Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum proteins and lipids in mild form of calf bronchopneumonia: candidates for reliable biomarkers

Abstract Calf bronchopneumonia is complex multifactorial disease and for its accurate diagnosis and therapy, besides clinical examination, microbiologic, hematologic and biochemical analyses could be necessary. In general, additional analyses are not implemented, mainly because the disease biomarkers are not defined. To establish which analysis might be useful for determining the severity of the disease, we analyzed 23 three-month old calves with mild clinical signs of bronchopneumonia and 15 age-matched healthy calves. Pasteurella multocida was isolated from deep nasal swabs of diseased calves. Peripheral blood erythrocyte and leukocyte count of bronchopneumonic and healthy calves showed no difference. Serum proteins, lipoproteins and lipids were analyzed with spectrophotometry, agarose gel electrophoresis, non-reducing SDS-PAGE, gel zymography, and thin-layer chromatography. The bronchopneumonic calves had an increased level of circulating immune complexes and α globulins, which contain some of the positive acute phase proteins. In diseased calves the increased concentration of total γ globulins (IgG), due to an increased concentration of anionic γ globulins (predominately IgG1), was detected. The increased concentration of anionic γ globulins followed by increased concentration of transferrin (negative acute phase protein) and HDL cholesterol, decreased concentration of LDL-cholesterol, unchanged activity of matrix metalloproteases and leukocyte counts might reflect the obvious absence of generalized inflammation. A positive correlation was found between the acquired results and the appearance of mild clinical signs. Therefore, we believe that the parameters analyzed in the peripheral blood could be applied as reliable disease markers to distinguish between severe (inflammatory) and mild forms of calf bronchopneumonia and to predict a better outcome for these calves.
Morphometric and Genetic Determination of Age Class and Sex for Fecal Pellets of Sika Deer (Cervus nippon)

Abstract. We aimed to validate a method to identify age class and sex of sika deer (Cervus nippon), which defecate fecal pellets. We collected 42 and 54 fecal samples in Nara and Yakushima, respectively. Both pellet width and length were significantly larger for adults than juveniles (1∼1.5 yrs). A discriminant model based on both width and length correctly assigned an age class for 92% of individuals in Nara and 98% in Yakushima. We genetically determined their sex based on the gel electrophoresis of two genes on sex chromosomes (SRY and ZFX/Y) amplified by PCR. For fresh feces, sex was not determined for 40% of the samples, but for the rest of the samples, sex was correctly assigned in almost all cases (28/29). However, sex was not determined in any of the samples that were analyzed at a half month or later after defecation. The proportion of young individuals could be estimated by the morphometry of fecal pellets, but the sex of the animals could not be confirmed.
Effect of maternal habitat, temperature and light on germination and salt tolerance of Suaeda vermiculata, a habitat-indifferent halophyte of arid Arabian deserts

Abstract Habitat-indifferent species that can grow well in both saline and non-saline soils offer a good opportunity for studying seed dormancy and salt tolerance during germination. Here, we assess interactive effects of maternal habitat and incubation conditions on salt tolerance during germination of the habitat-indifferent halophyte Suaeda vermiculata, a common perennial shrub of the arid Arabian deserts. Seeds collected from saline and non-saline habitats were germinated at six salinity levels (0–500 mM NaCl) and incubated at three temperatures and under two light regimes. Studied germination attributes were final germination, germination rate index (GRI) and germination recovery of non-germinated seeds when transferred to distilled water. The results showed insignificant difference in salt tolerance between seeds of the two habitat types at the lower salinities. At higher salinities (400 and 500 mM NaCl), germination of the saline habitat seeds was almost inhibited, but that of non-saline habitat seeds reached various levels depending on light and temperature. Both higher temperatures and darkness resulted in significant reductions of the final germination at the higher salinities. Seeds of the two habitats that did not germinate in the different treatments recovered their germination when transferred to distilled water, indicating that these seeds maintained their viability in saline solution and were able germinate upon the arrival of suitable conditions. Seeds of the two habitats germinated within 2 days at the lower salinities and GRI decreased with the increase in salinity level. Such reduction was obvious for seeds of the saline habitat. Recovery was faster for seeds of the saline habitats, especially for those incubated at higher salinities and in the dark. The difference in dormancy and germination attributes of seeds of the two habitat types reflects ecological adaptations for survival in salt marshes of arid deserts.
Characterization of Amaranthus spinosus collected from different regions: Phytochemical and biological properties

