Miracle-dz/UniFAR-FTUs huggingface dataset:
JOHANNES SMOLANDER DEEP LEARNING CLASSIFICATION METHODS FOR COM- PLEX DISORDERS

JOHANNES SMOLANDER: Deep Learning Classi cation Methods for Complex Disorders Tampere University of Technology Master of Science thesis, 59 pages, 8 Appendix pages March 2016 Master's Degree Programme in xxx Technology Major: Information Technology for Health and Biology Examiner: Prof. Frank Emmert-Streib
Construction, transfection and production of recombinant vigilin in mammalian expression system

Vigilin is an abundant, highly conserved, ubiquitous protein containing 15 related, but non-identical, K-homolous nucleic acid binding domains. The construction, transfection and production of recombinant vigilin in mammalian expression system were investigated. The whole length of vigilin was amplified by polymerase chain reaction (PCR) and ligated to pCEP- PU vector. The recombinant construct pCEP-PU with vigilin was produced and transfected into Human embryonic kidney cells in a specific culture medium. The secreted recombinant vigilin was purified from the serum-free medium to homogeneity by affinity chromatography. The conditioned and purified media were tested for the presence of vigilin by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting with specific antibody. An immunoreactive band with an apparent molecular mass of approximately 140 kDa was detected. Immunofluorescence staining of transfected cells with vigilin demonstrated that recombinant vigilin molecules are localized in the nucleus and cytoplasm. In summary, the purified recombinant vigilin will facilitate future studies that address the structure and function of vigilin.
Parallel-Observer-Based Predictive Current Control of Permanent Magnet Synchronous Machines With Reduced Switching Frequency

Model predictive control (MPC) strategies have attracted wide attention due to its inherently high dynamic characteristics and flexible control capability. When the MPC is adopted to regulate the currents of permanent magnet synchronous machines, the cost function is typically constructed based on tracking errors of current components. Reduced switching frequency can be obtained by means of minimizing a revised cost function which includes a penalty item related to the predicted switching frequency. This will inevitably affect current tracking performances and, meanwhile, increase the computational burden due to the required long-horizon minimization. In order to solve this problem, this paper proposes a predictive current controller which inherently takes the converter zero-order-hold characteristics and system delay into account. Besides, with the aim of simultaneously realizing system behavior prediction and disturbance estimation, a structure of parallel extended-state observers is proposed. Theoretical analyses and experimental validations are both conducted to confirm its effectiveness. It is demonstrated that, under the situation of reduced switching frequency, improved control performances can be expected when the proposed controller is adopted, including highly dynamic responses inherently presented by typical predictive controllers and enhanced steady-state performances with the help of parallel observation structure.
An Empirical Analysis of the Propagation Mechanism of Financial Globalization

This paper examines the mechanism of financial globalization and the preconditions needed for operating it, from the aspect of financial development. Using data on financial globalization and financial development during the period of 1988 to 2001, from 16 OECD countries, this paper also conducts an empirical analysis of the mechanism behind propagation of financial globalization, employing a dynamic panel data analysis presented by Arellano and Bond (1991). It argues that two preconditions play a significant role in accelerating financial globalization: a 'scale condition,' meaning that the initial assets of institutional investors need to exceed a certain level, and an 'institutional condition,' meaning that the economy should be equipped with a system in which the accumulated capital can be operated efficiently. When we conduct empirical analysis by dividing the 16 OECD countries into two groups - Anglo-Saxon countries and European continental countries - the results demonstrate that the 'scale condition' is in general supported in terms of financial globalization in both sample groups. The 'institutional condition', however, shows a little difference between the Anglo-Saxon countries with their market-based financial systems and the continental European countries with their bank-based ones. In order to utilize the advantages of financial globalization positively, it is concluded that Korea, with its bank-based financial system, should devise a scheme to achieve more efficient fund operation and risk management by development of its capital market. At the same time, to make Korea an attractive financial hub in quantitative terms, boosting of the sophistication of its capital markets, such as its pension fund and bond markets, is seen to be important.
LPS-elicited TSLPR expression enriches a functionally discrete subset of human CD14+ CD1c+ monocytes

