A computed tomography vertebral segmentation dataset with anatomical variations and multi-vendor scanner data.

With the advent of deep learning algorithms, fully automated radiological image analysis is within reach. In spine imaging, several atlas- and shape-based as well as deep learning segmentation algorithms have been proposed, allowing for subsequent automated analysis of morphology and pathology. The first "Large Scale Vertebrae Segmentation Challenge" (VerSe 2019) showed that these perform well on normal anatomy, but fail in variants not frequently present in the training dataset. Building on that experience, we report on the largely increased VerSe 2020 dataset and results from the second iteration of the VerSe challenge (MICCAI 2020, Lima, Peru). VerSe 2020 comprises annotated spine computed tomography (CT) images from 300 subjects with 4142 fully visualized and annotated vertebrae, collected across multiple centres from four different scanner manufacturers, enriched with cases that exhibit anatomical variants such as enumeration abnormalities (n = 77) and transitional vertebrae (n = 161). Metadata includes vertebral labelling information, voxel-level segmentation masks obtained with a human-machine hybrid algorithm and anatomical ratings, to enable the development and benchmarking of robust and accurate segmentation algorithms.

Effects of Cocoa Husk Feeding on the Composition of Swine Intestinal Microbiota.

A two-diet/two-period change over experiment was performed to investigate the effects of cocoa husks, as a source of dietary fiber and polyphenols, on pig intestinal microbial composition. Six pigs were fed a conventional cereal-based diet or a diet obtained by substitution of 7.5% of the conventional diet with cocoa husks for 3 weeks. Experimental diets were isoproteic and isoenergetic. At the end of each 3 week testing period, samples of fresh feces were collected and analyzed for microbial composition by fluorescence in situ hybridization. Cocoa husks did not affect feed intake, weight gain, and feed efficiency. Analysis of fecal microbial populations, grouped by phyla, showed a decrease of Firmicutes and an increase of Bacteroidetes in cocoa husk-fed pigs. Particularly, cocoa husks reduced fecal populations of the Lactobacillus-Enterococcus group and Clostridium histolyticum and increased the Bacteroides-Prevotella group and Faecalibacterium prausnitzii, suggesting a potential for cocoa husks in the improvement of intestinal microbial balance.

New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus).

Cattle (Bos taurus) and goat (Capra hircus) belong to the Bovidae family, and they share a common ancestor 19.7-21.5 Ma ago (MYA). The Bovidae family apparently experienced a rapid species radiation in the middle Miocene. The present day cattle and goat possess the same diploid chromosome number (2n = 60) and structurally similar autosomes, except that a small subcentromeric portion of cattle chromosome nine has been translocated to goat chromosome 14. In this study, we adopted a new strategy that involves the use of bioinformatics approach to detect unknown cryptic chromosome divergences between cattle and goat using and subsequent validation using the fluorescence in situ hybridization (FISH) of bacterial artificial chromosome clones. We identified two hypothetical discrepancies between the cattle and goat genome assemblies: an inversion in the goat chromosome 13 and a transposition in the goat chromosome 6. The FISH technique allowed clear validation of the existence of a new 7.4 Mb chromosomal inversion in the goat chromosome 13. Regarding the transposition in the goat chromosome six, FISH analyses revealed that the cattle and goat genomes shared the same organization, with the assembly of the goat genome being the correct one. Moreover, we defined, for the first time, the size and orientation of the translocated fragment involved in the evolutionary translocation between cattle chromosomes 9 and goat chromosome 14. Our results suggest that bioinformatics represents an efficient method for detecting cryptic chromosome divergences among species.

Effects of a selection of additives on in vitro ruminal methanogenesis and in situ and in vivo†NDF digestibility.

