Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 3: Small Molecules and Disease

“Big” molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. “Small” molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called “chemical bioinformatics” – a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules – either as the treatment, symptom or cause – to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.
An experimental technique for design of practical Wireless Power Transfer systems

Wireless Power Transfer using magnetically coupled resonators has been widely used for biomedical and consumer electronics applications. However, typical analysis of wireless power transfer has focused on standard operating conditions (linear power source and fixed impedances Zs = ZL = Z0) and is not applicable for practical applications. In this work we use experimentally obtained S-parameters to accurately model and analyze a WPT system driven by a linear or non-linear power source with arbitrary source impedance (Zs) delivering power to an arbitrary load impedance (ZL). Using this approach, we define a framework to evaluate the performance of WPT in terms of two metrics i.e. efficiency and power delivered to the load. The proposed technique can help designers accurately predict and analyze the behavior of WPT systems in practical applications.
Collective behavior with heterogeneous controllers

In this paper, we study the collective motion of individually controlled planar particles when they are coupled through heterogeneous controller gains. Two types of collective formations, synchronization and balancing, are described and analyzed under the influence of these heterogeneous controller gains. These formations are characterized by the motion of the centroid of the group of particles. In synchronized formation, the particles and their centroid move in a common direction, while in balanced formation the movement of particles possess a fixed location of the centroid. We show that, by selecting suitable controller gains, these formations can be controlled significantly to obtain not only a desired direction of motion but also a desired location of the centroid. We present the results for N-particles in synchronized formation, while in balanced formation our analysis is confined to two and three particles.
An improved registration algorithm based on geometric feature for the calibration of workpiece coordinate

Since target points could be generated quickly and accurately by off-line programming in the industrial robot machining, it is used widely in industrial robots. Due to installation error and mismachining tolerance which causes the offset of processing paths in the actual machining process, the registration algorithms for path calibration would be involved. While the traditional approach would converge to local optimal solution, an improved registration algorithm based on geometric properties of point clouds is proposed in the paper. Firstly, feature point sets are acquired by the curvature of point clouds and matched by traditional PCA algorithm, an initial value for precise registration is provided. Secondly, the improved ICP algorithm by curvature is utilized to modify the former result and reduce the execution time of precise registration, the path calibration can be achieved. The experimental result of the approach is validated in this paper which is significative for calibration of processing paths.
Improved viability of random pattern skin flaps with the use of bone marrow mesenchymal-derived stem cells and chicken embryo extract

Objective(s): Covering tissue defects using skin flaps is a basic surgical strategy for plastic and reconstructive surgery. The aim of this study was to evaluate the effects of chicken embryo extract (CEE) and bone marrow derived mesenchymal stem cells (BM-MSCs) on random skin flap survival (RSF) in rats. Using chicken embryo extract can be an ideal environment for the growth and proliferation of transplanted cells. Materials and Methods: Forty albino male Wistar rats were divided into 4 groups; each group consisted of 10 rats. BM-MSCs and CEE were transplanted into subcutaneous tissue in the area, where the flap would be examined. On the 7th postoperative day, the survival areas of the flaps were measured by using digital imaging with software assistance, and tissue was collected for evaluation. Results: Survival area was 19.54±2 in the CEE group and 17.90±2 in the CEE/BM-MSC group when compared to the rates of the total skin flaps, which were significantly higher than the control group (13.47±2) (P<0.05). The biomechanical assessment showed a slight difference, although there was no statistically significant difference between the experimental groups and the control group (P>0.05). Conclusion: The findings from this study demonstrated that in operative treatment with BM-MSCs and CEE transplantation could promote flap survival, but the biomechanical parameters were not contrasted with a saline injection.
Factors secreted by Schwann cells stimulate the regeneration of neonatal retinal ganglion cells

The adult mammalian central nervous system (CNS) does not repair after injury. However, we and others have shown in earlier work that the neonatal CNS is capable of repair and importantly of allowing regenerating axons to re‐navigate through the same pathways as they did during development. This phase of neonatal repair is restricted by the fragility of neurons after injury and a lack of trophic factors that enable their survival. Our aim is to define better the factors that sustain neurons after injury and allow regeneration to occur. We describe some of our work using Schwann cells to promote the regeneration of neurons from young postnatal rodents. We have established rapid methods for purifying Schwann cells without the use of either anti‐mitotic agents to suppress contaminating fibroblasts or mitotic stimulation to generate large numbers of Schwann cells. The rapidly purified Schwann cells have been used to generate conditioned medium that we have shown stimulates axon regeneration in cultured retinal ganglion cell neurons. We also show that the positive effects of Schwann cells are still present after pharmacological blockade of the neurotrophin receptors, suggesting that novel factors mediate these effects.
Genetics of the Pig Tapeworm in Madagascar Reveal a History of Human Dispersal and Colonization

