Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a Temporal Bibliographic Data Set for Entity Resolution

Entity resolution is the process of identifying groups of records within or across data sets where each group represents a real-world entity. Novel techniques that consider temporal features to improve the quality of entity resolution have recently attracted significant attention. However, there are currently no large data sets available that contain both temporal information as well as ground truth information to evaluate the quality of temporal entity resolution approaches. In this paper, we describe the preparation of a temporal data set based on author profiles extracted from the Digital Bibliography and Library Project (DBLP). We completed missing links between publications and author profiles in the DBLP data set using the DBLP public API. We then used the Microsoft Academic Graph (MAG) to link temporal affiliation information for DBLP authors. We selected around 80K (1%) of author profiles that cover 2 million (50%) publications using information in DBLP such as alternative author names and personal web profile to improve the reliability of the resulting ground truth, while at the same time keeping the data set challenging for temporal entity resolution research.
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks

Motivation Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results We present a seamless integration of domain knowledges and learning-based approaches. Under novel representations of structurally-annotatedprotein sequences, a semi-supervised deep learning model that unifies recurrent and convolutional neural networks has been proposed to exploit both unlabeled and labeled data, for jointly encoding molecular representations and predicting affinities. Our representations and models outperform conventional options in achieving relative error in IC50 within 5-fold for test cases and 20-fold for protein classes not included for training. Performances for new protein classes with few labeled data are further improved by transfer learning. Furthermore, separate and joint attention mechanisms are developed and embedded to our model to add to its interpretability, as illustrated in case studies for predicting and explaining selective drug-target interactions. Lastly, alternative representations using protein sequences or compound graphs and a unified RNN/GCNN-CNN model using graph CNN (GCNN) are also explored to reveal algorithmic challenges ahead. Availability Data and source codes are available at https://github.com/Shen-Lab/DeepAffinity Contact yshen@tamu.edu Supplementary information Supplementary data are available at http://shen-lab.github. io/deep-affinity-bioinf18-supp-rev.pdf.
Fine Needle Aspiration Cytology and Color Doppler Sonography for Evaluation of Azoospermic Patients

Azoospermia is defined as the absence of spermatozoa in the semen. If no spermatozoa are observed in the wet preparation, the World Health Organization (WHO) recommends an examination of the centrifuged sample (3000 X g or greater for 15 minutes). Approximately 1% of all men in the general population suffer from azoospermia, and azoospermic men constitute approximately 10 to 15% of all infertile men. This work aims to investigate whether color Doppler ultrasound can detect active spermatogenic foci within azoospermic testis or not. Also to evaluate the technique of FNAC as an alternative method for qualitative and quantitative analysis compared with open testicular histopathology. This work was carried out on 150 patients, complaining of infertility for at least one year. In conclusion, the results of this study demonstrate that color Doppler sonography represent promising methods for the assessment of patients affected by azoospermia allowing us to discriminate obstructive azoospermia (normal vessel distribution) from non-obstructive azoospermia (reduced or absent testicular vessels). FNAC of azoospermic testis is a cost-effective and safe method of evaluating male infertility.
2 Synthesis of Graphenes with Arc-Discharge Method

Carbon is one of the elements which form life. It plays a key function in nature and is very crucial for human beings. Carbon has many different kinds of allotropes, some known for thousands of years (graphite and diamond) and some known for several decades (fullerenes and nanotubes). The amazing two-dimensional form, which named graphene, is generated only several years ago. Graphene has raised a new tidal wave of research among the whole globe since its discovery and become a dazzling star in nanoscience. Graphene is one-atom-thick layer of sp2-hybridized carbon tightly packed into a honeycomb lattice, and is a basic building unit for graphitic materials of all other dimensionalities (Geim et al., 2007). Over the past several years, a great deal of intensive research has been generated by graphene due to its unique electrical, thermal, mechanical, optical and other characteristics(Du et al., 2008; Booth et al., 2008). With the understanding of their physical properties, the promises for application are growing in areas of nanoelectronics, sensors, composites, batteries and hydrogen storage (Li et al., 2008). Nevertheless, the large-scale production of high quality graphene is the principal question, which concerned with the graphene’s successful applications. The methods for synthesis of graphene include exfoliation of graphite(Novolesov et al., 2004; Niyogi et al., 2006; Li et al., 2008), chemical vapor deposition(Chae et al., 2009; Yuan et al., 2009; Li et al., 2009; Dervishi et al., 2009), epitaxial growth on electrically insulating surfaces such as SiC(Emtsev et al., 2009; Juang et al., 2009), chemical reduction of graphite oxide and graphite intercalation compounds(McAllister et al., 2007; Fan et al., 2008; Zhu et al., 2010), arc-discharge method(Subrahmanyam et al., 2009; Li et al., 2010a; Wang et al., 2010), other chemical methods(Choucair et al., 2009) and so on. Among the above methods, the arc-discharge method has its unique advantages: no metal catalyst is used; the process is timesaving and facile; high quality graphene could be synthesized in decagram-scale in low cost. In the following section, we will introduce the massive synthesis of graphene through arc-discharge method, including experimental details, characterization and formation mechanisms.
OPTIMIZATION OF FORMULATION OF FLOATING HYDROGELS CONTAINING GAS FORMING AGENT USING RESPONSE SURFACE METHODOLOGY

