: a tool for integrated differential expression analysis.

One of the fundamental aspects of genomic research is the identification of differentially expressed (DE) genes between two conditions. In the past decade, numerous DE analysis tools have been developed, employing various normalization methods and statistical modelling approaches. In this article, we introduce , an R package that leverages the capabilities of four state-of-the-art DE tools: edgeR, limma, DESeq2, and dearseq.

Proximal and Classic Epithelioid Sarcomas are Distinct Molecular Entities Defined by MYC/GATA3 and SOX17/Endothelial Markers, Respectively.

Epithelioid sarcoma (ES) is a rare tumor hallmarked by the loss of INI1/SMARCB1 expression. Apart from this alteration, little is known about the biology of ES. Despite recent advances in treatment, the prognosis of ES remains unsatisfactory.

Cocoa byproduct inclusion in dairy sheep diet: Effects on sensory, volatile, and antioxidant properties of cheese.

The possibility of inclusion of agro-industrial byproducts in the diet of small ruminants represents both an economic and an environmental strategy for reducing waste management by industries and costs of feeding as well as the impact of livestock farming. Large amounts of wastes from the cocoa industry are produced annually, with a considerable part represented by cocoa bean shells, considered a suitable ingredient to be included in the diet of ruminants within the limits established by European legislation. The aim of this study was to assess the effect of including cocoa bean shells in the diet of dairy sheep on the sensory, volatile, and antioxidant properties of cheese.

Feeding pigs with hazelnut skin and addition of a concentrated phenolic extract from olive-milling wastewaters during pork processing: Effects on salami quality traits and acceptance by the consumers.

Two groups of ten barrows received a conventional- (CTRL) or an experimental- (HZL) finishing diet containing 11% of hazelnut skin. From each barrow, two types of salami (namely, NITR, and PHEN) were obtained. NITR salami was added with E250 and E252.

Leveraging Google Earth Engine for a More Effective Grassland Management: A Decision Support Application Perspective.

Grasslands cover a substantial portion of the earth's surface and agricultural land and is crucial for human well-being and livestock farming. Ranchers and grassland management authorities face challenges in effectively controlling herders' grazing behavior and grassland utilization due to underdeveloped infrastructure and poor communication in pastoral areas. Cloud-based grazing management and decision support systems (DSS) are needed to address this issue, promote sustainable grassland use, and preserve their ecosystem services.

Polymorphism at the Locus and Energy Intake Level Affect Milk Traits and Casein Profiles in Rossa Mediterranea Goats.

A total of twenty-seven Rossa Mediterranea lactating goats, consisting of nine homozygous for strong alleles (), twelve heterozygous () and six homozygous for weak alleles () at the locus, were used to evaluate the effect of genotype, diet and genotype × diet interaction on goat milk traits and casein profile. The goats were used in a 3 × 3 factorial arrangement of treatments, with three genotypes (, and ) and three different energy intake levels: high (H), medium (M) and low (L). The diets supplied a complete pelleted feed containing 65% of alfalfa hay, respectively, at 150%, 100% and 70% of the total energy requirements.

Feeding hazelnut skin to lambs delays lipid oxidation in meat.

This study aimed to investigate the effect of dietary hazelnut skin (HNS), a by-product of confectionery industry, on the oxidative stability of lamb meat. Twenty-two finishing lambs were randomly assigned to 2 groups and fed ad libitum for 56 days on different concentrate-based diets: one control and one experimental, in which 150 g/kg of corn was replaced by HNS. After slaughter, the fat-soluble vitamins content and hydrophilic antioxidant capacity were assessed in fresh meat, as well as color, lipid and protein stability over 7 days of shelf-life trial.

Effect of dietary pomegranate by-product on lamb flavour.

This study evaluated the effect of the dietary inclusion of whole pomegranate by-product (WPB) on lamb flavour. Seventeen Comisana male lambs (body weight 14.82 kg ± 2 kg) were assigned to 2 treatments.

A quantitative review of on-farm feeding practices to enhance the quality of grassland-based ruminant dairy and meat products.

In the last decades, a large body of evidence has highlighted the major role of feeding management practices in improving specific nutritional, technological and sensory quality traits of ruminant products. However, results have been mostly obtained under controlled conditions, and have been rarely validated on-farm. Therefore, a quantitative review was conducted to quantify the effects of on-farm feeding management practices on carotenoids, fat-soluble vitamins, colour, fatty acids (FAs), terpenes and sensory properties in the main animal product categories (PCs): dairy products from cattle (DC), sheep (DS) and goat (DG), and meat from cattle (MC) and sheep (MS).

