Miracle-dz/UniFAR-FTUs huggingface dataset:
The genomic landscape of ANCA-associated vasculitis: Distinct transcriptional signatures, molecular endotypes and comparison with systemic lupus erythematosus

Introduction Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAVs) present with a complex phenotype and are associated with high mortality and multi-organ involvement. We sought to define the transcriptional landscape and molecular endotypes of AAVs and compare it to systemic lupus erythematosus (SLE). Methods We performed whole blood mRNA sequencing from 30 patients with AAV (granulomatosis with polyangiitis/GPA and microscopic polyangiitis/MPA) combined with functional enrichment and network analysis for aberrant pathways. Key genes and pathways were validated in an independent cohort of 18 AAV patients. Co-expression network and hierarchical clustering analysis, identified molecular endotypes. Multi-level transcriptional overlap analysis to SLE was based on our published data from 142 patients. Results We report here that “Pan-vasculitis” signature contained 1,982 differentially expressed genes, enriched in leukocyte differentiation, cytokine signaling, type I and type II IFN signaling and aberrant B-T cell immunity. Active disease was characterized by signatures linked to cell cycle checkpoints and metabolism pathways, whereas ANCA-positive patients exhibited a humoral immunity transcriptional fingerprint. Differential expression analysis of GPA and MPA yielded an IFN-g pathway (in addition to a type I IFN) in the former and aberrant expression of genes related to autophagy and mRNA splicing in the latter. Unsupervised molecular taxonomy analysis revealed four endotypes with neutrophil degranulation, aberrant metabolism and B-cell responses as potential mechanistic drivers. Transcriptional perturbations and molecular heterogeneity were more pronounced in SLE. Molecular analysis and data-driven clustering of AAV uncovered distinct transcriptional pathways that could be exploited for targeted therapy. Discussion We conclude that transcriptomic analysis of AAV reveals distinct endotypes and molecular pathways that could be targeted for therapy. The AAV transcriptome is more homogenous and less fragmented compared to the SLE which may account for its superior rates of response to therapy.
Self-construction and -configuration of functional neuronal networks

Biological processing systems are built in a way that enables them to become extremely performant. Every process relies solely on local information exchange, and no global controller. This building approach shapes the way the system functions. Therefore, understanding natural development and how it leads to function would extend our biological knowledge, but also enable technological progress. In this thesis we investigate the relationship between neuronal self-organization and function. We use the software framework Cx3D, which models 3D physical space and physical interactions, to simulate how two examples of neuronal networks, the superficial patch system and the winner-take-all (WTA) network, could develop in a self-organizing and biologically plausible way. The former denotes a patchy motif of clustered axonal connections that is observed in the superficial layers of various mammalian cortices. The latter is a computationally powerful candidate for the canonical microcircuit. Concerning the development of the superficial patch system, we hypothesize that a reaction-diffusion system exhibits stationary morphogenetic patterns. By sensing their local environment, cell bodies secrete morphogens following Gierer-Meinhardt dynamics. These morphogens steer the axonal growth and branching process. Our simulation results agree quantitatively with experimental measurements, such as the distribution of angles between neighboring patches, or the linear relationship between average patch diameter and spacing. Furthermore, by assuming that the morphogenetic specification happens early during development, we can simulate the expression of the patterns in a single layer (II/III) of the cortical structure. In order to bring neuronal function into this context, we investigated how a local cortical region (i.e. a single “patch” in the superficial patch system) could calibrate itself to express WTA behavior. Our simulations start from a single precursor cell, which incorporates a model of a gene regulatory network (GRN). This GRN gives rise to randomly distributed neurons, which extend their neurites based on developmental actions, such as retraction or bifurcation, that are expressed via their ’genetic code’. This neurite outgrowth generates the connectivity that is observed experimentally in layer II/III of cat visual cortex. In a rate-based approach, we also simulate the neuronal electrophysiology. We show that under the BCM rule, a Hebbian-type synaptic learning rule, the synapses can tune their weights, such that WTA functionality arises in a self-organizing way. This self-tuning occurs under the influence of input neurons, which are activated in a wave-like fashion, similar to the activity patterns evoked by retinal waves or subplate cells during cortical development. Besides, we also demonstrate the computational usefulness of a homeostatic form of synaptic adaptation. For example, we show that the synaptic scaling rule allows the
Efecto de la harina de champiñón y flavofosfolipol sobre la canal en pollos de engorda Effect of mushroom powder and flavophospholipol on carcass in broiler chickens

