Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first chromosome-scale genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07Gb genome, 894Mb (84.8%) was anchored onto 25 chromosomes resulting in a final scaffold N50 of 68.11 Mb. This high-quality bird genome assembly is also one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the zebrafinch (Taeniopygia) genetic map more closely resembles the fairy-wren map rather than the map from the more closely-related Ficedula flycatcher. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high quality, annotated genome assembly will be an invaluable resource not only to the superb fairy-wren species and relatives but also broadly across the avian tree by providing a new reference point for comparative genomic analyses.
Molecular phylogeny and systematics of cestodes with rudimentary rostellum (Cestoda: Hymenolepididae) from Holarctic Sorex shews (Eulipotyphla: Soricidae)

We analyse the phylogenetic relationships and taxonomic status of hymenolepidid cestodes with rudimentary rostellum, parasitic in Holarctic shrews of the genus Sorex. These cestodes were previously termed as a ‘Ditestolepis clade’ and encompass eight genera: Diorchilepis, Ditestolepis, Ecrinolepis, Gulyaevilepis, Mathevolepis, Novobrachylepis, Spalania and Spasskylepis. Representatives of seven of these were available for molecular study, including type species of all seven genera. Phylogenetic analysis based on partial sequences of the 28S rRNA gene supports this group of genera as monophyletic. The ‘Ditestolepis clade’ consists of two subclades. One of these includes genera containing cestodes having suckers positioned inside bothrium-like depressions (Ditestolepis, Gulyaevilepis and Spasskylepis). The second subclade contains cestodes with suckers expanding far beyond the margins of the scolex (Mathevolepis, Ecrinolepis, Spalania and Novobrachylepis). The relative taxonomic value of several additional morphological characters is discussed. Genetic data convincingly demonstrate that Ditestolepis diaphana, Spasskylepis ovaluteri and Mathevolepis macyi represent complexes of morphologically similar species. Based on the phylogenetic analysis, we resurrect the genus Spalania. Amended generic diagnoses and keys to identification of the genera in the Ditestolepis clade, as well as keys to the known species, are provided.
Genetic point mutation inducing antigenic drift in hypervariable region of avery virulant IBDV isolate in chickens in Egypt during 2014-2016

Infectious bursal disease (IBD) is a highly contagious viral disease affecting young chickens causing immune suppression, high morbidity and mortality. Its economic significance is recognized worldwide. In this study, suspected IBD samples (bursa of Fabricious) were collected from 45 chicken flocks in 3 Egyptian governorates from 2014 to 2016. The virus was inoculated in embryonated chicken eggs via chorio-allantoicmembrane (CAM) route inducing specific IBDV lesions in the embryos. Viral identification was carried out through Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) targeting VP2 gene. Fourteen positive IBDV isolates (31%) were confirmed by RT-PCR. Three pure IBDV isolates were subjected to partial VP2 gene sequence analysis from which 2 IBDV isolates No. 1 and 3 (Accession No. KX827589.1 and MK906027) were defined as a very virulent IBDV (vvIBDV) genogroup 3, while the third isolate (Accession No. KX827588.1) was closely related to a vaccine strain in cvIBDV genogroup 1. Nucleotide and amino acid sequence analysis and blast of the IBDV isolates indicated a close relationship with the previously recorded Egyptian IBDVs with 96 to 99% identity. Point mutation or amino acid substitution in positions P202M (conserved region); and A211T, D212Y (hypervariable region) of the VP2 gene in the isolate No. 3 vvIBDV (Accession No. MK906027) that differ from all the previously recorded Egyptian isolates in GenBank were present.
Algae as a Biofuel Feed Source