Amaranth is extensively cultivated as a green leafy vegetable and grain crop in many countries. The nutritional, chemical composition, antioxidant activity, and hemolytic potential of Amaranthus spinosus leaves collected from different locations in Tunisia were evaluated and compared. Leaves showed high levels of protein, carbohydrate, crude fiber, and ash. The leaves presented high contents in macro (K, Mg, Ca, and Na) and micronutrients (Fe, Zn, and Mn). Total phenolic and flavonoid contents ranged between 6.6 to 19.6 mg GAE/g DW and 4.07 to 10.48 mg CAE/g DW, respectively. The major compound in the essential oil was found to be α -thujone. The plant exhibited high antioxidant activity with EC50 values ranging from 25.55 to 54.58 μg/mL for DPPH radical scavenging capacity and 37.54–116.72 μg/mL for H2O2 scavenging activity, respectively. Moreover, A. spinosus leaves have the potential to protect red blood cells from hemolysis. Practical applications The results showed that A. spinosus could be a new source of nutrients and antioxidants and its use in human diet, nutraceutical development, and therapy is encouraged. Especially, it could be used to mitigate the risk of various diseases including cardiovascular, neurological, cancer, and Alzheimer's which are caused by reactive oxygen species (like H2O2).
NEUROBLASTOMA HOMING PEPTIDE SCREENING USING UNREFINED HOMOLOGY STRUCTURE OF NOREPINEPHRINE TRANSPORTER

The norepinephrine transporter (hNET) is a potential target for many antidepressants and for neuroblastoma therapeutics. The entrance channel of hNET and also dopamine transporter (DAT) serve as candidate site for targeting by large peptides e.g. α-helix-based. Targeting peptides, also known as homing peptides, are used to direct the delivery of cargo to specific cell types. Peptides of known secondary structures such as α-helix and β-sheet have predictable and stable folding. In this study, approx. 27 peptides, with predictable secondary structures, were evaluated by 20 dockings predictions on unrefined hNET homology model and DAT crystal structure using molecular mechanics (total ~1080 models). As anticipated, peptide size was detrimental for docking in channel space, whereas peptide isoelectrics point did not affect docking. Peptide’s initial non-bonded energy affected docking while overall peptide free energy and initial electrostatic energy did not. Two α-helices showed favorable docking in channel of hNET; namely, GASNGINAYL and SLWERLAYGI with binding energy of -106.2 kJ/mol and -128.6 kJ/mol, respectively. Prior to in vitro and in vivo applications, future work will focus on development of refined accurate model of hNET and application of solvated docking (in presence of water). This study provides new insight to the development of helix-based therapeutic peptides.
Vertical and horizontal distribution of the microcystin producer Planktothrix rubescens (Cyanobacteria) in a small perialpine reservoir