After showed its beneficial effects on chicken growth performance, a study was conducted to evaluate the effect of adding from birth and during the whole growth period, flavophospholipol and edible mushrooms powder on carcass characteristics, viscera weights and digestive tract measurements of male broiler chicken. A total of 300 one-dayold male broiler chicks were randomly distributed into 1 to 10 treatments with three replicates per treatment and 10 chicks per pen. The experiment consisted in a 2 x 5 factorial arrangement of treatments including five concentrations of mushrooms powder (0, 0.5, 1.0, 1.5 and 2.0 g/kg of diet) and the addition of 0.0 or 5.0 mg/kg of flavophospholipol from birth date to slaughter time at 42-d. Results show that the additions of dietary mushroom powder and flavophospholipol have a positive effect on weights of carcass parts with commercial importance as the breast and drumsticks. In contrast, there is no effect on wings weight. Regarding viscera weights, mushroom powder but not flavophospholipol or the interaction of both, affected the thymus, spleen, bursa of Fabricius and liver weights. Finally, despite weak statistically significant results on several measurements of the digestive tract, results show no effect of mushroom powder or the antibiotic addition on these variables.
Neural Correlates of Gain Control in Drosophila and Humans

Previous research has shown that visual sensitivity in human epilepsy patients is abnormal – characterized by increased responses at high contrast levels. These abnormalities have been linked to changes in neuronal gain control. Using animal models to study these changes is a useful approach. In this thesis, we used a steady-state visually evoked potential (SSVEP) technique similar to that used in humans to study photoreceptor-level and neuronal gain control in wild type (w-) Drosophila across a range of ages. We then compared these responses to those obtained from Drosophila carrying the kcc potassium channel mutation that renders young flies susceptible to light and shock-induced seizures. By taking into account the age and temperature dependence of the mutant (kccDHS1) flies, we were able to identify increased neural activity that recovers to the normal profile as they get older. We also found that these kccDHS1 flies are hypersensitive to light, particularly when young. These two findings are consistent with the fact that the level of the KCC protein increases with age. In addition, we found that kccDHS1 flies generate high frequency oscillations in their ERGs in response (50 – 100 Hz) to abrupt light onsets and offsets – a phenomenon that might be linked to abnormal changes in the gain control of neuronal feedback circuits. Studying visual abnormalities in Drosophila can reveal important information but eventually we need to link any visual abnormalities observed in animal models to humans. We therefore, attempted to measure subtle changes in gain control in humans due to adaptation, and at the same time make use of the human mental ability to measure another measure of gain control, attention, using an fMRI technique. Although our data did not show any interaction between adaptation and attention, it suggests that attention in early visual pathways largely affects the level of suppression in non-stimulated regions around the adaptor rather than responses to the probe itself. This is a manipulation that links to our work on adaptation in Drosophila in Chapter 6. Overall, the results presented in this thesis showed that fly models of epilepsy can be useful for studying changes in visual gain control, and showed that this work might be extended to humans.
Production potential of sugarbeet (Beta Vulgaris L.) under constraints of nitrogen irrigation and plant population

(.) The recommended levels of nitrogenous fertilizer (120 kg/ha) and plant population (one lac/ha) were found essential for maximum yields, whereas the number of irrigations could be reduced by 25 per cent without appreciable loss in root and sucrose yields. The nitrogen uptake in general was in conformity with root yield. The evapo-transpiration decreased with decrease in irrigation but was not much affected by the levels of nitrogen or the plant population. The water use efficiency increased with decrease in irrigation but decreased with decrease in levels of nitrogen and plant population
Chemical and Microbiological Assessments of Mackerel ( Scomber scombrus ) Stored in Ice.

