Miracle-dz/UniFAR-FTUs huggingface dataset:
Vertical distribution of Baltic sprat larvae: changes in patterns of diel migration?

Ontogenetic and diurnal vertical migration patterns of Baltic sprat larvae were investigated for the periods 1989–1990 and 1998–2002. Comparison of the results led to the hypothesis that the diel vertical migration behaviour of sprat larvae >10 mm has changed. In 1989 and 1990, sprat larvae migrated to the surface at night, whereas they stayed 30–50 m deep by day. From 1998 to 2002, sprat larvae showed no signs of diel vertical migration, remaining in warmer, near-surface water by day and night. This behavioural change coincided with a more general change in the Baltic ecosystem, i.e. an increase in near-surface temperature and a general increase in abundance of the major prey organism (Acartia spp.) of Baltic sprat larvae, with more pronounced aggregation in surface waters.
Web crawler and back-end for news aggregator system (Noox project)

The aim of this manuscript is to develop a web crawler, Content Management System (CMS), and Application Programming Interface (API) for a news aggregator system dubbed Noox project. News aggregator system requires a crawler to populate its content; however, different website may have a different page layout. This projects aims to create a back-end for Noox and open source and scalable web crawler that is capable to extract data from different page layout. The scope of this project includes the web crawler, CMS, API, scheduler for web crawler, and implementation of socket server. The development process utilizes PHP as the primary back-end language with Laravel as the web application framework. The PHP back-end hosts the CMS and the API. The API itself will implement Representational State Transfer (REST) as its architectural design. JavaScript Object Notation (JSON) is used as means of the API to communicate with the clients. The API also implements JSON Web Token (JWT) for client authentication purpose. Python programming language is used to develop the web crawler. The web crawler utilizes BeautifulSoup as the web extraction utility. The web crawler can be adapted to extract data from different page layout by utilizing user created configuration file. It can also be configured to export the extracted data into a JSON file or database system. The result of this project satisfies the requirement of the Noox project.
Analysis of spectral clustering algorithms for community detection: the general bipartite setting

We consider the analysis of spectral clustering algorithms for community detection under a stochastic block model (SBM). A general spectral clustering algorithm consists of three steps: (1) regularization of an appropriate adjacency or Laplacian matrix (2) a form of spectral truncation and (3) a k-means type algorithm in the reduced spectral domain. By varying each step, one can obtain different spectral algorithms. In light of the recent developments in refining consistency results for the spectral clustering, we identify the necessary bounds at each of these three steps, and then derive and compare consistency results for some existing spectral algorithms as well as a new variant that we propose. The focus of the paper is on providing a better understanding of the analysis of spectral methods for community detection, with an emphasis on the bipartite setting which has received less theoretical consideration. We show how the variations in the spectral truncation step reflects in the consistency results under a general SBM. We also investigate the necessary bounds for the k-means step in some detail, allowing one to replace this step with any algorithm (k-means type or otherwise) that guarantees the necessary bound. We discuss some of the neglected aspects of the bipartite setting, e.g., the role of the mismatch between the communities of the two sides on the performance of spectral methods. Finally, we show how the consistency results can be extended beyond SBMs to the problem of clustering inhomogeneous random graph models that can be approximated by SBMs in a certain sense.
K-Center: An Approach on the Multi-Source Identification of Information Diffusion