The effects of 18 essential oils, yeast, Quebracho tannin and Quillaja saponin on ruminal methane and gas production (GP) were studied in vitro. A lactating cow diet was incubated with rumen inoculum. Doses of the additives (mg/L) were: essential oils = 500; tannin = 67; yeast = 8.35 and 16.7; and saponin = 300. Lemongrass, estragole, eugenol, geraniol, limonen, thyme oil and thymol produced less gas (overall mean 33.8 mL/200 mg dry matter (DM)) than control (43.6 mL/200 mg DM; P < 0.001). Methane produced (mL/200 mg DM) by guaiacol (10.7), lemongrass (9.6), limonene (11.4), thyme oil (10.9) and thymol (2.1) was lower than control (12.5) (P < 0.001). Methane percentage on total GP was lower (P < 0.001) for cinnamic alcohol (25.4), guaiacol (24.5), thymol (19.7) and vanillin (26.3) than control (28.8). In a second experiment, thymol, guaiacol and yeast were added to the diet of dry fistulated cows to determine in situ neutral detergent fiber digestibility (NDFD) of six forages and in vivo dietary NDFD. Thymol and yeast decreased in situ NDFD after 24 h (33.9% and 33.5% vs. 38.1%; P = 0.008). Thymol decreased in vivo total tract NDFD (40.8% vs. 51.4%; P = 0.02). Differences in GP and methane levels were registered within classes of additives. A careful selection of additives may allow for the manipulation of ruminal fermentation.

Genomic analysis of cattle rob(1;29).

Robertsonian translocation (rob) involving chromosomes 1 and 29 represents the most frequent chromosome abnormality observed in cattle breeds intended for meat production. The negative effects of this anomaly on fertility are widely demonstrated, and in many countries, screening programs are being carried out to eliminate carriers from reproduction. Although rob(1;29) was first observed in 1964, the genomic structure of this anomaly is partially unclear. In this work, we demonstrate that, during the fusion process, around 5.4 Mb of the pericentromeric region of BTA29 moves to the q arm, close to the centromere, of rob(1;29). We also clearly show that this fragment is inverted. We find that no deletion/duplication involving sequences reported in the BosTau6 genome assembly occurred during the fusion process which originates this translocation.

Evaluating inhibition conditions in high-solids anaerobic digestion of organic fraction of municipal solid waste.

High-solids anaerobic digestion (HSAD) processes, when applied to different types of organic fractions of municipal solid waste (OFMSW), may easily be subjected to inhibition due to organic overloading. In this study, a new approach for predicting these phenomena was proposed based on the estimation of the putrescibility (oxygen consumption in 20 h biodegradation, OD(20)) of the organic mixtures undergoing the HSAD process. Different wastes exhibiting different putrescibility were subjected to lab-scale batch-HSAD. Measuring the organic loading (OL) as volatile solids (VS) was found unsuitable for predicting overload inhibition, because similar VS contents corresponded to both inhibited and successful trials. Instead, the OL calculated as OD(20) was a very good indicator of the inhibiting conditions (inhibition started for OD(20)>17-18 g O(2)kg(-1)). This new method of predicting inhibition in the HSAD process of diverse OFMSW may be useful for developing a correct approach to the technology in very different contexts.

Prediction of biogas potentials using quick laboratory analyses: upgrading previous models for application to heterogeneous organic matrices.

This study presents an upgrading of the mathematical models to predict anaerobic biogasification potential (ABP) through quick laboratory analyses that have been presented in an earlier study. The aim is to widen the applicability of the models to heterogeneous organic substrates and to improve their reliability through a deeper statistical approach. Three multiple-step linear regressions were obtained using biomass oxygen demand in 20 h (OD(20)) plus the volatile solids content (VS) of 23 new samples of heterogeneous organic matrices, of 46 samples presented in the earlier work and of the data set comprising all the 69 samples. The two variables chosen were found to be suitable for very heterogeneous materials. To judge the prediction quality, a validation procedure was performed with 12 new samples using model efficiency indexes. The proposed model had good prediction ability for a large variety of organic substrates, and allows the calculation of the ABP value within only 2-day's laboratory work instead of the 60-90 days required to obtain ABP by anaerobic test.