Thymic stromal lymphopoietin (TSLP) is a cytokine produced mainly by epithelial cells in response to inflammatory or microbial stimuli and binds to the TSLP receptor complex, a heterodimer composed of TSLP receptor (TSLPR) and IL-7 receptor α (CD127). TSLP activates multiple immune cell subsets expressing the TSLP receptor complex and plays a role in several models of disease. Although human monocytes express TSLPR and CD127 mRNAs in response to the TLR4 agonist LPS, their responsiveness to TSLP is ill-defined. We demonstrate that TSLP enhances human CD14+ monocyte CCL17 production in response to LPS and IL-4. Surprisingly, only a subset of CD14+ CD16− monocytes (TSLPR+ mono) expresses TSLP receptor complex upon LPS stimulation in an NF-κB- and p38-dependent manner. Phenotypic, functional and transcriptomic analysis revealed specific features of TSLPR+ mono, including higher CCL17 and IL-10 production and increased expression of genes with important immune functions (i.e. GAS6, ALOX15B, FCGR2B, LAIR1). Strikingly, TSLPR+ mono express higher levels of the dendritic cell marker CD1c. This evidence led us to identify a subset of peripheral blood CD14+ CD1c+ cells that expresses the highest levels of TSLPR upon LPS stimulation. The translational relevance of these findings is highlighted by the higher expression of TSLPR and CD127 mRNAs in monocytes isolated from patients with Gram-negative sepsis compared to healthy controls. Our results emphasize a phenotypic and functional heterogeneity in an apparently homogeneous population of human CD14+ CD16− monocytes and prompt further ontogenetic and functional analysis of CD14+ CD1c+ and LPS-activated CD14+ CD1c+ TSLPR+ monocytes.
A legal geography perspective on protected areas : lessons learnt from Table Mountain National Park (Cape Town, South Africa)

While legal geography is an emerging discipline, especially in North America, it is not yet a clearly defined field of research in France. In this article, we develop a conceptual framework based on a French legal theory applied to a protected area to show the convergence of perspectives between geography and law. Focused more specifically on how social values carried by law contribute to building space and place, this paper seeks to highlight a productive approach to the analysis of social relations.
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem

Motivation The Bioconductor project, a large collection of open source software for the comprehension of large-scale biological data, continues to grow with new packages added each week, motivating the development of software tools focused on exposing package metadata to developers and users. The resulting BiocPkgTools package facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches. Results The BiocPkgTools package has been incorporated into the Bioconductor project, installs using standard procedures, and runs on any system supporting R. It provides functions to load detailed package metadata, longitudinal package download statistics, package dependencies, and Bioconductor build reports, all in “tidy data” form. BiocPkgTools can convert from tidy data structures to graph structures, enabling graphbased analytics and visualization. An end-user-friendly graphical package explorer aids in task-centric package discovery. Full documentation and example use cases are included. Availability The BiocPkgTools software and complete documentation are available from Bioconductor (https://bioconductor.org/packages/BiocPkgTools).
The Impact of ‘IT’ Outsourcing on the Restaurant Industry

This research examines the impact of IT outsourcing on Restaurants’ Operations within the United Kingdom (UK). The study employs the theory of Transaction Cost Economics (TCE) and Resource-Based View (RBV) to conceptualise a theoretical framework. Data for the study was collected from 100 respondents consisting of supply chain managers, IT managers and senior management team members from three Restaurant Operations in the UK. The respondents were purposively sampled in order to ensure that only staffs with the relevant knowledge were contacted. A case study research design was adopted. Data was then analysed using both qualitative and quantitative techniques. The study established that increase in operational efficiency and cost reduction are recorded as benefits in IT outsourcing; companies have not experienced any serious post-contractual problems because they take the necessary safeguards to ensure that success is achieved in contracts; decision making is also the prerogative of top management and companies still talk about ‘giving out non-core functions in order to concentrate on core competencies’ without giving the necessary attention to other costs associated with the process. It was therefore recommended that due diligence and critical thinking have to be done by all stakeholders to be able to avert and manage any challenge that may occur in the process of outsourcing in restaurants’ operations.
Two Distinct Types of Extratropical Circulation Anomalies Associated with Cold Surges over the South China Sea