The global diffusion of epidemics, computer viruses, and rumors causes great damage to our society. It is critical to identify the diffusion sources and timely quarantine them. However, most methods proposed so far are unsuitable for diffusion with multiple sources because of the high computational cost and the complex spatiotemporal diffusion processes. In this paper, based on the knowledge of infected nodes and their connections, we propose a novel method to identify multiple diffusion sources, which can address three main issues in this area: 1) how many sources are there? 2) where did the diffusion emerge? and 3) when did the diffusion break out? We first derive an optimization formulation for multi-source identification problem. This is based on altering the original network into a new network concerning two key elements: 1) propagation probability and 2) the number of hops between nodes. Experiments demonstrate that the altered network can accurately reflect the complex diffusion processes with multiple sources. Second, we derive a fast method to optimize the formulation. It has been proved that the proposed method is convergent and the computational complexity is O(mn logα), where α = α(m, n) is the slowly growing inverse-Ackermann function, n is the number of infected nodes, and m is the number of edges connecting them. Finally, we introduce an efficient algorithm to estimate the spreading time and the number of diffusion sources. To evaluate the proposed method, we compare the proposed method with many competing methods in various real-world network topologies. Our method shows significant advantages in the estimation of multiple sources and the prediction of spreading time.
Failure to expand the motor unit size to compensate for declining motor unit numbers distinguishes sarcopenic from non‐sarcopenic older men

The age‐related loss of muscle mass is related to the loss of innervating motor neurons and denervation of muscle fibres. Not all denervated muscle fibres are degraded; some may be reinnervated by an adjacent surviving neuron, which expands the innervating motor unit proportional to the numbers of fibres rescued. Enlarged motor units have larger motor unit potentials when measured using electrophysiological techniques. We recorded much larger motor unit potentials in relatively healthy older men compared to young men, but the older men with the smallest muscles (sarcopenia) had smaller motor unit potentials than healthy older men. These findings suggest that healthy older men reinnervate large numbers of muscle fibres to compensate for declining motor neuron numbers, but a failure to do so contributes to muscle loss in sarcopenic men.
An Adaptive-Harvest-Then-Transmit Protocol for Wireless Powered Communications: Multiple Antennas System and Performance Analysis

This paper investigates a protocol so-called Adaptive Harvest Then Transmit (AHTT) for wireless powered communication networks (WPCNs) in multiple-input single-output (MISO) downlink systems, which assists in transmitting signals from a multi-antenna transmitter to a single-antenna receiver. Particularly, the power constrained relay is supplied with power by utilizing radio frequency (RF) signals from the source. In order to take advantage of multiple antennas, two different linear processing schemes, including Maximum Ratio Combining (MRC) and Selection Combination (SC) are studied. The system outage capacity and ergodic capacity are evaluated for performance analysis. Furthermore, the optimal power allocation is also considered. Our numerical and simulation results prove that the implementation of multiple antennas helps boost the energy harvesting capability. Therefore, this paper puts forward a new way to the energy efficiency (EE) enhancement, which contributes to better system performance.
Cortical Dynamics of Acoustic and Phonological Processing in Speech Perception

In speech perception, a functional hierarchy has been proposed by recent functional neuroimaging studies: Core auditory areas on the dorsal plane of superior temporal gyrus (STG) are sensitive to basic acoustic characteristics, whereas downstream regions, specifically the left superior temporal sulcus (STS) and middle temporal gyrus (MTG) ventral to Heschl's gyrus (HG) are responsive to abstract phonological features. What is unclear so far is the relationship between the dorsal and ventral processes, especially with regard to whether low-level acoustic processing is modulated by high-level phonological processing. To address the issue, we assessed sensitivity of core auditory and downstream regions to acoustic and phonological variations by using within- and across-category lexical tonal continua with equal physical intervals. We found that relative to within-category variation, across-category variation elicited stronger activation in the left middle MTG (mMTG), apparently reflecting the abstract phonological representations. At the same time, activation in the core auditory region decreased, resulting from the top-down influences of phonological processing. These results support a hierarchical organization of the ventral acoustic-phonological processing stream, which originates in the right HG/STG and projects to the left mMTG. Furthermore, our study provides direct evidence that low-level acoustic analysis is modulated by high-level phonological representations, revealing the cortical dynamics of acoustic and phonological processing in speech perception. Our findings confirm the existence of reciprocal progression projections in the auditory pathways and the roles of both feed-forward and feedback mechanisms in speech perception.
The complete mitochondrial DNA genome of a Chloridea (Heliothis) subflexa (Lepidoptera: Noctuidae) morpho-species

