Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis of Gating by the Outer Membrane Transporter FecA

Siderophore-mediated acquisition systems facilitate iron uptake. We present the crystallographic structure of the integral outer membrane receptor FecA from Escherichia coli with and without ferric citrate at 2.5 and 2.0 angstrom resolution. FecA is composed of three distinct domains: the barrel, plug, and NH2-terminal extension. Binding of ferric citrate triggers a conformational change of the extracellular loops that close the external pocket of FecA. Ligand-induced allosteric transitions are propagated through the outer membrane by the plug domain, signaling the occupancy of the receptor in the periplasm. These data establish the structural basis of gating for receptors dependent on the cytoplasmic membrane protein TonB. By compiling available data for this family of receptors, we propose a mechanism for the energy-dependent transport of siderophores.
Demographic Costs of Antipredator Defenses in Daphnia Pulex

Juvenile Daphnia pulex develop neck spines in response to a chemical agent released by predatory Chaoborus larvae. While these defensive structures reduce the vul- nerability of Daphnia to the insect predator, they also entail a demographic cost. We investigated the nature and degree of this cost through an analysis of cohort life tables involving both the typical morph (TM), which lacks neck spines, and spined morph (SM) at 22°C in two different food regimes: "natural" food conditions (53-,m filtered pond water) and "ideal" food conditions (1 x 105 cells/mL Chlamydomonas sp.). No consistent pattern of differences between TM and SM occurred with respect to survivorship, clutch sizes, body sizes, mean egg volume, or number of juvenile instars. Development rates of both juvenile and adult instars, however, were significantly slower in SM. The presence of neck spines increased the age at maturity for D. pulex by 8.4- 14.6%, and the duration of adult instars exposed to Chaoborus-factor, whose eggs will develop into SM, was 2.8% longer than for those not exposed. This caused delayed repro- duction in SM and resulted in a population growth rate (r) that was / 8-9% lower than in TM. This relatively large demographic cost of spine formation in D. pulex produces a strong selection pressure to forgo the formation of these spines when Chaoborus predators are absent.
Genetic evolution of infectious bursal disease virus in Senegal

In recent years very virulent (VV) IBDV strains and classical (CV) IBDV strains re-emerged and caused devastating outbreaks in different parts of the world. In this study, genetic evolution of fifteen IBDVs collected in Senegal in 1979, 1999, 2007, 2012, 2013 and 2014 was characterized to gain information for a better control of IBD. Following RT-PCR, nucleotide sequence of the VP2 hypervariable region was determined and compared with sequences available in GenBank. Phylogenetic analysis showed that the viruses diverged into two genotypes: Very virulent (VV) IBDV and classical virulent (CV) IBDV. The Senegalese field strains of the first genotype (VV) IBDV had 98.9 to 100% identity among themselves, whereas their identity with reported Nigerian (VV) IBDVs ranged between 96.7 and 99%. The close phylogenetic relationship of the Senegalese and Nigerian strains suggests that they likely derived from a common ancestor. In the phylogenetic tree, all the Senegalese (VV) IBDV strains belonged to the African very virulent types (VV2). The genotyping of senegalese field IBDV strains indicated that the majority of viruses circulating in Senegal are (VV) IBDVs and highlights a genetic stability. Key words: Infectious bursal disease, phylogenetic analysis, Senegal.
Minimalist art from cellular automata

