Finding academic concerns of the Three Gorges Project based on a topic modeling approach

The Three Gorges Project (TGP) has gone into the overall completion acceptance stage in 2014. As the world's largest hydropower project, the TGP has attracted worldwide attention over the past few decades. Previous studies mainly focused on a single aspect, such as engineering technologies, social impacts and environmental impacts, of the TGP. However, a large-scale review gathering systematic data to find academic concerns about the TGP is missing. Topic model is a text mining approach for discovering latent topics in a collection of documents. In this article, an emerging topic modeling approach, Latent Dirichlet Allocation (LDA), was introduced to uncover the intellectual structure of the academic literature focusing on the TGP. A collection of 8280 Chinese research articles highly related to the TGP was established with a time frame ranging from 2001 to 2013, and an 18-topic model was used to describe the intellectual structure. Two novel bibliometric indicators, including topic proportion and topic trend, were constructed to describe the academic concerns of the TGP. Topic proportion analysis shows that post-construction issues, including the social and environmental impacts brought by the TGP, have attracted more attention than the construction issues. “Ecology”, “Reservoir Operation”, “Land Administration”, and “Water Pollution”, have become the dominant research topics regarding the TGP during these years. Meanwhile, “Construction Technology” and “Design”, have gradually lost scholars’ interest. The results show that the approach reported in this study can provide sound and credible conclusions of the major academic concerns for a hydropower project. The topic modeling approach is expected to be widely applied as a methodological strategy in future hydropower and other infrastructure project assessment.     

Detecting Hotspot Information Using Multi-Attribute Based Topic Model

Microblogging as a kind of social network has become more and more important in our daily lives. Enormous amounts of information are produced and shared on a daily basis. Detecting hot topics in the mountains of information can help people get to the essential information more quickly. However, due to short and sparse features, a large number of meaningless tweets and other characteristics of microblogs, traditional topic detection methods are often ineffective in detecting hot topics. In this paper, we propose a new topic model named multi-attribute latent dirichlet allocation (MA-LDA), in which the time and hashtag attributes of microblogs are incorporated into LDA model. By introducing time attribute, MA-LDA model can decide whether a word should appear in hot topics or not. Meanwhile, compared with the traditional LDA model, applying hashtag attribute in MA-LDA model gives the core words an artificially high ranking in results meaning the expressiveness of outcomes can be improved. Empirical evaluations on real data sets demonstrate that our method is able to detect hot topics more accurately and efficiently compared with several baselines. Our method provides strong evidence of the importance of the temporal factor in extracting hot topics.     

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

Protein subcellular localization prediction based on compartment-specific features and structure conservation

Background  

Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins.     

A structural equation modeling approach for formalizing and evaluating ecological integrity in terrestrial ecosystems

Ecological integrity is a functional property that integrates habitat functions and species information for maintaining key ecological interactions in predator-prey systems. As a functional property, ecological integrity can be modeled as a latent concept from observable spatial attributes that measure the ecosystem's capacity to provide suitable habitat conditions for apex predators. Ecological integrity is a tri-dimensional concept that stems from “stable”, “concurrent” and “intact” conditions. A theoretical framework and a methodology is presented here for modeling ecological integrity from observable attributes (as GIS layers) to obtain a spatial representation of the integrity condition. From a theoretical framework, the ecological integrity concept is obtained with a structural equation modeling approach, where several other latent variables are obtained for characterizing a hierarchical network of spatial information. Later on, these observable attributes, and several latent modeled variables are translated into sources of geographic information that can be used to monitor changes in the natural remnant areas due to human impacts. When examining the direct, indirect and total effects of habitat loss and fragmentation on ecological integrity, spatial intactness (e.g., the amount of remnant habitat and connectivity) and stability (resistance in the interaction network and mobile links) are the attributes more affected by the pathway effects. The balance of the formative parameters obtained for the model supports the idea that ecosystems that have a high degree of integrity should maintain a high level of stability, self-organization and naturalness. These attributes are achieved when spatial habitat intactness and species interactions are maintained.     