The United States is the world’s largest importer of petroleum and is developing liquid fuel substitutes from biomass to displace fossil fuel consumption as a means of energy security of supply as well as secondary interests in reducing greenhouse gas emissions and supporting innovation. Algae based biofuel is a newer technology gaining momentum in the biofuel race due to very attractive growth properties and ease of distribution in current infrastructure. However, cost economics remain an issue. This study applies an experience curve as a basis for quantifying the investment needed for continued learning progress and scale up of algae biofuel production to reach cost parity with petroleum based fuels. The findings indicate investment will be substantial, perhaps exceeding $15 billion if progress is less than anticipated. This serves as the starting point for analysis of potential factions that would make these kinds of investments, their motivation and how investments might occur. Short term investments are best made in research to discover algae strains with high lipid yields combined with high productivity. Investment will most likely be a combination of public and private funding due to societal gains from research spillover effects and private gains from huge market potential and IP protection. Military support has the potential to be a game changer for algae technology. And, government policy support is important in the near term to encourage investment in continued research, development and commercialization.
Per-Unit Duties: Friends or Foes of Developing Country Exporters?

Protectionist instruments such as tariffs can distort the prices of traded goods. This paper explores the impact of specific (per-unit) duties on patterns of agricultural trade. Specific duties may encourage countries to export higher priced products, leading to an “Alchian-Allen effect” on unit values. Their restrictive effect on trade values is smaller for developed compared to developing countries. It can be explained by the specialization of these countries on low-priced products and by the low level of quality differentiation among their exports. Our results highlight the discriminating nature of specific duties for low-income countries.
Applicability of Satellite Remote Sensing in Accounting Above-Ground Carbon in Miombo Woodlands

The crisis of climate change has drawn attention of ecologists all over the world to explore ways that could effectively enhance the sequestration of carbon in forests and woodlands. This necessitates forest inventory, along with knowledge of techniques that are quick and manageable. The present study was carried out in Miombo woodlands of western Tanzania namely, Kitwe and Mgaraganza. The aim of the present study was to investigate the effectiveness of remote sensing in estimating the stock of carbon in Miombo woodlands. Two types of data namely, ground-truthing and satellite imagery were used. Ground-truthing data were obtained by measuring the diameter at breast height (DBH) of all trees in 30 and 20 concentric plots in Kitwe and Mgaraganza forests, respectively. The average DBH of trees in each forest was fitted in biomass allometric models to estimate the ground-truthing vegetation biomass. On the other hand, Landsat images of the two forests were used to compute the Normalised Vegetation Index (NDVI). The computed NDVI were regressed with the ground-truthing vegetation biomass to get the remotely sensed vegetation biomass which was assumed to be 50% carbon. The coefficients of determination between the ground-truthing above-ground biomass and the NDVI values were statistically significant at P<0.05. The above-ground carbon stock obtained by ground-truthing in Mgaraganza and Kitwe forests was 3 and 2 times higher than that of satellite remotely sensed data respectively. The above-ground carbon stock obtained from satellite remote sensing gives some impression thus a basis for remote sensing in Miombo woodlands.
The Diversity Management Approach to Equal Employment Opportunity in Australian Organisations

This article assesses the ‘Managing Diversity’ (MD) approach in Australia, examining its drivers, discussing its relationship to legislation designed to promote equity, and examining it as a set of management practices. It has been plausibly argued, on efficiency grounds, that responsibility for achieving equality objectives must be shifted to organisations as this links contextual conditions to organisational processes. However, even where there is some prescription and guidance such as that provided by Australian Equal Employment Opportunity (EEO) legislation targeted specifically to women employees, both practice and outcomes are variable. This is even more the case with MD where there are no guiding principles or legislative support. The article examines the best practice EEO and MD programs of Australian organisations to demonstrate the approaches and programs that are being developed at the workplace and to highlight the limitations of the ‘business case’ approach underlying such programs.
Interrogating the Treadmill of Production

