Miracle-dz/UniFAR-FTUs huggingface dataset:
Disease Protein Pathway Discovery using Higher-Order Network Structures

A disease pathway is a set of proteins that influence the disease. The discovery of disease pathways is an important problem because these pathways can reveal the underlying disease mechanism, uncover significant protein interactions, and elucidate potential treatment options. Finding the protein-protein interactions that accelerate or mitigate disease development may provide novel insight into safer drug targets. A greater understanding of the disease protein network further helps to trace diseases to their root biological causes and identify unforeseen side effects of current treatments. The disease pathway discovery problem is usually set up as follows: given a protein-protein interaction (PPI) network and a set of proteins known to be associated to the disease, predict other proteins in the network that are also part of the disease pathway. Generally speaking, previous research on this problem has primarily focused on local connectivity features of the known associated disease proteins. In other words, new proteins were predicted by building from the known associations using some lower-order network heuristic such as path length or common neighbors. It has been shown recently, however, that many disease pathways have a considerably more complicated network structure than a single tightly-connected component of protein nodes, as suggested by the use of local heuristics. Disease pathways actually exhibit more loosely connected subgraphs of network nodes that contribute to disease development through sophisticated interactions. Thus, it is critical to develop new methods for the analysis and determination of common motifs within such PPI network structures to more effectively elucidate disease pathways with similar patterns. In this project, we will focus on studying these higher-order network structures and applying the methods to a PPI network to robustly uncover disease protein pathways.
Etude et conception de l'anneau de désintégration d'une usine à neutrinos utilisant les décroissances bêta des noyaux hélium 6 et néon 18 produits par un faisceau intense de protons frappant diverses cibles

L'etude de l'oscillation du neutrino entre ses differentes saveurs requiert des flux purs et tres intenses de neutrinos energetiques, bien collimates, dont le spectre en energie est bien determine. Ainsi, une machine dediee apparait actuellement necessaire. Parmi les differents concepts proposes d'usines a neutrinos, celui etudie ici, denomme Beta-Beams, porte sur la production de neutrinos par la decroissance beta d'ions radioactifs prealablement acceleres. Plus precisement, la these est centree sur l'etude et la conception de l'anneau de stockage, en forme de champ de course, des ions acceleres. Sa finalite est de stocker les ions jusqu'a leur decroissance. Apres une breve description du mecanisme d'oscillation du neutrino et une revue des differentes experiences, une introduction sera donnee au concept des usines a neutrinos et plus particulierement sur les Beta-Beams. Ensuite, les problematiques liees aux Beta-Beams seront enoncees. Apres avoir decrit le formalisme du transport de particules dans un accelerateur, un premier design de l'anneau ainsi que ses proprietes optiques seront alors donnes. L'effet des defauts d'alignement ou de champ dans les dipoles a egalement ete etudie ainsi que l'optimisation de l'ouverture dynamique. Le traitement des pertes par decroissance ou par collimation en energie sera developpe. Le besoin d'injecter en presence d'un faisceau circulant necessite une injection off-momentum, qui sera decrite. Enfin, le melange des deux faisceaux necessite un programme radiofrequence specifique qui sera presente.
Analysis of FLT3 gene mutations in de novo myelodysplastic syndromes. FLT3 internal tandem duplication detected in a case of refractory anemia

