Relationships between Goat Foraging Behaviour and Pastoral Value in High Bassin Zone of Mandrare Rangeland in Southern of Madagascar

Goats have particular anatomical behaviour for browsing leaves to satisfy their energy requirements. In rangelands, available shrubs, leaves and biomass resources influence ruminant’s activities and rhythms such as foraging, walking, resting, ruminating and drinking. At semi-arid areas, this study aimed to determine how shrubs interact with pasture value to effect goat foraging behaviour

Optical map guided genome assembly

Background The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. Results We proposeOpticalKermitwhich directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler,OpticalKermitproduces an assembly with almost three times higher NGA50 with a lower number of misassemblies on realA. thalianareads. Conclusions OpticalKermitsuccessfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.Peer reviewe

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae

Nutraceutical approaches to non-alcoholic fatty liver disease (NAFLD): A position paper from the International Lipid Expert Panel (ILEP)

Non-Alcoholic Fatty Liver Disease (NAFLD) is a common condition affecting around 10–25% of the general adult population, 15% of children, and even > 50% of individuals who have type 2 diabetes mellitus. It is a major cause of liver-related morbidity, and cardiovascular (CV) mortality is a common cause of death. In addition to being the initial step of irreversible alterations of the liver parenchyma causing cirrhosis, about 1/6 of those who develop NASH are at risk also developing CV disease (CVD). More recently the acronym MAFLD (Metabolic Associated Fatty Liver Disease) has been preferred by many European and US specialists, providing a clearer message on the metabolic etiology of the disease. The suggestions for the management of NAFLD are like those recommended by guidelines for CVD prevention. In this context, the general approach is to prescribe physical activity and dietary changes the effect weight loss. Lifestyle change in the NAFLD patient has been supplemented in some by the use of nutraceuticals, but the evidence based for these remains uncertain. The aim of this Position Paper was to summarize the clinical evidence relating to the effect of nutraceuticals on NAFLD-related parameters. Our reading of the data is that whilst many nutraceuticals have been studied in relation to NAFLD, none have sufficient evidence to recommend their routine use; robust trials are required to appropriately address efficacy and safety

Step‐by‐step diagnosis and management of the nocebo/drucebo effect in statin‐associated muscle symptoms patients: a position paper from the International Lipid Expert Panel (ILEP)

Statin intolerance is a clinical syndrome whereby adverse effects (AEs) associated with statin therapy [most commonly statin-associated muscle symptoms (SAMS)] result in the discontinuation of therapy and consequently increase the risk of adverse cardiovascular outcomes. However, complete statin intolerance occurs in only a small minority of treated patients (estimated prevalence of only 3–5%). Many perceived AEs are misattributed (e.g. physical musculoskeletal injury and inflammatory myopathies), and subjective symptoms occur as a result of the fact that patients expect them to do so when taking medicines (the nocebo/drucebo effect)—what might be truth even for over 50% of all patients with muscle weakness/pain. Clear guidance is necessary to enable the optimal management of plasma in real-world clinical practice in patients who experience subjective AEs. In this Position Paper of the International Lipid Expert Panel (ILEP), we present a step-by-step patient-centred approach to the identification and management of SAMS with a particular focus on strategies to prevent and manage the nocebo/drucebo effect and to improve long-term compliance with lipid-lowering therapy

Pneumopathie organisée cryptogénique et secondaire

La pneumopathie organisée (PO) est une forme particulière de processus inflammatoire et fibroprolifératif du poumon, se traduisant par un syndrome radioclinique bien caractérisé. Dans sa forme idiopathique, elle est appelée pneumopathie organisée cryptogénique (POC). Lorsqu'elle survient dans un contexte déterminé ou en association avec une cause définie, on parle de pneumopathie organisée secondaire (POS). Le tableau classique est caractérisé par des symptômes généraux et respiratoires d'apparition subaiguë associés à des condensations alvéolaires plurifocales à l'imagerie thoracique. Le processus pathogénique débute par une lésion de l'épithélium alvéolaire conduisant à une exsudation de protéines plasmatiques dans les espaces aériens distaux, la formation d'amas de fibrine, puis la prolifération de myofibroblastes et la formation de bourgeons de tissu conjonctif intra-alvéolaires, avec préservation de l'architecture du parenchyme pulmonaire. Une caractéristique de la PO est la résolution généralement complète et sans séquelles des bourgeons fibroblastiques intra-alvéolaires, spontanément ou sous traitement corticoïde. La démarche diagnostique vise d'abord à établir le diagnostic de PO, puis à rechercher une cause éventuelle ou un contexte déterminé. La réponse aux corticoïdes est généralement rapide et complète et peut être considérée comme un élément diagnostique additionnel du syndrome clinique de PO. À l'inverse, une réponse au traitement insuffisante doit faire reconsidérer le diagnostic initial. Les rechutes sont fréquentes mais répondent bien à la reprise ou à l'augmentation des doses de prednisone et n'ont pas d'impact sur le pronostic final. Un schéma thérapeutique standardisé a été proposé dans le but de limiter les doses et les effets secondaires de la corticothérapie, sans en compromettre l'efficacité ni augmenter la fréquence des rechutes

Ultrasonic diagnostic in porous media and suspensions

An apparatus has been constructed to characterize transient fluid displacements in porous media, and probe sedimenting suspensions. The technique used is to propagate an ultrasonic wave in the sample. Both ultrasonic attenuation and velocity are related to the static and hydrodynamic properties of the medium. The system was built so as to perform array imaging (mapping) and tested with different fluids and suspensions. It is suggested that the ultrasonic technique can be suitable whenever transient, low cost and safe saturation and concentration measurements are to be performed.Nous avons réalisé un appareil pour étudier l'évolution temporelle des écoulements en milieux poreux et au cours de la sédimentation des suspensions. La technique employée utilise la propagation d'une onde ultrasonore dans l'échantillon. L'atténuation et la vitesse ultrasonores sont toutes deux reliées aux propriétés statique et dynamique du mileu. Le système d'imagerie acoustique permet une cartographie à deux dimensions de l'échantillon , ce système a été testé avec différents fluides et suspensions. Notre étude montre que la technique ultrasonore est bien adaptée à la détermination de la dépendance temporelle de la concentration et de la saturation dans des conditions de sécurité et de coût optimales

Lung function in Birt-Hogg-Dubé syndrome: a retrospective analysis of 96 patients.

Birt-Hogg-Dubé syndrome (BHD) is a rare autosomal dominant disorder caused by mutations in the FLCN gene coding for folliculin. Its clinical expression includes cutaneous fibrofolliculomas, renal tumors, multiple pulmonary cysts, and recurrent spontaneous pneumothoraces. Data on lung function in BHD are scarce and it is not known whether lung function declines over time. We retrospectively assessed lung function at baseline and during follow-up in 96 patients with BHD. Ninety-five percent of BHD patients had multiple pulmonary cysts on computed tomography and 59% had experienced at least one pneumothorax. Mean values of forced expiratory volume in 1 second (FEV <sub>1</sub> ), forced vital capacity (FVC), FEV <sub>1</sub> /FVC ratio, and total lung capacity were normal at baseline. Mean (standard deviation) residual volume (RV) was moderately increased to 116 (36) %pred at baseline, and RV was elevated > 120%pred in 41% of cases. Mean (standard deviation) carbon monoxide transfer factor (DLco) was moderately decreased to 85 (18) %pred at baseline, and DLco was decreased < 80%pred in 33% of cases. When adjusted for age, gender, smoking and history of pleurodesis, lung function parameters did not significantly decline over a follow-up period of 6 years. Cystic lung disease in BHD does not affect respiratory function at baseline except for slightly increased RV and reduced DLco. No significant deterioration of lung function occurs in BHD over a follow-up period of 6 years