Among cyanobacteria, Planktothrix rubescens (De Candolle ex Gomont) Anagnostidis & Komarek is a species that is well adapted to develop in moderately nutrient rich and deep lakes. In this typology of waterbodies, the competitive abilities of this species rely in its capacity to stand and growth in the dimly illuminated metalimnetic layer during the warmer months. I this work, we have studied the seasonal development and distribution of this species in Lake Ledro, a meso-oligotrophic reservoir located in the Eastern Alps. During the last decade, this species has given rise to numerous and extended surface bloom episodes, causing the reddening of vaste areas of the lake. In summer, the light intensities in the zone of the greater development of this cyanobacterium (in the metalimnion, between the euphotic depth and the layer of maximum development of the species) were bewteen 2 and 20 µmol m -2 s -1 , i.e. values that were well within the light intensities required to sustain the optimal growth of filaments. The formation of the autumn and winter blooms was triggered by the cooling of surface waters and increase of the mixed layer, which, eroding the metalimnion, entrained the filaments of Planktothrix in the surface mixed layers. The formation of the surface blooms was associated with the presence of high amounts of microcistins, which in a few occasions reached concentrations between 10 and 22 µg L -1 , posing potential problems for the exploitation of water resources.
A novel role for macrophages in peripheral nerve regeneration

Peripheral nerves are one of the few adult tissues which can regenerate following injury, and macrophages have many important roles in this multicellular process. Following nerve injury, regrowing axons must traverse tissue termed the ‘nerve bridge’, which forms spontaneously between the nerve stumps (proximal and distal), to reconnect with their original tissue target. Previously, we found that hypoxic macrophages in the bridge induce the formation of a polarised vasculature which dedifferentiated Schwann cells subsequently use as a scaffold to migrate along, taking axons with them into the distal stump. Here, macrophages together with Schwann cells function to clear debris and remodel the environment to facilitate axonal regeneration, demonstrating distinct functions for macrophages within discrete areas of the regenerating nerve. This thesis aims to characterise nerve macrophage populations and to determine whether there is a specific Schwann cell chemoattractant within the bridge. Resident nerve macrophages displayed a distinct gene expression pattern compared to other resident macrophage populations. Moreover, we found two distinct nerve resident populations which can be distinguished by CX3CR1 expression and physiological location. In the injured nerve, the origin and phenotype of macrophage populations is currently unknown. We determined that the majority of macrophages in the bridge and distal stump are monocyte-derived. In further characterisation of bridge macrophages, we have identified an intrinsic ability to differentially sense hypoxia. Here we show data to support a novel role for hypoxic bridge macrophages in promoting Schwann cell migration. Using in vitro chemotaxis assays, we found that hypoxic macrophages are able to induce Schwann cell migration and an unbiased screen identified the chemoattractant factor as CCL3. CCL3 is able to induce Schwann cell migration in chemotactic assays, and knockdown studies showed that CCL3 is the primary chemoattractant secreted by hypoxic macrophages. We also present preliminary in vivo experiments investigating the role of CCL3 following injury, as well as in models of nerve repair. A Schwann cell chemoattractant factor has wide therapeutic implications in peripheral nerve injury, as well as potential uses in the treatment of aberrant nerve growth and tumour spread.
Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank

Systematics is the science of discovering, organizing and interpreting the diversity of all living organisms. Recent developments in genomics and biodiversity informatics are transforming systematics and have opened up many new opportunities. Major digitization efforts and developments in biodiversity informatics have helped the systematics community explore ways to enhance the efficiency in organizing, publishing, and utilizing systematic information. At the same time, genomics is rapidly facilitating construction of the tree of life, improving taxonomic classification, and disentangling complex evolutionary histories. In the informatics and genomics era, systematics has an incredible capacity to integrate with computational and exploratory platforms for discovery as well as with other, related disciplines while maintaining its core strengths in biological collections and morphology. We call for the establishment of a new global cyberinfrastructure or Biodiversity Cyberbank that will function as the main repository of many types of biodiversity data to ensure the long‐term sustainability of the vast and growing amount of systematic data. This Biodiversity Cyberbank will contain new and efficient analytical pipelines for systematics research, especially for efficiently generating taxonomic treatments (revisions, e‐monographs and floras). Integrative systematics requires the training of the next‐generation systematists with taxonomic, phylogenomic and informatics skills to address grand questions about biodiversity and its assembly and continue to develop the Biodiversity Cyberbank. Integrative systematics must also proactively educate the public and policy makers on the importance of systematics and collections for addressing the biodiversity crisis of the Anthropocene, and a Biodiversity Cyberbank may represent one powerful tool for outreach.
Drosophila melanogaster as a Model Organism to Study Human Neurodegenerative Diseases

