A fully automated deep learning pipeline for micro-CT-imaging-based densitometry of lung fibrosis murine models

Idiopathic pulmonary fibrosis, the archetype of pulmonary fibrosis (PF), is a chronic lung disease of a poor prognosis, characterized by progressively worsening of lung function. Although histology is still the gold standard for PF assessment in preclinical practice, histological data typically involve less than 1% of total lung volume and are not amenable to longitudinal studies. A miniaturized version of computed tomography (µCT) has been introduced to radiologically examine lung in preclinical murine models of PF. The linear relationship between X-ray attenuation and tissue density allows lung densitometry on total lung volume. However, the huge density changes caused by PF usually require manual segmentation by trained operators, limiting µCT deployment in preclinical routine. Deep learning approaches have achieved state-of-the-art performance in medical image segmentation. In this work, we propose a fully automated deep learning approach to segment right and left lung on µCT imaging and subsequently derive lung densitometry. Our pipeline first employs a convolutional network (CNN) for pre-processing at low-resolution and then a 2.5D CNN for higher-resolution segmentation, combining computational advantage of 2D and ability to address 3D spatial coherence without compromising accuracy. Finally, lungs are divided into compartments based on air content assessed by density. We validated this pipeline on 72 mice with different grades of PF, achieving a Dice score of 0.967 on test set. Our tests demonstrate that this automated tool allows for rapid and comprehensive analysis of µCT scans of PF murine models, thus laying the ground for its wider exploitation in preclinical settings.

Pivotal role of micro-CT technology in setting up an optimized lung fibrosis mouse model for drug screening

Idiopathic pulmonary fibrosis (IPF) is a progressive disease with no curative pharmacological treatment. The most used animal model of IPF for anti-fibrotic drug screening is bleomycin (BLM)-induced lung fibrosis. However, several issues have been reported: the balance among disease resolution, an appropriate time window for therapeutic intervention and animal welfare remain critical aspects yet to be fully elucidated. In this study, C57Bl/6 male mice were treated with BLM via oropharyngeal aspiration (OA) following either double or triple administration. The fibrosis progression was longitudinally assessed by micro-CT every 7 days for 4 weeks after BLM administration. Quantitative micro-CT measurements highlighted that triple BLM administration was the ideal dose regimen to provoke sustained lung fibrosis up to 28 days. These results were corroborated with lung histology and Bronchoalveolar Lavage Fluid cells. We have developed a mouse model with prolonged lung fibrosis enabling three weeks of a curative therapeutic window for the screening of putative anti-fibrotic drugs. Moreover, we have demonstrated the pivotal role of longitudinal micro-CT imaging in reducing the number of animals required per experiment in which each animal can be its own control. This approach permits a valuable decrease in costs and time to develop disease animal models.

In-vivo lung fibrosis staging in a bleomycin-mouse model: a new micro-CT guided densitometric approach

Although increasing used in the preclinical testing of new anti-fibrotic drugs, a thorough validation of micro-computed tomography (CT) in pulmonary fibrosis models has not been performed. Moreover, no attempts have been made so far to define density thresholds to discriminate between aeration levels in lung parenchyma. In the present study, a histogram-based analysis was performed in a mouse model of bleomycin (BLM)-induced pulmonary fibrosis by micro-CT, evaluating longitudinal density changes from 7 to 21 days after BLM challenge, a period representing the progression of fibrosis. Two discriminative densitometric indices (i.e. 40th and 70th percentiles) were extracted from Hounsfield Unit density distributions and selected for lung fibrosis staging. The strong correlation with histological findings (r_Spearman = 0.76, p < 0.01) confirmed that variations in 70th percentile could reflect a pathological lung condition and estimate the effect of antifibrotic treatments. This index was therefore used to define lung aeration levels in mice distinguishing in hyper-inflated, normo-, hypo- and non-aerated pulmonary compartments. A retrospective analysis performed on a large cohort of mice confirmed the correlation between the proposed preclinical density thresholds and the histological outcomes (r_Spearman = 0.6, p < 0.01), strengthening their suitability for tracking disease progression and evaluating antifibrotic drug candidates.

Selection for growth in brown trout increases feed intake capacity without affecting maintenance and growth requirements1

The correlated responses in feed intake and G:F ratio with selection for increased growth rate were evaluated by comparing selected (S) and control (C) brown trout (Salmo trutta) reared under conditions known to affect feed efficiency: feed restriction and periods of compensatory growth. Nitrogen and energy requirements for maintenance and growth were also measured. Trout were allotted at comparable BW (3.7+/-0.06 and 3.8+/-0.04 g, for C and S respectively) to triplicate groups per treatment. The experiment lasted a total of 198 d, during which animals were successively submitted to a 116-d feeding phase and fed 10, 30, 50, 70, 100, and 140% of their usual daily ration (UDR), a 35-d phase of food deprivation, and a 47-d refeeding phase. The G:F of C and S were comparable in all experimental conditions tested. During the feeding phase, S grew better than C only when fed 100 and 140% UDR (P < 0.001). This was explained by a higher feed intake capacity. The requirements for growth and maintenance were similar among the lines, which is in agreement with their comparable loss of weight (mean energy loss of -53 and -55 kJ/(kg x d) for C and S, respectively; P > 0.38) observed during the feed deprivation phase and the lack of differences in carcass composition (fat, P > 0.35; protein, P > 0.54). During the refeeding phase, growth performance and G:F were high in all groups. The daily growth coefficient was higher in S than in C (P < 0.001) because of a higher feed intake (P < 0.001). An increase in absolute individual variability in final BW and length was associated with the level of food restriction in both lines; however, it always remained lower in S than in C. In conclusion, fish selected for growth under ad libitum conditions will only exhibit growth superiority when fed diets close to ad libitum, and there was no evidence that selection was associated with an improvement in efficiency of maintenance nor in retention of body tissues.

Li2VO(Si,Ge)O4, a prototype of a two-dimensional frustrated quantum heisenberg antiferromagnet

NMR and magnetization measurements in Li2VOSiO4 and Li2VOGeO4 are reported. The analysis of the susceptibility shows that both compounds are two-dimensional S = 1/2 Heisenberg antiferromagnets on a square lattice with a sizable frustration induced by the competition between the superexchange couplings J1 along the sides of the square and J2 along the diagonal. Li2VOSiO4 undergoes a low-temperature phase transition to a collinear order, as theoretically predicted for J2/J1>0.5. Just above the magnetic transition the degeneracy between the two collinear ground states is lifted by the onset of a structural distortion.

Stable and full rescue of the pigmentation in a medaka albino mutant by transfer of a 17 kb genomic clone containing the medaka tyrosinase gene

In the medaka Oryzias latipes, several albino strains have mutations in the tyrosinase gene that have been fully characterized at the molecular level. A genomic clone from wild-type medaka containing the 5 kb tyrosinase gene with its five exons, 10 kb of upstream sequences and 2 kb downstream sequences was introduced into fertilized eggs from a tyrosinase-negative albino strain. We show that the injection of this genomic clone predominantly conferred mosaic expression ending before the hatching stage. A minority of juveniles retained a variable number of pigmented cells, including four individuals keeping one pigmented eye through adulthood. Two of these could be mated, and one of these transmitted the transgene resulting in complete rescue of pigmentation to 16% of its offspring. The resulting transgenic line harbors a single copy of the wild-type tyrosinase gene and all fish are wild-type with respect to pigmentation. These experiments suggest that the tyrosinase genomic clone, or a future shorter version of it, can be used in fish to routinely detect transgenic lines. The apparent faithful and systematic expression of the tyrosinase transgene is most probably due to the presence of a locus control region (LCR) in the injected clone.

Effects of replacing fish meal with soy protein concentrate and of DL-methionine supplementation in high-energy, extruded diets on the growth and nutrient utilization of rainbow trout, Oncorhynchus mykiss

Our objectives were to test the potential replacement of fish meal by soy protein concentrate (SPC) in high-energy, extruded diets fed to rainbow trout (Oncorhynchus mykiss) and to evaluate the efficiency of DL-methionine supplementation of soy-based diets. Groups of trout (initial BW 103 to 106 g) were fed to visual satiety with isonitrogenous (6.6% DM) high-energy (22.8 MJ/kg DM gross energy), extruded diets, in which fish meal was progressively replaced with SPC (0, 50, 75, and 100%). Three 100% SPC diets were formulated to be either unsupplemented or supplemented with DL-methionine, so that total methionine content was .8 or 1.0% of DM. The quality of the SPC source used was assessed by measuring the antitryptic and antigenic activities and the concentrations of the isoflavones daidzein and genistein. Apparent digestibility of the diets was determined using the indirect method. A growth trial was conducted over 90 d at a water temperature of 18 degrees C. In addition to body composition analysis, plasma amino acid concentrations, anti-soy protein antibodies in the serum, and isoflavone concentrations in the bile were measured. The SPC source tested exhibited low antitryptic and antigenic activities, but it contained high concentrations of isoflavones (1,990 and 5,903 ppm for daidzein and genistein, respectively). Protein digestibility was high (92%) and was unaffected either the proportion of SPC in the diet or by DL-methionine supplementation. This was also true for the availability of amino acids, except phenylalanine. Digestibility of lipid and energy was reduced by 19% when SPC totally replaced fish meal. Growth rate was reduced when more than 50% of the dietary protein was of soy origin (daily growth coefficient of 3.2 and 2.1% for the control and the unsupplemented 100% SPC diet, respectively). The effect on growth was mainly explained by a general decline in feed intake (13.7 and 12.0 g DM x kg BW(-1) x d(-1) for the control and the unsupplemented 100% SPC diet, respectively) and in lipid and, thus, in energy digestibility. The DL-methionine supplementation partially reversed the depressive effects of high dietary SPC incorporation (+13% growth), mainly by enhancing intake. The negative effect of SPC incorporation either may be due to the high isoflavone concentration or to an interaction between the soy protein component and the dietary lipids.

Retention time of feed particles and liquids in the stomachs and intestines of dairy cows. Direct measurement and calculations based on faecal collection

To validate a method for analysing indigestible marker excretion patterns in terms of digesta passage, the mean retention time (MRT) of long hay, ground hay and concentrate, marked, respectively, with thulium, ytterbium and dysprosium was measured in the total digestive tract (TMRT) and in the stomachs (SMRT) of four cows fed on a diet of hay in the long form (17.7 kg DM/day). The MRT of the particulate and liquid phases in the intestines was obtained after faecal particles labelled by Europium and Chromium EDTA were pulse dosed through the duodenal cannula. Following test meals, total faecal collection and spot sampling of duodenal digesta were performed at fixed intervals. TMRT were 51.7, 45.6, 40.6 h and SMRT were 39.5, 31.9 and 28.0 h, respectively, for hay, ground hay and concentrate. The MRT of the liquids in the rumen (8.7 h) was shorter than the SMRT of particles but there was no differential passage between liquids and particles after the duodenum. Intestinal MRT averaged 11 h and was partitioned into 7.5 and 3.5, respectively, for MRT in the tubular sections and the caecum-proximal colon. The compartmental analysis of the faecal patterns of markers given during a test meal gives the following results. The time associated with the descending part of faecal kinetics (respectively, 25.3 and 22.9 h for hay and concentrate) is directly related to the escape of feed particles from the rumen. The delay of first appearance of markers mostly reflects transit in the post duodenal tubular sections for the concentrate. The time associated with the ascending part (respectively, 16.9 and 9.4 h for hay and concentrate) represents the time required to reduce the size of the forage particles (7 h according to the difference between TMRT of long and ground hay direct measurements) and caecal mixing (3.5 h) as well as other compartments or processes that are not clearly identified.

Effect of feeding time on hepatic nucleic acid, plasma T3, T4, and GH concentrations in rainbow trout

The effect of feeding time (dawn, midnight) on the growth performance and daily pattern of liver nucleic acid concentrations, plasma thyroid hormone, and growth hormone concentrations was studied in immature rainbow trout (Oncorhynchus mykiss, mean individual weight: 55 g). Fish were held in groups of 20 individuals (12 groups per treatment) and maintained in flow-through tanks supplied with river water under natural photoperiod. Food pellets (Aqualim, 49% crude protein) were delivered daily over a 30-min period by means of belt feeders. Growth performance and protein retention efficiency were higher for trout fed at dawn than for those fed at midnight, whereas both groups of fish ingested the same total amount of feed. All parameters studied showed significant daily variations. The daily patterns of liver RNA concentrations, RNA/DNA, and protein/DNA ratios were significantly different between fish fed at dawn and at midnight, indicative of a higher liver protein synthesis in the trout fed at dawn. On average, plasma thyroid hormone levels were higher and plasma GH concentrations were lower in trout fed at dawn compared with those fed at midnight. The hormonal patterns were only affected by feeding time when the fish were fed at dawn. These results suggested that the observed differences in growth and protein retention efficiency were linked to the observed differences in plasma hormone levels.

Mean retention time in digestive tract and digestion of fresh perennial ryegrass by lactating dairy cows: influence of grass maturity and comparison with a maize silage diet

The effects of grass maturity on the mean retention time of liquid and particles, digestibility and duodenal nutrient flows were measured by feeding second cuts of perennial ryegrass to 3 fistulated lactating dairy cows over 2 successive periods (late June and mid-July, 28 and 49 d regrowth, respectively). Fresh forage was given ad libitum with 12% (dry matter (DM) basis) concentrate. The increase in maturity lowered grass nitrogen content, organic matter (OM) digestibility and non-ammoniacal nitrogen flow into the duodenum, but did not affect OM intake (13.2 kg/d). Neither the fractional outflow rate of liquid in the rumen (FOR; 17.3%/h) nor the concentrate total mean retention time (TMRT; 32.9 h) were affected. With maturity forage TMRT tended to increase (43.0-48.8 h), certainly because of the longer comminution time of coarse particles. These results were compared with data obtained 2 months earlier with the same cows fed on a maize silage diet (25% DM basis of the same concentrate) ad libitum (17.4 kg OM/d). Despite a lower total OM intake, FOR was much higher with the grass than with the maize silage diet (12.1%/h) and this may explain the lower retention time in the rumen of the small particles when grass diets were given (19.0 vs 24.3 h for maize silage diet).

Changes in membrane ionic conductances and excitability characteristics of rat skeletal muscle during aging

Membrane electrical properties, component ionic conductances and excitability characteristics of extensor digitorum longus muscle from 3-4, 16 and 29 months old rats were measured "in vitro". Fiber diameter, membrane resistance (Rm) and membrane capacitance, increased with aging, and the increase was significant at 29 months. The increase of Rm was mostly due to a decrease of chloride conductance (GC1), whereas potassium conductance (GK) increased only slightly, at 16 and 29 months. Due to the lowered GC1, the latency of action potential increased at both ages with a consequent prolongation of the duration of action potential. Nevertheless, a decrease in the firing capability was recorded in the aged fibers. Our results indicate, that during aging, the most affected parameter of skeletal muscle fibers is GC1, although changes of this passive conductance alone cannot entirely account for the changes in the excitability characteristics recorded.

Faecal water content and egg survival of goat gastro-intestinal strongyles under dry tropical conditions in Guadeloupe

Faeces from naturally infected goats were deposited on a natural grassland during the dry season in Guadeloupe (French West Indies) at different times throughout the day. The grass was either 7 or 20-30 cm tall. After a period of between several hours and 7 days, the number of viable strongyle eggs and the faecal water content were measured. Faecal temperature was recorded continuously. Faecal temperature was greater than 40 degrees-45 degrees C at midday and dehydration was rapid between 8 a.m. and 2 p.m. Egg mortality was greater on short than on tall grass and higher in morning than in evening deposits. Minimal faecal water content during the first 36 h explained the 74%, 55% and 38% mortality rate for eggs of Oesophagostomum columbianum (OC), Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC), respectively. In all, 5%-22% of the eggs of the latter species remained viable in a state of anhydrobiosis after 7 days on the ground. A delay of only 2 days between goat departure and irrigation would be sufficient to ensure that greater than 95% of O. columbianum and H. contortus eggs and 70% of T. colubriformis eggs are destroyed.

The effects of taurine on pharmacologically induced myotonia

Taurine reduces the excitability of striated muscle fibers by increasing the membrane conductance to chloride ions (GCl). This action was tested on rats made myotonic by drugs that block GCl by different mechanisms. Experiments were made "in vivo" using electromyographic (EMG) recordings and "in vitro" with intracellular microelectrode recordings from extensor digitorum longus muscle fibers. Taurine did not antagonize the myotonic discharges produced in vivo by anthracene-9-carboxylic acid, nor did it restore GCl lowered in vitro by this agent. However, when myotonia was chronically induced by 20,25 diazacholesterol, taurine given chronically in vivo or acutely in vitro antagonized the EMG myotonia as well as the reduced GCl and increased excitability of single fibers. We conclude that taurine acts directly on chloride channels to modify their kinetics. Our findings suggest that further clinical studies on the use of taurine in muscle disease involving abnormal excitability or chloride channel function will be useful.

Membrane ionic conductances in normal and denervated skeletal muscle of the rat during development

The development of membrane ionic conductances of rat extensor digitorum longus (EDL) muscle fibers was studied in vitro using intracellular recordings. At 7-8 days after birth, the potassium conductance (GK) dominated the total membrane conductance while the chloride conductance (GCl) was very low. A rapid increase of GCl towards adult values was observed after few days (12-14 day old rats), whereas GK did not decrease up to day 23. Denervation at 7-8 days after birth suppressed the maturation of the electrical parameters measured, and 15 days after the nerve crush, GCl was just detectable. These results suggest that the maturation of the electrical properties, and in particular that of the resting chloride conductance in mammalian striated muscle fibers, occurs during the first weeks of postnatal life and is dependent on innervation.

The effect of diphenylamine-2-carboxylate on C1- channel conductance and on excitability characteristics of rat skeletal muscle

The effect of diphenylamine-2-carboxylate (DPC), a blocker of the C1- conductive pathway in C1- transporting epithelia, has been evaluated in-vitro on the electrophysiological variables of rat extensor digitorum longus muscle fibres. DPC (5-240 microM) caused a dose-related increase of membrane resistance which was attributed entirely to a fall in C1- channel conductance (IC50, 120 microM), since potassium conductance was not affected by the treatment. DPC also modified fibre excitability. A significant dose-dependent increase was observed in the latency of the action potential and in the excitability of the membrane. DPC was less potent on striated fibres than anthracene-9-carboxylic acid, another specific blocker of C1- channel conductance. Moreover DPC was less potent on skeletal muscle than on C1- transporting epithelia. Morphological differences in the C1- channels or of the drug binding sites may account for the differences between tissues.

Enantiomers of clofibric acid analogs have opposite actions on rat skeletal muscle chloride channels

The S-(-) isomers of a series of clofibric acid analogs produced only a block of chloride conductance of rat skeletal muscle fibers with increasing concentrations until block was nearly complete. The R-(+) isomers, on the other hand, at low concentrations increased chloride conductance by as much as 9% to 39% and at higher concentrations decreased chloride conductance, but never by more than 27% of the control value. The actions of the enantiomeric pairs to either produce or inhibit myotonic excitability paralleled their ability to block or increase chloride conductance, respectively.

The action of taurine on chloride conductance and excitability characteristics of rat striated muscle fibers

Taurine and related compounds were applied to rat extensor digitorum longus muscle fibers in vitro, and the effects on membrane potential, cable parameters, component conductances and excitability were observed with microelectrodes. After 20 min in 60 mM taurine the fibers hyperpolarized and there were decreases in the latency of a rheobasic stimulus, the duration of the action potential and the maximum number of spikes elicited by depolarizing pulses. The effects of taurine on membrane resistance are attributed to a specific dose-dependent increase in membrane chloride conductance (G) with little or no effect on membrane potassium conductance. C1Gamma-aminobutyric acid at 30-60 mM also produced a specific increase in GC1 but, unlike taurine it caused a significant depolarization. beta-alanine or sucrose at 60 mM did not mimic any of the effects observed with taurine at this concentration. It was concluded that the actions of taurine and GABA on excitability can be explained by increases in GC1.

Stereospecificity of the chloride ion channel: the action of chiral clofibric acid analogues

2-(p-Chlorophenoxy)isobutyric acid (clofibric acid (1) or CPIB) is a drug known to block chloride membrane conductance (GCl) in rat striated muscle. In the present study chiral analogues of CPIB (2-(p-chlorophenoxy)propionic acid (2) and 2-(p-chlorophenoxy)butyric acid (3)) have been tested to evaluate the influence of chirality on Cl ion flux in the channel. The results showed that the chloride channel conductance strongly depends on the absolute configuration: in fact, the S-(-) isomers of the tested compounds strongly decreased the GCl of skeletal muscle membrane, whereas the R-(+) isomers were virtually ineffective. These data allow the hypothesis that, like other ion channels present in various biological systems, the chloride channel of skeletal muscle membrane could also have a stereospecific binding site (or receptor) regulating chloride ion flux.

The influence of inactivity on membrane resting conductances of rat skeletal muscle fibres undergoing reinnervation

The role of activity in the maintenance of the normal component resting conductances of skeletal muscle fibres has been evaluated in vitro in rat extensor digitorum longus muscle during reinnervation from 2 to 40 days (a) after crushing of the peroneus nerve and (b) after local application of tetrodotoxin (TTX) to the crushed nerve. Whereas membrane conductances were regained after crushing alone, they were not completely restored when impulse propagation was blocked with TTX. It is concluded that nerve trophic factors are of primary importance in the control of muscular membrane conductances, and that transmission at the endplate and the muscle usage triggered by it have a minor but significant effect.