Prezygapophyseal articular facet shape in the catarrhine thoracolumbar vertebral column

Two contrasting patterns of lumbar vertebral morphology generally characterize anthropoids. “Long‐backed” monkeys are distinguished from “short‐backed” apes [Benton: The baboon in medical research, Vol. 2 (1967:201)] with respect to several vertebral features thought to afford greater spinal flexibility in the former and spinal rigidity in the latter. Yet, discussions of spinal mobility are lacking important functional insight that can be gained by analysis of the zygapophyses, the spine's synovial joints responsible for allowing and resisting intervertebral movements. Here, prezygapophyseal articular facet (PAF) shape in the thoracolumbar spine of Papio, Hylobates, Pongo, Gorilla, and Pan is evaluated in the context of the “long‐backed” versus “short‐backed” model. A three‐dimensional geometric morphometric approach is used to examine how PAF shape changes along the thoracolumbar vertebral column of each taxon and how PAF shape varies across taxa at corresponding vertebral levels. The thoracolumbar transition in PAF shape differs between Papio and the hominoids, between Hylobates and the great apes, and to a lesser extent, among great apes. At the level of the first lumbar vertebra, the PAF shape of Papio is distinguished from that of hominoids. At the level of the second lumbar vertebra, there is variation to some extent among all taxa. These findings suggest that morphological and functional distinctions in primate vertebral anatomy may be more complex than suggested by a “long‐backed” versus “short‐backed” dichotomy. Am J Phys Anthropol 142:600–612, 2010. © 2010 Wiley‐Liss, Inc.     

A partially function-to-topic model for protein function prediction

Background

Proteins are a kind of macromolecules and the main component of a cell, and thus it is the most essential and versatile material of life. The research of protein functions is of great significance in decoding the secret of life. In recent years, researchers have introduced multi-label supervised topic model such as Labeled Latent Dirichlet Allocation (Labeled-LDA) into protein function prediction, which can obtain more accurate and explanatory prediction. However, the topic-label corresponding way of Labeled-LDA is associating each label (GO term) with a corresponding topic directly, which makes the latent topics to be completely degenerated, and ignores the differences between labels and latent topics.

Result

To achieve more accurate probabilistic modeling of function label, we propose a Partially Function-to-Topic Prediction (PFTP) model for introducing the local topics subset corresponding to each function label. Meanwhile, PFTP not only supports latent topics subset within a given function label but also a background topic corresponding to a ‘fake’ function label, which represents common semantic of protein function. Related definitions and the topic modeling process of PFTP are described in this paper. In a 5-fold cross validation experiment on yeast and human datasets, PFTP significantly outperforms five widely adopted methods for protein function prediction. Meanwhile, the impact of model parameters on prediction performance and the latent topics discovered by PFTP are also discussed in this paper.

Conclusion

All of the experimental results provide evidence that PFTP is effective and have potential value for predicting protein function. Based on its ability of discovering more-refined latent sub-structure of function label, we can anticipate that PFTP is a potential method to reveal a deeper biological explanation for protein functions.

     

Two-enzyme active transport in vitro with ph induced asymmetrical functional structures.: III. Discussions based on numerical treatments of the time-dependent evolutions

Three complementary models have been considered in which pH gradients (step function. linear pH or linear H^?) impose asymmetry on a two-enzyme mixture. If the “combined pH dependences” of enzymes is pro-asymmetrical, the pH gradient induces an asymmetrical distribution of potential activities (“latent” asymmetry of functional structure). When substrate is added, “developed” asymmetry of effective activities appears which results in “substrate space wave” and pumping when the catalysed reaction couple is “inversible”. It is shown that only one steady state exists for a given boundary condition and is attained when the “combined effective activity” of enzymes is nil: the stationary flux with symmetrical boundaries or the stationary load with moving boundaries is proportional to “effective global activities” of enzymes. “Equivalent square models” could be proposed that would be able to describe “functional” or “permanent” structure pumps as well. These models belong to the thermodynamic branch and the asymmetrical “space wave” substrate concentration profiles obtained must be distinguished from dissipative structures. It appears that such primary active transport pumps are chemical equivalents of heat pumps.     

A text mining analysis of the climate change literature in industrial ecology

The literature on climate change research has evolved tremendously since the 1990s. The goal of this study is to use text mining to review the climate change literature and study the evolution of the main trends over time. Specific keywords from articles published in the special issue “ Industrial Ecology for Climate Change Adaptation and Resilience” in the Journal of Industrial Ecology are first selected. Details of over 35,000 publications containing these keywords are downloaded from the Web of Science from 1990 to 2018. The number of publications and co‐occurrence of keywords are analyzed. Moreover, latent Dirichlet allocation (LDA)—a probabilistic approach that can retrieve topics from large and unstructured text documents—is applied on the abstracts to uncover the main topics (consisting of new terms) that naturally emerge from them. The evolution in time of the importance of some emerging topics is then analyzed on the basis of their relative frequency. Overall, a rapid growth in climate change publications is observed. Terms such as “climate change adaptation” appear on the rise, whereas other terms are declining such as “pollution.” Moreover, several terms tend to co‐occur frequently, such as “climate change adaptation” and “resilience.” The database collected and the LiTCoF (Literature Topic Co‐occurrence and Frequency) Python‐based tool developed for this study are also made openly accessible. This article met the requirements for a gold – gold JIE data openness badge described http://jie.click/badges .     

Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder

While vision evokes a dense network of feedforward and feedback neural processes in the brain, visual processes are primarily modeled with feedforward hierarchical neural networks, leaving the computational role of feedback processes poorly understood. Here, we developed a generative autoencoder neural network model and adversarially trained it on a categorically diverse data set of images. We hypothesized that the feedback processes in the ventral visual pathway can be represented by reconstruction of the visual information performed by the generative model. We compared representational similarity of the activity patterns in the proposed model with temporal (magnetoencephalography) and spatial (functional magnetic resonance imaging) visual brain responses. The proposed generative model identified two segregated neural dynamics in the visual brain. A temporal hierarchy of processes transforming low level visual information into high level semantics in the feedforward sweep, and a temporally later dynamics of inverse processes reconstructing low level visual information from a high level latent representation in the feedback sweep. Our results append to previous studies on neural feedback processes by presenting a new insight into the algorithmic function and the information carried by the feedback processes in the ventral visual pathway.     

Acoustic communication in crocodilians: from behaviour to brain

Crocodilians and birds are the modern representatives of Phylum Archosauria. Although there have been recent advances in our understanding of the phylogeny and ecology of ancient archosaurs like dinosaurs, it still remains a challenge to obtain reliable information about their behaviour. The comparative study of birds and crocodiles represents one approach to this interesting problem. One of their shared behavioural features is the use of acoustic communication, especially in the context of parental care. Although considerable data are available for birds, information concerning crocodilians is limited. The aim of this review is to summarize current knowledge about acoustic communication in crocodilians, from sound production to hearing processes, and to stimulate research in this field. Juvenile crocodilians utter a variety of communication sounds that can be classified into various functional categories: (1) “hatching calls”, solicit the parents at hatching and fine‐tune hatching synchrony among siblings; (2) “contact calls”, thought to maintain cohesion among juveniles; (3) “distress calls”, induce parental protection; and (4) “threat and disturbance calls”, which perhaps function in defence. Adult calls can likewise be classified as follows: (1) “bellows”, emitted by both sexes and believed to function during courtship and territorial defence; (2) “maternal growls”, might maintain cohesion among offspring; and (3) “hisses”, may function in defence. However, further experiments are needed to identify the role of each call more accurately as well as systematic studies concerning the acoustic structure of vocalizations. The mechanism of sound production and its control are also poorly understood. No specialized vocal apparatus has been described in detail and the motor neural circuitry remains to be elucidated. The hearing capabilities of crocodilians appear to be adapted to sound detection in both air and water. The ear functional anatomy and the auditory sensitivity of these reptiles are similar in many respects to those of birds. The crocodilian nervous system likewise shares many features with that of birds, especially regarding the neuroanatomy of the auditory pathways. However, the functional anatomy of the telencephalic auditory areas is less well understood in crocodilians compared to birds.     

FloraGREIF – An Internet-Based Data Repository for Biogeographical Research in Mongolia

FloraGREIF presents an internet-based information tool on the vascular plant flora of Mongolia combining taxon- and record-specific information, text and image information with map information and digitized plant specimens with images of living species and their habitats. Based on an updated checklist as taxonomic backbone, information is split into the “taxon” and the “record” level. At the taxon level the user finds taxonomic diagnoses, habitat information, and species distribution within the floristic regions of Mongolia. The latter is visualized in a Web GIS application. The record level offers information for all records assigned to one taxon, which may include locality data only or additional, high-resolution scans of herbarium specimens combined with images from living species and their habitats. Several query masks allow a flexible search and display of species lists. The interactive Web GIS application links taxon or record information with various map layers, comprising administrative units, topography and orography, floristic regions and vegetation zones of Mongolia. They present background information for the display of species distribution or record localities. FloraGREIF offers a virtual research environment to make the substantial information on Mongolia’s flora mainly published in Russian accessible to the public.     

Metagenomic taxonomic classification using extreme learning machines

Next-generation sequencing technologies have allowed researchers to determine the collective genomes of microbial communities co-existing within diverse ecological environments. Varying species abundance, length and complexities within different communities, coupled with discovery of new species makes the problem of taxonomic assignment to short DNA sequence reads extremely challenging. We have developed a new sequence composition-based taxonomic classifier using extreme learning machines referred to as TAC-ELM for metagenomic analysis. TAC-ELM uses the framework of extreme learning machines to quickly and accurately learn the weights for a neural network model. The input features consist of GC content and oligonucleotides. TAC-ELM is evaluated on two metagenomic benchmarks with sequence read lengths reflecting the traditional and current sequencing technologies. Our empirical results indicate the strength of the developed approach, which outperforms state-of-the-art taxonomic classifiers in terms of accuracy and implementation complexity. We also perform experiments that evaluate the pervasive case within metagenome analysis, where a species may not have been previously sequenced or discovered and will not exist in the reference genome databases. TAC-ELM was also combined with BLAST to show improved classification results. Code and Supplementary Results: http://www.cs.gmu.edu/~mlbio/TAC-ELM (BSD License).     

Exploitation of gene context

Recently, a number of techniques have been proposed that use completely sequenced genomes for the function prediction of individual proteins encoded therein. They use the fusion of genes, their conserved location in operons or merely their co-occurrence in genomes to predict the existence of functional interactions between the proteins they encode. This type of information complements functional features that are predicted by classical homology-based search techniques.     

Bosmina (Eubosmina) longicornis longicornis SCHOEDLER, 1866 (Crustacea,Cladocera: Bosminidae) from the Postglacial Sediments of the Neuendorfer See,East-Germany

Analyses were made of subfossil Eubosmina remains from the Lake Neuendorfer See, a lake in the middle part of the river Spree in the “Urstromtal” of Baruth situated in the eastern part of Germany. In addition to Bosmina (Bosmina) longirostris (O. F. M., 1785) Bosmina (Eub.) longicornis longicornis Schoedler, 1866 occured in the lake from the Boreal (sediment depth 15.85 m) to the recent surface layers of the core. Other eubosminids did not occur during the history of the Lake Neuendorfer See with the exception of few remains of B. (Eub.) longispina, which were detected in the lowermost layers of the core during the late Pleistocene. In the present-day plankton, Bosmina (Eub.) l. longicornis was the only eubosminid found in the Lake Neuendorfer See. During the long period between colonization during the Boreal to the present, no changes were detected in typical morphological features of B. (Eub.) l. longicornis. All remains of Eubosmina in the layers above 15.85 m belong undoubtedly to the same taxon. No signs of any morphological instability (other then ontogenetic and cyclomorphic formchanges) or “morphological transition” (Hofmann, 1977) to other taxa could be found. By using paleolimnological analyses, the named taxon has proven to be a “good” entity within the group of long-spined taxa of the subgenus Eubosmina.     

