Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 2 Mathematical-Computational Simulation of Cytoskeletal Dynamics

Actin and microtubules are components of the cytoskeleton, and are key mediators of neuron growth and maintenance. Knowing how they are regulated enhances our understanding of neural development, ageing, degeneration, and regeneration. However, biological investigation alone will not unravel the complex cytoskeletal machinery. We expect that inquiries about the cytoskeleton can be significantly enhanced if their physico-chemical behavior is concealed and summarized in mathematical and computational models that can be coupled to concepts of biological regulation. Our computational modeling concerns the mechanical aspects associated with the dynamics of relatively simple, finger-like membrane protrusions called filopodia. Here we propose an alternative approach for representing the displacement of molecules and cytoplasmic fluid in the extremely narrow and long filopodia and discuss strategies to couple the particle-in-cell method with algorithms for laminar flow to model the two phases of actin dynamics: polymerization into filaments which are pulled back into the cell and compensatory G-actin drift towards its tip to supply polymerization. We use nerve cells of the fruit fly Drosophila as an effective, genetically amenable biological system to generate experimental data as the basis for the abstract models and their validation. C.A. de Moura ( ) Instituto de Matemática e Estatística IME, Universidade do Estado do Rio de Janeiro UERJ, Rio de Janeiro, Brazil e-mail: demoura@ime.uerj. br M.V. Kritz Laboratório Nacional de Computação Científica LNCC, Petrópolis, RJ, Brazil e-mail: kritz@lncc.br T.F. Leal Graduate Program on Mechanical Engineering, Universidade do Estado do Rio de Janeiro UERJ, Rio de Janeiro, Brazil Instituto Federal do Rio de Janeiro IFRJ, Paracambi, Brazil e-mail: thiagofranco@ime.uerj. br A. Prokop Faculty of Life Sciences FLS, University of Manchester, Manchester , UK e-mail: Andreas.Prokop@manchester.ac. uk © Springer International Publishing Switzerland 2016 A.J. da Silva Neto et al. (eds.), Mathematical Modeling and Computational Intelligence in Engineering Applications, DOI 10.1007/978-3-319-38869-4_2 15 16 C.A. de Moura et al.
Mining the Cultural Memory of Irish Industrial Schools Using Word Embedding and Text Classification

The Industrial Memories project aims for new distant (i.e., text analytic) and close readings (i.e., witnessing) of the 2009 Ryan Report, the report of the Irish Government’s investigation into abuse at Irish Industrial Schools. The project has digitised the Report and used techniques such as word embedding and automated text classification using machine learning to re-present the Report’s key findings in novel ways that better convey its contents. The Ryan Report exposes the horrific details of systematic abuse of children in Irish industrial schools between 1920 and 1990. It contains 2,600 pages with over 500,000 words detailing evidence from the 9year-long investigation. However, the Report’s narrative form and its sheer length effectively make many of it findings quite opaque. The Industrial Memories project uses text analytics to examine the language of the Report, to identify recurring patterns and extract key findings. The project represents the Report via an exploratory web-based interface that supports further analysis of the text. The methodology outlined is scalable and suggests new approaches to such voluminous state documents.
Mapping similarities in temporal parking occupancy behavior based on city-wide parking meter data

Abstract. The search for a parking space is a severe and stressful problem for drivers in many cities. The provision of maps with parking space occupancy information assists drivers in avoiding the most crowded roads at certain times. Since parking occupancy reveals a repetitive pattern per day and per week, typical parking occupancy patterns can be extracted from historical data. In this paper, we analyze city-wide parking meter data from Hannover, Germany, for a full year. We describe an approach of clustering these parking meters to reduce the complexity of this parking occupancy information and to reveal areas with similar parking behavior. The parking occupancy at every parking meter is derived from a timestamp of ticket payment and the validity period of the parking tickets. The similarity of the parking meters is computed as the mean-squared deviation of the average daily patterns in parking occupancy at the parking meters. Based on this similarity measure, a hierarchical clustering is applied. The number of clusters is determined with the Davies-Bouldin Index and the Silhouette Index. Results show that, after extensive data cleansing, the clustering leads to three clusters representing typical parking occupancy day patterns. Those clusters differ mainly in the hour of the maximum occupancy. In addition, the lo-cations of parking meter clusters, computed only based on temporal similarity, also show clear spatial distinctions from other clusters.
1 C / EBP β and NFAT differentially regulate Adamts-1 induction by stimuli 1 associated with vascular remodeling 2

