. In addition, the most important overrepresented pathways were MAPK, ErbB, JAK/STAT, Toll and Nod like receptors, Angiotensin II, Arachidonic acid metabolism, Wnt and coagulation cascade. Also, new insights were gained about the underlying protection mechanisms against renal IRI promoted by IPC and Hemin treatment. Venn diagram analysis allowed us to uncover common and exclusively differentially expressed genes between these two protective maneuvers, underscoring potential common and exclusive biological functions regulated in each case. In summary, IPC exclusively regulated the expression of genes belonging to stress, protein modification and apoptosis, highlighting the role of IPC in controlling exacerbated stress response. Treatment with the Hmox1 inducer Hemin, in turn, exclusively regulated the expression of genes associated with cell differentiation, metabolic pathways, cell cycle, mitosis, development, regulation of actin cytoskeleton and arachidonic acid metabolism, suggesting a pleiotropic effect for Hemin. These findings improve the biological understanding of how the kidney behaves after IRI. They also illustrate some possible underlying molecular mechanisms involved in kidney protection observed with IPC or Hemin treatment maneuvers.

Tricuspid Valve Injury After Heart Transplantation Due to Endomyocardial Biopsy: An Analysis of 3550 Biopsies

Introduction. Tricuspid regurgitation (TR) is the most commonly valvular dysfunction found after heart transplantation (HTx). It may be related to endomyocardial biopsy (EMB) performed for allograft rejection surveillance. Objective. This investigation evaluated the presence of tricuspid valve tissue fragments obtained during routine EMB performed after HTx and its possible effect on short-term and long-term hemodynamic status. Method. This single-center review included prospectively collected and retrospectively analyzed data. From 1985 to 2010, 417 patients underwent 3550 EMB after HTx. All myocardial specimens were reviewed to identify the presence of tricuspid valve tissue by 2 observers initially and in doubtful cases by a third observer. The echocardiographic and hemodynamic parameters were only considered for valvular functional damage analysis in cases of tricuspid tissue inadvertently removed during EMB. Results. The 417 HTx patients to 3550 EMB, including 17,550 myocardial specimens. Tricuspid valve tissue was observed in 12 (2.9%) patients corresponding to 0.07% of the removed fragments. The echocardiographic and hemodynamic parameters of these patients before versus after the biopsy showed increased TR in 2 cases (2/12; 16.7%) quantified as moderate without progression in the long term. Only the right atrial pressure showed a significant increase (P = .0420) after tricuspid injury; however, the worsening of the functional class was not significant enough in any of the subjects. Thus, surgical intervention was not required. Conclusions. Histological evidence of chordal tissue in EMB specimens is a real-world problem of relatively low frequency. Traumatic tricuspid valve injury due to EMB rarely leads to severe valvular regurgitation; only a minority of patients develop significant clinical symptoms. Hemodynamic and echocardiographic alterations are also less often observed in most patients.

Structural and resting state functional connectivity of the subthalamic nucleus: identification of motor STN parts and the hyperdirect pathway

Deep brain stimulation (DBS) for Parkinson's disease often alleviates the motor symptoms, but causes cognitive and emotional side effects in a substantial number of cases. Identification of the motor part of the subthalamic nucleus (STN) as part of the presurgical workup could minimize these adverse effects. In this study, we assessed the STN's connectivity to motor, associative, and limbic brain areas, based on structural and functional connectivity analysis of volunteer data. For the structural connectivity, we used streamline counts derived from HARDI fiber tracking. The resulting tracks supported the existence of the so-called "hyperdirect" pathway in humans. Furthermore, we determined the connectivity of each STN voxel with the motor cortical areas. Functional connectivity was calculated based on functional MRI, as the correlation of the signal within a given brain voxel with the signal in the STN. Also, the signal per STN voxel was explained in terms of the correlation with motor or limbic brain seed ROI areas. Both right and left STN ROIs appeared to be structurally and functionally connected to brain areas that are part of the motor, associative, and limbic circuit. Furthermore, this study enabled us to assess the level of segregation of the STN motor part, which is relevant for the planning of STN DBS procedures.

