Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of bioactive forages towards organic/sustainable control of gastrointestinal parasites in sheep

The aim of the present study was to investigate the potential effects of short-term grazing on bioactive forages towards (i) worm numbers and fecundity of established intestinal adult Trichostrongylus colubriformis population and (ii) the establishment and development of incoming T. colubriformis larvae. Forty-eight parasite-naïve lambs were infected with 8,000 T. colubriformis L3 on day 1 of the experiment. On day 28, lambs entered one of the experimental plots, which had been sown either with Lotus pedunculatus (lotus), or Hedysarum coronarium (sulla), or Cichorium intybus (chicory), or the control forage Lolium perenne/Trifolium repens (grass/clover). On day 35 of the experiment, all sheep were re-infected with 8,000 T. colubriformis L3 and were killed on day 42. Sheep grazing on lotus tended to have a lower FEC compared to sheep grazing on grass/clover (P = 0.06), however they also produced more faeces and thus daily faecal output was higher in these sheep grazing lotus compared to those grazing on the other forages (P < 0.05). Consequently, daily egg output was similar in all sheep suggesting that the reduction in faecal egg count was due to dilution effect of the faecal output. By day 42, all parasites of the primary infection would have been recovered as adults, whereas those of the secondary challenge would have only developed to the fourth stage larvae within a week (i.e. days 35-42). Grazing on the bioactive forages showed no evidence o f forage effect upon incoming T. colubriformis larvae within a week or against adult T. colubriformis worms during a two-week period. Comparisons between adult (primary) and immature (secondary challenge infection) worm burdens showed no reduction in parasite establishment of the second challenge dose suggesting that no effective immunity against T. colubriformis had been acquired in sheep.
Habitat use of the Wood Warbler Phylloscopus sibilatrix during spring migration versus breeding season based on citizen science data

ABSTRACT Capsule: Citizen science data on Wood Warblers Phylloscopus sibilatrix showed that the species non-selectively used a wide variety of habitats during migration but had a tendency for settling to breed in forest and natural areas. Aims: We tested the hypothesis that habitat used during spring stopovers in Spain differed from habitat use during the breeding period in Switzerland in a year of exceptional abundance as a result of persistent easterly winds in the Mediterranean. Methods: Habitat use during spring migration 2015 was compared by using bootstrapping resampling techniques on citizen science data from Spain and Switzerland, comparing the land-cover categories between locations of observations with random pseudo-absences. Results: Wood Warblers showed no preference for habitat features during migration and covered practically all available habitat types from urbanized areas to wetlands and forests, whereas in the breeding range birds showed an increasing tendency to be present in forest habitats. Conclusions: Habitat use during spring migration covered most available habitat types from urbanized areas to wetlands and forests. Breeding habitat use was restricted to forested areas. Citizen science allowed a quick collection of biological data over a wide area to potentially identify large-scale biological patterns. This is essential to potentially manage international conservation efforts for declining species.
Synchronization, Stochasticity, and Phase Waves in Neuronal Networks With Spatially-Structured Connectivity

Oscillations in the beta/low gamma range (10–45 Hz) are recorded in diverse neural structures. They have successfully been modeled as sparsely synchronized oscillations arising from reciprocal interactions between randomly connected excitatory (E) pyramidal cells and local interneurons (I). The synchronization of spatially distant oscillatory spiking E–I modules has been well-studied in the rate model framework but less so for modules of spiking neurons. Here, we first show that previously proposed modifications of rate models provide a quantitative description of spiking E–I modules of Exponential Integrate-and-Fire (EIF) neurons. This allows us to analyze the dynamical regimes of sparsely synchronized oscillatory E–I modules connected by long-range excitatory interactions, for two modules, as well as for a chain of such modules. For modules with a large number of neurons (> 105), we obtain results similar to previously obtained ones based on the classic deterministic Wilson-Cowan rate model, with the added bonus that the results quantitatively describe simulations of spiking EIF neurons. However, for modules with a moderate (~ 104) number of neurons, stochastic variations in the spike emission of neurons are important and need to be taken into account. On the one hand, they modify the oscillations in a way that tends to promote synchronization between different modules. On the other hand, independent fluctuations on different modules tend to disrupt synchronization. The correlations between distant oscillatory modules can be described by stochastic equations for the oscillator phases that have been intensely studied in other contexts. On shorter distances, we develop a description that also takes into account amplitude modes and that quantitatively accounts for our simulation data. Stochastic dephasing of neighboring modules produces transient phase gradients and the transient appearance of phase waves. We propose that these stochastically-induced phase waves provide an explanative framework for the observations of traveling waves in the cortex during beta oscillations.
The Grasp Strategy of a Robot Passer Influences Performance and Quality of the Robot-Human Object Handover

