Miracle-dz/UniFAR-FTUs huggingface dataset:
Étude biomécanique des pathomécanismes du rachis lombaire en conditions traumatiques et sportives : influence des propriétés ligamentaires

Le rachis est une structure osteo-disco-ligamentaire complexe jouant un role majeur dans la stabilite et la mobilite du corps humain. Dans certaines conditions, des blessures traumatiques ou de fatigue peuvent survenir. Chaque annee, plus de 700000 nouveaux traumas rachidiens sont comptabilises au niveau mondial. Les blessures de fatigue, resultant d’une sur-sollicitation des structures vertebrales, sont frequentes dans le domaine sportif. La spondylolyse est la blessure la plus commune parmi les blessures de fatigue dues au sport, notamment chez les adolescents. Cette these vise a ameliorer la comprehension des mecanismes de blessures du rachis lombaire dans des conditions traumatiques et sportives en tenant compte des facteurs intrinseques (posture, proprietes mecaniques des ligaments) et extrinseques (conditions de chargement). Le volet experimental decrit la caracterisation des ligaments du rachis thoracique et lombaire humain en traction uni-axiale dynamique. Le volet numerique porte sur l’analyse par elements finis des pathomecanismes du rachis lombaire en conditions traumatiques, d’une part, et pour l’etude des risques de spondylolyse dans le domaine sportif d’autre part. Cette these a ete realisee en cotutelle entre Polytechnique Montreal et le Laboratoire de Biomecanique Appliquee (UMRT21 Institut Francais des Sciences et Technologies des Transports, de l'Amenagement et des Reseaux/ Aix-Marseille Universite) et s’inscrit dans les travaux de recherche du Laboratoire international – Imagerie et biomecanique du rachis (iLab-Spine) et de la Chaire de recherche industrielle CRSNG/Medtronic en biomecanique de la colonne vertebrale.
Gradual divergence and diversification of mammalian duplicate gene functions

Gene duplication provides raw material for the evolution of functional innovation. We recently developed a phylogenetic method to classify the evolutionary processes underlying the retention and functional evolution of duplicate genes by quantifying divergence of their gene expression profiles. Here, we apply our method to pairs of duplicate genes in eight mammalian genomes, using data from 11 distinct tissues to construct spatial gene expression profiles. We find that young mammalian duplicates are often functionally conserved, and that functional divergence gradually increases with evolutionary distance between species. Examination of expression patterns in genes with conserved and new functions supports the “out-of-testes” hypothesis, in which new genes arise with testis-specific functions and acquire functions in other tissues over time. While new functions tend to be tissue-specific, there is no bias toward expression in any particular tissue. Thus, duplicate genes acquire a diversity of functions outside of the testes, possibly contributing to the origin of a multitude of complex phenotypes during mammalian evolution.
From Ethics to Analytics: Aspects of Participants' Orientations to the Presence and Relevance of Recording Devices

In discussions of sociological research based on the recording of interactional occasions, participants' awareness of the presence of recording devices is often deemed to have a detrimental effect on the `authenticity' or `naturalness' of the data collected. We propose an alternative approach to this issue by seeking to turn participants' observable orientations to the presence and relevance of recording devices into an analytic topic, and exploring the precise kinds of situated interactional work in which such orientations are involved. Drawing on a substantial data corpus from three distinct research settings, we analyse a range of interactional functions associated with participants' orientations to the fact of their talk being recorded. Instead of assuming that it will act as a constraint on the production of `natural' talk, we show how the relevance of a recording device is negotiated and used in situ as a participants' matter and interactional resource.
Detection of Leptospira in cattle and dogs in Dakahlia Governorate

This study was done to investigate the infection rates of leptospirosis in different Veterinary Clinics in Dakahlia Province during the period from September 2016 to December 2017, The study was applied on a total of 115 urine samples, collected from suspected cattle (97) and their in-contact dogs (18), which suffered from different clinical signs of leptospirosis. The collected samples were examined for Leptospira spp. by different methods as Dark Field Microscopy (DFM) and staining by Silver Impregnation Method “Fontana Method". The results of DFM showed that, 28 out of 97 (28.9%) cattle urine samples were positive, and eight out of 18 (44.4%) dogs' urine samples were positive. Additionally, the results of Fontana Method revealed that, 44 out of 97 (45.4%) cattle urine samples were positive, and 13 out of 18 (72.2%) dogs' urine samples were positive. To confirm these results, conventional polymerase chain reaction (PCR) targeting (23S rDNA) gene of Leptospira, was done on 6 urine samples, included 3 cattle urine samples and 3 dogs' urine samples (one sample was positive, and two samples were negative in each species). PCR result confirmed the DFM and Fontana method results. In addition, a treatment trial for three groups of cattle infected with leptospirosis was performed by Dihydrostreptomycin, Oxytetracycline and Amoxicillin, respectively for 3 days. This study showed higher prevalence of leptospirosis in Dakahlia by DFM and Fontana methods. Moreover, Dihydrostreptomycin, Oxytetracycline and Amoxicillin have been successfully affecting on leptospirosis.
How fluorescent tags modify oligomer size distributions of the Alzheimer-peptide Aβ(1-40)

Within the complex aggregation process of Aβ-peptides into fibrils, oligomeric species, play a central role and reveal fundamental properties of the underlying mechanism of aggregation. In particular, low molecular weight aggregates have attracted increasing interest because of their role in cytotoxicity and neuronal apoptosis, typical of aggregation related diseases. One of the main techniques used to characterize such early stages of aggregation is fluorescence spectroscopy. To this end, Aβ-peptide chains are functionalized with fluorescent tags, often covalently bound to the disordered N-terminus region of the peptide, with the assumption that functionalization and presence of the fluorophore will not modify the process of self-assembly nor the final fibrillar structure. Up to date, experimental findings reveal size distributions of thermodynamically stable oligomers ranging from very narrow distributions of dimers to octamers, to very broad distributions up to 50-mers. In the present investigation we systematically study the effects of five of the most commonly used fluorophores on the aggregation of Aβ(1-40)-peptides. Time-resolved and single-molecule fluorescence spectroscopy have been chosen to monitor the oligomer populations at different fibrillation times, TEM, AFM and X-ray diffraction to investigate the structure of mature fibrils. While the structures of the mature fibrils were only slightly affected by the fluorescent tags, the sizes of the detected oligomeric species varied significantly depending on the chosen fluorophore. In particular, we relate the presence of high molecular weight oligomers (as found for the fluorophores HiLyte 647, Atto 647N and Atto 655) to net-attractive, hydrophobic fluorophore-peptide interactions, which are weak in the case of HiLyte 488, and Atto 488. The latter form low molecular weight oligomers only. Our findings reveal the potentially high impact of the properties of fluorophores on transient aggregates which needs to be included in the interpretation of experimental data of oligomers of fluorescently labeled peptides.
Minimizing the impact of biologging devices: Using computational fluid dynamics for optimizing tag design and positioning

Biologging devices are used ubiquitously across vertebrate taxa in studies of movement and behavioural ecology to record data from organisms without the need for direct observation. Despite the dramatic increase in the sophistication of this technology, progress in reducing the impact of these devices to animals is less obvious, notwithstanding the implications for animal welfare. Existing guidelines focus on tag weight (e.g. the ‘5% rule'), ignoring aero/hydrodynamic forces in aerial and aquatic organisms, which can be considerable. Designing tags to minimize such impact for animals moving in fluid environments is not trivial, as the impact depends on the position of the tag on the animal, as well as its shape and dimensions. We demonstrate the capabilities of computational fluid dynamics (CFD) modelling to optimize the design and positioning of biologgers on marine animals, using the grey seal (Halichoerus grypus) as a model species. Specifically, we investigate the effects of (a) tag form, (b) tag size, and (c) tag position and quantify the impact under frontal hydrodynamic forces, as encountered by seals swimming at sea. By comparing a conventional versus a streamlined tag, we show that the former can induce up to 22% larger drag for a swimming seal; to match the drag of the streamlined tag, the conventional tag would have to be reduced in size by 50%. For the conventional tag, the drag induced can differ by up to 11% depending on the position along the seal's body, whereas for the streamlined tag this difference amounts to only 5%. We conclude by showing how the CFD simulation approach can be used to optimize tag design to reduce drag for aerial and aquatic species, including issues such as the impact of lateral currents (unexplored until now). We also provide a step‐by‐step guide to facilitate the implementation of CFD in biologging tag design.
Characteristics of Ongole Grade Cows in the Kebumen Regency, Central Java Province

The research was conducted to explore the characteristics of Ongole grade cows. The research was held in Klirong sub-district, Kebumen regency. Two hundred thirty of Ongole grade farmers were involved in this research and interviewed on cows reproduction characteristics and breeding management, while exterior characteristics and body size were measured directly on 217 head of Ongole grade cows. Data of body size and cows performance were analyzed using mean and standard deviation, while exterior characteristics were analyzed descriptively and presented in percentages. Exterior characteristics of Ongole grade cows were white color in body and face, have a hump, big dewlap, long and hanging ears. Body size of Ongole grade cows at the three to four years old in terms of heart girth, shoulder height, body length, hip height, hip width and head index were 168.60±13.15 cm; 131.10±8.71 cm; 135.57±13.70 cm; 136.20±13.03 cm; 45.23±1.03 cm and 0.41±0.01, while at cows more than four years old were 170.97±11.02 cm; 130.10±5.61 cm; 136.00±9.21 cm; 136.67±5.83 cm; 45.27±0.99 cm and 0.41±0.01. The PPE, PPM, and S/C of Ongole grade cows were 4.07±0.18 months, 5.01±0.38 months, and 1.71±0.14. It was concluded that body sizes and performance of Ongole grade cows still in the normal range and relatively better than another research.
Midkine-a is required for cell cycle progression of Müller glia during neuronal regeneration

In zebrafish, Müller glia function as intrinsic retinal stem cells that can regenerate ablated neurons. Understanding the mechanisms governing neuronal stem cells may provide clues to regenerate neurons in mammals. We report that in Müller glia the cytokine/growth factor, Midkine-a, functions as a core autocrine regulator of the cell cycle. Utilizing midkine-a mutants, we determined that Midkine-a regulates elements of an Id2a-retinoblastoma network in reprogrammed Müller glia that controls the expression of cell cycle genes and is required for transition from G1 to S phases of the cell cycle. In mutants, Müller glia that fail to divide undergo reactive gliosis, a pathological hallmark of Müller glia in mammals. Finally, we show that activation of the Midkine-a receptor, ALK, is required for Müller glia proliferation. These data provide mechanistic insights into Müller glia stem cells in the vertebrate retina and suggest avenues for eliciting neuronal regeneration in mammals.
Low Tunnels Reduce Irrigation Water Needs and Increase Growth, Yield, and Water-use Efficiency in Brussels Sprouts Production

Farmers use low tunnels (LTs) covered with spunbonded fabric to protect warm-season vegetable crops against cold temperatures and extend the growing season. Cool season vegetable crops may also benefit from LTs by enhancing vegetative growth and development. This study investigated the effect of the microenvironmental conditions under LTs on brussels sprouts growth and production as well as water requirements and use efficiency in comparison with those in open fields. Low tunnels increased minimum soil temperature in all trials. By contrast, LTs reduced evapotranspiration (ET) 54% to 68% by reducing solar radiation (SR) and blocking wind in spite of increased maximum air temperatures. Because of reduced ET, water needs and irrigation decreased by 24% to 40%. Furthermore, LTs enhanced vegetative growth (plant leaf area, plant height, and plant dry weight). Sprouts per plant and yield under LTs increased by 29% and 46% in Spring 2017, by 22% and 46% in Fall 2017, and by 29% and 22% in Spring 2018. Considering the increased growth and productivity and reduced irrigation, LTs increased water-use efficiency (WUE) in relation to yield by 62% to 107% in comparison with open fields. Increased total yield and improved WUE illustrate that LTs may be a useful management tool in sustainable production systems in addition to their traditional role for season extension.
Anwulignan Improves d-Galactose-Induced Learning and Memory Impairment via Regulating P38 MAPK-Nrf2-HO-1 Pathway in Mice

Schisandra sphenanthera has been used as a Chinese traditional medical herb with its restorative and antioxidant functions for hundreds of years. Anwulignan is a monomeric compound isolated from the total lignans of S. sphenanthera. Our previous study showed that anwulignan has a strong antioxidant activity in vitro. However, it is unclear if anwulignan possesses any function in improving learning and memory. In this study, we examined the effect of anwulignan on the learning and memory impairment induced by d-galactose (d-Gal) in mice. By using Morris water maze and step-through test for the observation of behavioral activities, we found that anwulignan significantly reduced the learning and memory impairment induced by d-Gal. Histological and biochemical analyses exhibited the hippocampal morphological damages as well as decreased superoxide dismutase (SOD) and increased malondialdehyde (MDA) in the blood and hippocampus in d-Gal-treated mice, whereas anwulignan could reverse the morphological change and reduce the oxidative damages in mice. Furthermore, the activation of p38 mitogen-activated protein kinase (MAPK) signaling and expression of nuclear factor [erythroid-derived 2]-like 2 (Nrf2) and heme oxygenase 1 (HO-1) were enhanced in anwulignan-treated mice, suggesting that anwulignan improves the learning and memory impairment induced by d-Gal through its antioxidative activity by activating the p38 MAPK-Nrf2-HO-1 pathway in the hippocampus of mice.
HistMapR: Rapid digitization of historical land-use maps in R

1. Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision. 2. Comparing land use between maps from different time periods allows estimation of the magnitude of habitat change in an area. However, digitizing historical maps manually is time-consuming and analyses of change are usually carried out at small spatial extents or at low resolutions. 3. We developed a method to semi-automatically digitize historical land-use maps using the R environment. We created a number of functions that use the existing raster package to classify land use according to a map’s colours, as defined by the RGB channels of the raster image. The method was tested on three different types of historical land-use map and results were compared to manual digitisations. 4. Our method is fast, and agreement with manually-digitised maps of around 80-92% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land-use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.
The Illusion of Statistical Control

The authors extend previous recommendations for improved control variable (CV) practice in management research by mapping the objectives for using statistical control to recommendations for research practice. Including CVs in research designs to permit statistical control of “nuisance” variance is a common research practice that is subject to well-documented and potentially serious problems. Yet because CVs are frequently weakly related to focal variables, they rarely influence the interpretation of results. As a result, current practice offers an illusion of statistical control when in fact little control actually occurs. The authors extend the growing literature on CV practice by examining the ambiguity of researchers' stated purposes for using statistical control that makes it difficult to determine whether common CV practice accomplishes any of these intents effectively. Guidelines for improving research practice are offered, including adopting a conservative stance toward the inclusion of CVs in the analysis of quasiexperimental and correlational designs guided by the principle “When in doubt, leave them out. ”
Identifying molecular determinants of prion conversion

Prion diseases have been widely studied, but despite many great leaps in our knowledge of prion and protein misfolding diseases in general, many gaps remain. One example is the structural triggers or provocators of prion conversion found within the prion protein (PrP) itself. While factors interacting on PrP can promote or dissuade conversion, it is also evident that inherent properties of differing PrP (presumably especially conformation) have an effect on the likelihood of prion conversion. Previous work from our lab found that the substitution of histidine 95 with a tyrosine increased prion conversion, while the same individual substitution at four other copper-binding histidines of PrP had no effect on prion conversion propensity. Therefore, we focused on the role of mutations at this amino acid of the mouse PrP (MoPrP), H95, to explore if this increase in prion conversion is unique to the H95Y mutation and better understand how mutations here affect conversion. In this original work, we perform an amino acid scan at H95, replacing the histidine with every other common amino acid and comparing the prion conversion propensity. The results are remarkable with the residues with hydrophobic side chains increasing prion conversion by about 150% and residues with electrically-charged side chains decreasing prion conversion by about 75%, both compared to WT PrP. We continued and provide the first robust data that mutations on the prion protein at residue 95 (specifically H95D, H95E, H95K and H95R) decrease the propensity for cellular PrP (PrPC) to misfold into scrapie PrP (PrPSc), with transient transfection of mutant proteins into ScN2a cells. We next biochemically characterize PrP H95E and PrP H95Y, the most promising mutant for reducing and increasing conversion, respectively, in N2aPrP−/− cells stably transfected with the mutant PrPs. We conclude that PrP H95E and PrP H95Y are biochemically similar to PrP WT. Also with these generated stable cell lines, we use immunofluorescence to study the localization and trafficking of the mutant PrPs relative to organelle markers. The only difference we observed was relative to the endosomal recycling compartments, with PrP H95E co-localizing less compared to PrP WT and PrP H95Y co-localizing more compared to PrP WT. This is in agreement with other work that links the endosomal recycling compartments with prion conversion. More work is required to understand what structural changes, if any, occur on the PrP H95E mutant and to understand if this plays a role in conversion, similar to the work carried out on the PrP H95Y mutant. At this point we conclude that the replacement of PrP H95 with electrically charged side chains decreases the prion conversion propensity, and after a detailed study of PrP H95E conclude that this is likely due to reduced co-localization with the endosomal recycling compartments, but we cannot rule out the influence of structural changes and would like to continue studies along this line.
The origin of animal multicellularity and cell differentiation

How animals evolved from their single-celled ancestors over 600 million years ago is poorly understood. Comparisons of genomes from animals and their closest relatives – choanoflagellates, filastereans and ichthyosporeans – have recently revealed the genomic landscape of animal origins. However, the cell and developmental biology of the first animals have been less well examined. Using principles from evolutionary cell biology, we reason that the last common ancestor of animals and choanoflagellates (the ‘Urchoanozoan’) used a collar complex - a flagellum surrounded by a microvillar collar – to capture bacterial prey. The origin of animal multicellularity likely occurred through the modification of pre-existing mechanisms for extracellular matrix synthesis and regulation of cytokinesis. The progenitors of animals likely developed clonally through serial division of flagellated cells, giving rise to sheets of cells that folded into spheres by a morphogenetic process comparable to that seen in modern choanoflagellate rosettes and calcareous sponge embryos. Finally, we infer that cell differentiation evolved in the animal stem-lineage by a combination of three mechanisms: division of labor from ancient plurifunctional cell types, conversion of temporally segregated phenotypes into spatially segregated cell types, and functional innovation.
Impact of probiotic and prebiotic on the lysozyme response of broilers against clostridial infection

A total of 75 one-day old chicks (Cobb local breed) At the 1 day old the chicks were randomly divided into 3 equal separate groups; 25 chicks each. Group 1 fed on prebiotic beta glucan 200gram/ton, group 2 fed on probiotic saccharomyces servicee 500gram/ton and group 3 control fed on balanced commercial ration. The result revealed that the group of broiler fed on prebiotic increase the lysozyme more than the group of broiler fed on probiotic and after artificial infection, the group treated with prebiotic was able to face the clostridial infection more than group treated with probiotic. The histopathological examination showed that increase length and width of intestinal villi of chicken treated with prebiotic more than that of probiotic.