This article is structured to answer a number of questions that have been raised over the years about the origin, structure, and application of the treadmill of production theory. The following questions are addressed: What was the theoretical structure of the treadmill of production? Why does the theory focus on production rather than consumption? Was the treadmill a dialectical or a linear change theory? How has the treadmill theory changed under the growing globalization of production since 1980? Has the treadmill been evaluated empirically? What forces have limited the diffusion of the treadmill in environmental sociology? Is the treadmill more/still useful today for ecological analyses? For social analyses?
A smartphone-based, privacy-aware recording system for the assessment of everyday listening situations

When trying to quantify hearing difficulties in every-day listening situations, mostly questionnaires are used to collect and evaluate subjective impressions. Obtaining objective data outside a laboratory is relatively difficult, given the required equipment and its proper handling as well as privacy concerns emerging from long-term audio recordings in a non-regulated and populated environment. Therefore, a smartphone-based system was developed that allows long-term ecological momentary assessment. Microphones are placed close to the ears to obtain signal characteristics, e.g., interaural level differences, similar to those perceived by a listener. Currently, root-meansquare, averaged spectra and the zero crossing rate are calculated. Additional features can be implemented and the flexibility of the smartphone itself allows for additional functionality, e.g., subjective ratings on predefined scales. A simple user interface ensures that the system can be properly handled by nontech-savvy users. As only the extracted features but not the audio-data itself are stored, screening and approval of the recorded data by the test subject is not necessary. Furthermore, additional standard features, e.g., the spectral centroid, can be computed offline, utilizing the recorded features.
Uniconazole effect on endogenous hormones, proteins and proline contents of barley plants (Hordeum vulgare) under salinity stress (NaCl)

Abstract. Bakheta MA, Hussein MM. 2014. Uniconazole effect on endogenous hormones, proteins and proline contents of barley plants (Hordeum vulgare) under salinity stress (NaCl). Nusantara Bioscience 6: 39-44. Pot experiments were carried out during two growth seasons 2010/2011 under greenhouse conditions of the National Research Centre, Dokki, Cairo, Egypt to investigate the response of barley plants (Hordeum vulgare L) grown under salinity stress (2500 or 5000 ppm) to spraying with solutions of uniconazole at 150 or 200 ppm. The obtained results showed that irrigation with saline solutions caused increases in the amounts of abscisic acid (ABA), crude protein, total soluble-protein, and proline contents. The results showed that spraying barley plants grown under saline solutions with uniconazole increased endogenous hormone contents of ABA, cytokinins, crude protein, total soluble protein, and proline but caused decreases in the amounts of endogenous indole acetic acid (IAA) and gibberellic acid (GA3). High protection of abscisic acid in treating plants with uniconazole and under salt stress (interaction effect) increases proline, proteins and soluble protein which has been proposed to act as compatible solutes that adjust the osmotic potential in the cytoplasm. Thus, these biochemical characters can be used as a metabolic marker in relation to salinity stress.
Interdimer “zipping” in the chemoreceptor signaling domain revealed by molecular dynamics simulations

Chemoreceptors are principal components of the bacterial sensory system that modulates cellular motility. They detect changes in the environment and transmit information to CheA histidine kinase, which ultimately controls cellular flagellar motors. The prototypical Tsr chemoreceptor in E. coli is a homodimer containing two principal functional modules: (i) a periplasmic ligand-binding domain and (ii) a cytoplasmic signaling domain. Chemoreceptor dimers are arranged into a trimer of dimers at the tip of the signaling domain comprising a minimal physical unit essential for enhancing the CheA activity several hundredfold. Trimers of dimers are arranged into highly ordered hexagon arrays at the cell pole; however, the mechanism underlying the trimer-of-dimer and higher order array formation remains unclear. Furthermore, molecular mechanisms of signal transduction that are likely to involve inter-dimer interactions are not fully understood. Here we apply all-atom, microsecond-time scale molecular dynamics simulations of the Tsr trimer of dimers atomic model in order to obtain further insight into potential interactions within the chemoreceptor signaling unit. We show extensive interactions between homodimers at the hairpin tip of the signaling domain, where strong hydrophobic interactions maintain binding. A subsequent zipping of homodimers is facilitated by electrostatic interactions, in particular by polar solvation energy and salt bridges that stabilize the final compact structure, which extends beyond the kinase interacting subdomain. Our study provides evidence that interdimer interactions within the chemoreceptor signaling domain are more complex than previously thought.
The RNA-Binding Protein KSRP Modulates Cytokine Expression of CD4+ T Cells