Task-aware robotic grasping is critical if robots are to successfully cooperate with humans. The choice of a grasp is multi-faceted; however, the task to perform primes this choice in terms of hand shaping and placement on the object. This grasping strategy is particularly important for a robot companion, as it can potentially hinder the success of the collaboration with humans. In this work, we investigate how different grasping strategies of a robot passer influence the performance and the perceptions of the interaction of a human receiver. Our findings suggest that a grasping strategy that accounts for the subsequent task of the receiver improves substantially the performance of the human receiver in executing the subsequent task. The time to complete the task is reduced by eliminating the need of a post-handover re-adjustment of the object. Furthermore, the human perceptions of the interaction improve when a task-oriented grasping strategy is adopted. The influence of the robotic grasp strategy increases as the constraints induced by the object's affordances become more restrictive. The results of this work can benefit the wider robotics community, with application ranging from industrial to household human-robot interaction for cooperative and collaborative object manipulation.
F-Type ATP Synthase Assembly Factors Atp11 and Atp12 in Arabidopsis

Atp11p and Atp12p are members of two chaperone families essential for assembly of the mitochondrial ATP synthase in Saccharomyces cerevisiae and Homo sapiens. However, the role of their homologs in higher plants is unclear with regard to the assembly of both chloroplast ATP synthase (cpATPase) and mitochondrial ATP synthase (mtATPase). Here, we show that loss of either Atp11 or Atp12 is lethal in Arabidopsis. While Atp12 is only localized in mitochondria, Atp11 is present both in chloroplasts and mitochondria. Yeast two-hybrid analyses showed that, as their homologs in yeast, Atp11 specifically interacts with the β subunit of the mtATPase and cpATPase, and Atp12 interacts with the α subunit of the mtATPase, implying that Atp11 and Atp12 fulfill a conserved task during assembly of ATP synthase. However, the binding sites for Atp11 in the β subunit of mtATPase and cpATPase are slightly different, suggesting that the mechanisms of action may have evolved in different ways. Although Atp11 interacts with cpATPase β subunit as the two assembly factors BFA3 and BFA1, they bind to different sites of the β subunit. These results indicate that Atp11 is involved in the assembly of both cpATPase and mtATPase but Atp12 is specifically required for the assembly of mtATPase in higher plants.
A Time-Resolved Spectroscopic Investigation of a Novel BODIPY Copolymer and Its Potential Use as a Photosensitiser for Hydrogen Evolution

A novel 4,4-difuoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) copolymer with diethynylbenzene has been synthesised, and its ability to act as a photosensitiser for the photocatalytic generation of hydrogen was investigated by time-resolved spectroscopic techniques spanning the ps- to ns-timescales. Both transient absorption and time-resolved infrared spectroscopy were used to probe the excited state dynamics of this photosensitising unit in a variety of solvents. These studies indicated how environmental factors can influence the photophysics of the BODIPY polymer. A homogeneous photocatalytic hydrogen evolution system has been developed using the BODIPY copolymer and cobaloxime which provides hydrogen evolution rates of 319 μmol h−1 g−1 after 24 h of visible irradiation.
Marine mammal subspecies in the age of genetics: Introductory remarks from the Associate Editor and Editor‐in‐Chief of Marine Mammal Science

Almost every conservation genetics and evolutionary biology textbook has a section questioning: “What is a species or subspecies? ” It has been one of the most discussed, nearly unanswerable questions in all of biology. At issue is how to logically divide a variable that is generally continuous, with some occasional discrete breaks. Answering this question is at times akin to addressing the questions: “How many colors are in a rainbow? ” or “Where does red end and orange begin? ” School children can tell the two colors apart at the middle part of their defined range, but defining the color of light at 589 nm (the arbitrary boundary between the colors) may be as much about the observer, their perceptual rules, and their experiences as it is about the physical experience of seeing a specific wavelength. How one defines a species is influenced by the concept of species, the tools used to evaluate that concept, and by scientific experience. Defining a species has historically conflated the philosophical and theoretical concepts of what a species is with the pragmatic and methodological problems of species delimitation (Mayden 1997, de Queiroz 2005). De Queiroz (2007) has argued that most species concepts share the common element that species are segments of separately evolving metapopulation lineages. Differences arise in the lines of evidence used to evaluate the evolutionary history and trajectory of each lineage. As segments of a metapopulation lineage journey on their own trajectory from other segments they accumulate changes. These changes can be in the genome or in morphological, behavioral, physiological, reproductive, or other biological traits of the species. Yet, these changes do not occur in the same sequential order, or at the
Prognostic value of miRNA-181a in human colorectal cancer evaluated by in situ hybridization