FLT3 (FMS-like receptor tyrosine kinase) gene, a member of the class III receptor tyrosine kinase family (RTK), is expressed on hematopoietic progenitor cells and mediates stem cell proliferation and differentiation [1]. In recent years, an internal tandem duplication (ITD) within JM/TK-1 domains as a somatic mutation of the FLT3 gene has been reported in 20 – 25% of adult patients with acute myeloid leukemia (AML) and 3% of adult MDS [2 – 7]. FLT3/ITDs have been detected in all FAB subtypes of AML and correlated with poor prognosis [3,8 – 9]. This mutation results in constitutive activation of FLT3 kinase with subsequent activation of proliferative pathways [1]. In addition, point mutations at aspartic acid within the activation loop of FLT3 have also been described in AML (7%), MDS (3.4%), and acute lymphoblastic leukemia (ALL) (2.8%) [10]. The most common is the D835 mutation (G! T! Asp! Tyr), which has also been associated with constitutive activation of receptor. The aim of the present study was the concurrent detection and clinical significance of FLT3 mutations (ITD and D835) in the bone marrow of 64 adult patients with de novo MDS at diagnosis. This study included 64 newly diagnosed patients with de novo MDS. Clinical characteristics of the patients are shown in Table I. Morphologic subtypes of MDS were classified according to the FAB criteria [11]. The karyotype was regularly performed and was normal in 36/48 examined cases. Clonal karyotypic abnormalities were found in 12/48 (25%) of cases including 3 RA, 7 RAEB, and 2 RAEB-t as depicted in Table I. Data allowing the calculation of risk scores according to the International Prognostic Scoring System (IPSS) [12] were available in 39 cases as shown in Table I. Bone marrow mononuclear cells from patients with MDS before the institution of any treatment were obtained after informed consent. Bone marrow mononuclear cells from patients with lymphoma without bone marrow involvement were used as a normal control. Bone marrow mononuclear cells were separated on Histopaque gradient. High molecular weight DNA was extracted using the phenol chloroform method. FLT3/ITD was examined by amplification of the JM domain from exon14 to exon15, using primers 14F: 50-GCAATTTAGGTATGAAAGC CAGC-30 and 15R: 50-CTTTCAGCATTTTGA CGGCAAC C-30, as previously described [2]. DNA from an AML patient known to carry the FLT3/ITD as demonstrated by direct sequencing was used as a positive control for the presence of the FLT3/ITD mutation. Exon 17 of FLT3 gene was amplified by PCR using the primers 17F: 50-CCG CCAGGAACG TGCTTG-30 and 17R: 50-GCAG CCTCACATTGCCCC-30 and digested with restriction enzyme EcoRV [10]. Normal products produce two bands of 68 bp and 46 bp following
Impact of Terrorism on Investment: Evidence from Pakistan

Terrorism destabilizes and demoralizes the nation, it also breeds depression and frustration in an economy. It is badly affecting factor of economic growth and development of Pakistan. In this study, we have tried to find out the impact of terrorism on domestic investment as well as foreign direct investment in Pakistan for the time frame of 1980-2015. The autoregressive distributed lag bound testing co-integration approach is used to examine the long run relationship. The results show that there is a long run relationship between terrorism and investment. The empirics also expose a negative effect of terrorism on both domestic and foreign investments while human capital and trade are playing a vital role to enhance the level of investment. The study suggests that the government should force all the people to leave the country who are illegally present. The need is to take steps to stop the illegal flow of arms and money into the country from abroad. It is the moral responsibility of all the secret agencies of Pakistan and media should work in the coordination with one another and try their utmost to detect and identify the terrorists.
Cardiac-resynchronization therapy with or without an implantable defibrillator in advanced chronic heart failure.

BACKGROUND We tested the hypothesis that prophylactic cardiac-resynchronization therapy in the form of biventricular stimulation with a pacemaker with or without a defibrillator would reduce the risk of death and hospitalization among patients with advanced chronic heart failure and intraventricular conduction delays. METHODS A total of 1520 patients who had advanced heart failure (New York Heart Association class III or IV) due to ischemic or nonischemic cardiomyopathies and a QRS interval of at least 120 msec were randomly assigned in a 1:2:2 ratio to receive optimal pharmacologic therapy (diuretics, angiotensin-converting-enzyme inhibitors, beta-blockers, and spironolactone) alone or in combination with cardiac-resynchronization therapy with either a pacemaker or a pacemaker-defibrillator. The primary composite end point was the time to death from or hospitalization for any cause. RESULTS As compared with optimal pharmacologic therapy alone, cardiac-resynchronization therapy with a pacemaker decreased the risk of the primary end point (hazard ratio, 0.81; P=0.014), as did cardiac-resynchronization therapy with a pacemaker-defibrillator (hazard ratio, 0.80; P=0.01). The risk of the combined end point of death from or hospitalization for heart failure was reduced by 34 percent in the pacemaker group (P<0.002) and by 40 percent in the pacemaker-defibrillator group (P<0.001 for the comparison with the pharmacologic-therapy group). A pacemaker reduced the risk of the secondary end point of death from any cause by 24 percent (P=0.059), and a pacemaker-defibrillator reduced the risk by 36 percent (P=0.003). CONCLUSIONS In patients with advanced heart failure and a prolonged QRS interval, cardiac-resynchronization therapy decreases the combined risk of death from any cause or first hospitalization and, when combined with an implantable defibrillator, significantly reduces mortality.
Integration and Development of Archives Information Resources in the Internet Age

