pinecone/core-2020-05-10-deduplication huggingface dataset:
Environmental variables affecting small‐scale distributions of five rotifer species in Lancaster Lake, Michigan

The small‐scale distributions of the rotifers  Polyarthra vulgaris, Synchaeta stylata, Conochilus unicornis, Hexarthra mira , and  Asplanchna priodonta  were investigated in Lancaster Lake, Cheboygan County, Michigan, July 21, 1974. Measurements were taken for 13 depths (at 1‐m intervals) and at 4 times of the day (1:00 AM, 7:00 AM, 1:00 PM, and 7:00 PM). In addition, the abundances of 6 crustacean, 2 planktonic dipteran, and 10 algal species, as well as temperature, light, oxygen, chlorophyll  a , alkalinity, pH and free carbon dioxide were measured. Whereas abiotic factors appeared to control large scale occupation of the lake, and excluded most species from the deeper portions of the hypolimnion, small‐scale distributional variation of the rotifers depended upon biotic interactions, particularly with the crustacean zooplankton
Taxonomy and Ecology of Sponge-AssociateMarionina spp. (Clitellata : Enchytraeidae) from the Horomatangi Geothermal System of Lake Taupo, New Zealand

The dissection of Heterorotula sponges collected in an area of geothermal activity at 126–145 m depth on the floor of Lake Taupo (de Rondeet al., 2002) revealed a dense population of associated Enchytraeidae. They represent three species of Marionina, two of which known but exotic (the Palaearctic M. ripariaBretscher, 1899 and the Chinese M. seminudaXie and Rota, 2001), and one new to science, M. spongicola sp. n. This is the first report of an ecological association between enchytraeids and poriferans in the lake profundal zone. The possible nature of such relationship (casual contact for feeding or dwelling for food and shelter) is discussed
Nutritional Limitation Travels up the Food Chain

It is a well accepted fact that nutrient limitation of plants affects the growth and survival of herbivores, generally leading to lower performance of herbivores feeding on nutrient stressed plants. The effect of plants' growing conditions on predatory organisms, feeding one trophic level up, has been much less studied, and there is a general consensus that such effects would be small as herbivores often show relatively strong homeostasis with respect to their nutrient content. Here, we challenge this view, and show from several examples that despite the fact that herbivores buffer much of the variance in nutrient stoichiometry of their food, effects of growing conditions of the primary producers can travel up the food chain. We discuss the implications of these findings, and argue that phosphorus limitation of secondary consumers might be more common in marine than in freshwater systems
Relationships between the Seasonal Variations of Macroinvertebrates, and Land Uses for Biomonitoring in the Xitiaoxi River Watershed, China

The impacts of differences in watershed land uses, and differences in seasonality on benthic macroinvertebrate communities, were evaluated in 12 stream sites within the Xitiaoxi River watershed, China, from April 2009 to January 2010. The composition of macroinvertebrate community differed significantly among three land use types. Forested sites were characterized by high taxa richness, diversity and the benthic‐index of biotic integrity (B‐IBI), while farmland and urban disturbed stream sites presented contrary patterns. The percentage of urban land use, conductivity, dissolved oxygen, ammonia nitrogen and total phosphorus were the major drivers for the variations. The land use related water quality stress gradients of the four sampling seasons were determined by means of four independent Principal Component Analyses. The responses of macroinvertebrate community metrics, to anthropogenic stressors, were explored using Spearman Rank Correlation analyses. All the selected metrics, including total numbers of taxa, numbers of Ephemeroptera, Plecoptera and Trichoptera taxa, percentage of non‐insect abundance, percentage of scrapers abundance, Pielou’s evenness index, Simpson diversity index, and the Benthic Index of Biotic Integrity were correlated significantly with environmental gradients (PC1) in autumn. In other seasons such correlations were less pronounced. Our results imply that autumn is the optimal time to sample macroinvertebrate communities, and to conduct water quality biomonitoring in this subtropical watershed. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim
The response of the rotifer community in Loch Leven,\ud
UK, to changes associated with a 60% reduction in\ud
phosphorus inputs from the catchment

Lakes across the world are suffering from anthropogenically induced nutrient enrichment\ud
problems and many attempts are being made to improve their water quality and ecosystem\ud
function. Most metrics that are being used to monitor recovery are based on relationships that\ud
have been established across a range of lakes. These may not respond quickly to in-lake\ud
changes in water quality when nutrient management strategies are put in place. This paper\ud
uses data routinely collected from Loch Leven, UK, to examine the immediate and longerterm\ud
responses of the rotifer community to a 60% reduction in phosphorus input from the\ud
catchment in the early 1990s. We conclude that changes in rotifer abundance and relative\ud
species composition are sensitive indicators of lake-specific changes in water quality,\ud
responding more quickly than more widely used metrics, such as total phosphorus and\ud
chlorophyll a concentrations. However, like all indicators of change, such indices must be\ud
used with care in situations where rotifer populations are subject to multiple stressors
Dynamic Interaction Networks in modelling and predicting the behaviour of multiple interactive stock markets

The behaviour of multiple stock markets can be described within the framework of complex dynamic systems. A representative technique of the framework is the dynamic interaction network (DIN), recently developed in the bioinformatics domain. DINs are capable of modelling dynamic interactions between genes and predicting their future expressions. In this paper, we adopt a DIN approach to extract and model interactions between stock markets. The network is further able to learn online and updates incrementally with the unfolding of the stock market time-series. The approach is applied to a case study involving 10 market indexes in the Asia Pacific region. The results show that the DIN model reveals important and complex dynamic relationships between stock markets, demonstrating the ability of complex dynamic systems approaches to go beyond the scope of traditional statistical methods
Curbing domestic violence: instantiating C-K theory with formal concept analysis and emergent self organizing maps

In this paper we propose a human-centered process for knowledge discovery from unstructured text that makes use of Formal Concept Analysis and Emergent Self Organizing Maps. The knowledge discovery process is conceptualized and interpreted as successive iterations through the Concept-Knowledge (C-K) theory design square. To illustrate its effectiveness, we report on a real-life case study of using the process at the Amsterdam-Amstelland police in the Netherlands aimed at distilling concepts to identify domestic violence from the unstructured text in actual police reports. The case study allows us to show how the process was not only able to uncover the nature of a phenomenon such as domestic violence, but also enabled analysts to identify many types of anomalies in the practice of policing. We will illustrate how the insights obtained from this exercise resulted in major improvements in the management of domestic violence cases.status: publishe
Factors contributing to IT industry success in developing countries: the case of Thailand

A stream of research exists that explores a country's information technology (IT) industry success. The theoretical model used in these studies is primarily focused on small developed countries. We contend that the factors that contribute to IT industry success in developing countries are likely to differ somewhat from those that play a role in small developed countries. Research to date on IT industry success has neglected developing countries. This study therefore presents an alternative IT industry success model for developing countries. It adapts Ein-dor, Myers, and Raman's (1997) model in developing such a conceptual model. The adapted framework is then applied in a study of IT industry in a developing country - Thailand. We found IT-related foreign direct investment to be vital to IT industry success in Thailand. Unlike findings from earlier studies on small developed countries, geographical location and to a lesser extent government investment promotion policies are also important to IT industry success in a developing country. These findings support the view that there are differences in the factors that affect IT industry success in developed and developing countries. Implications for research and practice are discussed. © 2005 Wiley Periodicals, Inc
Open Source Software and Economic Growth: A Classical Division of Labor Perspective

The article turns to classical economic insights on the division of labor and to institutional reasoning to identify some costs and benefits of Open Source Software (OSS) and proprietary software production. It suggests that, thanks to its licenses, OSS favors market expansion more than proprietary software does by tapping into spontaneous work input. The spontaneous tapping leads to a division of labor that exhibits what the article calls redundant economies. By generating a circle of knowledge growth, reuse, and sharing, redundant economies lead to increasing returns, which are crucial for economic growth.
Interpreting the trustworthiness of government mediated by information and communication technology: lessons from electronic voting in Brazil

The electronic voting system of Brazil is understood to be widely trusted by the citizens of the country and international observers. More precisely, it is seen as a trustworthy mechanism of producing election results that accurately represent the choices of the electorate. In this article, we discuss briefly the concepts of trust and trustworthiness, and focus to examine the formation of beliefs regarding the latter. We argue that the belief of trustworthiness is only partly attributable to the perception of the merits of the technical system and its enactment procedures. In our case study we found that the institutional actors responsible for the elections—the Superior and the Regional Electoral Courts—have played a key role in the formation of the belief that the electronic elections are trustworthy. We therefore conclude that, unlike common assumptions about the potential of e-government in developing countries to restore trust in government institutions that are considered untrustworthy, the production of trust in government services mediated by information and communication technology relies on citizens' perceptions of their trustworthiness
Vitronectin – master controller or micromanager?

The concept of the cellular glycoprotein vitronectin acts as a biological ‘glue’ and key controller of mammalian tissue repair and remodelling activity is emerging from nearly 50 years of experimental in vitro and in vivo data. Unexpectedly, the vitronectin-knock-out mouse was found to be viable and to have largely normal phenotype. However, diligent observation revealed that the VN-KO animal exhibits delayed coagulation and poor wound healing. This is interpreted to indicate that vitronectin occupies a role in the earliest events of thrombogenesis and tissue repair. That role is as a foundation upon which the thrombus grows in an organised structure. In addition to closing the wound, the thrombus also serves to protect the underlying tissue from oxidation, is a reservoir of mitogens and tissue repair mediators and provides a provisional scaffold for the repairing tissue. In the absence of vitronectin (e.g. VN-KO animal) this cascade is disrupted before it begins. \ud
\ud
Our data demonstrates that a wide variety of biologically active species associate with VN. While initial studies were focused on mitogens, other classes of bioactives (e.g. glycosaminoglycans, metalloproteinases) are now also known to specifically interact with VN. Many of these interactions are long-lived, often resulting in multi-protein complexes, while others are stable for prolonged periods. Multiprotein complexes provide several advantages: prolonging molecular interaction; sustaining local concentrations, facilitating co-stimulation of cell surface receptors and thereby enhancing cellular / biological responses. We contend that these, or equivalent, multi-protein complexes mediate vitronectin functionality in vivo. It is also likely that many of the species demonstrated to associate with vitronectin in vitro, also associate with vitronectin in vivo in similar multi-protein complexes. Thus the predominant biological function of vitronectin is that of a master controller of the extracellular environment; informing, and possibly instructing cells ‘where’ to behave, ‘when’ to behave, and ‘how’ to behave (i.e. appropriately for the current circumstance)
Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton

Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organization of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion, and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation, and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here, we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry, and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes.Full Tex
Quorum Sensing and Biofilm Formation in Mycobacteria: Role of c-di-GMP and Methods to Study This Second Messenger

Bacteria have evolved to survive the ever-changing environment using intriguing mechanisms of quorum sensing (QS). Very often, QS facilitates formation of biofilm to help bacteria to persist longer and the formation of such biofilms is regulated by c-di-GMP. It is a well-known second messenger also found in mycobacteria. Several methods have been developed to study c-di-GMP signaling pathways in a variety of bacteria. In this review, we have attempted to highlight a connection between c-di-GMP and biofilm formation and QS in mycobacteria and several methods that have helped in better understanding of c-di-GMP signaling. (c) 2014 IUBMB Life, 66(12):823-834, 201
Cardiolipin-cytochrome c complex: Switching cytochrome c from an electron-transfer shuttle to a myoglobin- and a peroxidase-like heme-protein

Cytochrome c (cytc) is a small heme-protein located in the space between the inner and the outer membrane of the mitochondrion that transfers electrons from cytc-reductase to cytc-oxidase. The hexa-coordinated heme-Fe atom of cytc displays a very low reactivity toward ligands and does not exhibit significant catalytic properties. However, upon cardiolipin (CL) binding, cytc achieves ligand binding and catalytic properties reminiscent of those of myoglobin and peroxidase. In particular, the peroxidase activity of the cardiolipin-cytochrome c complex (CL-cytc) is critical for the redistribution of CL from the inner to the outer mitochondrial membranes and is essential for the execution and completion of the apoptotic program. On the other hand, the capability of CL-cytc to bind NO and CO and the heme-Fe-based scavenging of reactive nitrogen and oxygen species may affect apoptosis. Here, the ligand binding and catalytic properties of CL-cytc are analyzed in parallel with those of CL-free cytc, myoglobin, and peroxidase to dissect the potential mechanisms of CL in modulating the pro- and anti-apoptotic actions of cytc
Intramuscular Lipid Metabolism, Insulin Action and Obesity

With the increasing prevalence of obesity, research has focused on the molecular mechanism(s) linking obesity and skeletal muscle insulin resistance. Metabolic alterations within muscle, such as changes in the cellular location of fatty acid transporter proteins, decreased mitochondrial enzyme activity and defects in mitochondrial morphology, likely contribute to obesity and insulin resistance. These defects are thought to play a role in the reduced skeletal muscle fatty acid oxidation (FAO) and increased intramuscular lipid (IMCL) accumulation that is apparent with obesity and other insulin resistant states, such as type 2 diabetes. Intramuscular triacylglycerol (IMTG) does not appear to be a ubiquitous marker of insulin resistance, although specific IMCL intermediates such as long-chain fatty acyl-CoAs (LCFA-CoAs), ceramide and diacylglycerol (DAG) may inhibit insulin signal transduction. In this review, we will briefly summarize the defects in skeletal muscle lipid metabolism associated with obesity, and discuss proposed mechanisms by which these defects may contribute to insulin resistance. Originally published IUBMB Life, Vol. 6, No. 1, Jan 200
Verprolin: A cool set of actin-binding sites and some very HOT prolines

Spatiotemporal organisation of eukaryotic cells is established and maintained by the cytoskeleton, a highly dynamic and complex network of structural and signalling proteins. Many components of the cytoskeleton are functionally and structurally conserved between humans and yeast. Among these are verprolin (Vrp1p) in yeast and its human ortholog Wiskott-Aldrich syndrome protein (WASP)-interacting protein (WIP). Much of our understanding of the function of these proteins has come from genetic analysis in yeast. Verprolin-deficient yeast cells exhibit defects in cytokinesis, endocytosis, and actin cytoskeleton polarisation. Verprolin binds actin, the yeast ortholog of human WASP (Las17p or Bee1p), and the yeast ortholog of human PSTPIP1 (Hof1p or Cyk2p). We propose that verprolin acts as a chaperone that by transient bimolecular interactions maintains the proper function of its partners. Verprolin-related proteins and partners are implicated in cancer, immunodeficiency, and neurodegeneration. Therefore, elucidating how verprolin functions will have major impacts in cell biology and medicine.Griffith Health, School of Medical ScienceFull Tex
ER stress response, peroxisome proliferation, mitochondrial unfolded protein response and Golgi stress response.

The endoplasmic reticulum (ER) response has been thought a cytoprotective mechanism to cope with accumulation of unfolded proteins in the ER. Recent progress has made a quantum leap revealing that ER stress response can be regarded as an autoregulatory system adjusting the ER capacity to cellular demand. This Copernican change raised a novel fundamental question in cell biology: how do cells regulate the capacity of each organelle in accordance with cellular needs? Although this fundamental question has not been fully addressed yet, research about each organelle has been advancing. The proliferation of the peroxisome is regulated by the PPAR alpha pathway, whereas the abundance of mitochondria appears to be regulated by mitochondrial retrograde signaling and the mitochondrial unfolded protein response. The functional capacity of the Golgi apparatus may be regulated by the mechanism of the Golgi stress response. These observations strongly suggest the existence of an elaborate network of organelle autoregulation in eukaryotic cells
Enzymatic processing of beta-dystroglycan recombinant ectodomain by MMP-9: identification of the main cleavage site

Dystroglycan (DG) is a membrane receptor belonging to the complex of glycoproteins associated to dystrophin. DG is formed by two subunits, alpha-DG, a highly glycosylated extracellular matrix protein, and beta-DG, a transmembrane protein. The two DG subunits interact through the C-terminal domain of alpha-DG and the N-terminal extracellular domain of beta-DG in a noncovalent way. Such interaction is crucial to maintain the integrity of the plasma membrane. In some pathological conditions, the interaction between the two DG subunits may be disrupted by the proteolytic activity of gelatinases (i.e. MMP-9 and/or MMP-2) that removes a portion or the whole beta-DG ectodomain producing a 30 kDa truncated form of beta-DG. However, the molecular mechanism underlying this event is still unknown. In this study, we carried out proteolysis of the recombinant extracellular domain of beta-DG, beta-DG(654-750) with human MMP-9, characterizing the catalytic parameters of its cleavage. Furthermore, using a combined approach based on SDS-PAGE, MALDI-TOF and HPLC-ESI-IT mass spectrometry, we were able to identify one main MMP-9 cleavage site that is localized between the amino acids His-715 and Leu-716 of beta-DG, and we analysed the proteolytic fragments of beta-DG(654-750) produced by MMP-9 enzymatic activity
miR-210: More than a silent player in hypoxi

Multiple studies have consistently established that miR (microRNA)-210 induction is a feature of the hypoxic response in both normal and transformed cells. Here, we discuss the emerging biochemical functions of this miRNA and anticipate potential clinical applications. miR-210 is a robust target of hypoxia-inducible factor, and its overexpression has been detected in a variety of cardiovascular diseases and solid tumors. High levels of miR-210 have been linked to an in vivo hypoxic signature and associated with adverse prognosis in cancer patients. A wide spectrum of miR-210 targets have been identified, with roles in mitochondrial metabolism, angiogenesis, DNA repair, and cell survival. Such targets may broadly affect the evolution of tumors and other pathological settings, such as ischemic disorders. Harnessing the knowledge of miR-210's actions may lead to novel diagnostic and therapeutic approaches
On a heuristic point of view concerning the expression of numerous genes during the cell cycle

The current model of the eukaryotic cell cycle proposes that numerous genes are expressed at different times during the cell cycle. The existence of myriad control points for gene expression leads to theoretical and logical problems for cell cycle control. Each expressed gene requires a control element to appear in a cell‐cycle specific manner; this control element requires another control element and so on,  ad infinitum . There are also experimental problems with the current model based on ineffective synchronization methods and problems with microarray measurements of mRNA. Equally important, the efficacy of mRNA variation in affecting changes in protein content is negligible. An alternative view of the cell cycle proposes cycle‐independent, invariant accumulation of mRNA during the cell cycle with decreases of specific proteins occurring only during the mitotic period of the cell cycle. © 2011 IUBMB IUBMB Life, 2011