Miracle-dz/UniFAR-FTUs huggingface dataset:
N6-Adenosine Methylation of Socs1 mRNA Is Required to Sustain the Negative Feedback Control of Macrophage Activation.

Bacterial infection triggers a cytokine storm that needs to be resolved to maintain the host's wellbeing. Here, we report that ablation of m6A methyltransferase subunit METTL14 in myeloid cells exacerbates macrophage responses to acute bacterial infection in mice, leading to high mortality due to sustained production of pro-inflammatory cytokines. METTL14 depletion blunts Socs1 m6A methylation and reduces YTHDF1 binding to the m6A sites, which diminishes SOCS1 induction leading to the overactivation of TLR4/NF-κB signaling. Forced expression of SOCS1 in macrophages depleted of METTL14 or YTHDF1 rescues the hyper-responsive phenotype of these macrophages in vitro and in vivo. We further show that LPS treatment induces Socs1 m6A methylation and sustains SOCS1 induction by promoting Fto mRNA degradation, and forced FTO expression in macrophages mimics the phenotype of METTL14-depleted macrophages. We conclude that m6A methylation-mediated SOCS1 induction is required to maintain the negative feedback control of macrophage activation in response to bacterial infection.
Preparation of Activated Carbon from Caribbean Pine by Chemical Activation

The main purpose for this project was to, by varying the parameters temperature (400 ˚C and 500 ˚C), acid concentration (10%, 25% and 40%), relative impregnation (0.75, 1.35 and 2.0) and impregnation time (1 h, 2 h and 3 h), evaluate which parameters that affect the product. Also, an investigation was made to determine the interaction of the different parameters. This was done by analysing the properties of the AC with gas adsorption of gasoline and ammonia. Liquid adsorption was analysed with iodine number and the yield of the AC was calculated with two different methods.In general an increasing of the temperature and the impregnation time results in a higher iodine number and higher capacity to absorb gasoline in the produced activated carbon. When the conditions were too strong the iodine number and the capacity to absorb gasoline decreased. The pore structure of the activated carbon is destroyed by too strong conditions.The results were also analysed with a computer program to establish statistical evidence of influence from the parameters indicating that temperature has strong effect on iodine number of the produced activated carbon. If the AC from Caribbean Pine would be commercially produced the recommended design is to keep all parameters low. This is both cost effective and energy efficient.Based on the experimental results it was determined that the AC from Caribbean Pine is better suited for adsorbing gasoline compared with ammonia. Furthermore, the adsorption of gasoline is increasing with an increasing temperature. An industrial manufactured AC was compared with the AC produced from Caribbean Pine and it had a better liquid and gas adsorption showing that more research and optimization of AC from Caribbean Pine must be done before commercializing the product.A suggestion for further research is to use the time in the oven as a parameter to be varied in the experimental setup. This could be valuable in order to determine the influence of the time in the oven both concerning the yield but also the adsorption ability of the AC.
A Game of Pawns

We introduce and study pawn games, a class of two-player zero-sum turn-based graph games. A turn-based graph game proceeds by placing a token on an initial vertex, and whoever controls the vertex on which the token is located, chooses its next location. This leads to a path in the graph, which determines the winner. Traditionally, the control of vertices is predetermined and fixed. The novelty of pawn games is that control of vertices changes dynamically throughout the game as follows. Each vertex of a pawn game is owned by a pawn. In each turn, the pawns are partitioned between the two players, and the player who controls the pawn that owns the vertex on which the token is located, chooses the next location of the token. Control of pawns changes dynamically throughout the game according to a fixed mechanism. Specifically, we define several grabbing-based mechanisms in which control of at most one pawn transfers at the end of each turn. We study the complexity of solving pawn games, where we focus on reachability objectives and parameterize the problem by the mechanism that is being used and by restrictions on pawn ownership of vertices. On the positive side, even though pawn games are exponentially-succinct turn-based games, we identify several natural classes that can be solved in PTIME. On the negative side, we identify several EXPTIME-complete classes, where our hardness proofs are based on a new class of games called Lock&Key games, which may be of independent interest.
Investigating Relationship Among Learning Self-efficacy, MOOC-satisfaction and MOOC-Loyalty of MOOC Learner Using Bagozzi’s Self-regulation Model