Jorge Oller*, Arántzazu Alfranca*, Nerea Méndez-Barbero, Silvia Villahoz , Noelia 3 Lozano-Vidal, Mara Martín-Alonso, Alicia G. Arroyo, Amelia Escolano, Angel Luis 4 Armesilla, Miguel R. Campanero‡, and Juan Miguel Redondo‡, 5 Department of Vascular Biology and Inflammation, Centro Nacional de Investigaciones 6 Cardiovasculares, Madrid, Spain; Unidad de Biotecnología Celular, Instituto de 7 Investigación en Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain; 8 Research Institute in Healthcare Science, School of Pharmacy, Faculty of Science and 9 Engineering, University of Wolverhampton, Wolverhampton, UK; Department of Cancer 10 Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain 11
Factors a!ecting investment bank initial public o!ering market share q

This paper examines the e! ect of several factors on the market share of investment banks that act as book managers in initial public o! erings (IPOs) between 1984 and 1995. For established banks, IPO "rst-day returns, one-year abnormal performance, abnormal compensation, industry specialization, analyst reputation, and association with withdrawn o! ers have a signi"cant impact on changes in market share. These factors have a more signi"cant e! ect on market share changes in low-volume IPO markets. These factors have a less signi"cant e! ect on market share, statistically and economically, for less established banks, consistent with the notion that less reputation is placed at risk. ( 2000 Elsevier Science S.A. All rights reserved. JEL classixcation: G24; C21
IN THE WORLD OF WISE MEN Control and Estimation under Constrained Information : Toward a Unique Theory of Control , Computation , and Communication 1

An attempt was made to review the actively developing area of research devoted to analysis and design of the control systems with due account taken of the constraints imposed by the available finite-capacity digital communication channels. The problem’s prehistory dating back to the 1960–1970’s, as well as the new approaches that appeared during the last decade were analyzed. Much attention was paid to various versions of the now popular data rate theorem. Consideration was given to the problems of control through the communication networks and some results obtained for the nonlinear systems. The basic application areas were listed in brief.
An object-based approach for tree species extraction from digital orthophoto maps

Abstract. Tree segmentation is an active and ongoing research area in the field of photogrammetry and remote sensing. It is more challenging due to both intra-class and inter-class similarities among various tree species. In this study, we exploited various statistical features for extraction of hazelnut trees from 1 : 5000 scaled digital orthophoto maps. Initially, the non-vegetation areas were eliminated using traditional normalized difference vegetation index (NDVI) followed by application of mean shift segmentation for transforming the pixels into meaningful homogeneous objects. In order to eliminate false positives, morphological opening and closing was employed on candidate objects. A number of heuristics were also derived to eliminate unwanted effects such as shadow and bounding box aspect ratios, before passing them into the classification stage. Finally, a knowledge based decision tree was constructed to distinguish the hazelnut trees from rest of objects which include manmade objects and other type of vegetation. We evaluated the proposed methodology on 10 sample orthophoto maps obtained from Giresun province in Turkey. The manually digitized hazelnut tree boundaries were taken as reference data for accuracy assessment. Both manually digitized and segmented tree borders were converted into binary images and the differences were calculated. According to the obtained results, the proposed methodology obtained an overall accuracy of more than 85 % for all sample images.
Intake of Bifidobacterium longum and Fructo-oligosaccharides prevents Colorectal Carcinogenesis