A great deal of our current understanding about the biology of neurodegenerative diseases has come from studying the function of genes linked to inherited forms of these disorders. Work performed in animal models, vertebrates as well as invertebrates, has been instrumental in deciphering the cellular, physiological and behavioural deficits arising from the expression of disease-causing genes. Using the fruit fly, Drosophila melanogaster, as a model we examined the normal and aberrant function of two genes linked to the onset of neurodegeneration in humans, presenilin and superoxide dismutase-1. Drosophila is an extremely versatile model and in many ways is ideal for studying the genetic basis of human disease. The high degree of genetic conservation coupled with low genetic redundancy make this model particularly well suited for studying the function of disease causing genes. We demonstrate a novel genetic, physical and physiological interaction between presenilin and calmodulin and describe how this interaction impacts a very early cellular defect associated with Alzheimer’s Disease, intracellular
First record of Aphidius ericaphidis (Hymenoptera, Braconidae) in Europe: North American hitchhiker or overlooked Holarctic citizen?

Aphidius ericaphidis, an aphid parasitoid originally described from North America, is recorded in Europe for the first time, based on morphological and molecular analyses. The species is recorded in Serbia, the Netherlands, Sweden and the United Kingdom. It was formerly recorded as Aphidius sp. /Ericaphis latifrons/Vaccinium uliginosum from the Alps (France). The possible origin of A. ericaphidis, as well as its likely distribution, is discussed in relation to its host. As it is a specific parasitoid of Ericaphis aphids, especially the invasive aphid Ericaphis scammelli on blueberries, its potential as a biocontrol agent is also discussed.
Density-dependent responses of the brittlestar Amphiura filiformis to moderate hypoxia and consequences for nutrient fluxes

Within coastal marine habitats, intense nutrient cycling, and near seabed primary production rates are strongly influenced by the transport and transformation of materials within the sediment and across the sediment-water interface. Through processes such as bioturbation and bio-irrigation, benthic infauna play a significant role in mediating this transport and modify many chemical and physical reactions. However, coastal ecosystems are experiencing growing impacts from a number of environmental stresses, one of which is reduced dissolved oxygen (DO), known as hypoxia. Hypoxic events in coastal areas are predicted to increase as global warming and human-induced eutrophication intensify, with predicted consequences for infaunal community diversity and ecosystem function. Using a mesocosm experiment, we investigated the effects of short-term, sub-lethal hypoxia (14 d, 3.59 mg O2 L-1) and organism density (500, 900, 1300, 1700, and 2100 indiv. m-2) on the bioturbation activity of the brittlestar Amphiura filiformis. Nutrient fluxes were measured as an important contribution to ecosystem function. Hypoxia resulted in reduced brittlestar activity (in terms of sediment surface bioturbation), increased efflux of ammonium and silicate, and an increase in the ratio of NH4+:NOx when brittlestar densities were high. No significant effects of hypoxia were detected on brittlestar burrow depth. Our results illustrated that population density plays a crucial role in exacerbating the effects of hypoxia, possibly due to greater biological oxygen demands and increased waste products as organism density increases. Consequently, during moderate reductions in DO, densely populated communities may actually be more vulnerable to hypoxic stress and exhibit greater shifts in ecosystem function than sparsely populated communities.
Evaluation of spices extracts for antifungal properties