Fatty acid metabolism in lambs supplemented with different condensed and hydrolysable tannin extracts.

Five groups of lambs (n = 9 each) were used to test the effect of plant extracts rich in hydrolysable (HT) or condensed tannin (CT) on animal performance, fatty acid composition of rumen content, liver and meat. The control group (CO) received a concentrate-based diet without tannins supplementation. The other groups received the same diet as the control lambs plus 4% chestnut (CH) and tara (TA) extracts as a source of HT and mimosa (MI) and gambier (GA) extracts as a source of CT.

Effect of dietary tannin supplementation on cow milk quality in two different grazing seasons.

Extensive farming systems are characterized by seasons with different diet quality along the year, as pasture availability is strictly depending on climatic conditions. A number of problems for cattle may occur in each season. Tannins are natural polyphenolic compounds that can be integrated in cows' diet to overcome these seasonal problems, but little is known about their effect on milk quality according to the season.

Phenotypic Characterization of Immortalized Chondrocytes from a Desbuquois Dysplasia Type 1 Mouse Model: A Tool for Studying Defects in Glycosaminoglycan Biosynthesis.

The complexity of skeletal pathologies makes use of in vivo models essential to elucidate the pathogenesis of the diseases; nevertheless, chondrocyte and osteoblast cell lines provide relevant information on the underlying disease mechanisms. Due to the limitations of primary chondrocytes, immortalized cells represent a unique tool to overcome this problem since they grow very easily for several passages. However, in the immortalization procedure the cells might lose the original phenotype; thus, these cell lines should be deeply characterized before their use.

Dietary cardoon meal modulates rumen biohydrogenation and bacterial community in lambs.

Cardoon meal is a by-product of oil extraction from the seeds of Cynara cardunculus and can serve as a novel alternative feedstuff for ruminants. This study examined the rumen fermentation, biohydrogenation of fatty acids (FA) and microbial community in lambs fed a concentrate diet containing 15% dehydrated lucerne (CON, n = 8) or cardoon meal (CMD, n = 7) for 75 days pre-slaughter. Diets did not influence rumen fermentation characteristics and the abundance of bacteria, methanogens, fungi, or protozoa.

Crosstalk between Macrophages and Myxoid Liposarcoma Cells Increases Spreading and Invasiveness of Tumor Cells.

Myxoid liposarcoma (MLPS) is the second most common subtype of liposarcoma and has tendency to metastasize to soft tissues. To date, the mechanisms of invasion and metastasis of MLPS remain unclear, and new therapeutic strategies that improve patients' outcomes are expected. In this study, we analyzed by immunohistochemistry the immune cellular components and microvessel density in tumor tissues from patients affected by MLPS.

Cheese quality from cows given a tannin extract in 2 different grazing seasons.

The aim of the present study was to compare the effect of dietary tannins on cow cheese quality in 2 different grazing seasons in the Mediterranean. Two experiments were performed on 14 dairy cows reared in an extensive system. The first experiment took place in the wet season (WS), and the second experiment took place in the dry season (DS).

Inclusion of cocoa by-product in the diet of dairy sheep: Effect on the fatty acid profile of ruminal content and on the composition of milk and cheese.

In this study, we hypothesized that dietary cocoa bean shell (CBS) as a partial replacer of human edible cereal grains in the diet of lactating ewes may affect performance and milk and cheese composition. Twenty Comisana lactating ewes allotted into control (CTRL; n = 10) or cocoa (CBS; n = 10) group received alfalfa hay ad libitum and 800 g of conventional (CTRL) or experimental (CBS) concentrate containing 11.7% CBS to partially replace corn and barley of the CTRL concentrate.

Feeding System Resizes the Effects of Polymorphism on Milk Traits and Fatty Acids Composition in Modicana Cows.

The interaction between genetic polymorphism and feeding system on milk traits and fatty acid composition was investigated in Modicana cows. Two K232A genotypes (AK and AA) and two feeding regimes, extensive system (EX) with 8 h of grazing without concentrate (EX) and semi-intensive systems (SI) with 2 h of grazing with concentrate, were investigated. genotype did not influence milk yield and composition.

Effect of Dietary Hazelnut Peels on the Contents of Fatty Acids, Cholesterol, Tocopherols, and on the Shelf-Life of Ripened Ewe Cheese.