An intricate history of human dispersal and geographic colonization has strongly affected the distribution of human pathogens. The pig tapeworm Taenia solium occurs throughout the world as the causative agent of cysticercosis, one of the most serious neglected tropical diseases. Discrete genetic lineages of T. solium in Asia and Africa/Latin America are geographically disjunct; only in Madagascar are they sympatric. Linguistic, archaeological and genetic evidence has indicated that the people in Madagascar have mixed ancestry from Island Southeast Asia and East Africa. Hence, anthropogenic introduction of the tapeworm from Southeast Asia and Africa had been postulated. This study shows that the major mitochondrial haplotype of T. solium in Madagascar is closely related to those from the Indian Subcontinent. Parasitological evidence presented here, and human genetics previously reported, support the hypothesis of an Indian influence on Malagasy culture coinciding with periods of early human migration onto the island. We also found evidence of nuclear-mitochondrial discordance in single tapeworms, indicating unexpected cross-fertilization between the two lineages of T. solium. Analyses of genetic and geographic populations of T. solium in Madagascar will shed light on apparently rapid evolution of this organism driven by recent (<2,000 yr) human migrations, following tens of thousands of years of geographic isolation.
Prostaglandin E2 promotes post-infarction cardiomyocyte replenishment by endogenous stem cells

Although self‐renewal ability of adult mammalian heart has been reported, few pharmacological treatments are known to promote cardiomyocyte regeneration after injury. In this study, we demonstrate that the critical period of stem/progenitor cell‐mediated cardiomyocyte replenishment is initiated within 7 days and saturates on day 10 post‐infarction. Moreover, blocking the inflammatory reaction with COX‐2 inhibitors may also reduce the capability of endogenous stem/progenitor cells to repopulate lost cells. Injection of the COX‐2 product PGE2 enhances cardiomyocyte replenishment in young mice and recovers cell renewal through attenuating TGF‐β1 signaling in aged mice. Further analyses suggest that cardiac stem cells are PGE2‐responsive and that PGE2 may regulate stem cell activity directly through the EP2 receptor or indirectly by modulating its micro‐environment in vivo. Our findings provide evidence that PGE2 holds great potential for cardiac regeneration.
Fusion pore expansion is a slow, discontinuous, and Ca2+-dependent process regulating secretion from alveolar type II cells

In alveolar type II cells, the release of surfactant is considerably delayed after the formation of exocytotic fusion pores, suggesting that content dispersal may be limited by fusion pore diameter and subject to regulation at a postfusion level. To address this issue, we used confocal FRAP and N-(3-triethylammoniumpropyl)-4-(4-[dibutylamino]styryl) pyridinium dibromide (FM 1-43), a dye yielding intense localized fluorescence of surfactant when entering the vesicle lumen through the fusion pore (Haller, T., J. Ortmayr, F. Friedrich, H. Volkl, and P. Dietl. 1998. Proc. Natl. Acad. Sci. USA. 95:1579–1584). Thus, we have been able to monitor the dynamics of individual fusion pores up to hours in intact cells, and to calculate pore diameters using a diffusion model derived from Fick's law. After formation, fusion pores were arrested in a state impeding the release of vesicle contents, and expanded at irregular times thereafter. The expansion rate of initial pores and the probability of late expansions were increased by elevation of the cytoplasmic Ca2+ concentration. Consistently, content release correlated with the occurrence of Ca2+ oscillations in ATP-treated cells, and expanded fusion pores were detectable by EM. This study supports a new concept in exocytosis, implicating fusion pores in the regulation of content release for extended periods after initial formation.
Worst-Case Optimal Algorithms for Parallel Query Processing

In this paper, we study the communication complexity for the problem of computing a conjunctive query on a large database in a parallel setting with $p$ servers. In contrast to previous work, where upper and lower bounds on the communication were specified for particular structures of data (either data without skew, or data with specific types of skew), in this work we focus on worst-case analysis of the communication cost. The goal is to find worst-case optimal parallel algorithms, similar to the work of [18] for sequential algorithms. We first show that for a single round we can obtain an optimal worst-case algorithm. The optimal load for a conjunctive query $q$ when all relations have size equal to $M$ is $O(M/p^{1/\psi^*})$, where $\psi^*$ is a new query-related quantity called the edge quasi-packing number, which is different from both the edge packing number and edge cover number of the query hypergraph. For multiple rounds, we present algorithms that are optimal for several classes of queries. Finally, we show a surprising connection to the external memory model, which allows us to translate parallel algorithms to external memory algorithms. This technique allows us to recover (within a polylogarithmic factor) several recent results on the I/O complexity for computing join queries, and also obtain optimal algorithms for other classes of queries.
A Novel Clustering Ant-Based QoS-aware Routing Algorithm in Large Scale Wireless Multimedia Sensor Networks