The KH-type splicing regulatory protein (KSRP) is a RNA-binding protein, which regulates the stability of many mRNAs encoding immune-relevant proteins. As KSRP regulates innate immune responses, for instance by the modulation of type I interferon mRNA stability, we were interested whether knockdown of the protein (KSRP−/−) interferes with T cell activation and polarization. Polyclonally stimulated KSRP−/− CD4+ T cells proliferated at a higher extent and higher frequency and expressed the activation marker CD25 more than wild-type T cells. In supernatants of stimulated KSRP−/− CD4+ T cells, levels of IL-5, IL-9, IL-10, and IL-13 were observed to be increased compared to those of the control group. KSRP−/− CD8+ T cells showed no altered proliferative capacity upon polyclonal stimulation, but supernatants contained lower levels of interferon-γ. Similar changes in the cytokine expression patterns were also detected in T cells derived from KSRP−/− mice undergoing arthritis induction indicative of a pathophysiological role of KSRP-dependent T cell polarization. We demonstrated the direct binding of KSRP to the 3′ untranslated region of IL-13, IL-10, and IFN-γ mRNA in in vitro experiments. Moreover, since IL-4 mRNA decay was reduced in KSRP−/− CD4+ T cells, we identify KSRP as a negative regulator of IL-4 expression. These data indicate that overexpression of IL-4, which constitutes the primary inducer of Th2 polarization, may cause the Th2 bias of polyclonally stimulated KSRP−/− CD4+ T cells. This is the first report demonstrating that KSRP is involved in the regulation of T cell responses. We present strong evidence that T cells derived from KSRP−/− mice favor Th2-driven immune responses.
Clinical Implications of Varying Degrees of Vancomycin Susceptibility in Methicillin-Resistant Staphylococcus aureus Bacteremia 1

aspects of bacteremia caused by methicillin-resistant Staphylococcus aureus (MRSA) with heterogeneously reduced susceptibility to vancomycin. Bloodstream MRSA isolates were screened for reduced susceptibility by using brain-heart infusion agar, including 4 mg/L vancomycin with and without 4% NaCl. Patients whose isolates exhibited growth (case-patients) were compared with those whose isolates did not (controls) for demographics, coexisting chronic conditions, hospital events, antibiotic exposures, and outcomes. Sixty-one (41%) of 149 isolates exhibited growth. Subclones from 46 (75%) of these had a higher MIC of vancomycin than did their parent isolates. No isolates met criteria for vancomycin heteroresistance. No differences in potential predictors or in outcomes were found between case-patients and controls. These data show that patients with vancomycin-susceptible MRSA bacteremia have similar baseline clinical features and outcomes whether or not their bacterial isolates exhibit growth on screening media containing vancomycin.
A new species of Chaetozone (Polychaeta, Cirratulidae) from the Bay of Biscay offshore France, together with a review of Chaetozone species from the North Atlantic and adjacent waters

A new cirratulid species of the genus Chaetozone has been discovered offshore in fine muddy sediments in the Bay of Biscay, France. This species is unusual in having an expanded fusiform anterior body region and numerous subdermal glands along the entire body that produce an elaborate and distinctive pattern when stained with Methyl Green. The new species is compared with closely related congeners and a review of Chaetozone species from the North Atlantic Ocean is presented.
How to Characterize Cylindrical Magnetic Nanowires