Introduction We aimed to investigate the effects of intake of yogurt containing Bifidobacterium longum (BB536-y) and fructo-oligosaccharides (FOS) in preventing colorectal carcinogenesis in healthy subjects, and the preventive effects of short-chain fatty acids (SCFA), whose production was enhanced by the intake of BB536-y and FOS, in human colon cancer cell lines. Materials and methods The subjects were 27 healthy persons who were divided into a group taking yogurt containing BB536 (BB536-y group; n = 14) and a group taking yogurt containing BB536 and FOS (BB536-y with FOS group; n = 13) once a day for 5 weeks. The feces were sampled before and after the intake to analyze the amount of SCFA in the feces and the profile of intestinal flora, such as putrefactive bacteria and Bacteroides fragilis enterotoxin (ETBF). Subsequently, human colon cancer cell lines (DLD-1 cells, WirDr cells) were cultured in the presence of SCFA (butyric acid, isobutyric acid, acetic acid) in order to evaluate the cell growth-inhibitory activity of SCFA (WST-8 assay) by calculating the IC50 value from the dose-response curve. Results Intake of BB536-y increased the total amount of SCFA in the feces and significantly suppressed the detection rate of ETBF and growth of putrefactive bacteria. Intake of BB536-y with FOS was associated with a higher Bifidobacterium detection rate than that of BB536-y alone. The contents of butyric acid, isobutyric acid, and acetic acid, namely, of SCFA, were also decreased. Analysis of the results of culture of DLD-1 cells and WirDr cells in the presence of butyric acid, isobutyric acid, and acetic acid revealed that each of the substances showed significant cell growth-inhibitory activity, with the activity being the highest for butyric acid, followed by that for isobutyric acid and acetic acid. Conclusion These findings suggest that intake of both BB536-y and BB536-y with FOS prevents colorectal carcinogenesis. How to cite this article: Ohara T, Suzutani T. Intake of Bifidobacterium longum and Fructo-oligosaccharides prevents Colorectal Carcinogenesis. Euroasian J Hepato-Gastroenterol 2018;8(1):11-17.
Morphological, mitochondrial DNA and allozyme evolution in representative amphibians and reptiles inhabiting each side of the Strait of Gibraltar

Patterns of differentiation in morphology, mitochondrial DNA and allozymes in amphibians and reptiles inhabiting northern and southern shores of the Strait of Gibraltar are not concordant, suggesting that each taxon was affected differently by events preceding or following the formation of the Strait of Gibraltar. Mitochondrial DNA and allozyme differentiation between Discoglossus jeanneae and Discoglossus scovazzi (Anura, Discoglossidae), Rana perezi and Rana saharica (Anura, Ranidae), and Blanus cinereus and Blanus tingitanus (Squamata, Amphisbaenia, Amphisbaenidae) is substantial, whereas morphological differentiation is moderate in Rana and Blanus, but is substantial in Discoglossus. Differentiation in mitochondrial DNA and morphology between Timon (Lacerta) lepidus and Timon (Lacerta) tangitanus (Squamata, Lacertoidea, Lacertidae) is considerable, but allozyme differentiation is low. In members of type-I and -II Podarcis vaucheri (Squamata, Lacertoidea, Lacertidae), morphology and mitochondrial DNA are moderately differentiated, but allozyme differentiation is low. Spanish and Moroccan populations of Hyla meridionalis (Anura, Hylidae), Mauremys leprosa (Testudines, Geoemydidae), and Macroprotodon brevis (Squamata, Serpentes, Colubridae) demonstrate little allozyme and mitochondrial DNA differentiation, but whereas morphological differentiation between Mauremys and Macroprotodon populations is moderate, Hyla demonstrate substantial morphological differentiation between continental populations. These data suggest that sex-limited mitochondrial markers are reflective of ancient phylogenetic history, whereas biparentally inherited allozyme markers and morphological characteristics reflect more recent population structure and movement. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 445–461.
An Introduction to Modulations and Waveforms for 5G Networks