Hazelnut peel (HNP), a by-product from the chocolate industry, is considered to be a suitable ingredient to be included in the diet of ruminants. This study aimed to evaluate the effect of feeding dairy ewes with a diet containing HNP on ripened cheese quality, including fatty acid (FA) profile, cholesterol, and tocopherol content, as well as stability during storage under commercial conditions. In total, 10 experimental cheeses were produced with bulk milk obtained from ewes fed a commercial concentrate (C group; = 5) or a concentrate containing 36% HNP in dry matter (HNP group; = 5).

Influence of dietary inclusion of tannin extracts from mimosa, chestnut and tara on volatile compounds and flavour in lamb meat.

Tannins are compounds able to form complexes with proteins limiting their ruminal degradation and thus the synthesis of some odour-active compounds may be inhibited. Tannins are broadly divided in condensed tannins (CT) and hydrolysable tannins (HT). The study aimed to assess the influence of dietary inclusion of three commercial tannin extracts, namely mimosa (Acacia mearnsii; CT), chestnut (Castanea sativa; HT) or tara (Caesalpinia spinosa; HT) on volatile profile and flavour of meat and kidney fat from lambs.

Effect of p.L127V Polymorphism and Feeding Systems on Milk Production Traits and Fatty Acid Composition in Modicana Cows.

Growth hormone participates in the regulation of lactation and lipid metabolism. A trial study was conducted to evaluate the effects of genetic polymorphism at GH p.L127V and its interaction with feeding system (extensive, EX; semi-intensive, SI) on milk traits and fatty acids composition in Modicana cows.

Effect of Feeding Hazelnut Skin on Animal Performance, Milk Quality, and Rumen Fatty Acids in Lactating Ewes.

The hazelnut skin is waste biomass rich in bioactive compounds that may affect lipid rumen metabolism, ruminant performance, and products' quality. Therefore, we investigated the effect of dietary hazelnut skin on milk production and composition and on rumen fatty acids in ewes. During 28 days, 20 Comisana lactating ewes received alfalfa hay plus 800g/head/day of pelleted concentrate containing 36% dried beet pulp (CTRL group; = 10) or 36% hazelnut skin (HS group; = 10).

Oxidative Status of Goats with Different CSN1S1 Genotypes Fed with Fresh and Dry Forages.

Forty late-lactation Girgentana goats were used to study the effect of diets fed ad libitum and αS1-casein (CSN1S1) genotype on redox balance. The goats genotyped at CSN1S1 locus (A/A, A/F) were subjected to four feeding treatments different for percentage inclusion of dry and fresh forage: DAF100 (98% of Dry Alfalfa Forage), DAF65 (65% of Dry Alfalfa Forage), FSF100 (100% of Fresh Sulla Forage) and FSF65 (65% of Fresh Sulla Forage). Blood samples were analyzed for superoxide dismutase (SOD) and glutathione peroxidase (GPX) activity, reactive oxygen metabolites (ROMs), biological antioxidant potential (BAP) and non-esterified fatty acids (NEFA), beta-hydroxybutyrate (BHBA), albumin, glucose and cholesterol contents.

Influence of dietary cardoon meal on volatile compounds and flavour in lamb meat.

Cardoon meal is a by-product retained after oil extraction from the seeds of cultivated Cynara cardunculus var. altilis that has been proposed as a valuable resource for animal feeding. The study aimed to assess the influence of its dietary inclusion on volatile profile and flavour of meat and kidney fat from lambs.

Recommendations for the Use of Tryptase in the Diagnosis of Anaphylaxis and Clonal Mastcell Disorders.

Tryptase is a serin-protease produced and released by mast cells after IgE-mediated or non-IgE mediated stimuli. We here review the various aspects related to the molecular characteristics of the enzyme and its biological effects, the genetic basis of its production and the release kinetics. Recommendations for the clinical use of tryptase measurement developed by a task force of Società Italiana di Patologia Clinica e Medicina di Laboratorio and Associazione Allergologi Immunologi Italiani Territoriali e Ospedalieri are given on the best procedure for a correct definition of the reference values in relation to the inter-individual variability and to the correct determination of tryptase in blood and other biological liquids, in the diagnosis of anaphylaxis (from drugs, food, insect sting, or idiophatic), death from anaphylaxis (post mortem assessment) and cutaneous or clonal mastcell disorders.