Background: Colorectal cancer (CRC) is one of the most common cancers in the world and the 5th leading cause of cancer death in China. CRC affects the gastrointestinal tract and has a high mortality rate. Recent studies have demonstrated the abnormal expression of miRNA-181a in a wide variety of tumors. However, the clinical significance of miRNA-181a in CRC is still unclear. Methods: The detection of miRNA-181a was performed by probe hybridization using 3' and 5' end LNA-modified DNA probes. And we evaluated the survival probabilities by the Kaplan-Meier method and the log-rank test. Furthermore, the univariate and multivariate Cox proportional hazard regression model were used for assessing the association of the miRNA-181a expression and prognosis. Results: MiRNA-181a was highly expressed in CRC (P Conclusions: These results indicated that expression levels of miRNA-181a could be an important indicator for prognosis and survival for CRC patients.
Evaluation of carbohydrate and phenol content of citrus fruits species

Carbohydrate content (Nutritional) and Phenol content (Anti-nutritional) of six varieties of citrus fruit species: Sweet orange (Citrus sinensis), Lemon (Citrus limonum), Mosambi (Citrus limetta), Pomelo (C. maxima), wild orange (Citrus aurantium) and mini orange (C. microcarpa) were analysed in this study. The results of the analysis revealed the presence of carbohydrate and phenol contents. Carbohydrate contents were found to be higher in Citrus maxima with the range of 3.690±0.705. In Citrus sinensis and Citrus limonum, carbohydrate content is low (2.983±0.0026 and 3.073±0.001) when compared with other citrus fruits. The total phenol content was higher in Citrus sinensis with the range of 1.3036±0.0031. Carbohydrate and Phenols have been responsible for the biological, antioxidant activities.
Patterns of Variation in the Cranial Osteology of Three Species of Endemic Australian Lizards (Ctenophorus: Squamata: Agamidae): Implications for the Fossil Record and Morphological Analyses made with Limited Sample Sizes

Abstract Australian Agamidae often are recovered from Australian Cenozoic fossil deposits but remain largely unidentified and unpublished. Accurate fossil identification could expand our understanding of the origin, distribution, evolution, and extinction of Australian agamid species over geologic time. We began to address this issue by critically examining skeletal morphologic features that were previously proposed for Australian Agamidae. We compared 60 morphological features (44 from the literature and 16 new features) for three taxa of the most speciose of the Australian agamid genera, Ctenophorus caudicinctus (n = 18), Ctenophorus isolepis (n = 20), and Ctenophorus reticulatus (n = 20). Of the 180 morphological features (60 per species) that were expected to be invariant for all specimens within a species, only 39 did not vary. All taxa have at least one unique feature that did not vary with ontogeny (i.e., apomorphy). Invariant features also are shared between two species or all three. Seventeen morphological features were invariant for all three taxa. In addition to invariant features, one to three morphological features varied within each species with either ontogeny or sex. We also found that few morphological features could be identified from disarticulated material. Given that the current museum collections are wholly inadequate for addressing these issues, larger collections of extant agamid skeletal material are needed to understand skeletal morphological variation. A fossil record of Australian Agamidae already exists; we just need to develop the tools to interpret it accurately.
Genetic Diversity and Association Analyses of Canadian Maize Inbred Lines with Agronomic Traits and Simple Sequence Repeat Markers

We evaluated genetic diversity and population structure in 32 Canadian maize inbred lines and performed association analysis for five agronomical traits and 50 simple sequence repeat (SSR) markers. Genetic diversity analysis revealed a total of 381 alleles at the 50 SSR loci. The average number of alleles per locus was 7.6. The average genetic diversity and polymorphic information content values were 0.709 and 0.676, respectively. The average major allele frequency was 0.414. Population structure analysis indicated that these maize inbred lines were comprised of four major groups and one admixed group based on a membership probability threshold of 0.80. A general linear model showed 20 marker-trait associations involving 12 SSR markers associated with the four agronomic traits except for leaf length. For these marker-trait associations, phi056, mmc0022, bnlg1621, bnlg1695, phi116, and bnlg1028 were associated with only one trait. The other nc005, bnlg1012, phi065, and umc1982 were associated with two traits. Two SSR markers, mmc0111 and umc1038, were associated with three traits. These results will help in optimizing the choice of parents for crossing combinations, as well as in selecting markers for marker-assisted selection for maize improvement.
Channa pseudomarulius , a valid species of snakehead from the Western Ghats region of peninsular India (Teleostei: Channidae), with comments on Ophicephalus grandinosus , O. theophrasti and O. leucopunctatus