Pepper cultivation is severely affected by anthracnose caused by Colletotrichum capsici. Conventional control of the diseases has been by the use of synthetic chemicals which are not readily available to farmers, expensive and environmentally hazardous. However, hazards associated with the use of chemicals have necessitated the search for alternatives particularly in botanicals. Two solvents (ethanol and Omi-ogi (supernatant solution of fermented maize slurry) were used to extract the active ingredients from dried parts of 5 spices (Ocimum gratissimum, Cymbopogon citratus, Allium sativum, Xylopia aethiopica, Aframomum melegueta) at 2.5, 5, 7.5 and 10% concentrations respectively. Generally, mycelia growth decreased with increase in each of the spices concentration. Also all the tested spices extract reduced significantly the mycelial growth of C. capsici. The most potent spice extract was O. gratissimum recording a growth of 0.9 mm compared to 4.4 mm at 10%. The same trend was recorded with supernatant of fermented maize extract where extract of O. gratissimum recorded significantly the least mycelial growth. Generally better antifungal activities were recorded with ethanol extracts compared to extracts from supernatant of fermented maize slurry.
Three Quinine and Cinchonidine producing Fusarium species from Indonesia

Five endophytic Fusarium isolates from Cinchona calisaya were characterized for their ability to produce cinchona alkaloids, such as quinine, quinidine, cinchonine and cinchonidine. Based on molecular identification using phylogenetic analysis of DNA sequence generated from the internal transcribed spacer (ITS) rDNA and the partial elongation factor (EF1–α) gene regions, these isolates were determined as F. incarnatum (strain IPBCC 15.1251 and IPBCC 15.1253), F. solani (strain IPBCC 15.1248 and IPBCC 15.1249) and F. oxysporum (strain IPBCC 15.1250). All strains, except F. solani strain IPBCC 15.1248, were detected capable in producing quinine and cinchonidine by using HPLC and UV–vis spectroscopy analyses. Only quinine was detected from the extract of the F. solani strain IPBCC 15.1248. This is the first report of Fusarium species capable of producing quinine and cinchonidine in synthetic liquid medium.
Flexible Learning-Free Segmentation and Reconstruction for Sparse Neuronal Circuit Tracing

Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically constructing more complete and realistic circuits. In practice, such algorithms are often too error-prone and computationally expensive to be immediately useful. We address these shortcomings with a new fast, flexible, learning-free method for sparse segmentation and reconstruction of neural volumes. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions, which are of sufficient quality for preliminary biological study. Compared to existing supervised learning methods, it is both significantly faster (up to several orders of magnitude) and produces high-quality reconstructions that are robust to noise and artifacts.
Using lake sediment records to reconstruct bark beetle disturbances in western North America - eScholarship

The recent outbreak of native bark beetles in western North America is unprecedented in severity and scale, at least during the historical period. The aim of this work is to develop a proxy-based methodology to understand how bark beetle disturbances are recorded in lake sediments. Three hypotheses are tested to determine how the ecological impacts of severe spruce beetle (Dendroctonus rufipennis) disturbances are recorded following mortality of Engelmann spruce (Picea engelmannii). Outbreaks are hypothesized to: (1) decrease the ratio of spruce to fir pollen; (2) increase soil erosion and mobilize terrestrial C; and (3) leach foliar N, enhancing algal productivity. To test these hypotheses, sediment cores from spruce beetle-affected basins were analyzed for pollen, insect remains, organic and minerogenic content, and isotopic and elemental concentrations. The dataset was tested statistically using generalized linear mixed models (GLMMs) to determine if the response variables differed significantly between outbreak and non-outbreak periods.
RNA Mimics of Green Fluorescent Protein

Selection for RNAs that bind and activate derivatives of the green fluorescent protein fluorophore yields a wide range of useful spectral properties. Green fluorescent protein (GFP) and its derivatives have transformed the use and analysis of proteins for diverse applications. Like proteins, RNA has complex roles in cellular function and is increasingly used for various applications, but a comparable approach for fluorescently tagging RNA is lacking. Here, we describe the generation of RNA aptamers that bind fluorophores resembling the fluorophore in GFP. These RNA-fluorophore complexes create a palette that spans the visible spectrum. An RNA-fluorophore complex, termed Spinach, resembles enhanced GFP and emits a green fluorescence comparable in brightness with fluorescent proteins. Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs.