Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological morphology : integrative organismal biology

Ecological morphology examines the relation between an animal's anatomy and physiology - its form and function - and how the animal has evolved in, and can inhabit, a particular environment. This book provides a synthesis of major concepts and a demonstration of the ways in which this integrative approach can yield rich and surprising results. Through this interdisciplinary study, scientists have been able to understand, for instance, how bat-wing design affects habitat use and bat diet; how the size of a predator affects its ability to capture and eat certain prey; and how certain mosquitoes have evolved physiologically and morphologically to tolerate salt-water habitats. "Ecological Morphology" also covers the history of the field, the role of the comparative method in studying adaptation and the use of data from modern organisms for understanding the ecology of fossil communities. This book provides an overview of the achievements and potential of ecological morphology for all biologists and students interested in the way animal design, ecology and evolution interact.
Acidiferrimicrobium australe gen. nov., sp. nov., an acidophilic and obligately heterotrophic, member of the Actinobacteria that catalyses dissimilatory oxido-reduction of iron isolated from metal-rich acidic water in Chile.

A novel acidophilic member of the phylum Actinobacteria was isolated from an acidic, metal-contaminated stream draining from an abandoned underground coal mine (Trongol mine), situated close to Curanilahue, Biobío Region, Chile. The isolate (USS-CCA1T) was demonstrated to be a heterotroph that catalysed under aerobic conditions the oxidation of ferrous iron and the reduction of ferric iron under anaerobic conditions, but not the oxidation of sulfur nor hydrogen. USS-CCA1T is a Gram-positive, motile, short rod-shaped, mesophilic bacterium with a temperature growth optimum at 30 °C (range 20-39 °C). It was categorized as an extreme acidophile growing between 1.7 and 4.5 and optimally at pH 3.0. The G+C content of the chromosomal DNA of the isolate was 74.1 mol%, which is highly related to Aciditerrimonas ferrireducens IC-180T , (the most closely related genus; 94.4 % 16S rRNA gene identity), and higher than other acidophilic actinobacteria. The isolate (USS-CCA1T) was shown to form a distinct 16S rRNA clade from characterized acidophilic actinobacteria, well separated from the genera Acidimicrobium, Ferrimicrobium, Ferrithrix, 'Acidithrix' and Aciditerrimonas. Genomic indexes (ANIb, DDH, AAI, POCP) derived from the USS-CCA1T draft genome sequence (deposited at DDBJ/ENA/GenBank under the accession WJHE00000000) support assignment of the isolate to a new species and a new genus within the Acidimicrobiaceae family. Isolate USS-CCA1T is the designated type strain of the novel species Acidiferrimicrobium australe (=DSM 106828T,=RGM 2506T).
An evaluation of taxonomic characters in the subsection Sessiles, section Corniculatae, of Vaucheria (Vaucheriaceae, Chrysophyta)

Abstract Taxonomic characters have been evaluated in the subsection Sessiles (section Comiculatae) of Vaucheria. Four isolates were tested in culture under a range of temperatures, photon flux densities, salinities and substrate gradients, and compared with 24 field populations. Oogonial orientation, L/D of oogonia, number of oogonia per gametangial group, antheridial shape and siphon diameter were found to be poor taxonomic characters. Oospore wall structure in transverse section, oogonial wall texture, oogonial shape and to some degree, oogonial length and diameter were found to be good distinguishing characters. As a result, V. sessilis (Vaucher) de Candolle, V. clavata sensu Klebs and V. repens Hassall have been placed in synonymy with V. bursata (O.F. Muller) C. Agardh; V. bursata and V. borealis Hirn have been delineated from V. dillwynii (Weber & Mohr) C. Agardh in having evenly textured rather than lamellate oospore walls, smooth rather than scrobiculate oogonial walls and ovoid to ovoid-reniform .
Herpes Simplex Virus 1 ICP34.5 Alters Mitochondrial Dynamics in Neurons

Herpes simplex virus persists lifelong in neurons and can reactivate to cause recurrent lesions in mucosal tissues. A key determinant of virulence is the viral protein ICP34.5, of which residues 68 to 87 significantly contribute to neurovirulence through an unknown mechanism. Our report provides evidence that residues 68 to 87 of ICP34.5 are required for binding mitochondrion-associated factors. These interactions alter mitochondrial dynamics in neurons, thereby facilitating viral replication and pathogenesis. ABSTRACT Expression of viral genes and activation of innate antiviral responses during infection result in an increase in reactive oxygen species (ROS) and toxic by-products of energy metabolism which can lead to cell death. The mitochondrion and its associated proteins are crucial regulators of these responses and related pathways such as autophagy and apoptosis. Through a mass spectrometry approach, we have shown that the herpes simplex virus 1 (HSV-1) neurovirulence- and autophagy-modulating protein ICP34.5 interacts with numerous mitochondrion-associated factors. Specifically, we showed that amino acids 68 to 87 of ICP34.5, the domain that binds beclin1 and controls neurovirulence, are necessary for interactions with PGAM5, KEAP1, and other regulators of the antioxidant response, mitochondrial trafficking, and programmed cell death. We further show that while this domain interacts with multiple cellular stress response factors, it does not alter apoptosis or antioxidant gene expression. That said, the attenuated replication of a recombinant virus lacking residues 68 to 87 (termed Δ68-87) in primary human fibroblasts was restored by addition of ferric nitrate. Furthermore, in primary mouse neurons, the perinuclear localization of mitochondria that follows infection with HSV-1 was notably absent following Δ68-87 infection. Through this 20-amino-acid domain, ICP34.5 significantly reduces mitochondrial motility in axons of neurons. We propose the hypothesis that ICP34.5 promotes perinuclear mitochondrial localization by modulating transport of mitochondria through interaction with PGAM5. These data expand upon previous observations of altered mitochondrial dynamics following alphaherpesvirus infections and identify a key determinant of this activity during HSV-1 infections. IMPORTANCE Herpes simplex virus persists lifelong in neurons and can reactivate to cause recurrent lesions in mucosal tissues. A key determinant of virulence is the viral protein ICP34.5, of which residues 68 to 87 significantly contribute to neurovirulence through an unknown mechanism. Our report provides evidence that residues 68 to 87 of ICP34.5 are required for binding mitochondrion-associated factors. These interactions alter mitochondrial dynamics in neurons, thereby facilitating viral replication and pathogenesis.
Deceleration of the Trend in Inequality of Educational Outcome in the Netherlands∗

The association between family socioeconomic status and the offspring’s educational attainment has long been studied in social stratification and social mobility research (for example Breen and Jonsson, 2005; Hout and DiPrete, 2006). A strong positive association means that people with a high socioeconomic background are more likely to achieve higher levels of education than people with a low socioeconomic background. The strength of the association is for this reason often referred to as educational inequality. In this article I will focuss on the association between socioeconomic background and the highest achieved level of education. Following Buis (2008a), the association between social background and highest achieved level of education will be called Inequality of Educational Outcome (IEOut) in order to distinguish it from the association between highest social background and the probabilities of continuing from one level of education to the next, which is referred to as Inequality of the Educational Opportunities (IEOpp). This article will have a primary and a subsidiary aim: The primary aim is to provide a detailed description of the trend in IEOut in the Netherlands between 1912 and 1988. Previous literature has found for the Netherland that IEOut decreased linearly over time (De ∗DRAFT: Please request permission before citing. I am grateful for comments and suggestions made by John Fox, Harry B.G. Ganzeboom, Adriaan Hoogendoorn, and Gerben Moerman.
Basic insights into Zika virus infection of neuroglial and brain endothelial cells

Zika virus (ZIKV) has recently emerged as an important human pathogen due to the strong evidence that it causes disease of the central nervous system, particularly microcephaly and Guillain–Barré syndrome. The pathogenesis of disease, including mechanisms of neuroinvasion, may include both invasion via the blood–brain barrier and via peripheral (including cranial) nerves. Cellular responses to infection are also poorly understood. This study characterizes the in vitro infection of laboratory-adapted ZIKV African MR766 and two Asian strains of (1) brain endothelial cells (hCMEC/D3 cell line) and (2) olfactory ensheathing cells (OECs) (the neuroglia populating cranial nerve I and the olfactory bulb; both human and mouse OEC lines) in comparison to kidney epithelial cells (Vero cells, in which ZIKV infection is well characterized). Readouts included infection kinetics, intracellular virus localization, viral persistence and cytokine responses. Although not as high as in Vero cells, viral titres exceeded 104 plaque-forming units (p.f.u.) ml−1 in the endothelial/neuroglial cell types, except hOECs. Despite these substantial titres, a relatively small proportion of neuroglial cells were primarily infected. Immunolabelling of infected cells revealed localization of the ZIKV envelope and NS3 proteins in the cytoplasm; NS3 staining overlapped with that of dsRNA replication intermediate and the endoplasmic reticulum (ER). Infected OECs and endothelial cells produced high levels of pro-inflammatory chemokines. Nevertheless, ZIKV was also able to establish persistent infection in hOEC and hCMEC/D3 cells. Taken together, these results provide basic insights into ZIKV infection of endothelial and neuroglial cells and will form the basis for further study of ZIKV disease mechanisms.
Exploring the Link between Income Inequality, Poverty Reduction and Economic Growth: An ASEAN Perspective

The main objective of the current study is to investigate the role of economic growth and income inequality in poverty reduction. In the emerging economies, there are more significant challenges of income inequalities as compared with the vibrant economies. For dealing with the issues of poverty in a successful way, there is a need to tackle the income inequalities. It has been proposed that policies working at redistribution of income should be implemented by the governments to support low-income families. Increase of income inequality is linked with economic growth. For development of economy, high-income inequality is essential as it decreases the advantages of economic growth for poor people. The increasing inequality of income and extensive poverty are major issues in the process of development. The key objective for most of the policies on economic growth is to reduce these issues. The previous research studies have used the traditional measures for income poverty, including index of the poverty gap and a headcount ration. However, the measures of human poverty that have become crucial estimators of social development and living conditions have been used in this research. The study has employed the dynamic panel data approach and used the data of 13 years from the period starting from 2004 to 2017. It has been suggested by the empirical analysis, that poverty levels reduce through economic growth in the emerging world. The levels of income poverty and poverty have a downward trend. It is implied by the results of research that the incomes of the poor should not be the only focus on countries to reduce poverty. Instead, there is a need to improve the provision of necessary facilities and an improvement in life expectancy rates to eliminate the poverty levels.
LIPOPOLYSACCHARIDES ASSOCIATION ON THE SURFACE OF A SILICON CRYSTAL ADDRESSED BY THz SPECTROSCOPY AND MOLECULAR MODELLING

Gram-negative bacteria lipopolysaccharides (LPS) are lipids with a chemical structure comprising a lipidic region with several hydrocarbonate chains and a large saccharide region. Due to their structure, LPS can associate through hydrophobic forces, but also can dissolve in water. Here we investigated the association of LPS molecules on the surface of a silicon crystal by terahertz (THz) spectroscopy. We measured the THz absorption of LPS molecules directly deposited on the crystal or deposited on the crystal coated with a CaCl2 solution. Resulting spectra present a non-linear increase of THz absorption, with two absorption shoulders at 1.05 THz (~35 cm) and 1.37 THz (~45 cm). The presence of the CaCl2 solution does not influence the shoulders localization, suggesting a similar association of LPS molecules in both situations. Based on the comparison with previous THz studies on phospholipid bilayers, we suggested a layer ordering of LPS molecules in our samples that was validated through molecular modelling methods. We modelled LPS monolayers and simulated the THz spectra by normal modes analysis (NMA) and molecular dynamics (MD). The NMA spectrum of a LPS monolayer resulted in agreement with experiments, allowing us to validate the proposed LPS layer organization and the spectra simulation method.
Genetic differentiation among local Japanese populations of the starfish Asterias amurensis inferred from allozyme variation

The starfish Asterias amurensis that is a common species in Japanese waters shows the remarkable morphological variation in several characters such as colour pattern of body between local populations. The genetic differentiation and relationships among seven local Japanese populations were investigated by allozyme analysis. From the allozyme variation observed in 25 genetic loci coding for 14 enzymes, Nei’s genetic distances between seven local populations were calculated and a biochemical dendrogram for seven populations was constructed. The dendrogram indicated that the Akkeshi (Hokkaido), Ushimado (Inland Sea), and Ise (Ise Bay) populations are much genetically differentiated from the other four populations, and that the degree of genetic differentiation between them was much higher than that between conspecific local populations. Judging from allozyme and morphological data, we conclude that the starfish A. amurensis from Japanese waters consists of at least three groups that are largely genetically divergent at subspecies or sibling species level.
Preventive effects of fatty acids and phytochemicals in ApcMin/+ mouse, a model of colorectal cancer

3 ABBREVIATIONS . 8 LIST OF TABLES . 10 LIST OF FIGURES . 12 ACKNOWLEDGMENTS . 14 1. GENERAL INTRODUCTION . 15 1.1. COLORECTAL CANCER . 15 1.1.1. Basic concepts and epidemiology . 15 1.1.2. Types of colorectal cancer . 17 1.1.2.1. Hereditary non-polyposis colorectal cancer (HNPCC) . 17 1.1.2.2. Familial Adenomatous polyposis (FAP) . 19 1.1.2.3. Sporadic Colorectal Cancer . 23 1.1.2.4. Sporadic MSI-Colorectal Cancer . 24 1.1.3. Adenocarcinoma Sequence . 25 1.1.4. Risk Factors for Colorectal Cancer . 28 1.1.4.1. Obesity . 28 1.1.4.2. Dietary Fibre . 30 1.1.4.3. Meat Consumption . 31 1.1.4.4. Fruits and Vegetable Intake . 31 1.1.4.5. Alcohol . 32 1.1.4.6. Physical Activity . 32 1.2. INFLAMMATION AND COLORECTAL CANCER . 33 1.2.1. Overview of Inflammation . 33 1.2.2. Chronic Inflammation Associated with Cancer . 34 1.2.3. Inflammation and Tumour Growth . 36 1.2.4. Diet and Inflammation . 37 1.3. APCMIN/+ MOUSE MODEL OF COLORECTAL CANCER . 43 1.3. 1. Basic concepts . 43 1.3. 2. Genetic and Phenotype characteristics in ApcMin/+ Mouse Model . 43 1.3. 3. Other types of ApcMin/+ Mouse Model of Colorectal Cancer . 46 1.4. FATTY ACIDS AND COLORECTAL CANCER . 47 1.4.1. Definition . 47 1.4.2. Metabolism of Fatty Acids . 49 1.4.3. Animal and Epidemiological evidence of the effects of Fatty Acids . 51 1.4.4. Chemopreventive Mechanism of Fatty Acids . 53 1.5. PHYTOCHEMICAL AND COLORECTAL CANCER . 56 1.5. 1. Definition . 56 1.5. 2. Metabolism of Phenolics . 58 1.5. 3. Epidemiological Evidence . 59 1.5. 4. Coffee . 61 1.5. 5. Walnuts . 62 1.5. 6. Cocoa . 62 1.5. 7. Turmeric and Thyme . 63 1.5. 8. Berries . 64 1.5. 9. Chemopreventive Mechanism of Phytochemicals . 64 2. AIMS OF THE STUDY . 68
Generalized Bitcoin-Compatible Channels

—The widespread adoption of decentralized cryp-tocurrencies, such as Bitcoin or Ethereum, is currently hindered by their inherently limited transaction rate. One of the most prominent proposals to tackle this scalability issue are payment channels which allow mutually distrusted parties to exchange an arbitrary number of payments in the form of off-chain authenticated messages while posting only a limited number of transactions onto the blockchain. Speciﬁcally, two transactions sufﬁce, unless a dispute between these parties occurs, in which case more on-chain transactions are required to restore the correct balance. Unfortunately, popular constructions, such as the Lightning network for Bitcoin, suffer from heavy communication complexity both off-chain and on-chain in case of dispute. Concretely, the communication overhead grows exponentially and linearly, respectively, in the number of applications that run in the channel. In this work, we introduce and formalize the notion of generalized channels for Bitcoin-like cryptocurrencies. Generalized channels signiﬁcantly extend the concept of payment channels so as to perform off-chain any operation supported by the underlying blockchain. Besides the gain in expressiveness, generalized channels outperform state-of-the-art payment channel constructions in efﬁciency, reducing the communication complexity and the on-chain footprint in case of disputes to linear and constant, respectively. We provide a cryptographic instantiation of generalized channels that is compatible with Bitcoin, leveraging adaptor signatures
Local sensitivity analysis of cardiovascular system parameters

Cardiovascular disease is one of the major problems in today’s medicine and the number of patients increase worldwide. To treat these types of diseases, prior knowledge about function and dysfunction of the cardiovascular system is essential for identifying the disease in an early stage. Mathematical modeling is a powerful tool for prediction and investigation of the cardiovascular system. It has been shown, that the Windkessel model, drawing an analogy between electrical circuits and fluid flow, is an effective method to model the human cardiovascular system. The aims of this work are the derivation of a computational cardiovascular model for the arm arteries, and to analyze the behavior of the vascular network structure by parameter sensitivity analysis. Sensitivity analysis is essential for parameter estimation and simplification of cardiovascular models. In optimal experiment design (OED) sensitivity analysis is used to construct experiments and corresponding models that allow the interpretation of cardiovascular measurements in an effective manner. In this paper we have applied sensitivity analysis to a linear elastic model of the arm arteries to find sensitive parameters and their confidence intervals that guide us to the estimation of cardiovascular network parameters. To calculate the percentage effect on the measurable state variables pressure and flow, with respect to percentage change in cardiovascular input parameters, we use norms. This method allows us to quantify and verify results obtained by sensitivity analysis. The sensitivities with respect to flow resistance, arterial compliance and flow inertia, reveal that the flow resistance and diameter of the vessels are the most Modelling in Medicine and Biology X 155 www.witpress. com, ISSN 1743-3525 (on-line) WIT Transactions on Biomedicine and Health, Vol 17, © 2013 WIT Press doi:10.2495/BIO130141 sensitive parameters. Those parameters play a key role in diagnoses of severe stenosis and aneurysms. In contrast, wall thickness and elastic modulus are found to be less sensitive.
Genetic variation in Heritiera littoralis (Malvaceae) from east and south Asia revealed by AFLP markers

Abstract Heritiera littoralis Dryand (Malvaceae) is a mangrove tree that can grow in both intertidal wetland and inland habitats. Due to natural and human impacts, populations of this species have been fragmented. We used amplified fragment length polymorphism markers to determine the genetic variations in 13 natural populations of H. littoralis from China, Japan, and Thailand. Our results revealed a relatively high level of genetic variation (at population level: P = 35.71%, H = 0.127, and I = 0.190; at species level: P = 77.47%, H = 0.221, and I = 0.342) and a high level of genetic differentiation among populations (G ST = 0.336) in this species. The results also suggest that the origins of the current populations of H. littoralis in Asia lie in two gene pools. These findings imply that as many populations as possible should be preserved in situ for the conservation of this species. Given their genetic variability and origin, the Thai populations should be assigned priority for conservation.
Statistical Methods in Genetic Epidemiology

Statistical Estimation of Epidemiological Risk is a concise, organized, and well-written text that provides the derivations of statistical formulas underlying much epidemiological research and practice. The book is divided into eight chapters covering formulas for estimating population prevalence under different sampling designs and familiar risk estimators such as the relative risk, odds ratio, and attributable risk. In addition, the book covers less frequently used risk estimators, including the risk difference (the absolute difference in risk between two populations), the relative difference (excess effect due to an exposure or treatment), the generalized odds ratio (used for ordinal response variables), and the number needed to treat (the average number of persons who would require treatment to prevent one adverse outcome on average). Each section is organized similarly, covering estimation under binomial, cluster, and inverse sampling designs, and uses clear examples to illustrate the appropriate application of each method. There are ample references for readers interested in the original research motivating each method. Statistical exercises follow each chapter, most focusing on the derivation of formulas given in the text. There are two audiences for this text. The primary audience includes biostatisticians and statistically sophisticated epidemiologists, who will be interested in the mathematical derivations and have the necessary skills to apply the resulting formulas. The secondary audience is epidemiologic researchers, who will find the book a valuable addition to the classic text by Fleiss, Levin, and Paik (2003). For most epidemiologists who are not “current” with the biostatistical literature, this book can serve as a guide to the broad range of risk estimation statistics applied to both simple and complex study designs. An epidemiologist could use this text to make an informed selection of study design, knowing that statistical methods will subsequently be available for its analysis. An epidemiologist may also find the text useful while working with biostatisticians, both in directing a collaborating statistician to appropriate methods and in giving an explanation of methods that may not be readily accessible to epidemiologists.