This research aims to examine the relationship among Learners’ self-efficacy, MOOC-satisfaction and MOOC-Loyalty of the credit-bearning MOOCs at Taylor’s University using Bagozzi’s self-regulation Model. Online questionnaire included 10-item of learning self-efficacy, 6-item of MOOC-satisfaction, and 5-item of MOOC-Loyalty. It also included another two factors which affected the learning self-efficacy and MOOC-satisfaction: 9-item on Ease of learning and 5-item on Quality of MOOC content. Pearson correlation coefficient between pair of variables among all the variables were obtained. The results of zero order correlation analysis showed a strong positive correlation between the predictors and outcome variables. The research findings provided positive impact to lecturers who plan to convert from traditional teaching pedagogy to MOOC mode as Malaysian students have higher degree of MOOC-loyalty and they were in favor of continuing to take up the credit bearing MOOC throughout their study at Taylor’s university. Besides, it also alarmed the university administrator to provide the best infrastructure for the MOOC platform and best quality of MOOC content so as to raise the MOOC-satisfaction which enhance the MOOC-loyalty.
Cell stress response and hypoxia in breast cancer

During severe hypoxia (<0.01% oxygen) the protein folding machinery becomes dysfunctional, resulting in the accumulation of unfolded proteins with consequent endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) and autophagy, a process involved in the physiological turnover of cytoplasmic components. The link between the UPR and autophagy is not clearly defined. The aim of this thesis is to investigate the role of the induction of UPR under severe hypoxia in tumour survival and resistance to therapy. The results of this research suggest that the activating transcription factor 4 (ATF4), a component of the PKR-like ER kinase (PERK) pathway, fundamental in the UPR, is required for the ER-stress induced upregulation of autophagy. Mechanisms other than hypoxia for UPR induction were investigated, using the proteasome inhibitor bortezomib (BZ). BZ treatment increased ATF4 protein levels in MCF7 cells, even transfected with short-interference RNA (siRNA) against the classical UPR activator PERK, suggesting that the proteasomal stabilization is likely the main mechanism for ATF4 protein accumulation. The induction of autophagy by BZ is dependent upon the upregulation of the microtubule-associated protein 1 light chain 3B (LC3B), an autophagy marker, by ATF4 and acts as a survival mechanism. Hypoxia, UPR and autophagy markers (such as Pimonidazole, carbonic anhydrases IX (CAIX), C/EBP homologous protein (CHOP) and LC3B) were evaluated by immunohistochemical approach in spheroids, xenografts models and breast cancer samples. CHOP immunohistochemical staining was performed in breast cancer sections from a series of patients. CHOP was expressed in cells surrounding necrotic areas. No correlation were found with clinical outcome and further studies are needed.
Roman Hoffmann and Raya Muttarak Learn from the Past, Prepare for the Future: Impacts of Education and Experience on Disaster Preparedness in the Philippines and Thailand

Hoffmann, Roman and Muttarak, Raya (2017) Learn from the Past, Prepare for the Future: Impacts of Education and Experience on Disaster Preparedness in the Philippines and Thailand. World Development, 96. pp. 32-51. ISSN 0305750X This version is available at: https://epub.wu. ac.at/5561/ Available in ePubWU: May 2017 License: Creative Commons: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BYNC-ND 4.0) ePubWU, the institutional repository of the WU Vienna University of Economics and Business, is provided by the University Library and the IT-Services. The aim is to enable open access to the scholarly output of the WU. This document is the publisher-created published version.
Normal mode analysis : theory and applications to biological and chemical systems

Normal mode theory and harmonic potential approximations Konrad Hinsen All-atom normal mode calculations of large molecular systems using iterative methods Liliane Mouawad and David Perahia The Gaussian network model: Theory and applications A.J. Radar, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar Normal mode analysis of macromolecules: from enzyme activity site to molecular machines Guohui Li, Adam Van Wynsbergh, Omar N.A. Demerdash, Qiang Cui Functional information from slow mode shapes Yves-Henri Sanejouand Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis Florence Tama, Charles L. Brooks III Applications of normal mode analysis in structural refinement of supramolecular complexes Jianpeng Ma Normal mode analysis in studying protein motions with x-ray crystallography George N. Phillips, Jr. Optimizing the parameters of the Gaussian network model for ATP-binding proteins Taner Z. Sen, Robert L. Jernigan Effects of sequence, cyclization, and superhelical stress on the internet motions of DNA Atsushi Matsumoto, Wilma K. Olson Symmetry in normal mode analysis of icosahedral viruses Herman W.T. van Vlijmen Extension of the normal mode concept: Principal component analysis, jumping-among-minima model, and their applications to experimental data analysis Akio Kitao Imaginary-frequency, unstable instantaneous normal modes, the potential energy landscape, and diffusion in liquids T.Keyes Driven molecular dynamics for normal modes of biomolecules without the Hessian, and beyond Martina Kaledin, Alexey L. Kaledin, Alex Brown, and Joel Bowman Probing vibrational energy relaxation in proteins using normal modes Hiroshi Fujisaki, Lintao Bu, and John E. Straub Anharmonic decay of vibrational state in proteins Xin Yu, David M. Leitner Collective coordinate approaches to extended conformational sampling Michael Nilges, Rogher Abseher Using collective coordinates to guide conformational sampling in atomic simulations Haiyan Liu, Zhiyong Zhang, Jianbin He, Yunyu Shi
Physico-chemical and functional properties of deoiled rice bran and its utilization in the development of extruded product