Cylindrical magnetic nanowires made through the help of nanoporous alumina templates are being fabricated and characterized since the beginning of 2000. They are still actively investigated nowadays, mainly due to their various promising applica‐ tions, ranging from high-density magnetic recording to high-frequency devices, passing by sensors, and biomedical applications. They also represent suitable systems in order to study the dimensionality effects on a given material. With time, the development in fabrication techniques allowed to increase the obtained nanowire complexity (control‐ led crystallinity, modulated composition and/or geometry, range of materials, etc.), while the improvements in nanomanipulation permitted to fabricate system based either on arrays or on single nanowires. On the other side, their increased complexity requires specific physical characterization methods, due to their particular features such as high anisotropy, small magnetic volume, dipolar interaction field between them, and interesting electronic properties. The aim of this chapter was to offer an ample overview of the magnetic, electric, and physical characterization techniques that are suitable for cylindrical magnetic nanowire investigation, of what is the specific care that one needs to take into account and which information will be extracted, with typical and varied examples.
ontext-dependent cheating : Experimental evidence from 6 countries

Policy makers use several international indices that characterize countries according to the quality of their institutions. However, no effort has been made to study how the honesty of citizens varies across countries. This paper explores the honesty among citizens across 16 countries with 1440 participants. We employ a very simple task where participants face a trade-off between the joy of eating a fine chocolate and the disutility of having a threatened self-concept because of lying. Despite the incentives to cheat, we find that individuals are onesty orruption ultural differences mostly honest. Further, international indices that are indicative of institutional honesty are completely uncorrelated with citizens’ honesty for our sample countries. © 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). ∗ Corresponding author at: Department of Financial Economy and Accounting, Universidad Complutense Madrid, Campus Somosaguas, Madrid, 28223, pain. Tel. : +34 630176315; fax: +34 910102708. E-mail addresses: david.pascual@ccee.ucm. es (D. Pascual-Ezama), tf@ifro.ku. dk (T.R. Fosgaard), jccarden@gmail.com (J.C. Cardenas), kujal@gmail.com (P. Kujal), rveszteg@gmail.com (R. Veszteg), bgil.gomezdelianno@uam.es (B. Gil-Gómez de Liaño), brian.gunia@jhu.edu (B. Gunia), oris.Weichselbaumer@jku.at (D. Weichselbaumer), khilken@vub.ac. be (K. Hilken), armenak.antinyan@fau.de (A. Antinyan), J.M. J.Delnoij@uu.nl J. Delnoij), antonios.proestakis@ec.europa. eu (A. Proestakis), michael.d. tira@gmail.com (M.D. Tira), yulius.pratomo@staff.uksw. edu (Y. Pratomo), arekjaberlopez@gmail.com (T. Jaber-López), branasgarza@gmail.com (P. Brañas-Garza). http://dx.doi. org/10.1016/j.jebo. 2015.04.020 167-2681/© 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license http://creativecommons.org/licenses/by-nc-nd/4.0/). 380 D. Pascual-Ezama et al. / Journal of Economic Behavior & Organization 116 (2015) 379–386
ANAEROBIC DIGESTION OF MUNICIPAL BIOWASTE FOR THE PRODUCTION OF RENEWABLE ENERGY: EFFECT OF PARTICLE SIZE

In recent years, Anaerobic Digestion (AD) has become an important technological alternative for the management of municipal biowaste (MBW) for both pollution control and obtaining renewable energy such as methane. One of the factors that most affects the AD of MBW is the particle size, particularly in the hydrolysis and lag phases, this last being in general the limiting stage of solid waste AD. This research evaluated on a laboratory scale the AD of MBW by evaluating Biochemical Methane Potential (BMP) at a temperature of 30 °C during 30 days and the influence of particle size. The particle sizes ranged between < 2 mm to 12.5 mm. Along the study, better results were observed for particle sizes < 2 mm, obtaining productions of methane and electrical energy of 128 mL gVS-1 and 2960.4 kWh week-1 respectively (19% higher than in reactors with larger particles), thus indicating lower costs for design and maintenance.