Kernel-PCA data integration with enhanced interpretability

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.

Optoelectronic studies in nanocrystalline silicon Schottky diodes obtained by Hot-Wire Chemical Vapour Deposition

The very usual columnar growth of nanocrystalline silicon leads to electronic transport anisotropies. Whereas electrical measurements with coplanar electrodes only provide information about the electronic transport parallel to the substrate, it is the transverse transport which determines the collection efficiency in thin film solar cells. Hence, Schottky diodes on transparent electrodes were obtained by hot-wire CVD in order to perform external quantum efficiency and surface photovoltage studies in sandwich configuration. These measurements allowed to calculate a transverse collection length, which must correlate with the photovoltaic performance of thin film solar cells. Furthermore, the density of charge trapped at localized states in the bandgap was estimated from the voltage dependence of the depletion capacitance of these rectifying contacts.

Financial integration, capital misallocation and global imbalances

This paper shows that in a stylized model with two countries, characterized by different levels of financial development, the following facts can be replicated: 1) persistent current account surpluses and 2) high TFP growth in China. Under autarky, entrepreneurs in the emerging country overinvest in short-term projects and underinvest in long-term projects because short-term assets help them secure long-term investments in the presence of credit constraints. This creates an aggregate misallocation of capital. When financial markets integrate, entrepreneurs with long-term projects can have access to cheaper short-term assets abroad, which leaves them more resources to invest in their projects. This both reduces capital misallocations and generates capital outflows.

Problems of the architecture design in the system integration

This thesis studies the problems and their reasons a software architect faces in his work. The purpose of the study is to search and identify potential factors causing problens in system integration and software engineering. Under a special interest are non-technical factors causing different kinds of problems. Thesis was executed by interviewing professionals that took part in e-commerce project in some corporation. Interviewed professionals consisted of architects from technical implementation projects, corporation's architect team leader, different kind of project managers and CRM manager. A specific theme list was used as an guidance of the interviews. Recorded interviews were transcribed and then classified using ATLAS.ti software. Basics of e-commerce, software engineering and system integration is described too. Differences between e-commerce and e-business as well as traditional business are represented as are basic types of e-commerce. Software's life span, general problems of software engineering and software design are covered concerning software engineering. In addition, general problems of the system integration and the special requirements set by e-commerce are described in the thesis. In the ending there is a part where the problems founded in study are described and some areas of software engineering where some development could be done so that same kind of problems could be avoided in the future.

Stock and Bond Market Integration: Evidence from Russian Financial Markets

Minimizing the risks of an investment portfolio but not in the favour of expected returns is one of the key interests of an investor. Typically, portfolio diversification is achieved using two main strategies: investing in different classes of assets thought to have little or negative correlations or investing in similar classes of assets in multiple markets through international diversification. This study investigates integration of the Russian financial markets in the time period of January 1, 2003 to December 28, 2007 using daily data. The aim is to test the intra-country and cross-country integration of the Russian stock and bond markets between seven countries. Our test methodology for the short-run dynamics testing is the vector autoregressive model (VAR) and for the long-run cointegration testing we use the Johansen cointegration test which is an extension to VAR. The empirical results of this study show that the Russian stock and bond markets are not integrated in the long-run either at intra-country or cross-country level which means that the markets are relatively segmented. The short-run dynamics are also relatively low. This implies a presence of potential gains from diversification.

Dual and Opposite Effects of hRAD51 Chemical Modulation on HIV-1 Integration.

The cellular DNA repair hRAD51 protein has been shown to restrict HIV-1 integration both in vitro and in vivo. To investigate its regulatory functions, we performed a pharmacological analysis of the retroviral integration modulation by hRAD51. We found that, in vitro, chemical activation of hRAD51 stimulates its integration inhibitory properties, whereas inhibition of hRAD51 decreases the integration restriction, indicating that the modulation of HIV-1 integration depends on the hRAD51 recombinase activity. Cellular analyses demonstrated that cells exhibiting high hRAD51 levels prior to de novo infection are more resistant to integration. On the other hand, when hRAD51 was activated during integration, cells were more permissive. Altogether, these data establish the functional link between hRAD51 activity and HIV-1 integration. Our results highlight the multiple and opposite effects of the recombinase during integration and provide new insights into the cellular regulation of HIV-1 replication.

Synaptic Integration of Adult-Born Hippocampal Neurons Is Locally Controlled by Astrocytes.

Adult neurogenesis is regulated by the neurogenic niche, through mechanisms that remain poorly defined. Here, we investigated whether niche-constituting astrocytes influence the maturation of adult-born hippocampal neurons using two independent transgenic approaches to block vesicular release from astrocytes. In these models, adult-born neurons but not mature neurons showed reduced glutamatergic synaptic input and dendritic spine density that was accompanied with lower functional integration and cell survival. By taking advantage of the mosaic expression of transgenes in astrocytes, we found that spine density was reduced exclusively in segments intersecting blocked astrocytes, revealing an extrinsic, local control of spine formation. Defects in NMDA receptor (NMDAR)-mediated synaptic transmission and dendrite maturation were partially restored by exogenous D-serine, whose extracellular level was decreased in transgenic models. Together, these results reveal a critical role for adult astrocytes in local dendritic spine maturation, which is necessary for the NMDAR-dependent functional integration of newborn neurons.

Content and Language Integration as a part of a degree reform at Tampere University of Technology

Tampere University of Technology is undergoing a degree reform that started in 2013. One of the major changes in the reform was the integration of compulsory Finnish, Swedish and English language courses to substance courses at the bachelor level. The integration of content and language courses aims at higher quality language learning, more fluency in studies, and increased motivation toward language studies. In addition, integration is an opportunity to optimize the use of resources and to offer courses that are more tailored to the students' field of study and to the skills needed in working life. The reform also aims to increase and develop co-operation between different departments at the university and to develop scientific follow up. This paper gives an overview of the integration process conducted at TUT and gives examples of adjunct CLIL implementations in three different languages.

Maturation and Functional Integration of New Granule Cells into the Adult Hippocampus.

The adult hippocampus generates functional dentate granule cells (GCs) that release glutamate onto target cells in the hilus and cornus ammonis (CA)3 region, and receive glutamatergic and γ-aminobutyric acid (GABA)ergic inputs that tightly control their spiking activity. The slow and sequential development of their excitatory and inhibitory inputs makes them particularly relevant for information processing. Although they are still immature, new neurons are recruited by afferent activity and display increased excitability, enhanced activity-dependent plasticity of their input and output connections, and a high rate of synaptogenesis. Once fully mature, new GCs show all the hallmarks of neurons generated during development. In this review, we focus on how developing neurons remodel the adult dentate gyrus and discuss key aspects that illustrate the potential of neurogenesis as a mechanism for circuit plasticity and function.

An affected core drives network integration deficits of the structural connectome in 22q11.2 deletion syndrome.

Chromosome 22q11.2 deletion syndrome (22q11DS) is a genetic disease known to lead to cerebral structural alterations, which we study using the framework of the macroscopic white-matter connectome. We create weighted connectomes of 44 patients with 22q11DS and 44 healthy controls using diffusion tensor magnetic resonance imaging, and perform a weighted graph theoretical analysis. After confirming global network integration deficits in 22q11DS (previously identified using binary connectomes), we identify the spatial distribution of regions responsible for global deficits. Next, we further characterize the dysconnectivity of the deficient regions in terms of sub-network properties, and investigate their relevance with respect to clinical profiles. We define the subset of regions with decreased nodal integration (evaluated using the closeness centrality measure) as the affected core (A-core) of the 22q11DS structural connectome. A-core regions are broadly bilaterally symmetric and consist of numerous network hubs - chiefly parietal and frontal cortical, as well as subcortical regions. Using a simulated lesion approach, we demonstrate that these core regions and their connections are particularly important to efficient network communication. Moreover, these regions are generally densely connected, but less so in 22q11DS. These specific disturbances are associated to a rerouting of shortest network paths that circumvent the A-core in 22q11DS, "de-centralizing" the network. Finally, the efficiency and mean connectivity strength of an orbito-frontal/cingulate circuit, included in the affected regions, correlate negatively with the extent of negative symptoms in 22q11DS patients, revealing the clinical relevance of present findings. The identified A-core overlaps numerous regions previously identified as affected in 22q11DS as well as in schizophrenia, which approximately 30-40% of 22q11DS patients develop.

Institutional legacies, employment and professional integration of non EU/EEA doctors in France

Internationally, policies for attracting highly-skilled migrants have become the guidelines mainly used by the Organisation for Economic Co-operation and Development (OECD) countries. Governments are implementing specific procedures to capture and facilitate their mobility. However, all professions are not equal when it comes to welcoming highly-skilled migrants. The medical profession, as a protective market, is one of these. Taking the case of non-EU/EEA doctors in France, this paper shows that the medical profession defined as the closed labour market, remains the most controversial in terms of professional integration of migrants, protectionist barriers to migrant competition and challenge of medical shortage. Based on the path-dependency approach, this paper argues that non-EU/EEA doctors' issues in France derive from a complex historical process of interaction between standards settled in the past, particularly the historical power of medical corporatism, the unexpected long-term effects of French hospital reforms of 1958, and budgetary pressures. Theoretically, this paper shows two significant findings. Firstly, the French medical system has undergone a series of transformations unthinkable in the strict sense of a path-dependence approach: an opening of the medical profession to foreign physicians in the context of the Europeanisation of public policy, acceptance of non-EU/EEA doctors in a context of medical shortage and budgetary pressures. Secondly, there is no change of the overall paradigm: significantly, the recruitment policies of non-EU/EEA doctors continue to highlight the imprint of the past and reveal a significant persistence of prejudices. Non-EU/EEA doctors are not considered legitimate doctors even if they have the qualifications of physicians which are legitimate in their country and which can be recognised in other receiving countries.

jxSensor: a sensor network integration layer for JXTA

Nowadays, Wireless Sensor Networks (WSN) arealready a very important data source to obtain data about the environment. Thus, they are key to the creation of Cyber-Physical Systems (CPS). Given the popularity of P2P middlewares as ameans to efficiently process information and distribute services, being able to integrate them to WSN¿s is an interesting proposal. JXTA is a widely used P2P middleware that allows peers to easily exchange information, heavily relying on its main architectural highlight, the capability to organize peers with common interests into peer groups. However, right now, approaches to integrate WSNs to a JXTA network seldom take advantage of peer groups. For this reason, in this paper we present jxSensor, an integrationlayer for sensor motes which facilitates the deployment of CPS¿s under this architecture. This integration has been done taking into account JXTA¿s idiosyncrasies and proposing novel ideas,such as the Virtual Peer, a group of sensors that acts as a single entity within the peer group context.

Synergy Sources, Target Autonomy and Integration in Acquisitions

Determining the appropriate level of integration is crucial to realizing value from acquisitions. Most prior research assumes that higher integration implies the removal of autonomy from target managers, which in turn undermines the functioning of the target firm if it entails unfamiliar elements for the acquirer. Using a survey of 86 acquisitions to obtain the richness of detail necessary to distinguish integration from autonomy, the authors argue and find that integration and autonomy are not the opposite ends of a single continuum. Certain conditions (e.g., when complementarity rather than similarity is the primary source of synergy) lead to high levels of both integration and autonomy. In addition, similarity negatively moderates the relationship between complementarity and autonomy when the target offers both synergy sources. In contrast, similarity does not moderate the link between complementarity and integration. The authors' findings advance scholarly understanding about the drivers of implementation strategy and in particular the different implementation strategies acquiring managers deploy when they attempt to leverage complementarities, similarities, or both.

Integration of a Bioethanol Process to a Pulp Mill

Tässä diplomityössä tutkittiin puuhakkeen esihydrolyysi- ja hakkuujätteen hydrolyysiprosessien integroimista sellutehtaaseen bioetanolin tuottamiseksi. Tällaisesta ns. biojalostamosta luotiin WinGEMS-simulointiohjelmalla simulointimalli, jonka avulla tutkittiin bioetanoliprosessin vaikutusta sellutehtaan massa- ja energiataseisiin sekä alustavaa biojalostamon kannattavuutta. Simuloinnissa tarkasteltiin kolmea eri tapausta, joissa mäntysellun tuotannon ajateltiin olevan 1000 tonnia päivässä ja hakkuujätettä käytettävän 10 % tarvittavan kuitupuun määrästä: 1) Puuhakkeen esihydrolyysi ja hakkuujätteen hydrolyysi etanolin tuottamiseksi 2) Puuhakkeen esihydrolyysi, hakkuujäte kuorikattilaan poltettavaksi 3) Ei esihydrolyysiä, hakkuujäte kuorikattilaan poltettavaksi Verrattuna tapaukseen 3, puun kulutus kasvaa 16 % esihydrolysoitaessa puuhake ennen keittoa tapauksissa 1 ja 2. Kasvaneella puun kulutuksella tuotetaan tapauksessa 1 149 tonnia etanolia ja 240 MWh enemmän ylimääräsähköä päivässä. Tapauksessa 2 tuotetaan 68 tonnia etanolia ja 460 MWh enemmän ylimääräsähköä päivässä. Tämä tuottaisi vuotuista lisäkassavirtaa 18,8 miljoonaa euroa tapauksessa 1 ja 9,4 miljoonaa euroa tapauksessa 2. Hydrolyysin tuoteliuoksen, hydrolysaatin, haihduttaminen sekä hydrolyysiprosessien orgaanisten jäännöstuotteiden haihduttaminen ja polttaminen kasvattavat haihduttamon ja soodakattilan kuormitusta. Verrattuna tapaukseen 3, tapauksissa 1 ja 2 haihduttamon vaiheiden määrä on kasvatettava viidestä seitsemään ja tarvittavat lämmönsiirtopinta-alat lähes kaksinkertaistettava. Soodakattilan kuormitus kasvaa 39 % tapauksessa 1 ja 26 % tapauksessa 2.