Insights into a putative hinge region in elastin using molecular dynamics simulations

The resiliency and elasticity of vertebrate tissues are traced to elastin, a crosslinked protein with extensive hydrophobic regions. There is little discussion in the literature on the structure and dynamics of the alanine-rich crosslinking regions of elastin that comprise a significant part of the native protein. In particular, the region encoded by exons 21 and 23, a contiguous splice form found in all types of human elastin, is believed to be strategically positioned for proper function of the protein, namely, in the reversible elongation and contraction of tissue. Hence, molecular dynamics (MD) calculations on the EX21/23 domain are reported here. This crosslinking domain has been assumed to adopt an architecture in which the putative hinge region links two α-helices. In this paper, we use a homology-based approach to obtain starting structures in the hinge region. The subsequent MD brings new insights into the possibility of fluctuations between “open” and “closed” states, as well as distinguishing structural features of the latter. The significance of these findings towards an enhanced understanding of structure–function relationships in elastin and the elastic fiber is discussed.     

Delimitation of evolutionary units in Cuvier’s dwarf caiman, <Emphasis Type="Italic">Paleosuchus palpebrosus</Emphasis> (Cuvier, 1807): insights from conservation of a broadly distributed species

An important goal of evolutionary and conservation biology is the identification of units below the species level, such as Evolutionarily Significant Units (ESUs), providing objectively delimited units for species conservation and management. In this study we tested the hypothesis that Cuvier’s dwarf caiman (Paleosuchus palpebrosus)—a species broadly distributed across several biomes and watersheds of South America—is comprised of different ESUs. We analyzed mitochondrial cytochrome b sequences of 206 individuals and 532 unlinked ddRAD loci of 20 individuals chosen from amongst the mitochondrial haplogroups. Analysis of the cytochrome b sequences revealed four mitochondrial clusters, while STRUCTURE analysis of ddRAD loci detected three genomic clusters with different levels of mixture between them. Using the Adaptive Evolutionary Conservation (AEC) framework we identified three ESUs: “Amazon”, “Madeira-Bolivia” and “Pantanal”; one of them composed of two different Management Units (MUs), “Madeira” and “Bolivia”. In general, based on the comparisons with other crocodilian species, genetic diversity of each lineage was moderate however, the Madeira MU showed fivefold lower genetic diversity than other geographic groups. Considering the particularities of each Paleosuchus palpebrosus conservation unit, we recommend that the conservation status of each is evaluated separately. Tropical biodiversity is largely underestimated and in this context the broadly distributed species are the most likely candidates to harbor distinct evolutionary lineages. Thus, we suggest that conservation research should not neglect species that are generally considered of Least Concern by IUCN due to the taxon’s broad geographic distribution.     

Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis

To probe signal propagation and genetic actuation in microbial consortia, we have coopted the components of both redox and quorum sensing (QS) signaling into a communication network for guiding composition by “programming” cell lysis. Here, we use an electrode to generate hydrogen peroxide as a redox cue that determines consortia composition. The oxidative stress regulon of Escherichia coli, OxyR, is employed to receive and transform this signal into a QS signal that coordinates the lysis of a subpopulation of cells. We examine a suite of information transfer modalities including “monoculture” and “transmitter-receiver” models, as well as a series of genetic circuits that introduce time-delays for altering information relay, thereby expanding design space. A simple mathematical model aids in developing communication schemes that accommodate the transient nature of redox signals and the “collective” attributes of QS signals. We suggest this platform methodology will be useful in understanding and controlling synthetic microbial consortia for a variety of applications, including biomanufacturing and biocontainment.     

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.