An investigation integrating morphological and molecular data to address the taxonomic status of Indian Channa marulius -like fishes reveals the presence of two species within Indian Rivers. As a consequence, Channa pseudomarulius is resurrected as a valid species and removed from the synonymy of C. marulius . Channa pseudomarulius appears to be restricted to the southern Western Ghats region of peninsular India and can be distinguished from the more widespread C. marulius by fewer lateral-line scales, fewer dorsal- and anal-fin rays, fewer vertebrae, and by a difference of about 8% in mitochondrial cytochrome c oxidase subunit 1 gene sequences. Channa marulius and C. pseudomarulius both possess low levels of genetic diversity across their range suggestive of small historical population sizes. This is especially interesting in the case of C. marulius , which is shown to have a large natural geographical range spanning at least the Indian subcontinent and parts of the Indo-Burman ranges in westernmost Myanmar. The synonymy of Channa marulius with Ophicephalus grandinosus , O. theophrasti , and O. leucopunctatus is confirmed based on examination of type specimens. A lectotype is designated for O. grandinosus.
Genetic structure of the bumble bee Bombus hypocrita sapporoensis, a potential domestic pollinator for crops in Japan

The European bumble bee, Bombus terrestris, is an excellent commercial pollinator. In Japan, B. terrestris is categorized as an invasive alien species, and the use of the bee is restricted. In this study, we identify the native bumble bee Bombus hypocrita sapporoensis as a candidate commercial pollinator in Hokkaido Island. To evaluate the risk of disturbing the natural genetic structure if this bee is used as a commercial pollinator, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene to elucidate the phylogenetic relationship of B. h. sapporoensis in Hokkaido Island and the Asian continent. In addition, we analyzed six microsatellites to further investigate the population genetic structure in Hokkaido Island. The mitochondrial analyses revealed that there is little differentiation within Hokkaido Island; however, there is considerable differentiation between Hokkaido and the Asian continent. Microsatellite analyses using STRUCTURE showed that B. h. sapporoensis in Hokkaido was divided into two genetic groups. Individuals belonging to each group were distributed throughout Hokkaido Island, and no clear geographical differentiation was observed. These results indicate that there would be little risk of genetic disturbance if bees from Hokkaido Island were used. However, it would be advisable to avoid importing continental bees as a pollinating insect in Hokkaido Island.
On operator semigroups arising in the study of incompressible viscous fluid flows

This article concentrates on various operator semigroups arising in the study of viscous and incompressible flows. Of particular concern are the classical Stokes semigroup, the hydrostatic Stokes semigroup, the Oldroyd as well as the Ericksen–Leslie semigroup. Besides their intrinsic interest, the properties of these semigroups play an important role in the investigation of the associated nonlinear equations. This article is part of the theme issue ‘Semigroup applications everywhere’.
DEVELOPMENT AND APPLICATION OF AN EXPANDED STREPTOMYCES GENETIC CODE

Actinobacteria, especially those of genus Streptomyces, are a prominent source of bioactive natural products. The ability to site-specifically incorporate unnatural amino acids (UAAs) into natural product biosynthetic enzymes and ribosomally derived peptides in these organisms would constitute a valuable tool for drug discovery and development. The work described in this dissertation focuses on development and application of an expanded Streptomyces genetic code, including development of UAA incorporation systems based on amber suppression and sense codon reassignment, structural diversification of the model thiopeptide natural product thiostrepton using UAAs, and mapping protein-protein interactions in type II polyketide biosynthetic enzymes using photocrosslinking UAAs. First, we developed an amber suppression-based system of site-specific incorporation of p-iodo-L-phenylalanine (pIPhe) and p-azido-L-phenylalanine (pAzPhe) into superfolder GFP (sfGFP) in the model natural product producer Streptomyces venezuelae ATCC 15439.
A Recurrent Neural Network Approach for Automated Neural Tracing in Multispectral 3D Images

Neuronal morphology reconstruction in fluorescence microscopy 3D images is essential for analyzing neuronal cell type and connectivity. Manual tracing of neurons in these images is time consuming and subjective. Automated tracing is highly desired yet is one of the foremost challenges in computational neuroscience. The multispectral labeling technique, Brainbow utilizes high dimensional spectral information to distinguish intermingled neuronal processes. It is particular interesting to develop new algorithms to include the spectral information into the tracing process. Recently, deep learning approaches achieved state-of-the-art in different computer vision and medical imaging applications. To benefit from the power of deep learning, in this paper, we propose an automated neural tracing approach in multispectral 3D Brainbow images based on recurrent neural net-work. We first adopt VBM4D approach to denoise multispectral 3D images. Then we generate cubes as training samples along the ground truth, manually traced paths. These cubes are the input to the recur-rent neural network. The proposed approach is simple and effective. The approach can be implemented with the deep learning toolbox ‘Keras’ in 100 lines. Finally, to evaluate our approach, we computed the average and standard deviation of DIADEM metric from the ground truth results to our tracing results, and from our tracing results to the ground truth results. Extensive experimental results on the collected dataset demonstrate that the proposed approach performs well in Brainbow labeled mouse brain images.