: Under the background of the Internet as the main feature, archive informationization has become an important direction for the development of college archives. With the introduction and application of new technologies, new ideas and new methods in the archives work of colleges and universities, the archives work has undergone different degrees of change in the work procedures, links and contents.
DEPARTMENT OF ECONOMICS, MANAGEMENT AND STATISTICS UNIVERSITY OF MILAN – BICOCCA

Digital skills are increasingly important for labor market outcomes and social participation. Do they also matter for academic performance? This paper investigates the effects of digital literacy on educational outcomes by merging data from the Italian National Assessment in secondary schools with an original data set on performance tests of Internet skills for 10 grade students. Our identification strategy relies on a rich set of individual, family, school and classroom control variables that are not commonly available in previous studies. The findings indicate that, overall, Internet skills have a positive impact on academic achievement. This effect is stronger for students with low academic performance or low family background. It is also stronger for students in technical or vocational schools.
Use of Baculovirus-Expressed Glycoprotein H in an Enzyme-Linked Immunosorbent Assay Developed To Assess Exposure to Chelonid Fibropapillomatosis-Associated Herpesvirus and Its Relationship to the Prevalence of Fibropapillomatosis in Sea Turtles

ABSTRACT Chelonid fibropapillomatosis-associated herpesvirus (CFPHV) is an alphaherpesvirus believed to cause marine turtle fibropapillomatosis (FP). A serodiagnostic assay was developed for monitoring sea turtle populations for CFPHV exposure. CFPHV glycoprotein H (gH) expressed in recombinant baculovirus was used in an enzyme-linked immunosorbent assay (ELISA) to detect virus-specific 7S turtle antibodies. Using captive-reared green turtles (Chelonia mydas) with no history of virus exposure as “known negatives” and others with experimentally induced FP as “known positives,” the assay had 100% specificity but low sensitivity, as seroconversion was detected in only half of the turtles bearing experimentally induced tumors. Antibodies were detected only in samples collected after cutaneous fibropapillomas appeared, consistent with observations that tumors are significant sites of virion production and antigen expression and the possibility that prolonged/repeated virus shedding may be required for adequate stimulation of 7S antibody responses to gH. Natural routes of infection, however, may produce higher seroconversion rates. High gH antibody seroprevalences (∼80%) were found among wild green turtles in three Florida localities with different FP prevalences, including one site with no history of FP. In addition, all eight loggerhead turtles (Caretta caretta) tested were seropositive despite FP being uncommon in this species. The possibility that CFPHV infection may be common relative to disease suggests roles for environmental and host factors as modulators of disease expression. Alternatively, the possibility of other antigenically similar herpesviruses present in wild populations cannot be excluded, although antibody cross-reactivity with the lung/eye/trachea disease-associated herpesvirus was ruled out in this study.
Professionals' role in building organization's brand equity

Author: Kristina Mantilanaho Title: Professionals’ role in building organization’s brand equity Faculty: LUT School of Business and Management Master’s programme: International Marketing Management Year: 2018 Master’s Thesis: 77 pages, 12 figures, 3 tables, 1 appendix Examiners: Associate Professor Anssi Tarkiainen, Professor SannaKatriina Asikainen
Iterative multiuser detection for asynchronous CDMA with concatenated convolutional coding