The storage time of mackerel stored in ice was determined by sensory, chemical, and bacterial analyses. Ice: fish ratios of 1:2, 1:3, and 1:4 were used. Sensory analysis revealed that the storage time was directly related to ice: fish ratio and was 9, 8, and 6 d, respectively, At time of rejection, the levels of total volatile bases, trimethylamine and histamine were 23, 5, and 2 mg/100 g, respectively. At this time, a bacterial load limit of 1 × 106 CFU/g was reached for all the flora studied (total mesophilic aerobic, psychrotrophic, moderately halophilic) except the sulfide-producing flora. The data presented show the efficiency of adequate icing and allow for the recommendation of chemical standards for the evaluation of mackerel deterioration and/or for determination of different classes of freshness.
Scottish racing pigeons killed by Peregrine Falcons Falco peregrinus: estimation of numbers from ring recoveries and Peregrine daily food intake

Capsule Daily food intake gave the best indication, with 7–23% of the pigeon population estimated to have been taken. Aims To assess the numbers of Scottish racing pigeons taken by Peregrines, based on the recovery of racing pigeon rings from Peregrine eyries and on the daily food intake (DFI) of Peregrines. Methods The estimate based on ring recoveries was derived from examination of the flight histories of birds whose rings had been recovered during searches at Peregrine eyries. The DFI-based approach involved deriving estimates of the biomass and number of Scottish racing pigeons taken based on the Peregrines' mean daily food requirements, and involved a comprehensive synthesis of available Peregrine dietary data. Results Estimates of the number of Scottish racing pigeons killed by Peregrines, during the 2002 racing season, were a minimum of 3083 from ring recoveries and between 25 283 and 78 385 based on DFI. This represented 1% and 7–23% of the estimated total Scottish loft population respectively. The estimated Peregrine kills based on DFI represented 13–40% of total losses of Scottish racing pigeons to all causes; conversely 60–87% of total losses could not be attributed to Peregrines. Conclusions The recovery of racing pigeon rings from eyries provided only a minimum figure for the total losses of Scottish racing pigeons to Peregrines. Calculations based on Peregrine DFI, however, provided a good indication of the magnitude of Peregrine impact. The DFI technique is constrained by the lack of comprehensive data on relevant parameter values, leading to a broad range of estimates. Further research is encouraged to derive or refine parameter estimates for the DFI calculations in order to refine the estimates of potential kills from this approach.
Rare disease: a focus on metabolomics

ABSTRACT Introduction: A disease or disorder is defined rare when it affects less than 1 in 2000 subjects. 400 million people worldwide are living with a rare disease; approximately 50% of these patients are children, and 30% of them die within the first 5 years of life. The wide aetiology diversity leads to high variability in symptomatology, and clinical manifestations and consequently to challenging diagnosis. New experimental approaches are therefore recommended to improve diagnosis, and for the development of new therapeutic strategies. In the last years, metabolomics have allowed to better understand the metabolic processes associated with several rare diseases. Areas covered: This review describes the use of metabolomics for the study of the metabolic alterations related to some of the most studied pediatric rare disorders. Metabolomics, by means of 1H NMR spectroscopy and MS spectrometry, allows the identification and the quantification of a large number of metabolites (biomarkers) in different biofluids. Expert opinion: Metabolomics proved to be a powerful tool for the clinical investigation of rare diseases. The power of discrimination seems to be reliable for all the considered biofluids (urine, blood, and amniotic fluid). Standardization of the analytical and statistical steps is still needed for further studies with larger populations and meta-analysis.
INHERITANCE OF BACTERIAL BLIGHT RESISTANCE IN RICE

SUMMARY Inheritance of bacterial blight resistance in rice was studied in two crosses, viz., Tffl 6 (resistant) x Karuna (susceptible) and IR 20 (resistant) x Dular (susceptible). Segregation pattern in both the crosses showed that the resistance was governed by a single dominant gene.
Prevalence of Clostridium perfringens β2-toxin in sheep and goat population in Punjab, Pakistan