QoS-aware routing algorithm is important in wireless multimedia sensor networks. This paper formulates a generalized QoS-aware routing model on the basis of multiple routing metrics and priorities of packets. It first introduces a 2D plain-based routing algorithm IPACR which improves the standard ant colony algorithm by optimizing the initial distribution of artificial pheromone in order to accelerate the algorithm convergence rate. Then it presents a clustering-based routing algorithm ICACR which can be well applied in a large scale network. Both the numerical algorithm performance analysis and simulation of IPACR and ICACR are given. The results show that ICACR outperforms IPACR in terms of both network lifetime and QoS-aware routing metrics in large scale wireless multimedia sensor networks. Moreover, the simulation based on the real video traces shows that the extension of the multi-path to ICACR for different priorities of video frames can achieve better performance.
Socio-Spatial Properties of Online Location-Based Social Networks

The spatial structure of large-scale online social networks has been largely unaccessible due to the lack of available and accurate data about people’s location. However, with the recent surging popularity of location-based social services, data about the geographic position of users have been available for the first time, together with their online social connections. In this work we present a comprehensive study of the spatial properties of the social networks arising among users of three main popular online location-based services. We observe robust universal features across them: while all networks exhibit about 40% of links below 100 km, we further discover strong heterogeneity across users, with different characteristic spatial lengths of interaction across both their social ties and social triads. We provide evidence that mechanisms akin to gravity models may influence how these social connections are created over space. Our results constitute the first large-scale study to unravel the socio-spatial properties of online location-based social networks.
Real world data of a veterinary teaching hospital in Japan: a pilot survey of prescribed medicines

The prescription data from a digital accounting system of a veterinary teaching hospital collected between 2008 and 2011 in Japan were downloaded, stored in a database and analysed using a statistical analysis software, SAS. Seventy-six per cent of all prescriptions were drugs approved for human beings. The most frequently prescribed category was ‘Agents against pathogenic organisms’, such as antibiotics and chemotherapeutic agents, followed by ‘Cardiovascular agents’. Seventy-five per cent of prescribed oral formulations in the category ‘Agents against pathogenic organisms’ were drugs approved for human beings, while 78 per cent of the injectable prescriptions were those for veterinary. A total of 36 oral antipathogenic products were prescribed, and among them amoxicillin was prescribed the most, followed by cephalexin for human beings and enrofloxacin for veterinary. The pattern of cyclosporin prescription, which is the most prescribed product other than ‘Agents against pathogenic organisms’, was surveyed. The capsule formulation was primarily used for dogs, while oral solutions were preferably used for cats. This pilot study is the first analytical data of real prescription in hospitals in Japan and one of the longest surveys in veterinary world.
The Tully–Fisher relation of galaxies at z∼ 0.85 in the DEEP2 survey

Local and intermediate redshift (z∼ 0.5) galaxy samples obey well correlated relations between the stellar population luminosity and maximal galaxy rotation that define the Tully–Fisher (TF) relation. Consensus is starting to be reached on the TF relation at z∼ 0.5, but work at significantly higher redshifts is even more challenging, and has been limited by small galaxy sample sizes, the intrinsic scatter of galaxy properties, and increasing observational uncertainties. We present here the TF measurements of 41 galaxies at relatively high redshift, spectroscopically observed with the Keck/DEIMOS instrument by the DEEP2 project, a survey which will eventually offer a large galaxy sample of the greatest depth and number yet achieved towards this purpose. The ‘first-look’ sample analyzed here has a redshift range of 0.75 < z < 1.3 with 〈z〉= 0.85 and an intrinsic magnitude range from MB of −22.66 to −20.57 (Vega). We find that compared to local fiducial samples, a brightening of 1.5 mag is observed, and consistent with passive evolutionary models.
Small area estimation strategy for the 2011 Census in England and Wales