1.1 Motivation and Background 3 1.1.1 The LTE Solution: OFDM and SC-FDMA 6 1.2 New Modulation Formats: FBMC, GFDM, BFDM, UFMC and TFP 7 1.2. 1 Filter-bank Multicarrier 7 1.2. 2 Generalized Frequency Division Multiplexing 10 1.2. 3 Bi-orthogonal Frequency Division Multiplexing 13 1.2. 4 Universal Filtered Multicarrier 14 1.2. 5 Time-frequency Packing 15 1.2. 6 Single-carrier Schemes 18 1.3 Waveform Choice 19 1.4 Discussion and Concluding Remarks 20 References 22
Imaging features of bilateral primary megaureter in a senior dog: a case report

An 8-year-old dog weighing 45 kg presented with symmetric alopecia, diarrhoea and undescended testes with no associated urinary symptoms. Abdominal ultrasonography and computed tomographic excretory urography revealed extensive dilation and reduced peristalsis of both ureters, except for the distal parts, which showed normal insertion into the urinary bladder, and normal calibre without peristalsis. No abnormalities of the urinary bladder or urethra that may have caused obstruction were identified. A diagnosis of primary megaureter was made. This is the first known reported case of primary megaureter in a dog. To our knowledge, this is first known case report in the veterinary literature that describes the ultrasonographic features of primary megaureter.
Distributed Compressive Sensing Augmented Wideband Spectrum Sharing for Cognitive IoT

The increasing number of Internet of Things (IoT) objects has been a growing challenge of the current spectrum supply. To handle this issue, the IoT devices should have cognitive capabilities to access the unoccupied portion of the wideband spectrum. However, most IoT devices are difficult to perform wideband spectrum sensing using either conventional Nyquist sampling system or sub-Nyquist sampling system since both power-hungry sampling components and intricate sub-Nyquist sampling hardware are unrealistic in the power-constrained IoT paradigm. In this paper, we propose a blind joint sub-Nyquist sensing scheme by utilizing the surround IoT devices to jointly sample the spectrum based on the multicoset sampling theory. Thus, only the off-the-shelf low-rate analog-to-digital converters on the IoT devices are required to form coset samplers and only the minimum number of coset samplers are adopted without the prior knowledge of the number of occupied channels and signal-to-noise ratios. Moreover, to further reduce the number of coset samplers and transfer part of the computational burden from the IoT devices to the core network, we adopt the data from geo-location database when applicable. The experimental results on both simulated and real-world signals verify the theoretical results and effectiveness of the proposed scheme. At the meanwhile, it is shown that the adaptive number of coset samplers could be adopted without causing the degradation of the detection performance and the number of coset samplers could be further reduced with the assists from geo-location database even when the obtained information is partially correct.
The Effect of Furfural Compounds in Corncob Hydrolysate on Microbial Lipids Accumulation of Trichosporon Cutaneum for Biomass-to-Oil Bioprocessing

Oleaginous yeast Trichosporon cutaneum is an ideal strain to produce microbial lipids by fermentation on corncob hydrolysate. However, furfural, routinely generated during lignocellulose hydrolysis, shows detrimental effects on microbial lipids accumulation, which mechanism has not been well marked so far. In this paper, corncob biomass was hydrolyzed by 0.12 M dilute H2SO4 and directly used as the T. cutaneum fermentation medium. The different initial furfural content was obtained by adding the proportional amount of furfural into the detoxified corncob hydrolysates. To explore the furfural-mediated mechanism on microbial lipids accumulation in this work, atomic force microscopy was used for visualizing the morphology characteristics and high performance liquid chromatograph was employed for evaluating the furfural metabolism of the yeast during the furfural-detrimental process. Furthermore, flow cytometry was used to monitor the yeast growth and fluorescence spectroscopy was imaged in the dynamics process of microbial lipids accumulation. Analysis reveals that furfural at a low concentration (≤ 0.4 g/L) can be metabolized by the yeast into 2-furoic acid with little detrimental effect on microbial lipids accumulation. The furfural detriment mechanism relating to the damage of cytomembrane for preventing the yeast cell growth is proposed as the main cause of no microbial lipids accumulation of T. cutaneum in high concentration furfural situations (≥ 0.6 g/L). These results provide valuable information for developing and designing a more efficient biomass-into-lipid fermentation bioprocess. Graphical Abstract
Overcoming Data Sparsity for Relation Detection in German Novels

Within the context of social network analysis (SNA) for literary texts the automatic detection of family relations and similar social relations between characters in novels would be an important step for any macroscopic analysis. Manual labeling is rather inefficient since the text snippets that explicitly describe a relation are sparse within the long text documents; therefore we combine two techniques, active learning and distant supervision, which are often used to overcome data sparsity. Inspired by distant supervision which uses a high quality information resource to support information extraction from other data, we used expert summaries of literary texts, German novels mainly from the 19th century, since relevant text snippets are much more frequent in summaries. Then we applied an uncertainty-based active learning strategy labeling selected sentences from the novels and the complete summaries. The results show that training on summaries and evaluating on data derived from novels yields reasonable results with high precision and low recall similar to humans solving this task. After a brief discussion of related work in the next section, the data set and the necessary preprocessing for this work are explained in section three. Section four describes our method in detail and shows strengths and weaknesses.
Tunicamycin Mediated Inhibition of Wall Teichoic Acid Affects Staphylococcus aureus and Listeria monocytogenes Cell Morphology, Biofilm Formation and Virulence

The emergence of bacterial resistance to therapeutic antibiotics limits options for treatment of common microbial diseases. Subinhibitory antibiotics dosing, often aid in the emergence of resistance, but its impact on pathogen’s physiology and pathogenesis is not well understood. Here we investigated the effect of tunicamycin, a cell wall teichoic acid (WTA) biosynthesis inhibiting antibiotic at the subinhibitory dosage on Staphylococcus aureus and Listeria monocytogenes physiology, antibiotic cross-resistance, biofilm-formation, and virulence. Minimum inhibitory concentration (MIC) of tunicamycin to S. aureus and L. monocytogenes was 20–40 μg/ml and 2.5–5 μg/ml, respectively, and the subinhibitory concentration was 2.5–5 μg/ml and 0.31–0.62 μg/ml, respectively. Tunicamycin pre-exposure reduced cellular WTA levels by 18–20% and affected bacterial cell wall ultrastructure, cell membrane permeability, morphology, laser-induced colony scatter signature, and bacterial ability to form biofilms. It also induced a moderate level of cross-resistance to tetracycline, ampicillin, erythromycin, and meropenem for S. aureus, and ampicillin, erythromycin, vancomycin, and meropenem for L. monocytogenes. Pre-treatment of bacterial cells with subinhibitory concentrations of tunicamycin also significantly reduced bacterial adhesion to and invasion into an enterocyte-like Caco-2 cell line, which is supported by reduced expression of key virulence factors, Internalin B (InlB) and Listeria adhesion protein (LAP) in L. monocytogenes, and a S. aureus surface protein A (SasA) in S. aureus. Tunicamycin-treated bacteria or the bacterial WTA preparation suppressed NF-κB and inflammatory cytokine production (TNFα, and IL-6) from murine macrophage cell line (RAW 264.7) indicating the reduced WTA level possibly attenuates an inflammatory response. These results suggest that at the subinhibitory dosage, tunicamycin-mediated inhibition of WTA biosynthesis interferes with cell wall structure, pathogens infectivity and inflammatory response, and ability to form biofilms but promotes the development of antibiotic cross-resistance.
A Lean Experience of Game Fabrication From School to University and Back

Gamification of educational contexts can be used to playfully engage all for diverse goals. This paper shows how we gamified school contexts for co-designing educational games (sic) for schools. In our gamified co-design, mixed teams of children and designers fabricated game prototypes together, by resolving missions and challenges as in a game context. The paper then shows how such low-fidelity prototypes were further developed, following a lean user experience design approach: the fabricated prototypes of games were evaluated by mixed teams, then by other schools and finally developed as high-fidelity prototypes at university.