Objective: The objective of present study was to determine the optimum gas forming agent concentration to enhance the floating ability and drug release pattern of floating hydrogels by using factorial design. Methods : In this article calcium carbonates as gas forming agents was synthesized in modified floating kappa carrageenan hydrogels. Ranitidine Hydrochloride was used as drug. 3 2 full factorial design was utilized for the optimization of gas forming agents. Polymer ratio (X 1 ) and calcium carbonates concentration (X 2 ) were used as independent variables. The floating hydrogels were characterized and the results obtained are swelling ratio study, drug entrapment efficiency, floating lag time and cumulative drug release. Results : From the factorial batches, it was observed that formulation containing 0.5% of calcium carbonates with 80:20 ƙC: NaCMC showed the optimum floating properties, swelling ratio, drug entrapment efficiency and cumulative drug release. Conclusion : Thus, formulation containing 0.5% of calcium carbonates with 80:20 ƙC:NaCMC appear to be a potential approach to develop sustains drug release in gastrointestinal condition. Keywords : Floating hydrogels, Calcium carbonates, Kappa carrageenan, Sodium salt of carbomethylcellulose, Ranitidine hydrochloride, Optimization, Factorial design.
Objective Definition of the Indian Summer Monsoon Onset

Abstract The onset of the Indian summer monsoon (ISM) over the southern tip of the Indian peninsula [also known as monsoon onset over Kerala (MOK)] has been considered the beginning of India’s rainy season. The Indian Meteorological Department (IMD) makes an official prediction of ISM onset every year using a subjective method. Based on an analysis of the past 60-yr (1948–2007) record, the authors show that the onset date can be objectively determined by the beginning of the sustained 850-hPa zonal wind averaged over the southern Arabian Sea (SAS) from 5° to 15°N, and from 40° to 80°E. The rapid establishment of a steady SAS westerly is in excellent agreement with the abrupt commencement of the rainy season over the southern tip of the Indian peninsula. In 90% of the years analyzed, this simple and objective index has excellent agreement with the onset dates that are subjectively defined by the IMD. There are only 3 yr of the past 60 yr during which the two onset dates differ by more than 10 days, and non.
Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations

In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant and frequently exchange conspecifics. Here, we use an individual‐based modelling approach, combined with a population genetics projection model, to consider the impacts of a warming climate on the population connectivity of two contrasting Antarctic fish species, Notothenia rossii and Champsocephalus gunnari. Focussing on the Scotia Sea region, sea surface temperatures are predicted to increase significantly by the end of the 21st century, resulting in reduced planktonic duration and increased egg and larval mortality. With shorter planktonic durations, the results of our study predict reduced dispersal of both species across the Scotia Sea, from Antarctic Peninsula sites to islands in the north and east, and increased dispersal among neighbouring sites, such as around the Antarctic Peninsula. Increased mortality modified the magnitude of population connectivity but had little effect on the overall patterns. Whilst the predicted changes in connectivity had little impact on the projected regional population genetic structure of N. rossii, which remained broadly genetically homogeneous within distances of ~1,500 km, the genetic isolation of C. gunnari populations in the northern Scotia Sea was predicted to increase with rising sea temperatures. Our study highlights the potential for increased isolation of island populations in a warming world, with implications for the resilience of populations and their ability to adapt to ongoing environmental change, a matter of high relevance to fisheries and ecosystem‐level management.
Evolving PSO algorithm design in vector fields using geometric semantic GP

This paper investigates the possibility of evolving new particle swarm equations representing a collective search mechanism, acting in environments with unknown external dynamics, using Geometric Semantic Genetic Programming (GSGP). The proposed method uses a novel initialization technique - the Evolutionary Demes Despeciation Algorithm (EDDA)- which allows to generate solutions of smaller size than using the traditional ramped half-and-half algorithm. We show that EDDA, using a mixture of both GP and GSGP mutation operators, allows us to evolve new search mechanisms with good generalization ability.
GeoSparkViz: a scalable geospatial data visualization framework in the apache spark ecosystem

Data Visualization allows users to summarize, analyze and reason about data. A map visualization tool first loads the designated geospatial data, processes the data and then applies the map visualization effect. Guaranteeing detailed and accurate geospatial map visualization (e.g., at multiple zoom levels) requires extremely high-resolution maps. Classic solutions suffer from limited computation resources and hence take a tremendous amount of time to generate maps for large-scale geospatial data. The paper presents GeoSparkViz a large-scale geospatial map visualization framework. GeoSparkViz extends a cluster computing system (Apache Spark in our case) to provide native support for general cartographic design. The proposed system seamlessly integrates with a Spark-based spatial data management system, GeoSpark. It provides the data scientist a holistic system that allows her to perform data management and visualization on spatial data and reduces the overhead of loading the intermediate spatial data generated during the data management phase to the designated map visualization tool. GeoSparkViz also proposes a map tile data partitioning method that achieves load balancing for the map visualization workloads among all nodes in the cluster. Extensive experiments show that GeoSparkViz can generate a high-resolution (i.e., Gigapixel image) Heatmap of 1.7 billion Open-StreetMaps objects and 1.3 billion NYC taxi trips in ≈4 and 5 minutes on a four-node commodity cluster, respectively.
miR-196b promotes lung cancer cell migration and invasion through the targeting of GATA6

MicroRNAs (miRNAs) have been proven to regulate gene expression at the protein translation level. miRNA abnormal expression has been associated with the development of lung cancer. In the present study, we aimed to investigate the mechanism of miR-196 in non-small cell lung cancer (NSCLC). The miR-196b and GATA-6 (GATA6) expression levels were examined in NSCLC by RT-qPCR and western blot analysis. Transwell assay was used to assess cell migration and invasion. Moreover, the specific target of miR-196b in NSCLC was verified by the luciferase reporter assay. The expression of miR-196b was higher in both NSCLC tissues and cells than the normal levels. Specifically, the miR-196b mimic group in NSCLC cells markedly promoted cell migration and invasion, while the miR-196b inhibitor group exhibited the opposite effect. Furthermore, GATA6 was verified as a specific target of miR-196b in NSCLC cells and GATA6 could attenuate the migratory and invasive ability of NSCLC cells regulated by miR-196b. In addition, the relationship between GATA6 and miR-196b expression was negatively correlated in NSCLC tissues. Thus, miR-196b enhanced NSCLC cell migration and invasion via the downregulation of GATA6, indicating its potential application in NSCLC diagnosis and therapy.
A Survey on the Security of Pervasive Online Social Networks (POSNs)

Pervasive Online Social Networks (POSNs) are the extensions of Online Social Networks (OSNs) which facilitate connectivity irrespective of the domain and properties of users. POSNs have been accumulated with the convergence of a plethora of social networking platforms with a motivation of bridging their gap. Over the last decade, OSNs have visually perceived an altogether tremendous amount of advancement in terms of the number of users as well as technology enablers. A single OSN is the property of an organization, which ascertains smooth functioning of its accommodations for providing a quality experience to their users. However, with POSNs, multiple OSNs have coalesced through communities, circles, or only properties, which make service-provisioning tedious and arduous to sustain. Especially, challenges become rigorous when the focus is on the security perspective of cross-platform OSNs, which are an integral part of POSNs. Thus, it is of utmost paramountcy to highlight such a requirement and understand the current situation while discussing the available state-of-the-art. With the modernization of OSNs and convergence towards POSNs, it is compulsory to understand the impact and reach of current solutions for enhancing the security of users as well as associated services. This survey understands this requisite and fixates on different sets of studies presented over the last few years and surveys them for their applicability to POSNs.
Vascularization of Biomaterials for Bone Tissue Engineering: Current Approaches and Major Challenges

Tissue engineering uses various approaches to restore bone loss and heal critical-size defects resulting from trauma, infection, tumor resection or other musculoskeletal diseases. The success of bone tissue engineering strategies critically depends on the extent of blood vessel infiltration into the scaffolds. It has been demonstrated that blood vessel invasion from the host tissue into scaffolds is limited to a depth of several hundred micrometers. Limited vessel perfusion restricts the formation of bone in central regions of the scaffold, leads to loss of cell viability in this region and ultimately does not support healing of the defect. This review addresses the importance of vascularization in bone tissue engineering, discusses the key factors regulating the process of angiogenesis, and provides an overview of current approaches to direct blood vessel formation in biomaterials.
Propagation of obstructed Bessel and Bessel-Gauss beams

The investigation into Bessel beams has been a topic of immense research during the past 20 years, due to the interesting properties they display. Bessel beams not only exhibit diffraction free propagation, but also reconstruction of the amplitude and phase of the beam after encountering an obstruction. Although this self reconstruction property has been previously modelled by numerous groups, the techniques involve rigorous, time-consuming computations. In this work we present an efficient method to accurately calculate the reconstruction of a Bessel beam after an arbitrary obstruction. Our method considers the well-known conical wave features of Bessel beams and looks at the projection of the obstruction in space as a result of the travelling conical waves that produce the Bessel beams.
Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

Abstract A detailed network describing asparagine metabolism in plants was constructed using published data from Arabidopsis (Arabidopsis thaliana) maize (Zea mays), wheat (Triticum aestivum), pea (Pisum sativum), soybean (Glycine max), lupin (Lupus albus), and other species, including animals. Asparagine synthesis and degradation is a major part of amino acid and nitrogen metabolism in plants. The complexity of its metabolism, including limiting and regulatory factors, was represented in a logical sequence in a pathway diagram built using yED graph editor software. The network was used with a Unique Network Identification Pipeline in the analysis of data from 18 publicly available transcriptomic data studies. This identified links between genes involved in asparagine metabolism in wheat roots under drought stress, wheat leaves under drought stress, and wheat leaves under conditions of sulfur and nitrogen deficiency. The network represents a powerful aid for interpreting the interactions not only between the genes in the pathway but also among enzymes, metabolites and smaller molecules. It provides a concise, clear understanding of the complexity of asparagine metabolism that could aid the interpretation of data relating to wider amino acid metabolism and other metabolic processes.
Leaching of Oil from Tuna Fish Liver by Using Solvent of Methyl-Ethyl Ketone

Research of oil leaching from Tuna Fish Liver has been carried out by extracting of tuna fish liver in soxhlet by using methyl-ethyl ketone as solvent. Liver of fresh tuna fish is blended, put into soxhlet, and extracted at temperatures of 60oC, 65oC, 70oC, 75oC, and 80oC. After obtaining the oil, separation between solvent and oil is carried out by distillation. Oil obtained is analyzed by testing the yield, acid number, Iodine value, viscosity, and its impurities content. Yield obtained is influenced by temperature and time of leaching. Both variables indicates that the higher the variables, the more fish liver oil obtained. Maximum yield obtained is 25.552% at operating condition of leaching temperature 80oC, and leaching duration of 5 hours.
Icosahedral gold cage clusters : M @ Au 12 À „ M Ä V , Nb , and Ta ...

We report the observation and characterization of a series of stable bimetallic 18-valence-electron clusters containing a highly symmetric 12-atom icosahedral Au cage with an encapsulated central heteroatom of Group VB transition metals, M@Au12 2 (M5V,Nb,Ta). Electronic and structural properties of these clusters were probed by anion photoelectron spectroscopy and theoretical calculations. Characteristics of the M@Au12 2 species include their remarkably high binding energies and relatively simple spectral features, which reflect their high symmetry and stability. The adiabatic electronic binding energies of M@Au12 2 were measured to be 3.70 6 . 03, 3.7760. 03, and 3.7660. 03 eV forM5V, Nb, and Ta, respectively. Comparison of density-functional calculations with experimental data established the highly symmetric icosahedral structures for the 18-electron cluster anions, which may be promising building blocks for cluster-assembled nanomaterials in the form of stoichiometric@M@Au12 2 #X salts. © 2004 American Institute of Physics. @DOI: 10.1063/1.1799574 #
A Moderated Mediation Model of Internet Use for Health Information

Background: Using technology acceptance model (TAM), prior studies revealed that attitude towards Internet use for health information differently affected behavioral intention to use the Internet for health information. In other words, some results showed a smaller influence of attitude on Internet use for health information as compared to results of other researches. The level of health consciousness could explain the differences in the existing literature on magnitude of the influence of attitude towards Internet use for health information on the Internet use. The main objective of the study is to examine the moderating effect of health consciousness on the influence of attitude towards using the Internet for health-related information on Internet use for health information seeking in TAM framework. Furthermore, the study aims to test the mediating role of attitude towards Internet for health information in the effect of cognitive beliefs (i.e. perceived usefulness and perceived ease of Internet use) on Internet use for health information seeking. Data for the present study were collected using convenience sampling. The sample consisted of female Internet users living in the state of Selangor, Malaysia. Partial Least Squares-Structural Equation Modeling method was used to test the research hypotheses based on the response from a total of 303 participants. The results of this study showed that when there is a high level of health consciousness (i) attitude partially mediates the influence of perceived usefulness on Internet use for health information and (ii) perceived ease of Internet use has an indirect effect on Internet use for health information through attitude towards using the Internet for health-related information.