Deoiled rice bran was investigated for proximate composition and functional characteristics to assess its capability as protein and fibre source. The presence of anti-nutritional factors such as oxalates, tannins, polyphenols and phytates in rice bran is one of the major drawbacks, which restrict its direct utilization in the diet. However, for effective utilization of bran for human nutrition, the elimination of these undesirable constituents is required. Processing treatments such as extrusion cooking can be used for elimination of undesirable components. Deoiled rice bran was incorporated with cereal base by an extrusion process to obtain a functional, ready-to-eat breakfast cereal. The carbohydrate content of deoiled rice bran was improved after extrusion processing, but the protein content was reduced in the extruded product of deoiled rice bran, which can be related to the denaturation of proteins. The extrusion process improves some functional and nutritional properties of deoiled rice bran which are valuable to industrial applications and have potential as food ingredient for the betterment of consumer health.
Indexing Highly Repetitive String Collections, Part I

Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through applications like bioinformatics, the string collections experienced a growth that outperforms Moore’s Law and challenges our ability to handle them even in compressed form. It turns out, fortunately, that many of these rapidly growing string collections are highly repetitive, so that their information content is orders of magnitude lower than their plain size. The statistical compression methods used for classical collections, however, are blind to this repetitiveness, and therefore a new set of techniques has been developed to properly exploit it. The resulting indexes form a new generation of data structures able to handle the huge repetitive string collections that we are facing. In this survey, formed by two parts, we cover the algorithmic developments that have led to these data structures. In this first part, we describe the distinct compression paradigms that have been used to exploit repetitiveness, and the algorithmic techniques that provide direct access to the compressed strings. In the quest for an ideal measure of repetitiveness, we uncover a fascinating web of relations between those measures, as well as the limits up to which the data can be recovered, and up to which direct access to the compressed data can be provided. This is the basic aspect of indexability, which is covered in the second part of this survey.
Sulfites, selenites and tellurites

Foreword. Preface. Introduction to the solubility of solids in liquids. Sodium sulfite. Sodium pyrosulfite. Potassium sulfite. Potassium pyrosulfite. Ammonium sulfite. Ammonium pyrosulfite. Beryllium sulfite. Magnesium sulfite. Calcium sulfite. Strontium sulfite. Barium sulfite. Manganese(II) sulfite. Iron(II) sulfite. Cobalt(II) sulfite. Nickel(II) sulfite. Copper(I) sulfite. Copper(I,II) sulfite. Silver sulfite. Zinc sulfite. Cadmium sulfite. Mercury(I) sulfite. Lead(II) sulfite. Sodium selenite. Potassium selenite. Alkali metal selenites. Sparingly soluble selenites. Tellurites. System index. Registry number index. Author index.
High expression of disabled homolog 2-interacting protein contributes to tumor development and proliferation in cutaneous squamous cell carcinoma

Background Disabled homolog 2-interacting protein (DAB2IP), a Ras GTPase-activating protein, is downregulated in several cancers. Its depletion is involved in tumor cell proliferation, apoptosis, and metastasis, as well as epithelial–mesenchymal transition. The present study aimed to explore the potential role of DAB2IP in cutaneous squamous cell carcinoma (cSCC) and provide a theoretical basis for the diagnosis and targeted therapy of cSCC. Methods The clinicopathological features of DAB2IP expression in cSCC were analyzed by immunohistochemistry, and the effects of DAB2IP on SCL-1 cell behavior were determined via genetic interference in vitro. SCL-1 cell lines that exhibited reduced expression of DAB2IP and a scrambled shRNA control were constructed using a lentivirus vector-based shRNA technique. RNA extraction, reverse transcription-quantitative PCR (RT-qPCR), MTT assay, colony formation test, cell cycle analysis, apoptosis test, transwell assay, wound-healing assay, in vitro invasive assay were used in this study. Results The immunohistochemical results demonstrated that the expression of DAB2IP was higher in cSCC tissues than in soft fibroma. The level of DAB2IP expression was associated with the degree of malignancy and the depth of tumor infiltration; however, it had no association with patients’ sex, tumor size, location, or phenotype. The results of the MTT, cell cycle, apoptosis, and invasion experiments demonstrated that knockdown of DAB2IP inhibited the viability and invasion of SCL-1 cells in vitro. Conclusions High expression of DAB2IP may contribute to the development and proliferation of cSCC.
Thermal Decomposition of Sugars as an Eco-friendly and Inherent Safe Process for Carbon Nanoparticles Production