Functional error modeling for uncertainty quantification in hydrogeology

Approximate models (proxies) can be employed to reduce the computational costs of estimating uncertainty. The price to pay is that the approximations introduced by the proxy model can lead to a biased estimation. To avoid this problem and ensure a reliable uncertainty quantification, we propose to combine functional data analysis and machine learning to build error models that allow us to obtain an accurate prediction of the exact response without solving the exact model for all realizations. We build the relationship between proxy and exact model on a learning set of geostatistical realizations for which both exact and approximate solvers are run. Functional principal components analysis (FPCA) is used to investigate the variability in the two sets of curves and reduce the dimensionality of the problem while maximizing the retained information. Once obtained, the error model can be used to predict the exact response of any realization on the basis of the sole proxy response. This methodology is purpose-oriented as the error model is constructed directly for the quantity of interest, rather than for the state of the system. Also, the dimensionality reduction performed by FPCA allows a diagnostic of the quality of the error model to assess the informativeness of the learning set and the fidelity of the proxy to the exact model. The possibility of obtaining a prediction of the exact response for any newly generated realization suggests that the methodology can be effectively used beyond the context of uncertainty quantification, in particular for Bayesian inference and optimization.

Chow–Liu trees are sufficient predictive models for reproducing key features of functional networks of periictal EEG time-series

Seizure freedom in patients suffering from pharmacoresistant epilepsies is still not achieved in 20–30% of all cases. Hence, current therapies need to be improved, based on a more complete understanding of ictogenesis. In this respect, the analysis of functional networks derived from intracranial electroencephalographic (iEEG) data has recently become a standard tool. Functional networks however are purely descriptive models and thus are conceptually unable to predict fundamental features of iEEG time-series, e.g., in the context of therapeutical brain stimulation. In this paper we present some first steps towards overcoming the limitations of functional network analysis, by showing that its results are implied by a simple predictive model of time-sliced iEEG time-series. More specifically, we learn distinct graphical models (so called Chow–Liu (CL) trees) as models for the spatial dependencies between iEEG signals. Bayesian inference is then applied to the CL trees, allowing for an analytic derivation/prediction of functional networks, based on thresholding of the absolute value Pearson correlation coefficient (CC) matrix. Using various measures, the thus obtained networks are then compared to those which were derived in the classical way from the empirical CC-matrix. In the high threshold limit we find (a) an excellent agreement between the two networks and (b) key features of periictal networks as they have previously been reported in the literature. Apart from functional networks, both matrices are also compared element-wise, showing that the CL approach leads to a sparse representation, by setting small correlations to values close to zero while preserving the larger ones. Overall, this paper shows the validity of CL-trees as simple, spatially predictive models for periictal iEEG data. Moreover, we suggest straightforward generalizations of the CL-approach for modeling also the temporal features of iEEG signals.

Social attitude toward sustainable development in 2025: A case for reinforcing scenario design

This paper shows the role that some foresight tools, such as scenario design, may play in exploring the future impacts of global challenges in our contemporary Society. Additionally, it provides some clues about how to reinforce scenario design so that it displays more in-depth analysis without losing its qualitative nature and communication advantages. Since its inception in the early seventies, scenario design has become one of the most popular foresight tools used in several fields of knowledge. Nevertheless, its wide acceptance has not been seconded by the urban planning academic and professional realm. In some instances, scenario design is just perceived as a story telling technique that generates oversimplified future visions without the support of rigorous and sound analysis. As a matter of fact, the potential of scenario design for providing more in-depth analysis and for connecting with quantitative methods has been generally missed, giving arguments away to its critics. Based on these premises, this document tries to prove the capability of scenario design to anticipate the impacts of complex global challenges and to do it in a more analytical way. These assumptions are tested through a scenario design exercise which explores the future evolution of the sustainable development paradigm (SD) and its implications in the Spanish urban development model. In order to reinforce the perception of scenario design as a useful and added value instrument to urban planners, three sets of implications –functional, parametric and spatial— are displayed to provide substantial and in-depth information for policy makers. This study shows some major findings. First, it is feasible to set up a systematic approach that provides anticipatory intelligence about future disruptive events that may affect the natural environment and socioeconomic fabric of a given territory. Second, there are opportunities for innovating in the Spanish urban planning processes and city governance models. Third, as a foresight tool, scenario design can be substantially reinforced if proper efforts are made to display functional, parametric and spatial implications generated by the scenarios. Fourth, the study confirms that foresight offers interesting opportunities for urban planners, such as anticipating changes, formulating visions, fostering participation and building networks

