Miracle-dz/UniFAR-FTUs huggingface dataset:
A network-based integrated framework for predicting virus–prokaryote interactions

Abstract Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$s_2^*$\end{document} and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus–host interactions.
Response of Orthoptera species (Tettigoniidae and Acrididae) to wildfires in a Central European dry grassland

Abstract The effects of wildfires on the Orthoptera fauna of extensive dry grasslands were investigated at 25 random sites in a military training area in Eastern Austria. using a space-for-time substitution, a time span of 1 to about 20 y after fire was considered. Fire-induced trajectories of habitat characteristics such as microclimate proved to have a determining effect on the occurrence of most acridids and some tettigoniids. Dispersal capacity and fire-shelter characteristics of egg deposition sites did not significantly influence postbum occurrence patterns ofthe investigated species. Of a total of 20 species, seven were favored by wildfires, two were adversely affected by fire and eleven did not show significant responses to postburn age. Four species, amongst them Celes variabilis, which is highly endangered in Central Europe, can be considered fire-dependent in the study area. Therefore, fire can have beneficial effects for the conservation of acridid grasshoppers in particular. A reconsideration of the present legal ban on the use of prescribed burning in Central Europe is recommended.
Estuarine relationships between zooplankton community structure and trophic gradients

Zooplankton and water quality parameters were investigated at eight mesohaline stations in the lower Chesapeake Bay and Elizabeth River from January through December 1994 to identify the changes of zooplankton community structure with increased eutrophication. The total micro- and mesozooplankton biomass decreased with the increase of eutrophication. However, the relative proportion of microzooplankton increased with increased eutrophication. Within highly eutrophied waters, the small oligotrichs (<30 µm) and rotifers dominated the total zooplankton biomass (as carbon). However, tintinnids, copepod nauplii and mesozooplankton significantly decreased with the increase of eutrophication. These patterns were consistent throughout the seasons and had significant relationships statistically. These results suggest zooplankton community structures characterize an increasing eutrophication of an ecosystem.
One hundred and seventy-five new species of Graphidaceae: closing the gap or a drop in the bucket?

Recent studies of the global diversity of the lichenized fungal family Graphidaceae suggest that there are a large number of species remaining to be discovered. No less than 640 species have been described since 2002, including 175 new species introduced in a collaborative global effort in a single issue in this journal. These findings suggest that the largest family of tropical crustose lichens may have an even higher number of species than Parmeliaceae. To estimate whether the discovery of 175 new species is a significant step forward in cataloguing extant diversity in this family, we employed a parametric method to predict global species richness of Graphidaceae using a GIS-based grid map approach. The model employs linear regression between observed species richness and sample score and vegetation composition per grid to predict individual grid species richness, and interpolation of species grid distributions to predict global species richness. We also applied a non-parametric species-area curve approach and non-parametric species richness estimators (Chao, Jackknife, Bootstrap) to compare the results from the different methods. Our approach resulted in a prediction of 4,330 species of Graphidaceae, including approximately 3,500 (sub-)tropical species in the core subfamilies Fissurinoideae, Graphidoideae, Redonographoideae, plus 125 species restricted to extratropical regions (outside the zone between 30° northern and 30° southern latitude) and 700 species in subfamily Gomphilloideae. Currently, nearly 2,500 species are known in the family, including species not yet formally described. Thus, our model suggests that even after describing 175 species in this issue and with another approximately 140 awaiting publication, the number of species still to be discovered and described is more than 1,800, and much work remains to be done to close this substantial gap. Based on our approach, we predict that most of this undiscovered diversity is to be found in Mexico, the northern Andean region, the eastern Amazon and central and southern Brazil, tropical West Africa, continental Southeast Asia, Indonesia, and Papua New Guinea.
Genetic structure and dispersal of Macrobrachium australiense (Decapoda: Palaemonidae) in western Queensland, Australia