This study investigated the extratropical circulation anomalies responsible for cold surges over the South China Sea in winter. The surge events were identified by the intensity of northerly winds over 110°–117.5°E along 15°N at 925 hPa. Two distinct patterns of sea level pressure (SLP) anomalies in East Asia were found to have a crucial role in inducing cold surges over the South China Sea. Accordingly, the cold surge events were classified into two types. The first type of cold surge is characterized by a pair of SLP anomalies with positive and negative ones centered over China and Japan, respectively, whereas the second type of cold surge is characterized by widespread and persistent positive SLP anomalies over East Asia. Furthermore, the first type of cold surge is accompanied by a deepened East Asian trough and precursory Rossby wave trains across the Eurasian continent in the mid- and upper troposphere, but the latter is not. Prior to both types of the cold surges, the Siberian high is significantly intensified. However, diagnosis of the SLP tendency indicates that the intensification is related to different physical processes. In the first type of cold surge, the Rossby wave trains favor negative vorticity advection and cold advection, inducing intensification of the Siberian high. By contrast, in the second type of cold surge, vorticity advection can be ignored due to the lack of Rossby wave trains, and only the lower-tropospheric cold advection induced by anomalous northerly winds, resulting from the anomalous Siberian high, contributes to the further intensification of the Siberian high.
Changing contribution of snow to Hudson Bay river discharge

Hudson Bay (HB) in northern Canada has experienced changing volumes and seasonality of streamflows in the last 100 years. These shifts may be due to changing snow accumulation and ablation regimes. This study quantifies the changing contribution of snow to river discharge from 20 major river basins draining into HB (including James Bay) between 1980 and 2013. The analysis is based on daily snow water equivalent (SWE) data from GlobSnow, and daily streamflow data from the Water Survey of Canada, Hydro-Qu~bec, and Le Centre d\u2019Expertise Hydrique du Qu~bec. The contribution of snowmelt to streamflow generation is estimated from the ratio of water year maximum SWE to runoff. The Mann-Kendall test is performed for evaluation of trends and their significance. In HB, the snowmelt contribution to streamflow generation during 1980 to 2013 decreased by 15.9% (34 yr)\u207b~ and changed in hydrological conditions are observed. The potential impacts of these changes on ecological and socio-economic systems across much of Canada\u2019s North are discussed.
Comparative evaluation of KOH mount, fungal culture and PAS staining in onychomycosis

<p class="abstract"><strong>Background:</strong> Onychomycosis is a common ailment associated with significant physical and psychological morbidity. Increased prevalence in the recent years has attributed to enhanced longitivity, co morbid conditions like diabetes, avid spots participation and emergence of HIV. The objective of the study was to evaluate KOH mount, fungal culture and PAS staining of affected nail plate in diagnosis of onychomycosis. </p><p class="abstract"><strong>Methods:</strong> The present study was carried out in OPD of Dermatology, PESIMSR, Kuppam, Andhra Pradesh during the period of October 2010 to October 2012 including all patients showing classical clinical features of onychomycosis. <strong></strong></p><p class="abstract"><strong>Results:</strong> Majority of patients were from 21-40 years age group i.e. 46%. 56% of finger nails were commonly involved than 36% toe nails. DLSO is the most common clinical variant accounting for 80%. Most common isolated species as <em>Trichophyton rubrum </em>(31.6%) followed by <em>T. mentagrophytes</em> and <em>Aspergillus niger</em> 15.8% each. The sensitivity of KOH (81.82%), PAS (84.56%) and culture 57%. Both PAS and KOH were more sensitive than culture (p<0.001). PAS was also more sensitive than KOH. The specificity of KOH 92.86%, culture 92.86% and PAS 57.14%. </p><p class="abstract"><strong>Conclusions:</strong> Fungal culture though is the gold standard for the identification of pathogens but it takes minimum 2-3 weeks. Histopathological examination of nail clippings with PAS stain is simple, highly sensitive screening test. </p>
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