The use of model-based small area estimation methods for adjusting census results in the UK was first introduced in the 2001 Census. The aim was to obtain local level population estimates (local authority totals) by age-sex groups, adjusted for the level of undercount based on regression models combining results from the census and the Census Coverage Survey. A similar approach was adopted for the 2011 Census but with new features and this paper describes the work carried out to arrive at the chosen small area strategy. Simulation studies are used to investigate three proposed small area estimation methods: a local fixed effects model (the 2001 Census approach), a direct estimator and a synthetic estimator. The results indicate that both the synthetic and the local fixed models constitute good options to produce accurate and reliable local authority population estimates. A proposal is made to implement a small area estimation procedure that accommodates both the synthetic and local fixed models, as in some selected areas with differing local authority under-coverage rates a local fixed effects model may perform best. We examine this strategy under real census conditions based on the final results from the 2011 census.
Secure Beamforming in Full-Duplex SWIPT Systems with Loopback Self-Interference Cancellation

Security is a critical issue in full duplex (FD) communication systems due to the broadcast nature of wireless channels. In this paper, joint design of information and artificial noise beamforming vectors is proposed for the FD simultaneous wireless information and power transferring (FD-SWIPT) systems with loopback self-interference cancellation. To guarantee high security and energy harvesting performance of the FD-SWIPT system, the proposed design is formulated as a secrecy rate maximization problem under energy transfer rate constraints. Although the secrecy rate maximization problem is non-convex, we solve it via semidefinite relaxation and a two-dimensional search. We prove the optimality of our proposed algorithm and demonstrate its performance via simulations.
Multiscale Direct Envelope Inversion: Algorithm and Methodology for Application to the Salt Structure Inversion

For the full‐waveform inversion, obtaining a globally optimal solution is difficult when the seismic data do not contain sufficient low‐frequency information and the inversion object is a salt structure with a large‐scale salt dome. The large salt dome presents difficulty for the inversion of the salt structure; however, it also confers a convenience that can be utilized: A large salt dome makes the events in the seismic record sparse and isolated. We use the envelope to obtain the arrival time of the events in the seismic data and apply multiscale strategies to extract the low‐frequency information of the seismic data that relates to the long‐wavelength components of the subsurface. In calculating the gradient, the envelope Fréchet derivative is used to take advantage of the multiscale envelope for the characteristics of the salt structure. Therefore, the multiscale direct envelope inversion using the window‐averaged envelope and the direct envelope Fréchet derivative is proposed. To further improve the computational efficiency and inversion quality of the multiscale direct envelope inversion, several auxiliary strategies are proposed: A joint misfit function is designed to make the inversion method more adaptable, and an offset weighting factor is introduced to implement the multioffset inversion method to improve the inversion quality of subsalt. We analyze the antinoise performance of the multiscale direct envelope inversion. The SEG/EAGE salt model is used to test the application effect of the multiscale direct envelope inversion. The antinoise ability and insensitivity to low‐frequency data of the method are verified in the numerical experiments.
Phytoplankton photosynthesis and biomass in Lake Superior: Effects of nutrient enrichment

Several investigators have measured the rate of photosynthesis in Lake Superior during the past two decades (PUTNAM & OLSON 1966, PARKOS et al. 1969, VERDUIN 1975, NALEwAjKO et al. 1981, FAHNENSTIEL & GLIME 1983, NALEwAJKo & VOLTOLINA 1986). Neither experimental approaches nor methods for data reporting have been consistent among investigators (FAHNENSTIEL et al. 1989) and thus, not all rates are comparable. Furthermore, the factor(s) controlling the rate of photosynthesis in Lake Superior may still be open to question. The role of nutrients and in particular, phosphorus, in controlling photosynthesis and phytoplankton yield in Lake Superior has been documented. SCHELSKE et al. (1972) performed a series of large enclosure experiments that were designed to determine the limiting element in the Great Lakes. In these experiments, large volumes of water (> 1000 I) were spiked with various combinations of plant nutrients and the response of the phytoplankton community in terms of chlorophyll, phytoplankton abundance, and photosynthesis was monitored. Results from these experiments suggested that phosphorus was the limiting element in the Great Lakes. These and other nutrient enrichment studies on the Great Lakes (SCHELSKE 1979) provided the scientific cornerstone for eutrophication control. More recent information, however, has questioned the role of phosphorus in controlling primary production and algal growth in Lake Superior. NALEwAjKO et al. (1981) suggested that phytoplankton growth in Lake Superior was not limited by phosphorus but by light, and even suggested that the entire concept of phosphorus control to maintain phytoplankton biomass at present levels may need to be reevaluated. Light control of primary production was suggested to occur even in the epilimnion during thermal stratification. In a subsequent paper, NALEwAjKO & VOLTOLINA (1986) suggested that physical factors were more important than phosphorus in controlling primary production during isothermal mixing periods.