Abstract We investigate the complete mitogenome of a pheromone-trapped morpho-species of Chloridea subflexa from Brazil (initially identified by the Sanger sequencing of partial mtCOI gene) as 15 323 bp (KT598688) via next generation sequencing platform. The mitogenome has an A/T rich base composition (A: 40.4%; T: 40.3%; C: 11.5%; G: 7.8%), and included 13 protein-coding genes (PCGs), 22 tRNAs, 2 ribosomal RNAs and a putative replication region (ca. 323 bp). All PCGs start with a methionine (M) amino acid except the COI gene which has an arginine (R). The trnL2 and trn-Lys genes were partially embedded within the COII gene, while the trn-His gene was completely embedded within the ND4 gene. All PCGs ends with the “TAA” stop codon except ND3 which has a “TAG” stop codon.
Directly Optimize Diversity Evaluation Measures

The queries issued to search engines are often ambiguous or multifaceted, which requires search engines to return diverse results that can fulfill as many different information needs as possible; this is called search result diversification. Recently, the relational learning to rank model, which designs a learnable ranking function following the criterion of maximal marginal relevance, has shown effectiveness in search result diversification [Zhu et al. 2014]. The goodness of a diverse ranking model is usually evaluated with diversity evaluation measures such as α-NDCG [Clarke et al. 2008], ERR-IA [Chapelle et al. 2009], and D#-NDCG [Sakai and Song 2011]. Ideally the learning algorithm would train a ranking model that could directly optimize the diversity evaluation measures with respect to the training data. Existing relational learning to rank algorithms, however, only train the ranking models by optimizing loss functions that loosely relate to the evaluation measures. To deal with the problem, we propose a general framework for learning relational ranking models via directly optimizing any diversity evaluation measure. In learning, the loss function upper-bounding the basic loss function defined on a diverse ranking measure is minimized. We can derive new diverse ranking algorithms under the framework, and several diverse ranking algorithms are created based on different upper bounds over the basic loss function. We conducted comparisons between the proposed algorithms with conventional diverse ranking methods using the TREC benchmark datasets. Experimental results show that the algorithms derived under the diverse learning to rank framework always significantly outperform the state-of-the-art baselines.
Ocean Acidification Affects Redox-Balance and Ion-Homeostasis in the Life-Cycle Stages of Emiliania huxleyi

Ocean Acidification (OA) has been shown to affect photosynthesis and calcification in the coccolithophore Emiliania huxleyi, a cosmopolitan calcifier that significantly contributes to the regulation of the biological carbon pumps. Its non-calcifying, haploid life-cycle stage was found to be relatively unaffected by OA with respect to biomass production. Deeper insights into physiological key processes and their dependence on environmental factors are lacking, but are required to understand and possibly estimate the dynamics of carbon cycling in present and future oceans. Therefore, calcifying diploid and non-calcifying haploid cells were acclimated to present and future CO2 partial pressures (pCO2; 38.5 Pa vs. 101.3 Pa CO2) under low and high light (50 vs. 300 µmol photons m−2 s−1). Comparative microarray-based transcriptome profiling was used to screen for the underlying cellular processes and allowed to follow up interpretations derived from physiological data. In the diplont, the observed increases in biomass production under OA are likely caused by stimulated production of glycoconjugates and lipids. The observed lowered calcification under OA can be attributed to impaired signal-transduction and ion-transport. The haplont utilizes distinct genes and metabolic pathways, reflecting the stage-specific usage of certain portions of the genome. With respect to functionality and energy-dependence, however, the transcriptomic OA-responses resemble those of the diplont. In both life-cycle stages, OA affects the cellular redox-state as a master regulator and thereby causes a metabolic shift from oxidative towards reductive pathways, which involves a reconstellation of carbon flux networks within and across compartments. Whereas signal transduction and ion-homeostasis appear equally OA-sensitive under both light intensities, the effects on carbon metabolism and light physiology are clearly modulated by light availability. These interactive effects can be attributed to the influence of OA and light on the redox equilibria of NAD and NADP, which function as major sensors for energization and stress. This generic mode of action of OA may therefore provoke similar cell-physiological responses in other protists.
Canine Distemper Virus Fusion Activation: Critical Role of Residue E123 of CD150/SLAM