Thermal Decomposition of Sugars as an Eco-friendly and Inherent Safe Process for Carbon Nanoparticles Production Andrea Pietro Reverberi*, Marco Vocciante, Marco Salerno, Simone Lauciello, Bruno Fabiano DCCI – Department of Chemistry and Industrial Chemistry, Genova University, via Dodecaneso 31, 16146 Genova, Italy Nanophysics Department, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy Nanochemistry Department, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy DICCA – Department of Civil, Chemical and Environmental Engineering, Polytechnic School, Genova University, via Opera Pia 15, 16145 Genova, Italy reverb@dichep.unige. it
Ordered Search: Equilibrium and Optimum

We introduce an ordered-search model with a heterogeneous consumer search-cost distribution to model firm pricing with both consumer and firm heterogeneity. This enables us to leverage recent theoretical results from differentiated-oligopoly theory to provide a rich cross-section characterization of industry mark-ups, demand, and consumer search patterns. We characterize the unique equilibrium with hidden prices, with advertised prices, with positively correlated search costs, and when consumers have idiosyncratic mean product qualities. For iid match-value distributions, firms with higher quality-costs have higher equilibrium mark-ups but still sell more. Comparing optimal to equilibrium search, consumers search more products in a sufficiently covered market, while consumers search less if firms are symmetric. Equilibrium pricing compresses the distribution of search orders. These results are more pronounced if prices are hidden compared to advertised: equilibrium pricing expands the distribution of search orders. We next allow firms to differ in search accessibility and mean quality, benchmarking so that the advertised price equilibrium is symmetric. Then we find a composition effect under hidden prices that more accessible firms (with corresponding lower intrinsic quality) have lower mark-ups, higher demands, and tend to be searched earlier and more often. JEL Classifications: D43, D83, L13.
Considerations in the development of a follow-up exploratory quantitative design for student's motivation regarding to work industry-related activities in higher engineering education

This Work in Progress paper describes considerations relative to the development of a follow-up exploratory quantitative design for examining student motivation in higher engineering education. The intent of the current work is to build on the outcomes of a previous qualitative study exploring the perceptions of students with regard to work industry-related activities included as part of their formal study experience in Swedish university settings. In the follow-up study design discussed in this paper we focus on a quantitative approach to assessing the impact of such experiences on student motivation. Findings from our previous study indicate both that how these different work industry-related activities are conducted and how the different relationships that are present can effect students’ motivation for learning in tertiary engineering education. However, while the earlier study provides understanding of which scenarios can affect student motivation, there is a need to consider relative effect sizes. To address this issue in this paper, we present considerations for a survey design and discuss the determination of population and sample size and study variables for a preliminary survey instrument. We also propose methods with which to establish validity and reliability, as well as presenting a data analysis plan. At this juncture, the development of a follow-up exploratory quantitative study will contribute to a better understanding of students’ perceptions about work industry-related activities which is currently a prime concern in higher engineering education, providing guidelines for a more critical planning of these activities in the future.
Current State and Next Steps on Automated Hints for Students Learning to Code

The core of this work-in-progress is that the best way to learn how to code is to practice by solving problems. However, if students have trouble with this, they can get frustrated and give up. Automated Tutoring Systems (ATS) aim to provide hints to help them solve the problems they encounter. Many of the existing systems offer general hints, e.g., "check the conditional statement" or help the student interpret the compiler or test-case errors. While this can be useful, we think that an ATS should provide interactive and specialized feedback for each program. We snowballed through publications on promising ATS and found that there are several such systems (in 27 publications), but we could also identify many challenges and that our requirements were not met by any existing system. For example, few of them work on general-purpose programming languages, e.g., Java, or scale to realistic problems consisting of multiple methods and classes. From the search, we find ATS based on Automated Program Repair (APR) shows the most promise. However, while program repair has the potential to generate specialized hints to help guide the student to a working state, studies that looked into these have identified further challenges. For example, many APR ATS tools only show the repaired program to the students, who then have to compare and modify their program accordingly. Another issue is that APR generally only modifies a few lines, so if the student solution is far from correct, the repair might fail. This can be solved by partial repair, i.e., the program is repaired so at least one additional test-case passes. While this increases the repair rate, it might make hints more difficult or point the students in a non-obvious or even "wrong" direction. The APR can take several minutes, which also makes it unsuitable for interactive ATS. We take a design science approach to define an ATS based on APR that attempts to address the identified challenges. We give a review of the state-of-the-art for the required components, e.g., APR, how to generate hints from differences between two programs. From this, we suggest a three-step roadmap; 1. identify suitable APR-tools, 2. construct an oversized test-suite, and 3. adopt APR to the tutoring context.