We propose iterative multiuser detectors for asynchronous code-division multiple-access with parallel-concatenated convolutional codes (turbo codes) and with serially concatenated convolutional codes (SCCC). At each iteration we update and exchange the extrinsic information from the multiuser detector and channel decoders and regenerate soft information between constituent convolutional decoders. Simulation results show that with the proposed structure, near-single-user performance can be achieved. We also propose two reduced-complexity techniques, i.e., the reduced-state iterative multiuser detector based on the T-MAP algorithm and the iterative interference canceler based on a noise-whitening filter. Simulation results show a small performance degradation for these two techniques, particularly for the T-MAP receiver.
Methodological weakness in using correlation coefficients for assessing the interchangeability of analyte data between samples collected under different sampling conditions – the example of matrix metalloproteinase 9 determined in serum and plasma samples

Klaus Jung* and Chun-Ying Wu 1 Department of Urology, Charité Universitätsmedizin Berlin, Germany 2 Berlin Institute for Urological Research, Berlin, Germany 3 Division of Gastroenterology, Taichung Veterans General Hospital, Taichung, Taiwan 4 Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan 5 Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan
Comparison of quantitative methods for cell‐shape analysis

Morphology is an important large‐scale manifestation of the global organizational and physiological state of cells, and is commonly used as a qualitative or quantitative measure of the outcome of various assays. Here we evaluate several different basic representations of cell shape – binary masks, distance maps and polygonal outlines – and different subsequent encodings of those representations – Fourier and Zernike decompositions, and the principal and independent components analyses – to determine which are best at capturing biologically important shape variation. We find that principal components analysis of two‐dimensional shapes represented as outlines provide measures of morphology which are quantitative, biologically meaningful, human interpretable and work well across a range of cell types and parameter settings.
Factors for the Emergence and Growth of Environmental Technology Industries in Upper Austria

Environmental technologies are considered a growing industry driven by urging climate, energy and waste problems and related regulations, among others. However, not all locations have the same preconditions for its emergence and growth. Based on regional economic, geographic and cluster theories it can be argued that particular factor and demand conditions, regional industry structures and institutional configurations play a role, but so far this has not been sufficiently explored. This paper focuses on the region of Upper Austria [Oberosterreich] that has a highly developed environmental technology industry. The sector has evolved since the beginning of the 1970s with roots in engineering, machinery, and instruments firms and has experienced fast growth and transformation. The paper explores the development of this sector in Upper Austria and the factors and conditions affecting it. Characteristics and performance of the regional industry are compared to the national level. Empirical findings are based on national survey data covering the period 1993 to 2007, exploratory interviews with local industry experts and stakeholders and recent materials. Findings suggest that the region is one of the dominant locations for environmental technologies in Austria in terms of number of firms and employees and that it has been characterised by high growth and expanding export markets. The sector seems to benefit from pre-existing industries and engineering competences and is supported by two cluster initiatives in the region. (authors' abstract)
Compressive simultaneous full-waveform simulation

The fact that the computational complexity of wavefield simulation is proportional to the size of the discretized model and acquisition geometry and not to the complexity of the simulated wavefield is a major impediment within seismic imaging. By turning simulation into a compressive sensing problem, where simulated data are recovered from a relatively small number of independent simultaneous sources, we remove this impediment by showing that compressively sampling a simulation is equivalent to compressively sampling the sources, followed by solving a reduced system. As in compressive sensing, this reduces sampling rate and hence simulation costs. We demonstrate this principle for the time-harmonic Helmholtz solver. The solution is computed by inverting the reduced system, followed by recovering the full wavefield with a program that promotes sparsity. Depending on the wavefield's sparsity, this approach can lead to significant cost reductions, particularly when combined with the implicit preconditioned Helmholtz solver, which is known to converge even for decreasing mesh sizes and increasing angular frequencies. These properties make our scheme a viable alternative to explicit time-domain finite differences.
Comparison of the activities of protein disulphide-isomerase and thioredoxin in catalysing disulphide isomerization in a protein substrate.