Pulse phase-coherent timing and spectroscopy of CXOU J164710.2−45521 outbursts

We present a long-term phase-coherent timing analysis and pulse-phase resolved spectroscopy for the two outbursts observed from the transient anomalous X-ray pulsar CXOU J164710.2−455216. For the first outburst we used 11 Chandra and XMM–Newton observations between 2006 September and 2009 August, the longest baseline yet for this source. We obtain a coherent timing solution with P = 10.61065583(4) s, Ṗ = 9.72(1) × 10−13 s s−1 and P̈ = –1.05(5) × 10−20 s s−2. Under the standard assumptions this implies a surface dipolar magnetic field of ∼1014 G, confirming this source as a standard B magnetar. We also study the evolution of the pulse profile (shape, intensity and pulsed fraction) as a function of time and energy. Using the phase-coherent timing solution we perform a phase-resolved spectroscopy analysis, following the spectral evolution of pulse-phase features, which hints at the physical processes taking place on the star. The results are discussed from the perspective of magnetothermal evolution models and the untwisting magnetosphere model. Finally, we present similar analysis for the second, less intense, 2011 outburst. For the timing analysis we used Swift data together with 2 XMM–Newton and Chandra pointings. The results inferred for both outbursts are compared and briefly discussed in a more general framework.

Unpacking Japan's 21st century "National Conversation" : images of the future beyond the iron cage of the "Catch Up" model

How does the image of the future operate upon history, and upon national and individual identities? To what extent are possible futures colonized by the image? What are the un-said futurecratic discourses that underlie the image of the future? Such questions inspired the examination of Japan’s futures images in this thesis. The theoretical point of departure for this examination is Polak’s (1973) seminal research into the theory of the ‘image of the future’ and seven contemporary Japanese texts which offer various alternative images for Japan’s futures, selected as representative of a ‘national conversation’ about the futures of that nation. These seven images of the future are: 1. Report of the Prime Minister’s Commission on Japan’s Goals in the 21st Century—The Frontier Within: Individual Empowerment and Better Governance in the New Millennium, compiled by a committee headed by Japan’s preeminent Jungian psychologist Kawai Hayao (1928-2007); 2. Slow Is Beautiful—a publication by Tsuji Shinichi, in which he re-images Japan as a culture represented by the metaphor of the sloth, concerned with slow and quality-oriented livingry as a preferred image of the future to Japan’s current post-bubble cult of speed and economic efficiency; 3. MuRatopia is an image of the future in the form of a microcosmic prototype community and on-going project based on the historically significant island of Awaji, and established by Japanese economist and futures thinker Yamaguchi Kaoru; 4. F.U.C.K, I Love Japan, by author Tanja Yujiro provides this seven text image of the future line-up with a youth oriented sub-culture perspective on that nation’s futures; 5. IMAGINATION / CREATION—a compilation of round table discussions about Japan’s futures seen from the point of view of Japan’s creative vanguard; 6. Visionary People in a Visionless Country: 21 Earth Connecting Human Stories is a collection of twenty one essays compiled by Denmark born Tokyo resident Peter David Pedersen; and, 7. EXODUS to the Land of Hope, authored by Murakami Ryu, one of Japan’s most prolific and influential writers, this novel suggests a future scenario portraying a massive exodus of Japan’s youth, who, literate with state-of-the-art information and communication technologies (ICTs) move en masse to Japan’s northern island of Hokkaido to launch a cyber-revolution from the peripheries. The thesis employs a Futures Triangle Analysis (FTA) as the macro organizing framework and as such examines both pushes of the present and weights from the past before moving to focus on the pulls to the future represented by the seven texts mentioned above. Inayatullah’s (1999) Causal Layered Analysis (CLA) is the analytical framework used in examining the texts. Poststructuralist concepts derived primarily from the work of Michel Foucault are a particular (but not exclusive) reference point for the analytical approach it encompasses. The research questions which reflect the triangulated analytic matrix are: 1. What are the pushes—in terms of current trends—that are affecting Japan’s futures? 2. What are the historical and cultural weights that influence Japan’s futures? 3. What are the emerging transformative Japanese images of the future discourses, as embodied in actual texts, and what potential do they offer for transformative change in Japan? Research questions one and two are discussed in Chapter five and research question three is discussed in Chapter six. The first two research questions should be considered preliminary. The weights outlined in Chapter five indicate that the forces working against change in Japan are formidable, structurally deep-rooted, wide-spread, and under-recognized as change-adverse. Findings and analyses of the push dimension reveal strong forces towards a potentially very different type of Japan. However it is the seven contemporary Japanese images of the future, from which there is hope for transformative potential, which form the analytical heart of the thesis. In analyzing these texts the thesis establishes the richness of Japan’s images of the future and, as such, demonstrates the robustness of Japan’s stance vis-à-vis the problem of a perceived map-less and model-less future for Japan. Frontier is a useful image of the future, whose hybrid textuality, consisting of government, business, academia, and creative minority perspectives, demonstrates the earnestness of Japan’s leaders in favour of the creation of innovative futures for that nation. Slow is powerful in its aim to reconceptualize Japan’s philosophies of temporality, and build a new kind of nation founded on the principles of a human-oriented and expanded vision of economy based around the core metaphor of slowness culture. However its viability in Japan, with its post-Meiji historical pushes to an increasingly speed-obsessed social construction of reality, could render it impotent. MuRatopia is compelling in its creative hybridity indicative of an advanced IT society, set in a modern day utopian space based upon principles of a high communicative social paradigm, and sustainability. IMAGINATION / CREATION is less the plan than the platform for a new discussion on Japan’s transformation from an econo-centric social framework to a new Creative Age. It accords with emerging discourses from the Creative Industries, which would re-conceive of Japan as a leading maker of meaning, rather than as the so-called guzu, a term referred to in the book meaning ‘laggard’. In total, Love Japan is still the most idiosyncratic of all the images of the future discussed. Its communication style, which appeals to Japan’s youth cohort, establishes it as a potentially formidable change agent in a competitive market of futures images. Visionary People is a compelling image for its revolutionary and subversive stance against Japan’s vision-less political leadership, showing that it is the people, not the futures-making elite or aristocracy who must take the lead and create a new vanguard for the nation. Finally, Murakami’s Exodus cannot be ruled out as a compelling image of the future. Sharing the appeal of Tanja’s Love Japan to an increasingly disenfranchised youth, Exodus portrays a near-term future that is achievable in the here and now, by Japan’s teenagers, using information and communications technologies (ICTs) to subvert leadership, and create utopianist communities based on alternative social principles. The principal contribution from this investigation in terms of theory belongs to that of developing the Japanese image of the future. In this respect, the literature reviews represent a significant compilation, specifically about Japanese futures thinking, the Japanese image of the future, and the Japanese utopia. Though not exhaustive, this compilation will hopefully serve as a useful starting point for future research, not only for the Japanese image of the future, but also for all image of the future research. Many of the sources are in Japanese and their English summations are an added reason to respect this achievement. Secondly, the seven images of the future analysed in Chapter six represent the first time that Japanese image of the future texts have been systematically organized and analysed. Their translation from Japanese to English can be claimed as a significant secondary contribution. What is more, they have been analysed according to current futures methodologies that reveal a layeredness, depth, and overall richness existing in Japanese futures images. Revealing this image-richness has been one of the most significant findings of this investigation, suggesting that there is fertile research to be found from this still under-explored field, whose implications go beyond domestic Japanese concerns, and may offer fertile material for futures thinkers and researchers, Japanologists, social planners, and policy makers.

Statistical methods for electromyography data and associated problems

This thesis proposes three novel models which extend the statistical methodology for motor unit number estimation, a clinical neurology technique. Motor unit number estimation is important in the treatment of degenerative muscular diseases and, potentially, spinal injury. Additionally, a recent and untested statistic to enable statistical model choice is found to be a practical alternative for larger datasets. The existing methods for dose finding in dual-agent clinical trials are found to be suitable only for designs of modest dimensions. The model choice case-study is the first of its kind containing interesting results using so-called unit information prior distributions.

Memory of past random wave conditions in submarine groundwater discharge

Submarine groundwater discharge (SGD) is an integral part of the hydrological cycle and represents an important aspect of land-ocean interactions. We used a numerical model to simulate flow and salt transport in a nearshore groundwater aquifer under varying wave conditions based on yearlong random wave data sets, including storm surge events. The results showed significant flow asymmetry with rapid response of influxes and retarded response of effluxes across the seabed to the irregular wave conditions. While a storm surge immediately intensified seawater influx to the aquifer, the subsequent return of intruded seawater to the sea, as part of an increased SGD, was gradual. Using functional data analysis, we revealed and quantified retarded, cumulative effects of past wave conditions on SGD including the fresh groundwater and recirculating seawater discharge components. The retardation was characterized well by a gamma distribution function regardless of wave conditions. The relationships between discharge rates and wave parameters were quantifiable by a regression model in a functional form independent of the actual irregular wave conditions. This statistical model provides a useful method for analyzing and predicting SGD from nearshore unconfined aquifers affected by random waves

Latent TGF-β binding proteins -3 and -4 : transcriptional control and extracellular matrix targeting

Extracellular matrix (ECM) is a complex network of various proteins and proteoglycans which provides tissues with structural strength and resilience. By harvesting signaling molecules like growth factors ECM has the capacity to control cellular functions including proliferation, differentiation and cell survival. Latent transforming growth factor β (TGF-β) binding proteins (LTBPs) associate fibrillar structures of the ECM and mediate the efficient secretion and ECM deposition of latent TGF-β. The current work was conducted to determine the regulatory regions of LTBP-3 and -4 genes to gain insight into their tissue-specific expression which also has impact on TGF-β biology. Furthermore, the current research aimed at defining the ECM targeting of the N-terminal variants of LTBP-4 (LTBP-4S and -4L), which is required to understand their functions in tissues and to gain insight into conditions in which TGF-β is activated. To characterize the regulatory regions of LTBP-3 and -4 genes in silico and functional promoter analysis techniques were employed. It was found that the expression of LTBP-4S and -4L are under control of two independent promoters. This finding was in accordance with the observed expression patterns of LTBP-4S and -4L in human tissues. All promoter regions characterized in this study were TATAless, GC-rich and highly conserved between human and mouse species. Putative binding sites for Sp1 and GATA family of transcription factors were recognized in all of these regulatory regions. It is possible that these transcription factors control the basal expression of LTBP-3 and -4 genes. Smad binding element was found within the LTBP-3 and -4S promoter regions, but it was not present in LTBP-4L promoter. Although this element important for TGF-β signaling was present in LTBP-4S promoter, TGF-β did not induce its transcriptional activity. LTBP-3 promoter activity and mRNA expression instead were stimulated by TGF-β1 in osteosarcoma cells. It was found that the stimulatory effect of TGF-β was mediated by Smad and Erk MAPK signaling pathways. The current work explored the ECM targeting of LTBP-4S and identified binding partners of this protein. It was found that the N-terminal end of LTBP-4S possesses fibronectin (FN) binding sites which are critical for its ECM targeting. FN deficient fibroblasts incorporated LTBP-4S into their ECM only after addition of exogenous FN. Furthermore, LTBP-4S was found to have heparin binding regions, of which the C-terminal binding site mediated fibroblast adhesion. Soluble heparin prevented the ECM association of LTBP-4S in fibroblast cultures. In the current work it was observed that there are significant differences in the secretion, processing and ECM targeting of LTBP-4S and -4L. Interestingly, it was observed that most of the secreted LTBP-4L was associated with latent TGF-β1, whereas LTBP-4S was mainly secreted as a free form from CHO cells. This thesis provides information on transcriptional regulation of LTBP-3 and -4 genes, which is required for the deeper understanding of their tissue-specific functions. Further, the current work elucidates the structural variability of LTBPs, which appears to have impact on secretion and ECM targeting of TGF-β. These findings may advance understanding the abnormal activation of TGF-β which is associated with connective tissue disorders and cancer.

Orbital evolution studies of two HMXB pulsars

High mass X-ray binary (HMXB) pulsars are of two types, persistent and transient. 4U1538-52 is a persistent HMXB whose orbit was previously measured to be circular but the RXTE observations revealed an eccentric orbit. We observed this system with RXTE-PCA in August 2003 and our timing analysis supports the eccentric orbit of the system. However, we do not find any evidence for orbital evolution. Rotational and tidal interactions between the stars of a closed binary system result in apsidal motion which can be measured in systems with eccentric orbit. 4U0115+63 is a Be-transient HMXB whose eccentric orbit was well-determined during its 1978 outburst. We report preliminary results from analysis of data obtained during the 1999 outburst of this source with the RXTE-PCA.

Orbital evolution and orbital phase resolved spectroscopy of the HMXB pulsar 4U 1538-52 with RXTE-PCA and BeppoSAX

We report here results from detailed timing and spectral studies of the high mass X-ray binary pulsar 4U 1538-52 over several binary periods using observations made with the Rossi X-ray Timing Explorer (RXTE) and BeppoSAX satellites. Pulse timing analysis with the 2003 RXTE data over two binary orbits confirms an eccentric orbit of the system. Combining the orbitial parameters determined from this observation with the earlier measurements we did not find any evidence of orbital decay in this X-ray binary. We have carried out orbital phase resolved spectroscopy to measure changes in the spectral parameters with orbital phase, particularly the absorption column density and the iron line flux. The RXTE-PCA spectra in the 3-20 keV energy range were fitted with a power law and a high energy cut-off along with a Gaussian line at similar to 6.4 keV, whereas the BeppoSAX spectra needed only a power law and Gaussian emission line at similar to 6.4keV in the restricted energy range of 0.3-10.0 keV. An absorption along the line of sight was included for both the RXTE and BeppoSAX data. The variation of the free spectral parameters over the binary orbit was investigated and we found that the variation of the column density of absorbing material in the line of sight with orbital phase is in reasonable agreement with a simple model of a spherically symmetric stellar wind from the companion star.

Orbital evolution studies of two HMXB pulsars

High mass X-ray binary (H M X B) pulsars are of two types, persistent and transient. 4U 1538-52 is a persistent HMXB whose orbit was previously measured to be circular but the RXTE observations revealed an eccentric orbit. We observed this system with RXTE-PCA in August 2003 and our timing analysis supports the eccentric orbit of the system. However, we do not find any evidence for orbital evolution. Rotational and tidal interactions between the stars of a closed binary system result in apsidal motion which can be measured in systems with eccentric orbit. 4U0115+63 is a Be-transient HMXB whose eccentric orbit was well-determined during its 1978 outburst. We report preliminary results from analysis of data obtained during the 1999 outburst of this source with the RXTE-PCA.

Petri net-based modeling of a class of complex digital systems

We present through the use of Petri Nets, modeling techniques for digital systems realizable using FPGAs. These Petri Net models are used for logic validation at the logic design phase. The technique is illustrated by modeling practical circuits. Further, the utility of the technique with respect to timing analysis of the modeled digital systems is considered. Copyright (C) 1997 Elsevier Science Ltd