Clustering is an essential step in the analysis of single cell RNA-seq (scRNA-seq) data to shed light on tissue complexity including the number of cell types and transcriptomic signatures of each cell type. Due to its importance, novel methods have been developed recently for this purpose. However, different approaches generate varying estimates regarding the number of clusters and the single-cell level cluster assignments. This type of unsupervised clustering is challenging and it is often times hard to gauge which method to use because none of the existing methods outperform others across all scenarios. We present SAME-clustering, a mixture model-based approach that takes clustering solutions from multiple methods and selects a maximally diverse subset to produce an improved ensemble solution. We tested SAME-clustering across 15 scRNA-seq datasets generated by different platforms, with number of clusters varying from 3 to 15, and number of single cells from 49 to 32,695. Results show that our SAME-clustering ensemble method yields enhanced clustering, in terms of both cluster assignments and number of clusters. The mixture model ensemble clustering is not limited to clustering scRNA-seq data and may be useful to a wide range of clustering applications.
Ice‐margin fluctuation sequences and grounding zone wedges: The record of the Late Palaeozoic Ice Age in the eastern Karoo Basin (Dwyka Group, South Africa)

In the eastern part of the Karoo Basin of South Africa, the sedimentary record of the Late Palaeozoic Ice Age, the Dwyka Group, consists of an up to 200 m thick accumulation of massive to crudely stratified diamictite occasionally interstratified with siltstone, sandstone and conglomerate horizons. Three distinct sedimentary units, separated by intervening glacial erosion surfaces, are viewed as ice‐margin fluctuation sequences. The lowermost one, resting on highly uneven, glacially abraded Archaean basement, has been interpreted as a grounding zone wedge deposited after the retreat and stabilization of the ice margin after the inundation of the Karoo Basin. The grounding zone wedge interpretation is based on its thickness (up to 100 m), the dominance of diamictite, and its facies assemblage and inferred depositional processes (rain‐out of debris, dropstone dumping, mass and debris flow, till). Overlying the grounding zone wedge, deposits are sedimentary units interpreted as glaciofluvial or ice‐contact delta and grounding zone wedges, respectively. By analogy with Quaternary sedimentary sequences, deposition of the Dwyka Group in the study area might have been very rapid (tens to hundreds of thousand years) and may hence correlate with the ultimate deglacial sequence of the Western Karoo Basin, as both successions are covered by the postglacial Ecca Group. Although commonly observed and imaged on modern, high‐latitude continental shelves, grounding zone wedges have never been interpreted in the ancient geological record. This paper therefore outlines a model defining criteria necessary for their identification.
Single-Ended-Fed High-Gain LTCC Planar Aperture Antenna for 60 GHz Antenna-in-Package Applications

This paper presents new single-ended-fed planar aperture antennas (SPAAs) using low-temperature co-fired ceramics (LTCC) process technology. The SPAA element is proposed first, which not only inherits the merits of the aperture antennas including high gain and wide bandwidth but also exhibits advantages of low profile and compact size. The aperture is excited by a cross-shaped patch, and a loop-shaped balun structure placed below the patch is introduced to convert the single-ended signal into differential one to drive the patch. In this way, the energy can propagate on the patch in a traveling waveform and illuminate the aperture with uniform E-field distributions. Therefore, the antenna achieves good electrical and radiation performances, which are comparable to its balanced-fed counterparts, while processing a simplified structure. Measured results demonstrate that the impedance bandwidth of the antenna covers the 60 GHz license-free band (57–64 GHz), and the maximum gain can reach 11.5 dBi with a cavity area of only about 27 mm2. Furthermore, the element is successfully extended to a $4\,\,\times \,\,4$ element array using a substrate-integrated-waveguide based feeding network to further increase the gain up to 20.4 dBi. The measured results show that the impedance bandwidth of the array is from 57.5 to 65.7 GHz and the radiation performances are very stable over the operating frequency band.
Modeling of mesoscale phenomena using WRF-BEP-BEM-CIM in a complex region