1. The activities of protein disulphide-isomerase (PDI) and thioredoxin in catalysing disulphide bond isomerization in a protein substrate were compared by using the standard assay, namely the re-activation of 'scrambled' RNAase. 2. The specific activity of PDI was 25-fold greater than that of thioredoxin. 3. The greater efficiency of PDI compared with thioredoxin is considered to be due more to the presence of multiple catalytic domains in PDI than to differences in their active-site sequences. 4. Data and procedures were defined for expressing enzyme activity in standard units, i.e. mumol of active RNAase generated/min.
Effects of butyrate and glucocorticoids on gamma- to beta-globin gene switching in somatic cell hybrids

Butyrate and its analogs have been shown to induce fetal hemoglobin in humans and primates and in erythroid cell cultures. To obtain insights concerning the cellular mechanisms of butyrate action, we analyzed the effects of butyrate on human globin gene expression in hybrids produced by fusing mouse erythroleukemia cells (MEL) with human fetal erythroid cells (HFE). These hybrids initially express human fetal hemoglobin but subsequently switch to adult globin expression after several weeks in culture. We found that alpha-aminobutyric acid, a butyrate analog which does not induce terminal maturation, strikingly delays the rate of the gamma- to beta-globin gene (gamma-to-beta) switch in the HFE x MEL hybrids. The effect of butyrate on globin expression is transient, with the result that the delay of globin gene switching requires the continuous presence of this compound in culture. Furthermore, butyrate fails to induce fetal hemoglobin expression in hybrids which have switched, suggesting that the effect of this compound on gamma-globin expression is due to inhibition of gamma gene silencing rather than to induction of gamma gene transcription. Since in other cellular systems, glucocorticoids antagonize the action of butyrate, the effect of dexamethasone on the gamma-to-beta switch in HFE x MEL hybrids was examined. Dexamethasone strikingly accelerated the gamma-to-beta switch, and its effect was irreversible. The effects of dexamethasone and butyrate on the gamma-to-beta switch of the HFE x MEL hybrids appear to be codominant. These results indicate that steroids can have a direct effect on globin gene switching in erythroid cells.
An obstacle segmentation and classification system for the visually impaired

In the majority of cases blindness is caused by retinal degenerative conditions such as Age-Related Macular Degeneration (AMD) and Retinitis Pigmentosa (RP). However, blind individuals still retain central visual pathways and processing mechanisms. Recent advances in Time of Flight (TOF) imaging technology have presented new opportunities to develop improved sensory substitution systems for compensation of visual sensory loss. In sensory substitution information from an artificial receptor/sensor is coupled to the brain via a Human Machine Interface (HMI). The brain is able to utilise this information in place of what is usually transmitted from an intact sense organ such as the eye. The human brain has an adaptive capacity called plasticity. Research has shown that inputs from sensory substitution devices can reach numerous brain structures including those anatomically and physiologically related to the lost sensory modality. This is provided that the information from the HMI/artificial receptors is appropriate to restore function. The authors segmentation and classification system (VisionRE) aims at improving the shortcomings of the current state of the art by accurately segmenting and classifying 3D objects/obstacles in real-time and presenting the 3D information to the user in a more intuitive manner via a multimodal electro-tactile and audio HMI.
Reference dosimetry and small-field dosimetry in external beam radiotherapy: Results from a Danish intercomparison study

A comparison of dosimetry methods at different clinics can be used as a means to uncover systematic uncertainties in radiotherapy. To assess the current status of reference dosimetry and small-field dosimetry in clinical practice, a collaborative comparison study involving several dosimetry methods was performed by DTU Nutech at six Danish clinics. The first part of the intercomparison regarded the consistency of reference dosimetry. Absorbed dose to water under reference conditions was measured using a Farmer ionization chamber