My interest in algorithmic, generative and evolutionary art stems from my exposure to artists featured in the SIGGRAPH art exhibitions of the early 1980s such as Roman Verostko, Hans Dehlinger, Yoichiro Kawaguchi, Mark Wilson, Jean-Pierre Hébert, Karl Sims, andWilliam Latham to name just a few. My own computer generated artworks arise from visualizations of mathematical, physical or biological processes. My objective is to draw the viewer’s attention to the complexity and intricacy underlying such processes. Previously, in this journal, I have written about minimalist art derived from maximal planar graphs (Greenfield, 2008). Elsewhere, I have written about various generative art projects using cellular automata (Greenfield, 2016, 2018, 2019). Here, I will provide details about an artwork from a recent project onminimalist art derived from the so-called ‘rotor router’ model used for simulating deterministic random walks in the plane (Doerr & Friedrich, 2009; Holroyd & Propp, 2010). I first became aware of this model thanks to an archiv preprint of Neumann, Neumann, and Friedrich (2019). Consider a 200 × 300 toroidal grid such that each cell has four rotors that advance independently. Assume the rotors have 8, 5, 4 and 4 segments numbered 1–8, 1–5, 1–4 and 1–4, respectively. For each cell, randomly initialize its rotor settings and colour the cell grey. Next, select four cells to receive ‘painting objects’. The painting objects have finite tapes over the alphabet (R)ight, (D)own, (L)eft, (U)p. There are purple, blue, green and orange objects with tapes of length 8, 5, 4 and 4 respectively. At each time step, those cells with objects assume the colour of the object, use the value of the appropriate rotor as an index for decidingwhere to send the object, and then advance the appropriate rotor. For example, using the randomly chosen cell positions (52,68), (32,222), (65, 71) and (32,246) plus the randomly generated tapes DLULL, DUURLDDR, RUDL and DULU for the purple, blue, green and orange objects, respectively, after 15,000 time steps the random walk painting on the left of Figure 1 is obtained. At first glance, it may not be clear that I have specified a two-dimensional cellular automaton. Space prohibits providing the formal details, but if one thinks about what is happening from the point of view of the cells this claim should seem plausible. The random painting on the left in Figure 1 was selected from an initial randomly generated population
Haplotype variation in the spiny-cheek crayfish Orconectes limosus: colonization of Europe and genetic diversity of native stocks

Abstract The North American spiny-cheek crayfish, Orconectes limosus (Rafinesque, 1817), a widespread invader in Europe, seems to have been introduced there successfully only once. According to available literature, 90 individuals of unclear origin were released in Poland in 1890. Despite this apparent bottleneck, the species has successfully colonized various aquatic habitats and has displaced native crayfish species in many places. To test whether different European populations were likely to have come from a single source and to identify their possible origin, we analyzed the diversity of the mitochondrial gene for cytochrome c oxidase subunit I (COI) of O. limosus individuals from Europe and from its original range in North America, including the presumed source region of European populations, the Delaware River watershed (eastern USA). Two haplotypes were found in European populations. One haplotype was widespread; the other was present in a single population. In contrast, 18 haplotypes were detected in North America. This result supports the hypothesis of a single overseas introduction of O. limosus and suggests that the high invasion success of this species was not limited by an introduction bottleneck. Two divergent clades were detected in North American O. limosus populations. One, which includes the dominant haplotype in Europe, was found in a large part of the species' present range. The 2nd (diverging by >1%) was mostly restricted to a limited area in southeastern Pennsylvania. Orconectes limosus populations in the northern part of the species' North American range, at least some of which are nonindigenous themselves, may share the source area with European O. limosus. The endangered status of O. limosus populations in southeastern Pennsylvania and northeastern Maryland, where much of the species' genetic diversity resides, should be considered in conservation management.
Large, Deployable S-Band Antenna for a 6U Cubesat

Small satellites in general and cubesats in particular have been limited in their ability to perform RF science and communications missions by the size of the RF aperture. A large deployable membrane antenna approach has been developed to address the limits in aperture size and provide both high gain communications and sensing from UHF to C-band. The paper describes the general approach and presents performance results from ground test articles of an S-Band implementation of the architecture. The test article deploys a 1.53 m 2 active area out of a 2U (2,000 cm 3 ) volume from a 6U cubesat. The antenna array is formed from two tensioned membranes. The membranes are folded compactly for launch along with four deployable boom structures. Once on orbit, the booms deploy, unfolding and tensioning the membranes and then hold them in place for operation. Ground test articles have shown a gain of 30.5 dB at 3.6 GHz. The antenna has a 3 dB beamwidth of 3.4°, has an overall aperture efficiency of 56% and sidelobes 10 dB lower than the main lobe. The system architecture can be applied to payload volumes as small as 1⁄2U and to frequencies from UHF to K-band.
Assessment of the losses caused to potatoes by the potato cyst nematodes, Globodera rostochiensis and G. pallida.