Clostridium perfringens presents persistent threat to small animals in causing moderate to severe enterotoxemia. The pathogenicity of C. perfringens depends on the production of four major toxins. In addition to the major toxins, beta2 (β2) toxin, a minor toxin, is also produced by some strains of C. perfringens. In this study, a total of 107 fecal samples collected from healthy and diseased sheep and goats were cultured and processed for biochemical analysis. On the basis of biochemical characterization, 61 isolates were confirmed as C. perfringens. In order to detect C. perfringens types, multiplex PCR assay was carried out for the confirmed isolates. Results indicated that the gene encoding beta2 (β2) toxin was found in 73% of type A isolates and 67% of type D isolates. There was no significant difference in the presence of this gene in the sheep and goats. An association between beta2 (β2) gene and disease occurrence was also found non-significant in both sheep and goat species. The present study suggests the high prevalence of C. perfringens beta2 gene (β2) in fecal isolates of both sheep and goats. However, the role of beta2 (β2) toxin gene in pathogenesis of enteric diseases needs further investigations.
64) Effect of Backfill Composition on Posttransplant Root Growth of Kalmia latifolia L.

Post-transplant root growth is critical for landscape plant establishment. The HorhizotronTM provides a way to easily measure root growth in a wide range of rhizosphere conditions. Mountain laurel (Kalmia latifolia L.) plants were removed from their containers and planted in Horhizotrons in a greenhouse in Auburn, AL, and outdoors in Blacksburg, VA. Each Horhizotron contained four glass quadrants extending away from the root ball, and each quadrant within a Horhizotron was filled with a different substrate (treatment) : 1) 100% pine bark (Pinus taeda L., PB), 2) 100% soil, 3) a mixture of 50:50 (by vol) PB:soil, or 4) 100% soil along the bottom of the quadrant to a depth of 10 em (4 in) and 100% PB layered 10 em (4 in) deep on top of the soil. Root growth along the glass panes of each quadrant was measured bi-weekly in Auburn and weekly in Blacksburg. In both locations, roots were longer in all treatments containing pine bark than in 100% soil. When pine bark was layered on top of soil, roots grew into the pine bark but did not grow into the soil. Results suggest that amending soil backfill with pine bark can increase post-transplant root growth of container-grown mountain laurel.
Acoustic surveys of birds using electronic recordings: new potential from an omnidirectional microphone system

Conventional acoustic surveys of avian communities require expert skills that are rare, particularly during the relatively short singing periods of most temperate North American species. We investigated the use of 2 newlydeveloped omnidirectional microphones for field recordings of forest bird communities. Our study compared richness and abundance of species recorded by field experts and those inferred from simultaneous recordings later analyzed by the same observers. The acoustic recording technique worked well for bird communities associated with the southern boreal mixedwoods of central Saskatchewan and western Ontario. Similarity measures for both presence-absence and abundance data ranged from 83 to 97%. The acoustic recording technique, particularly in a stereo configuration, could be used to analyze species composition and relative abundance of forest bird communities. Moreover, this approach had numerous advantages, including an archived record of point counts, the use of non-expert field staff to collect recordings, and the standardization of field data through time.
A parametric index of community evenness

Abstract Species relative abundance or community evenness is a basic component of any biodiversity measure. Several evenness indices have thus far been proposed in ecological literature. However, despite its vast potential applicability in ecological research, none seems to be generally preferred. Furthermore, only very few parametric evenness families have thus far been proposed. While traditional evenness indices supply point descriptions of community evenness, according to a parametric evenness family E(α), there is a continuum of possible evenness measures that differ in their sensitivity to the presence of dominant and rare species as a function of the parameter α. Therefore, changing α allows for vector descriptions of community structure represented by its diversity profile of E(α) versus α. In this paper, we propose that Hill’s parametric evenness family Eα,0 has a number of properties that may render it a desirable measure of evenness for ecological diversity studies. Two artificial communities are used to evaluate the performance of Eα,0 in quantifying community evenness.
Effect of Crude Aqueous Extracts of Some Medicinal Plant Flowers on Solid Ehrlich Tumor in Mice