Because of the global warming, urban planning strategies must be investigated to reduce building energy consumption and increase thermal comfort in urban areas. It is thus proposed in this study to use a mesoscale meteorological model to study the impact of multiple urban planning scenarios in the Canton of Vaud. The Weather Research and Forecast (WRF) model is used to conduct simulations. The urban parameterizations, Building Effect Parameterization + Building Energy Model + Canopy Interface Model (BEP-BEM-CIM), developed in previous studies are already integrated in the WRF model. We demonstrate that the models perform well in plateaued regions (<10% difference) but some important deviations (20%-30% difference) are noted in particularly complex regions with complex topography. Two possible improvements will be addressed in the future: there is a need to improve the topography representation in the model itself and other scenarios including the impact of future climate will also be assessed.
A COMPARATIVE STUDY OF DOA ESTIMATION ALGORITHMS WITH APPLICATION TO TRACKING USING KALMAN FILTER

Tracking the Direction of Arrival (DOA) Estimation of a moving source is an important and challenging task in the field of navigation, RADAR, SONAR, Wireless Sensor Networks (WSNs) etc. Tracking is carried out starting from the estimation of DOA, considering the estimated DOA as an initial value, the Kalman Filter (KF) algorithm is used to track the moving source based on the motion model which governs the motion of the source. This comparative study deals with analysis, significance of Non-coherent, Narrowband DOA (Direction of Arrival) Estimation Algorithms in perception to tracking. The DOA estimation algorithms Multiple Signal Classification (MUSIC), Root-MUSIC& Estimation of Signal Parameters via Rotational Invariance Technique (ESPRIT) are considered for the purpose of the study, a comparison in terms of optimality with respect to Signal to Noise Ratio (SNR), number of snapshots and number of Antenna elements used and Computational complexity is drawn between the chosen algorithms resulting in an optimum DOA estimate. The optimum DOA Estimate is taken as an initial value for the Kalman filter tracking algorithm. The Kalman filter algorithm is used to track the optimum DOA Estimate.
Effects of silibinin on hepatic warm ischemia-reperfusion injury in the rat model

Objective(s): Liver ischemia-reperfusion injuries (I/RI) are typically the main causes of liver dysfunction after various types of liver surgery especially liver transplantation. Radical components are the major causes of such direct injuries. We aimed to determine the beneficial effects of silibinin, a potent radical scavenger on liver I/RI. Materials and Methods: Thirty-two rats were divided into 4 groups. Group I: VEHICLE, the rats underwent laparotomy and received DMSO, group II: SILI, laparotomy was done and silibinin was administered. Group III: I/R, the rats received DMSO and were subjected to a liver I/R procedure and group IV: I/R+SILI, the animals underwent the I/R procedure and received silibinin. After 1 hr of ischemia followed by 3 hr reperfusion, blood was collected to evaluate the serum marker of liver injuries. Hepatic tissue was harvested to investigate glycogen content, histological changes, and vasoregulatory gene expression. Results: Results showed that serum AST, ALT, LDH, GGT, ALP, and hyaluronic acid (HA) increased significantly in I/R group compared with the VEHICLE group. Silibinin reduced this elevation except for GGT. Silibinin inhibited hepatocyte vacuolization and degeneration, endothelium damages, sinusoidal congestion and inflammation, and glycogen depletion during I/R. ET-1 mRNA was overproduced in the I/R group compared with the VEHICLE group which was decreased by silibinin. KLF2 and eNOS expression was reduced during I/R compared with the VEHICLE group. Silibinin elevated KLF2 expression but had no meaningful effect on eNOS expression. Conclusion: Silibinin protected the liver from I/RI. Silibinin could improve liver circulation by preventing sinusoidal congestion, inflammation, and perhaps modification of the vasoregulatory gene expression.