ABSTRACT Measles virus (MeV) and canine distemper virus (CDV) possess tetrameric attachment proteins (H) and trimeric fusion proteins, which cooperate with either SLAM or nectin 4 receptors to trigger membrane fusion for cell entry. While the MeV H-SLAM cocrystal structure revealed the binding interface, two distinct oligomeric H assemblies were also determined. In one of the conformations, two SLAM units were sandwiched between two discrete H head domains, thus spotlighting two binding interfaces (“front” and “back”). Here, we investigated the functional relevance of both interfaces in activating the CDV membrane fusion machinery. While alanine-scanning mutagenesis identified five critical regulatory residues in the front H-binding site of SLAM, the replacement of a conserved glutamate residue (E at position 123, replaced with A [E123A]) led to the most pronounced impact on fusion promotion. Intriguingly, while determination of the interaction of H with the receptor using soluble constructs revealed reduced binding for the identified SLAM mutants, no effect was recorded when physical interaction was investigated with the full-length counterparts of both molecules. Conversely, although mutagenesis of three strategically selected residues within the back H-binding site of SLAM did not substantially affect fusion triggering, nevertheless, the mutants weakened the H-SLAM interaction recorded with the membrane-anchored protein constructs. Collectively, our findings support a mode of binding between the attachment protein and the V domain of SLAM that is common to all morbilliviruses and suggest a major role of the SLAM residue E123, located at the front H-binding site, in triggering the fusion machinery. However, our data additionally support the hypothesis that other microdomain(s) of both glycoproteins (including the back H-binding site) might be required to achieve fully productive H-SLAM interactions. IMPORTANCE A complete understanding of the measles virus and canine distemper virus (CDV) cell entry molecular framework is still lacking, thus impeding the rational design of antivirals. Both viruses share many biological features that partially rely on the use of analogous Ig-like host cell receptors, namely, SLAM and nectin 4, for entering immune and epithelial cells, respectively. Here, we provide evidence that the mode of binding between the membrane-distal V domain of SLAM and the attachment protein (H) of morbilliviruses is very likely conserved. Moreover, although structural information revealed two discrete conformational states of H, one of the structures displayed two H-SLAM binding interfaces (“front” and “back”). Our data not only spotlight the front H-binding site of SLAM as the main determinant of membrane fusion promotion but suggest that the triggering efficiency of the viral entry machinery may rely on a local conformational change within the front H-SLAM interactive site rather than the binding affinity.
Compression-Dependent Transform-Domain Downward Conversion for Block-Based Image Coding

Transform-domain downward conversion (TDDC) for image coding is usually implemented by discarding some high-frequency components from each transformed block. As a result, a block of fewer coefficients is formed, and a lower compression cost is achieved due to the coding of only a few low-frequency coefficients. In this paper, we focus on the design of a new TDDC-based coding method by using our proposed interpolation-compression directed filtering (ICDF) and error-compensated scalar quantization (ECSQ), leading to the compression-dependent TDDC (CDTDDC)-based coding. More specifically, ICDF is first used to convert each $16\times 16$ macro-block into an $8\times 8$ coefficient block. Then, this coefficient block is compressed with ECSQ, resulting in a smaller compression distortion for those pixels that locate at some specific positions of a macro-block. We select these positions according to the 4:1 uniform sub-sampling lattice and use the pixels locating at them to reconstruct the whole macro-block through an interpolation. The proposed CDTDDC-based coding can be applied to compress both grayscale and color images. More importantly, when it is used in the color image compression, it offers not only a new solution to reduce the data-size of chrominance components but also a higher compression efficiency. Experimental results demonstrate that applying our proposed CDTDDC-based coding to compress still images can achieve a significant quality gain over the existing compression methods.
Patient health monitoring system based on Internet of Things

Internet of Things provides us a connectivity between the real world and the physical world. It can provide us connectivity anywhere, any-time and at any place. Basically internet of things is a network of physical objects that senses, communicate and gathers all the important information from the data which is universal language for the objects and on the basis of that information, it takes decision accordingly. In this paper, we have developed a circuit which can sense the temperature and heart-beat of the human body, and if it exceeds a certain set limit, then an alarm would be raise over "IOT Geeko" platform on internet.
Discovery of Oxime Ethers as Hepatitis B Virus (HBV) Inhibitors by Docking, Screening and In Vitro Investigation

A series of oxime ethers with C6-C4 fragment was designed and virtually bioactively screened by docking with a target, then provided by a Friedel–Crafts reaction, esterification (or amidation), and oximation from p-substituted phenyl derivatives (Methylbenzene, Methoxybenzene, Chlorobenzene). Anti-hepatitis B virus (HBV) activities of all synthesized compounds were evaluated with HepG2.2. 15 cells in vitro. Results showed that most of compounds exhibited low cytotoxicity on HepG2.2. 15 cells and significant inhibition on the secretion of HBsAg and HBeAg. Among them, compound 5c-1 showed the most potent activity on inhibiting HBsAg secretion (IC50 = 39.93 μM, SI = 28.51). Results of the bioactive screening showed that stronger the compounds bound to target human leukocyte antigen A protein in docking, the more active they were in anti-HBV activities in vitro.
The endothelial adaptor molecule TSAd is required for VEGF-induced angiogenic sprouting through junctional c-Src activation

The adaptor protein TSAd helps endothelial cells disconnect so that they can migrate and form new blood vessels. Disconnecting endothelial cells for new blood vessels The endothelial cells lining blood vessels are linked together by adherens junctions, where VE-cadherin protein complexes must come apart so that endothelial cells can migrate and proliferate to form new blood vessels. This process is triggered by activation of the receptor VEGFR2, which stimulates the kinase c-Src. Gordon et al. showed that the adaptor protein TSAd linked these two signaling molecules in the developing trachea. TSAd recruited active c-Src to adherens junctions, which resulted in the breakdown of VE-cadherin complexes and enabled the rearrangement of endothelial cells to form a new blood vessel sprout. Because TSAd was required for blood vessel formation in developing trachea, but not in the developing retina, TSAd could be targeted to prevent abnormal vascular growth in a tissue-specific manner. Activation of vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) by VEGF binding is critical for vascular morphogenesis. In addition, VEGF disrupts the endothelial barrier by triggering the phosphorylation and turnover of the junctional molecule VE-cadherin, a process mediated by the VEGFR2 downstream effectors T cell–specific adaptor (TSAd) and the tyrosine kinase c-Src. We investigated whether the VEGFR2-TSAd–c-Src pathway was required for angiogenic sprouting. Indeed, Tsad-deficient embryoid bodies failed to sprout in response to VEGF. Tsad-deficient mice displayed impaired angiogenesis specifically during tracheal vessel development, but not during retinal vasculogenesis, and in VEGF-loaded Matrigel plugs, but not in those loaded with FGF. The SH2 and proline-rich domains of TSAd bridged VEGFR2 and c-Src, and this bridging was critical for the localization of activated c-Src to endothelial junctions and elongation of the growing sprout, but not for selection of the tip cell. These results revealed that vascular sprouting and permeability are both controlled through the VEGFR2-TSAd–c-Src signaling pathway in a subset of tissues, which may be useful in developing strategies to control tissue-specific pathological angiogenesis.