SUMMARY Nine field trials were carried out from 1967 to 1973 on sandy loam soils in Staffordshire and Worcestershire to study the relationship between potato yield and numbers of potato cyst nematodes (Globodera spp.). Three (probably five) of these trial sites appeared to be infested with G. rostochiensis only, whereas both species occurred on the remaining four sites which grew the resistant variety, Maris Piper. Although mixtures of the two species occurred on some plots they tended to have different distributions within each trial site. The results from this work have been analysed, together with those from earlier work in the Eastern Counties on peat and silt soils, over two population density ranges, 0–40 eggs/g (5 sites) and 0–160 eggs/g (16 sites). There is no evidence of any difference in the regression of yield on eggs/g amongst the five sites in the lower range (b =–0.90 + 0.11) nor amongst 15 of the 16 sites in the higher range (b = -0–40 ± 0–02). Analysis of 10 sites with sufficient data in the 40–160 eggs/g range gave b = -0.24 ± 0.06. Thus the regression lines are essentially parallel for each of the two ranges, covering several potato varieties, soil textures and different potential yields and suggest that the varieties used are equally tolerant. The losses are 6.25 t/ha/20 eggs/g for the 0.40 eggs/g range, 1.67 t/ha/20 eggs/g for the 40–160 eggs/g range, and 2.75 t/ha/20 eggs/g as a mean for the whole range. A maximum loss of 22 t/ha is indicated. Peat soils are less dense than mineral soils but there was no need for adjustment in nematode counts. Losses caused by potato cyst nematodes are better expressed as actual yield losses rather than as percentage decreases.
The APOE∗3-Leiden Heterozygous Glucokinase Knockout Mouse as Novel Translational Disease Model for Type 2 Diabetes, Dyslipidemia, and Diabetic Atherosclerosis

Background There is a lack of predictive preclinical animal models combining atherosclerosis and type 2 diabetes. APOE∗3-Leiden (E3L) mice are a well-established model for diet-induced hyperlipidemia and atherosclerosis, and glucokinase+/− (GK+/−) mice are a translatable disease model for glucose control in type 2 diabetes. The respective mice respond similarly to lipid-lowering and antidiabetic drugs as humans. The objective of this study was to evaluate/characterize the APOE∗3-Leiden.glucokinase+/− (E3L.GK+/−) mouse as a novel disease model to study the metabolic syndrome and diabetic complications. Methods Female E3L.GK+/−, E3L, and GK+/− mice were fed fat- and cholesterol-containing diets for 37 weeks, and plasma parameters were measured throughout. Development of diabetic macro- and microvascular complications was evaluated. Results Cholesterol and triglyceride levels were significantly elevated in E3L and E3L.GK+/− mice compared to GK+/− mice, whereas fasting glucose was significantly increased in E3L.GK+/− and GK+/− mice compared to E3L. Atherosclerotic lesion size was increased 2.2-fold in E3L.GK+/− mice as compared to E3L (p = 0.037), which was predicted by glucose exposure (R 2 = 0.636, p = 0.001). E3L and E3L.GK+/− mice developed NASH with severe inflammation and fibrosis which, however, was not altered by introduction of the defective GK phenotype, whereas mild kidney pathology with tubular vacuolization was present in all three phenotypes. Conclusions We conclude that the E3L.GK+/− mouse is a promising novel diet-inducible disease model for investigation of the etiology and evaluation of drug treatment on diabetic atherosclerosis.
Improving the estimation of soil-available nutrients at the sub-field scale using time-series UAV observations

ABSTRACT Soil-available nutrients (SANs)are essential for crop growth and yield formation. Appropriate variable rate fertilization (VRF) can control SAN at a normal level to avoid unnecessary damage to sustainable production capacity. The precondition of optimizing the application of VRF is obtaining the real-time status of SAN. A new method for SAN estimation has been proposed by integrating modified World Food Studies (WOFOST) and time-series satellite remote sensing (RS) data. This method can provide field scale SAN estimations with high accuracy. However, the estimation accuracy at a subfield scale was low for VRF application because of the poor spatial resolution of common satellite imagery. In this letter, the subfield SAN estimations were optimized to ensure the VRF value. Time-series multispectral images acquired by an unmanned aerial vehicle (UAV) were used to replace common satellite data, and the SAN values for haplic phaeozem in selected spring maize plot in Hongxing Farm (48°09ʹ N, 127°03ʹ E) were estimated. Based on the field SAN data, the estimation accuracies using satellite data and UAV data were analyzed. The results show that the UAV data improved SAN estimations at the subfield scale).
Network optimization with big data and uncertain data

Network optimization is a branch of mathematical programming studying how to plan, optimize, and manage the network to improve its performance, which has been widely investigated and practiced in the fields of transportation, logistics, supply chain, and so on. In recent years, one of the hot research directions on network optimization is to consider the interactions with big data. On one hand, big data is able to achieve the network transparency and visualization, which is helpful on reducing information asymmetry and bullwhip effect. On the other hand, big data can not exclude all uncertainties related to indeterminate quantity or imprecise parameters, such as customer demand, transportation time, etc. In practice, most network optimization approaches are challenged by both transparency and indeterminacy. Therefore, network optimization with big data and uncertain data has received more and more attentions from both academia and industry. A query of Web of Science clearly demonstrates a rapid growth in this research area. The special issue has collected five high-quality papers which develop network optimization models or algorithms in uncertain environments or based on the background of big data. First, as newly strategic analysis of the emerging online marketplace considering risk attitude and channel power, Chen, Hao, and Yan (2020) studied whether the e-tailer and the manufacturer can reach a consensus on introducing the marketplace channel. Second, in order to investigate the multi-level warehouse layout problem with indeterminate information, He et al. (2020) proposed two novel uncertain network optimization models and an effective solution approach, where the indeterminate factors such as the monthly demands and horizontal transportation distances were described by uncertain data. Third, Li et al. (2020) formulated a bi-objective integrated routing optimization approach for rapid and detailed post-disaster needs assessment, and proposed a tabu search algorithm for handling the large-scale optimization problem. The effects of site familiarity and route familiarity were considered in order to achieve a better balance between the contradictory objectives. Fourth, uncertain time series analysis is a new tool to predict future values based on imprecise observations, which are usually described by uncertain data. Lu et al. (2020) proposed two methods for predicting the future value of uncertain time series based on the autoregressive moving average models. Compared with the existing prediction methods, the effectiveness of their work were demonstrated by computational results. Finally, Zhang, Liu, and Liu (2020) proposed least absolute deviations estimations for unknown parameters in uncertain multivariate regression models with imprecise observations. In summary, each article hasmade certain contribution onmodels and algorithms to the development of network optimization with big data and uncertain data.
Meiobenthos in earthen ponds used for semi-intensive shrimp farming (New Caledonia, South Pacific)

We analysed the temporal variability of meiobenthic (meiofauna and protists) abundance and community structure in the sediments of two shrimp farms located in New Caledonia. In each farm, sediment samples were collected weekly from February to June 2006 at two ponds, and analysed for quantity and composition of sedimentary organic matter, meiofaunal abundance, taxa richness and community composition. Independently of the initial conditions, sedimentary contents of biopolymeric C and total phytopigment varied significantly during shrimp rearing, although not consistently in the two ponds. Changes in the quantity and biochemical composition of sedimentary organic matter were associated with changes in total meiofaunal abundance and taxa richness, as well as in total and rare (<1% of total abundance) meiobenthic community composition. We show that the slight eutrophication of the sediment during the shrimp rearing cycle determined significant effects on the meiofaunal community composition as well as on the relative importance of metazoan vs. protists abundance. The results of this study suggest that the study of meiobenthic communities represents a reliable descriptor of the environmental quality of shrimp farming ponds.
Complementary Viewpoints: Scientific and Local Knowledge of Ungulates in the Brazilian Atlantic Forest