SUMMARY 1. The freshwater prawn, Macrobrachium australiense (Decapoda: Palaemonidae), is an abundant species throughout the rivers of western Queensland, and it is thought to have effective dispersal capabilities. Given the very low topographical relief of the western Queensland landscape and the vast nature of episodic flooding, it was predicted that widespread dispersal in this species would occur within, and possibly between the four major catchments of the region: the Darling, Bulloo, Cooper and Diamantina. We analysed eight polymorphic allozyme systems and a fragment of the cytochrome c oxidase subunit 1 (COI) mitochondrial DNA (mtDNA) gene to determine the extent of recent and historical patterns of dispersal at nested spatial scales, within and between catchments. 2. Large and significant levels of allozyme and mtDNA differentiation were revealed among all catchments, indicating that dispersal of M. australiense does not occur across catchment boundaries, although this species is reportedly capable of overland movement. In contrast, no significant patterns of genetic differentiation were resolved between major subcatchments of the Darling and Cooper, or between sites within these subcatchments, indicating that populations of M. australiense are panmictic within catchments. 3. The MtDNA data resolved two divergent and reciprocally monophyletic clades, with the first representing the Darling catchment, and the second corresponding to the Bulloo, Cooper and Diamantina catchments. We postulate that extreme variation in historical climatic patterns and palaeohydrologic conditions played an important role in shaping the population structure of M. australiense throughout western Queensland during the Quaternary.
The Ethical Implications of Community-Based Research

Researchers need to provide evidence that they have met ethical requirements before entering the field—rightly so, since the power and privilege embedded in academic researchers is considerable. However, given the calls for universities to decolonize and democratize research, we need to question whether the ethical norms developed to cater for objective, researcher-driven enquiries are appropriate and sufficient to ensure ethical conduct for qualitative designs that are more subjective, participatory, and community-based. This conceptual article argues for the need to rethink the standards against which ethics boards evaluate community-based research projects and suggests some ways this could be done.
Lipoprotein metabolism in poultry

Understanding the metabolism of lipoproteins in birds is important to enable nutritionists to design diets aimed at obtaining better meat characteristics and egg quality, and can furnish useful information for future studies. In comparison to mammals, there are a number of expressive differences in the metabolism of lipids in birds, such as the transport of dietary lipids to the liver, hepatic lipogenesis and the presence of unique lipoproteins in the blood (portomicrons). Greater differences are found in egg-laying hens during the production phase, in which lipoproteins produced in the liver, under the action of oestrogen, are used for the formation of the egg yolk. The regulation of the lipid metabolism by hormones and the participation of key enzymes associated to advances in molecular biology techniques could assist in the genetic selection of more productive birds and better quality products for consumers.
Correction: Enhanced deacetylation of p53 by the anti-apoptotic protein HSCO in association with histone deacetylase 1.

Abstract HSCO (hepatoma subtracted-cDNA library clone one, also called ETHE1) was originally identified by its frequent overexpression in hepatocellular carcinomas. HSCO inhibits function of NF-κB by binding to RelA and accelerating its export from the nucleus. We show here that HSCO exhibits anti-apoptotic activity in cells exposed to DNA-damaging agents by suppressing transcriptional activity of p53. Induction of pro-apoptotic genes, Noxa, Perp, PIG3, and Bax were suppressed in cells over-expressing HSCO. By increasing ubiquitylation and degradation of p53, HSCO reduces p53 protein levels. HSCO specifically associates with histone deacetylase 1 (HDAC1) independently of Mdm2 and facilitates deacetylation of p53 at Lys-373/382 by HDAC1. The metallo-β-lactamase family consensus sequence in HSCO is important for its effect on p53 deacetylation. Co-immunoprecipitation and immunofluorescence studies suggested that HSCO, HDAC1, and p53 form a complex in the nucleus. Thus, HSCO is a cofactor that increases the deacetylase activity of HDAC1 toward p53, leading to suppression of apoptosis. Treatment of hepatocellular carcinomas that retain wild-type p53 and overexpress HSCO with anti-HSCO agents might re-establish the p53 response and revert chemoresistance.
The NMDA Receptor Antibody Paradox: A Possible Approach to Developing Immunotherapies Targeting the NMDA Receptor

N-methyl-D-aspartate receptors (NMDAR) play a key role in brain development and function, including contributing to the pathogenesis of many neurological disorders. Immunization against the GluN1 subunit of the NMDAR and the production of GluN1 antibodies is associated with neuroprotective and seizure-protective effects in rodent models of stroke and epilepsy, respectively. Whilst these data suggest the potential for the development of GluN1 antibody therapy, paradoxically GluN1 autoantibodies in humans are associated with the pathogenesis of the autoimmune disease anti-NMDA receptor encephalitis. This review discusses possible reasons for the differential effects of GluN1 antibodies on NMDAR physiology that could contribute to these phenotypes.
Lineage Diversification of Lizards (Phrynosomatidae) in Southwestern North America: Integrating Genomics and Geology

In the first chapter of my dissertation, I provide an ultimate tectonic hypothesis for several well-studied zoogeographic boundaries along the west coast of North America, specifically along the San Andreas Fault system. Reviewing the literature, I demonstrate that four Great Pacific Fracture Zones correspond with spatially concordant phylogeographic breaks for a variety of marine and terrestrial animals. I hypothesize that the four zoogeographic boundaries reviewed here ultimately originated via the same tectonic process (triple junction evolution along the San Andreas Fault system), and I suggest how a comparative phylogeographic approach can be used to test this hypothesis. In the second chapter, I investigate the systematics and species delimitation of fringe-toed lizards of the Uma notata complex in the deserts of southwestern North America. Ten nuclear loci were Sanger sequenced and genome-wide sequence and single-nucleotide polymorphism (SNP) data were collected using restriction-associated DNA (RAD) sequencing. I validated five species-level lineages within the U. notata complex, three of which were previously described as full species, one originally described as a subspecies but later synonymized, and one previously documented yet undescribed species from Mohawk Dunes, Arizona, USA. The results support the hypothesis that Pleistocene glacial cycles promoted allopatric speciation via dispersal across a landscape matrix shaped by older tectonic events, but I also recovered evidence for a vicariant role of the Colorado River during the Pleistocene epoch. In the third chapter, I studied the comparative phylogeography of lizards (Phrynosomatidae) of the Baja California Peninsula, including the genera Callisaurus, Petrosaurus, Urosaurus, and Sceloporus. I collected sequence/SNP data from 228 individual lizards from the peninsula and eight islands using RADseq. The estimated divergence dates across co-distributed clades revealed that for each of the five regions where comparisons are possible, at least two or three episodes of divergence are required to explain the observed patterns. I tested for range expansions or bottlenecks associated with Pleistocene glacial cycles or continent-to-peninsula invasions. The results are consistent with the hypothesis that plate tectonic events established a complex landscape matrix with numerous barriers to dispersal that ultimately facilitated divergence, generating the idiosyncratic patterns observed among co-distributed lineages.
Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development

Many cell surface and secreted proteins are modified by the covalent addition of glycans that play an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signaling. Aberrant protein glycosylation has been associated with the development of several muscular diseases suggesting essential glycan- and lectin-mediated functions in myogenesis and muscle development but our molecular understanding of the precise glycans, catalytic enzymes and lectins involved remain only partially understood. Here, we quantified dynamic remodeling of the membrane-associated proteome during a time-course of myogenesis in cell culture. We observed wide-spread changes in the abundance of several important lectins and enzymes facilitating glycan biosynthesis. Glycomics-based quantification of released N-linked glycans confirmed remodeling of the glycome consistent with the regulation of glycosyltransferases and glycosidases responsible for their formation including a previously unknown di-galactose-to-sialic acid switch supporting a functional role of these glycoepitopes in myogenesis. Furthermore, dynamic quantitative glycoproteomic analysis with multiplexed stable isotope labelling and analysis of enriched glycopeptides with multiple fragmentation approaches identified glycoproteins modified by these regulated glycans including several integrins and growth factor receptors. Myogenesis was also associated with the regulation of several lectins most notably the up-regulation of galectin-1 (LGALS1). CRISPR/Cas9-mediated deletion of Lgals1 inhibited differentiation and myotube formation suggesting an early functional role of galectin-1 in the myogenic program. Importantly, similar changes in N-glycosylation and the up-regulation of galectin-1 during postnatal skeletal muscle development were observed in mice. Treatment of new-born mice with recombinant adeno-associated viruses to overexpress galectin-1 in the musculature resulted in enhanced muscle mass. Our data form a valuable resource to further understand the glycobiology of myogenesis and will aid the development of intervention strategies to promote healthy muscle development or regeneration.
Oxidative stability and quality of raw Saanen and Alpine goats milk

The milk composition and concentration of thiobarbituric acid reactive substances (TBARS) and superoxide dismutase (SOD) activity in fresh and refrigerated raw goat milk of Saanen and Alpine breed at the breeding period were investigated. Low average milk fat, SNF and lactose content were determined in both breeds with no significant differences between breeds regarding the milk yield and milk composition. The significantly higher somatic cell count (SCC) was detected in Saanen goats. The SOD activity and TBARS concentration were significantly higher 14 h after the collection and cold storage in both breeds of dairy goats with no difference between the breeds. In the Alpine goats the TBARS concentration was negatively correlated with urea concentration, and in the milk of the Saanen goats the TBARS was positively correlated with proteins and SCC. The higher SCC in the Saanen goats may have caused higher production of secondary oxidative products catalysed by the enzyme superoxide dismutase from polymorphonuclear granulocytes present in the udder, or by some other enzymes that participate in oxidation of the milk constituents. The energy shortage and protein surplus in the diet of the dairy goats may have induced the higher degree of lipid mobilisation and a consequent increase of polyunsaturated fatty acids (PUFA) that are easily prone to oxidation and formation of the secondary oxidative products.
Generics and Alternatives

In this paper we argue that for the (probabilistic) interpretation of generic sentences of the form “Gs are f,” three types of alternatives play a role: (i) alternative features of f, (ii) alternative groups, or kinds, of G, and (iii) alternative causal background factors. In the first part of this paper we argue for the relevance of these alternatives. In the second part, we describe the results of some experiments that empirically tested in particular the second use of alternatives.
Influence of infestation with Echinochloa crus-galli species on crop production in corn.

The problem of the influence of different species of weeds on the production of agricultural plants has been studied by many researchers. The damage caused by weeds in maize crop is mostly of 30-70%, and when the infestation is strong the culture can be fully compromised. Our research highlight takes place in Transylvania, and focuses on the influence of Echinochloa crus-galli species (L.) Pal. Beauv. and other weeds on corn production, according to the degree of infestation. The research was conducted at the University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania. The research was done on two agrofunds: unfertilized and mineral fertilized with NPK 100 kg s.a. /ha. The unfertilized maize crop has been made in four variants with different degrees of infestation of Echinochloa crus-galli, from about 40 to 100 plants/m 2 . Four herbicides (isoxaflutol 750 g/l; acetoclor 860 g/l; dimetenamid 900 g/l; bentazon 320 g/l + dicamba 90 g/l) were used for weed control in fertilized plots . Weed biomass and corn plant and grain production were measured in the ripening stage. Corn invaded by weeds grew weakly and had a yellowish green color; in unfertilized corn plots a stratified weed population developed: Echinochloa crus-galli dominated in the upper layer, Setaria glauca (L.) Beauv. developed in the middle and a number of dicotyledonous species in the lower layer. In fertilized variant, the competition between weeds and maize on one hand and between monocotyledonous and dicotyledonous species on the other hand was more balanced, the biomass of dicotyledonous species ranged from 1700 kg/ha in unfertilized plots to 4100 kg/ha in mineral fertilized plots. The amount of weeds, obviously influenced production levels of maize grain and green mass. Production losses in terms of green mass per hectare can be considered equal to the weight of green weeds. At a density of 104 plants/m 2 of Echinochloa crus-galli with green mass of 18,052 kg/ha corn crop was fully compromised.
The relationship between vegetation density and its protective value depends on the densities and traits of prey and predators

Densities of submerged vegetation and those of associated animals tend to co-vary. This relationship is often attributed to the positive correlation between the density of vegetation and its protective value against predators. However, two counteracting basic elements underlying this paradigm limit its generality. That is, increasing vegetation density should result in decreased predator–prey encounters, whilst at the same time predator–prey encounters should increase as animal densities increase. These two mechanisms should thus counteract each other when the densities of vegetation and associated animals, including both prey and predators, co-vary. Experimental designs that expose fixed densities of prey and preda tors to varying densities of vegetation assess only the former mechanism and may thus not properly evaluate the protective value of vegetation in such conditions. By contrast, designs that mimic the naturally co-varying organism densities test both mechanisms and thus their counteractive impacts on predator–prey encounters. We compared the outcomes of the two alternative designs and carried out additional experiments to explain the putative discrepancy. Increasing vegetation density (mimics of Potamogeton pectinatus) enhanced prey (Daphnia magna) survival only when fixed densities of prey and predators (Perca fluviatilis or Rutilus rutilus) were used. When the animal densities were allowed to co-vary with vegetation density, vegetation had no impact on prey survival. Instead, prey survival was determined by the aggregate density of prey and predators, shaped by the species-specific traits of the latter. Thus, the impact of the increased animal densities overrode the impact of the increased vegetation density on predator–prey encounters. It may be insufficient to attribute the co-variation of vegetation, prey and predator densities simply to the association between vegetation density and its protective value. Increased food resources and reduced competition within vegetation may promote prey and thereby also predator abundance to a greater extent than previously thought.