Crude aqueous extracts of Cynara Cardunculus, Achillea millefolium, Calendula officinalis and Matricaria chamomilla flowers belong to family Compositeae were used in this work to study their efficiency to relief solid ehrlich tumor in mice. The more effective extract was C. officinalis which decreased tumor size from 513.6 to 139.8mm at a dose of 200mg/kg body weight comparing with doxorubicin which reduced tumor size to 98.2mm in concentration of 15mg/kg after 21 days, followed by M. chamomilla which showed the mean value of 168.7mm. While, the lowest values were showed with C. cardunculus and A. millefolium flowers extract which were 198.7 and 223.5mm, respectively. Also, the more effective treatments were doxorubicin in concentration of 15mg/kg and C. officinalis, followed by M. chamomilla, C. cardunculus and A. millefolium flowers extract for blood tests in tumor mice, e.g. antioxidant markers (MDA, TAC, SOD), liver functions (ALT, AST, Total proteins, Albumin and Globulins), kidney functions (Creatinine and Urea) lipid profile (triglycerides, total cholesterol, HDL, LDL and vLDL) and haematological parameters (HB, RBCs, Plt and WBCs) comparing with control tumor mice at a dose of 200mg/kg body weight for 21 days.
Morphological diversity of the medial cortex neurons in the common Indian wall lizard, Hemidactylus flaviviridis

The medial cortex of lizards is a simple three layered brain region displaying cyto- and chemoarchitectonical, connectional and ontogenetics that relate it to the hippocampal fascia dentata of mammals. Its neurons in the cell layer-II show a morphologically diverse population, partly as a result of the prominent continuous growth of this telencephalic region. We describe here the morphology of the neurons present in the medial cortex of the common Indian wall lizard (Hemidactylus flaviviridis) by using the classical Golgi-Colonnier procedure. According to classification criteria of dendritic tree pattern and dendritic spine covering we have observed seven different types of neurons in the cell layer-II of the medial cortex. Three of them, "bipolar", "aspinous monotufted monopolar", "aspinous monotufted bipolar", were without spines; whereas the four others having spines were classified as "spinous monotufted monopolar", "spinous monotufted bipolar", "spinous bitufted bipolar", "spinous multipolar". These neurons in the middle layer send their projection dendrites and axon towards the outer plexiform layer and inner plexiform layer. These neuronal types were compared with those reported previously by different workers in the other reptilian medial cortex and in the mammalian dentate area.
Does wing size shape insect biogeography? Evidence from a diverse regional stonefly assemblage

Aim: Dispersal ability has traditionally been seen as a key influence on species distributions, but recent biogeographical analyses have cast doubt on the strength of this association. Here we present biogeographical evidence from New Zealand's entire plecopteran fauna (100 species) to test for associations between flight ability and species range, and to determine the extent of wing reduction that is required to influence biogeographical patterns. Location: The main islands of New Zealand, representing a land area of 270,000 km. These islands host a diverse assemblage of endemic stoneflies, including a substantial number of wing-reduced taxa. Methods: We analyse biogeographical data, encompassing over 7000 species/locality records, across all 100 stonefly taxa recorded from New Zealand's mainland. Distributional data are analysed together with morphological data, in a phylogenetic framework, to test the hypothesis that wing length (dispersal ability) has a significant association with range size. Results: Our analyses indicate a strong relationship between species wing length and area of occupancy, unconfounded by phylogenetic relationships. A significant positive correlation was also observed between geographical range and relative wing length in both sexes, with consistent patterns observed in distinct families. When the analysis was confined only to macropterous species the relationship between wing length and area of occupancy remained significant. Main conclusions: This study shows that rapid switches in dispersal ability are linked to dramatic biogeographical contrasts. While complete wing loss is associated with major range reduction, it is also clear that even small reductions in wing size can significantly influence biogeographical patterns. Broadly, the analysis demonstrates that by focusing on a major regional assemblage of ecologically, and phylogenetically, similar taxa, it is possible to show that even subtle morphological shifts can be correlated with substantial biogeographical change.