Abstract This article compares the local ecological knowledge (LEK) of quilombolas in the Atlantic Forest (Brazil) to scientific knowledge about the diet of four ungulate taxa (Tapirus terrestris L., Mazama spp., Pecari tajacu L., Tayassu pecari Link). LEK was gathered through interviews conducted with the freelisting method and through closed questionnaires. Ecological studies were compiled via a systematic review of the specialized academic literature. The research detected points of convergence and divergence between these knowledge systems. Local knowledge of the food classes in the ungulate diet indicated a wider range of items than that observed in 65 scientific studies of the foraging habits of these species. Certain characteristics of the LEK, such as its principal focus on environments that are not commonly investigated by ecological studies, form the basis of these divergences and reveal the complementary potential of LEK relative to scientific data in this field.
Comparing the potential of stereo aerial photographs, stereo very high-resolution satellite images, and TanDEM-X for estimating forest height

ABSTRACT Airborne laser scanning (ALS) is generally known as the most accurate and primary source providing the 3D structure of forest canopy model (CHM) information; however, in many countries, it is not updated as needed for continuous forest management planning due to its high costs. Image-based point clouds derived from airborne stereo aerial photographs, space-borne stereo very high-resolution WorldView-2, and TerraSAR-X add-on for Digital Elevation Measurement (TanDEM-X) can also be used for the generation of the CHM. In this study, we compared the performance of three types of 3D data, i.e. stereo aerial photographs, stereo very high-resolution WorldView-2, and TanDEM-X for the retrieval of forest CHM. Digital surface models (DSMs) generated from image-based point clouds produced from stereo aerial photographs and stereo WorldView-2 using image-matching algorithms and from TanDEM-X data using interferometry. Finally, three types of CHMs generated by subtracting ALS-based digital terrain model (DTM) from the above three DSMs. Plot-level heights and density metrics extracted from the CHMs and regressed with the field-based Lorey’s mean, and maximum height. Stereo aerial photographic CHM showed the most accurate results with root-mean-square error (RMSE) = 1.71 m, followed by high-resolution stereo WorldView-2 with RMSE = 2.04 m, and TanDEM-X with RMSE = 2.13 m, respectively. Also, for maximum height, we obtained higher accuracy for image-based point clouds with RMSE = 2.33 m, followed by high-resolution stereo WorldView-2 with RMSE = 2.71 m, and TanDEM-X with RMSE = 2.81 m, respectively. Our overall finding indicated that stereo aerial photography is the most accurate option followed by stereo very high-resolution WorldView-2 and TanDEM-X data for estimating forest heights. The study shares valuable information for the generation and regular update of forest structure information in the presence of pre-existing ALS DTM.
Purification and Characterization of Acid Phosphatase from the Egg of the Lady Beetle, Harmonia axyridis (Coccinellidae: Coleoptera)

Acid phosphatase (AP) in the egg of the lady beetle, Harmonia axyridis, was purified and characterized. Ammonium sulfate precipitation, CM column and isoelectrofocusing (IEF) were applied to purify an estimated molecular weight of 66 kDa AP. The purity was checked by SDS PAGE, native PAGE and Western blot. AP was detected in the hemolymph of the female and the egg, but not in the male on the blotting. Km of AP for a substrate, p‐nitrophenyl phosphate (p‐NPP), was 1.64 x 10‐4 M. AP had the optimum enzymatic activity at pH 3.5. In inhibition tests performed with various chemicals, ammonium molybdate suppressed 99% of the enzyme activity of AP even at the concentration of 5 x 10‐4 mM. AP was stable up to 50°C.
Place, emotions and aesthetics: young Tamil Hindu religiosity in north-western Norway

ABSTRACT This article explores how young transnationally oriented Tamil Hindus experience and reflect upon local places of Hindu worship in rural Norway. They compare such places to the larger and more aesthetically elaborate temples they experience elsewhere. Perspectives from the work of Ole Riis and Linda Woodhead (2010) and Abby Day (2011, 2013) are employed in the analysis of the interrelations between individuals, places, emotions, religiosity, and beliefs. The findings suggest that different places evoke different emotions. Some places generate strong religious emotions, while others produce embodied emotions of peace, wellbeing, and belonging. These emotions can, in some settings, be considered as religious, while in other settings this is not necessarily the case. The material on which this article is based consists of field notes from observations, written responses to a questionnaire with open-ended questions (N=25), and transcripts from photo-elicitation interviews (N=7). The participants were between 16 and 25 years of age and had been raised in north-western Norway, where the density of Hindus and Hindu organisations is relatively low.