Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of the Anabas testudineus (Perciformes, Anabantidae)

Abstract We present the complete mitochondrial genome of the Anabas testudineus in this study. The mitochondrial genome is 16,603 bp in length and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 29.40% of C, 28.63% of A, 25.79% of T, and 16.18% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. All the protein-coding genes begin with an ATG initiation codon except for COXІ with GTG. Four types of termination codons revealed are TAA (COXІ, ATP8, ND4L, CYTB), T (COXП, ND3, ND4), TA (ND2, ATP6, COXШ), and TAG (ND1, ND5, ND6). Most genes are either abutted or overlapped and many features keep consistent with the other vertebrates.
ENHANCING EARLY-AGE RESISTANCE TO CRACKING IN HIGH-STRENGTH CEMENT-BASED MATERIALS BY MEANS OF INTERNAL CURING USING SUPER ABSORBENT POLYMERS

This paper reports on the effectiveness of internal curing to reduce two major causes of early-age cracking in high-strength cementitious materials, i.e. autogenous and plastic shrinkage. As a measure to develop such curing, the materials, including fine-grained UHPC and cement paste, were enriched using varied amounts of Super Absorbent Polymers (SAP) and extra water whilst mixing. Investigations of shrinkage under free and restrained conditions demonstrated that internal curing can diminish the likelihood of early-age cracking significantly. The amount of SAP and extra water added was found to be decisive both in determining the magnitude of such changes and the history of evolution of autogenous shrinkage. Some deterioration of the early-age mechanical properties in internally cured materials resulted from the retarding of their setting behaviour and from particular changes in their porosity.
Distance Exploration for Scalable Batch Bayesian Optimization

Bayesian optimization (BO) is posed as a sequential problem where each experiment is completed before selecting a next one. However, it is often desirable to simultaneously explore using batches of parameters, especially when parallel processing facilities are available. Existing works have addressed batch BO in different ways. Still, the existing approaches are not scalable to large batch size or when the function evaluations are cheap. In this paper, we propose a computationally efficient batch Bayesian optimization based on a new exploration strategy using geometric distance. Our relaxation reduces the complexity in computing batch BO and also provides an alternative way for exploration, selecting a point far from the already observed locations. We theoretically formulate that our new strategy is a special case of the standard GP variance. We derive convergence analysis for the proposed batch BO approach. We present extensive experiments to show that our distance-based approach outperforms the state-of-the-art methods in both computational efficiency and performance.
Planning for Sustainable and Reliable Robotic Part Handling in Manufacturing Automation

Robots have been used effectively in factories for many years, however, it is only recently that they have begun to take on roles requiring large amounts of autonomy and high-level reasoning capabilities. Autonomy is becoming increasingly necessary due to greater variability in factorygenerated products (e.g., end-user customisation) leading to assembly lines that must involve more than just simple repetitions of the same task with the same components. For example, in car manufacturing—the application domain for this work—each car is built to the specification of the user, meaning that the parts required for assembly may be different for each car on the line. Not only does this require more complex assembly line robots, but robots are starting to be used in preparing the parts for delivery to the assembly line. This system demonstration illustrates work that is being performed as part of the STAMINA1 project to address this latter task: using autonomous mobile robots with the ability to pick parts from around the factory to be delivered to the assembly line at the appropriate time (see Figure 1), a process called kitting. In particular, we focus on the high-level reasoning components in our framework consisting of a logistic planner, which acts as the central information provider in the system; a mission planner, which is tasked with creating and assigning initial high-level plans and goals to the robots in the fleet; and a task planner, which is responsible for managing planning activities for individual robots. Additionally, the robot fleet uses a skills framework which modularises robot capabilities into high-level, symbolic planning actions, meaning that the robots are pre-calibrated to use planning-like constructs. Plans are produced in a format that maps planned actions to skills to facilitate execution. This setup allows the technology to be quickly adapted to new situations when robot capabilities or the environment change, as happens when the factory floor is rearranged, new parts become available, or new robots are added to the fleet.
2 Potential Methods for Patterning Metallic Glass

Metallic glass (MG) with a long-range topological disorder structure exhibits some unique mechanical, physical, and chemical properties compared to its crystalline counterpart, such as high hardness and strength, large elastic limit as well as superior resistance to wear and corrosion. These features make MGs to be regarded as very promising materials. Recent studies indicate that patterned MG H. Huang (*) School of Mechanical Science and Engineering, Jilin University, Changchun, Jilin, China Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, Yokohama, Japan e-mail: huanghu@jlu.edu. cn J. Yan Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, Yokohama, Japan e-mail: yan@mech.keio. ac.jp # Springer Nature Singapore Pte Ltd. 2018 J. Yan (ed.), Micro and Nano Fabrication Technology, Micro/Nano Technologies, https://doi.org/10.1007/978-981-10-6588-0_15-2 1 surface with micro-/nanostructures on it can hugely enhance its biological activity and compatibility, catalytic activity, and hydrophobicity, extending the application of MGs in biomedicine, waterproof material, industrial catalysis, sewage treatment, etc. This chapter summarizes the potential methods for patterning MGs firstly, mainly including mechanical machining, thermoplastic shaping, chemical etching, and laser irradiation. Then, the emphasis is on nanosecond pulsed laser patterning of MGs, and its recent achievement and development will be addressed. The surface structures patterned by single nanosecond pulsed laser irradiation as well as line laser irradiation under various experimental parameters and environmental atmospheres will be introduced, and their formation mechanisms will be discussed. Accordingly, a new surface patterning method of MGs, i. e. , nanosecond pulsed laser irradiation inducing selective thermoplastic extrusion in nitrogen gas, will be provided. Furthermore, the effect of patterned microstructures on the surface hydrophobicity will be briefly discussed.
Appeared in: Has the Last Word Been Said on Classical Electrodynamics? —New Horizons A. Chubykalo, A. Espinosa, V. Onochin and R. Smirnov-Rueda (eds.) (Rinton Press, Princeton, 2004) pp. 118-132. ELECTRODYNAMICS: ACTION-AT- NO-DISTANCE?

An action-at-a-distance (on the lightcone) theory of the electromagnetic interaction is described. It is argued that this theory is internally consistent and avoids several of the infamous pitfalls of field theories such as advanced interaction and divergent self energy of a single charge (or background radiation). In addition, a resolution for problems posed by asymmetric kinematical ageing is proposed.
Developing Autonomy in an East Asian Classroom : from Policy to Practice

Education will not take place without autonomy (Kenny, 1993). In accordance with global trends, Vietnam has identified developing learner autonomy (LA) as one key strategy of its higher education. The aim of this paper is to propose an action research which is planned to promote LA of Vietnamese students of English at tertiary level. Firstly, a survey questionnaire will be conducted to a class of English majored students to explore students' views of their responsibilities and decision-making abilities, their actual and preferred learning activities. The students will then join in several activities, which are designed to develop their autonomous learning. The learning tasks will include individual short talks, group discussion, group presentation (oral or written), debate and drama. Finally, in-depth interviews will be taken with three random students to obtain students' ideas about autonomous EFL learning, especially, the changes of their learning style after the recommended activities. The paper implies suggestions for pedagogy of an autonomous classroom in the East Asian context.
Processing of social emotion in patients with schizophrenia and substance use disorder: An fMRI study

Abstract The lifetime prevalence of substance use disorders among schizophrenia patients is close to 50%. The negative consequences of substance abuse in schizophrenia are well documented, but the aetiology of this comorbid condition remains unknown. Mounting evidence suggests that dual-diagnosis patients have fewer negative symptoms and better social skills, compared to non-abusing patients. We hypothesized that schizophrenia patients with substance use disorder (SCZ–SUD) would display increased cerebral activations in response to socioemotional stimuli, relative to patients with no SUD (SCZ). Schizophrenia patients (DSM-IV criteria) were divided into two groups: patients with (n=12) and without (n=11) substance use (alcohol and/or cannabis). Using functional magnetic resonance imaging (fMRI), patients were scanned during passive viewing of an emotional film excerpt with social content. Loci of activation were identified in the right mPFC (BA 10) and the right supramarginal gyrus (BA 40) in SCZ–SUD patients, and in the left pons in SCZ patients. Relative to SCZ patients, increased loci of activation were found in the right superior parietal cortex (BA 7) and the left medial prefrontal cortex (BA 10) in SCZ–SUD patients, who reported higher subjective emotional experience on a self-report scale. To our knowledge, this is the first fMRI study to assess social emotions in dual-diagnosis schizophrenia. Our results suggest that socioemotional processing may be less impaired in dual diagnosis, which recruited brain regions seemingly involved in “social cognition. ” Further studies on the topic are warranted.
Expression of Cell Cycle Regulatory Proteins and Analysis of Apoptosis in Normal Nasal Mucosa and in Nasal Polyps

Background The etiopathogenesis of nasal polyps still is to be clarified. Although hyperplasia is a typical feature of these pathological processes, little attention has been paid to specific aspects of cellular growth in polyps. We have evaluated the expression and localization of some of the regulatory proteins that direct the cell through the specific sequence of events culminating in mitosis or apoptosis in nasal polyps. Methods Twenty samples of nasal polyps and 20 samples of normal nasal mucosa have been analyzed for apoptotic index by detecting the DNA 3’ OH ends deriving from DNA fragmentation. Moreover, they have been evaluated by immunohistochemical staining for expression of Ki-67, cyclins A and B1, p53, p21, p27, murine double minute clone 2, and Bcl-2. Results We have identified a greater proportion of proliferating cells in the lining epithelial cells of the polyps when compared with the normal mucosa as stained with anti–Ki-67 antibodies. An overexpression of p53, MDM2, and Bcl-2 and an increased apoptosis were observed in nasal polyps compared with the normal mucosa, whereas no variation of p27 expression was observed. The p21 and cyclins A and B1 were rarely expressed in both pathological and normal tissue. Conclusion The p53-based control system of cell cycle progression appears to be altered in nasal polyps, potentially leading to an abrogation of the DNA damage checkpoint. Evaluation of the expression of the regulatory proteins that direct the cells throughout their cycle in nasal polyps may allow a better understanding of the biological behavior and clinical outcome of these benign pathological entities.
Organisation of Xenopus oocyte and egg cortices

The division of the Xenopus oocyte cortex into structurally and functionally distinct “animal” and “vegetal” regions during oogenesis provides the basis of the organisation of the early embryo. The vegetal region of the cortex accummulates specific maternal mRNAs that specify the development of the endoderm and mesoderm, as well as functionally‐defined “determinants” of dorso‐anterior development, and recognisable “germ plasm” determinants that segregate into primary germ cells. These localised elements on the vegetal cortex underlie both the primary animal‐vegetal polarity of the egg and the organisation of the developing embryo. The animal cortex meanwhile becomes specialised for the events associated with fertilisation: sperm entry, calcium release into the cytoplasm, cortical granule exocytosis, and polarised cortical contraction. Cortical and subcortical reorganisations associated with meiotic maturation, fertilisation, cortical rotation, and the first mitotic cleavage divisions redistribute the vegetal cortical determinants, contributing to the specification of dorso‐anterior axis and segregation of the germ line. In this article we consider what is known about the changing organisation of the oocyte and egg cortex in relation to the mechanisms of determinant localisation, anchorage, and redistribution, and show novel ultrastructural views of cortices isolated at different stages and processed by the rapid‐freeze deep‐etch method. Cortical organisation involves interactions between the different cytoskeletal filament systems and internal membranes. Associated proteins and cytoplasmic signals probably modulate these interactions in stage‐specific ways, leaving much to be understood. Microsc. Res. Tech. 44:415–429, 1999. © 1999 Wiley‐Liss, Inc.
A small‐molecule enhancer of autophagy decreases levels of Aβ and APP‐CTF via Atg5‐dependent autophagy pathway

The hallmarks of Alzheimer's disease are the aggregates of amyloid‐β (Aβ) peptide and tau protein. Autophagy is one major cellular pathway leading to the removal of aggregated proteins. We examined the possibility of inducing autophagy to reduce Aβ peptide and the amyloid precursor protein (APP)‐derived fragment APP‐CTF levels in cell lines and primary neuronal cultures. We found that induction of autophagy either by small‐molecule enhancers of rapa‐mycin (SMER)28, a small‐molecule enhancer of autophagy, or following starvation greatly decreased the levels of Aβ peptide (apparent EC50 of ~10 µM) and APP‐CTF (apparent EC50 of ~20 µM) in a γ‐secretase‐independent manner. Pharmacological inhibition of autophagy led to a significant accumulation of Aβ peptide and APP‐CTF and diminished the effect of SMER28. Three essential components of the autophagic pathway, autophagy‐related protein (Atg)5, Beclin1, and Ulk1, were shown to be involved in the degradation of Aβ and APP‐CTF, and Atg5 was necessary for the effect of SMER28. In addition, the autophagic marker light chain 3‐II cocompartmentalized with APP‐CTF. These results support the involvement of autophagy in the clearance of Aβ and APP‐CTF. We therefore propose that small molecule enhancers of autophagy, such as SMER28, may have therapeutic potential for the treatment of Alzheimer's disease and other proteinopathies. —Tian, Y. , Bustos, V. , Flajolet, M. , Greengard, P. A small‐molecule enhancer of autophagy decreases levels of Aβ and APP‐CTF via Atg5‐dependent autophagy pathway. FASEB J. 25, 1934‐1942 (2011). www.fasebj. org
Animmune local concentration based virus detection approach

Along with the evolution of computer viruses, the number of file samples that need to be analyzed has constantly increased. An automatic and robust tool is needed to classify the file samples quickly and efficiently. Inspired by the human immune system, we developed a local concentration based virus detection method, which connects a certain number of two-element local concentration vectors as a feature vector. In contrast to the existing data mining techniques, the new method does not remember exact file content for virus detection, but uses a non-signature paradigm, such that it can detect some previously unknown viruses and overcome the techniques like obfuscation to bypass signatures. This model first extracts the viral tendency of each fragment and identifies a set of statical structural detectors, and then uses an information-theoretic preprocessing to remove redundancy in the detectors’ set to generate ‘self’ and ‘nonself’ detector libraries. Finally, ‘self’ and ‘nonself’ local concentrations are constructed by using the libraries, to form a vector with an array of two elements of local concentrations for detecting viruses efficiently. Several standard data mining classifiers, including K-nearest neighbor (KNN), radial basis function (RBF) neural networks, and support vector machine (SVM), are leveraged to classify the local concentration vector as the feature of a benign or malicious program and to verify the effectiveness and robustness of this approach. Experimental results show that the proposed approach not only has a much faster speed, but also gives around 98% of accuracy.
Variability of Chlorophyll-a in Relation to Physico-Chemical Variables in Zanzibar Coastal Waters

The relationships between chlorophyll-a (Chl-a), nutrients and other physico-chemical variables are important for marine water management strategies. In this study, monthly Chlorophyll-a (Chl-a) concentration, temperature, salinity, pH, dissolved oxygen and nutrients were measured at two sites (Bawe and Chwaka Bay) in Zanzibar coastal waters from May 2012 to May 2013. The mean Chl-a concentration ranged from 0.69 mg/m to 1.86 mg/m, with insignificant variation between the sites, and significant differences among the stations being higher in near shore stations than in open seawater stations (t= 5.296, P < 0.0001). The results revealed significant higher Chl-a concentration during the southeast monsoon (SEM) than the northeast monsoon (NEM) (t = 2.871, P < 0.0152). In addition, the results showed that, the concentration was significantly correlated positively with salinity (r = 0.640; p = 0.019) and negatively with NO3 (r = -0.563; p = 0.044). The results of this study suggest that high Chl-a concentration to the near shore station is due to sewage system which influence nutrients concentrations, hence result into high Chl-a concentration. Furthermore, the SEM experienced high Chl-a concentration due to strong winds which bring nutrients to the sea surface which favour growth of phytoplankton hence result into high concentration.
SoC Design Of A Novel Cluster-Based Approach for Real-Time Lane Detection in Low Quality Images

In this paper, we present a novel System on Chip design for real time lane detection approach on low-quality grayscale images. The proposed method leverages the sequential read out from image sensors to progressively build clusters. The decision to allocate pixels to existing lines (clusters) is made on the fly as pixels flow from the image sensor into the system. We propose a hardware/software partitioning that places low-level computational intensive parts in a pipelined chain in hardware. The pipeline first applies morphological operations on incoming images to enhance their quality. Later canny edge detection followed by Probabilistic Hough Transform is used for accurate line detection. The lines are then filtered and clustered before being fitted into road lanes using weighted least squares method. We prototype our design on a system on FPGA with a precision above 90% and demonstrate a speedup of 2.09x compared to a software only implementation on an embedded processor.
Applying a Neural Network Ensemble to Intrusion Detection

Abstract An intrusion detection system (IDS) is an important feature to employ in order to protect a system against network attacks. An IDS monitors the activity within a network of connected computers as to analyze the activity of intrusive patterns. In the event of an ‘attack’, the system has to respond appropriately. Different machine learning techniques have been applied in the past. These techniques fall either into the clustering or the classification category. In this paper, the classification method is used whereby a neural network ensemble method is employed to classify the different types of attacks. The neural network ensemble method consists of an autoencoder, a deep belief neural network, a deep neural network, and an extreme learning machine. The data used for the investigation is the NSL-KDD data set. In particular, the detection rate and false alarm rate among other measures (confusion matrix, classification accuracy, and AUC) of the implemented neural network ensemble are evaluated.
Anesthesia View in Percutaneous Nephrolithotomy : A 3-year Experience of a Referral Hospital

Results: A total of 521 patients were included in this study. The mean age was 48.32±0.61 years. The mean stone size was 22.48±0.47 mm. The mean duration of the operation was 106.30±1.56 minutes, and 79.07% of patients were stone-free after the procedure. The mean fluoroscopy time was 23.30±1.45 seconds and the mean irrigation fluid volume was measured as 8.70±0.23 L. The decrease in the hemoglobin and hematocrit levels after the procedure was statistically significant (p<0.0001), with a transfusion rate of 4.99%. Fever after surgery and hemorrhage not requiring blood transfusion were the major complications (13.4% and 10.74%, respectively) seen, using the Clavien classification system. Difficult intubation (1.2%), post-extubation laryngospasm (2.3%), refractory nausea (1.5%), bronchospasm (0.38%), ischemic electrocardiography changes (0.19%), and delirium (0.19%) were the major anesthesia problems.
The Aspergillus nidulans yA gene is regulated by abaA.

The developmentally regulated Aspergillus nidulans yA gene encodes a p‐diphenol oxidase that is needed for synthesis of green conidial pigment. We subjected the yA 5′ flanking region to mutational analysis in A. nidulans and Saccharomyces cerevisiae to identify DNA sequence elements involved in its transcriptional control, and identified two functionally distinct elements. Element I contained potential BrlA binding sites and was required for full level yA transcription, but not for developmental regulation in the presence of element II. Element II contained putative TEF‐1 binding sites flanking a CCAAT element and was sufficient for developmental regulation of transcription. Mutation of the TEF‐1 binding sites eliminated developmental regulation, whereas mutation of the CCAAT element led to elevated levels of transcription. Element II was also sufficient to induce transcription in S. cerevisiae when the A.nidulans developmental regulatory gene abaA was expressed from the GAL1 promoter. As AbaA and TEF‐1 possess similar DNA binding domains, the abaA‐yA interaction in yeast is probably direct. Thus, abaA appears to be a direct activator of yA, but yA regulation may also involve interactions with BrlA and a member of the CCAAT class of DNA binding proteins.