Using unsupervised learning techniques to assess interactions among complex traits in soybeans

Soybean yield components and agronomic traits are connected through physiological pathways that impose tradeoffs through genetic and environmental constraints. Our primary aim is to assess the interdependence of soybean traits by using unsupervised machine learning techniques to divide phenotypic associations into environmental and genetic associations. This study was performed on large scale, jointly analyzing 14 quantitative traits in a large multi-parental population designed for genetic studies. We collected phenotypes from 2012 to 2015 from a soybean nested association panel with 40 families of approximately 140 individuals each. Pearson and Spearman correlations measured phenotypic associations. A multivariate mixed linear model provided genotypic and environmental correlations. To evaluate relationships among traits, the study used principal component and undirected graphical models from phenotypic, genotypic, and environmental correlation matrices. Results indicate that high phenotypic correlation occurs when traits display both genetic and environmental correlations. In genetic terms, length of reproductive period, node number, and canopy coverage play important roles in determining yield potential. Optimal grain yield production occurs when the growing environment favors faster canopy closure and extended reproductive length. Environmental associations found among yield components give insight into the nature of yield component compensation. The use of unsupervised learning methods provides a good framework for investigating interactions among various quantitative traits and defining target traits for breeding.     

Effect of phenylbutazone on the haemodynamic, acid-base and eicosanoid responses of horses to sustained submaximal exertion

The systemic haemodynamic and acid-base effects of the administration of phenylbutazone (4·4 mg kg⁻¹ intravenously) to standing and running horses were investigated. Phenylbutazone, or a placebo, was administered to each of six mares either 15 minutes before, or after 30 minutes of a 60-minute submaximal exercise test which elicited heart rates approximately 55 per cent of maximal, and to the same horses at rest. The variables examined included the cardiac output, heart rate, systemic and pulmonary arterial pressures, right atrial and right ventricular pressures, and arterial and mixed venous blood gases and pH. Serum sodium, potassium and chloride concentrations, and plasma thromboxane B₂, 6-keto-prostaglandin F_1α (6-keto-PGF_1α), and prostaglandin E₂ (PGE₂) concentrations were measured in separate studies using similar protocols in the same horses. Running produced increases in heart rate, cardiac output, mean arterial and right ventricular pressure, and decreases in total peripheral resistance. The acid:base responses to exertion were characterised by respiratory alkalosis. Exertion did not significantly influence plasma 6-keto-PGF_1α or PGE₂ concentrations but plasma thromboxane B₂ concentrations were increased significantly by 60 minutes of exertion in the untreated horses. This exercise-induced increase in plasma thromboxane B₂ concentration was inhibited by the previous administration of phenylbutazone, but phenylbutazone did not produce detectable changes in systemic haemodynamic or acid-base variables in either standing or running horses.     

Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters

Accuracy of prediction of estimated breeding values based on genome-wide markers (GEBV) and selection based on GEBV as compared with traditional Best Linear Unbiased Prediction (BLUP) was examined for a number of alternatives, including low heritability, number of generations of training, marker density, initial distributions, and effective population size (Ne). Results show that the more the generations of data in which both genotypes and phenotypes were collected, termed training generations (TG), the better the accuracy and persistency of accuracy based on GEBV. GEBV excelled for traits of low heritability regardless of initial equilibrium conditions, as opposed to traditional marker-assisted selection, which is not useful for traits of low heritability. Effective population size is critical for populations starting in Hardy-Weinberg equilibrium but not for populations started from mutation-drift equilibrium. In comparison with traditional BLUP, GEBV can exceed the accuracy of BLUP provided enough TG are included. Unfortunately selection rapidly reduces the accuracy of GEBV. In all cases examined, classic BLUP selection exceeds what was possible for GEBV selection. Even still, GEBV could have an advantage over traditional BLUP in cases such as sex-limited traits, traits that are expensive to measure, or can only be measured on relatives. A combined approach, utilizing a mixed model with a second random effect to account for quantitative trait loci in linkage equilibrium (the polygenic effect) was suggested as a way to capitalize on both methodologies.     

Serum Biomarkers of Clinical and Cytologic Response in Dogs with Idiopathic Immune‐Mediated Polyarthropathy

Background

Immune‐mediated polyarthopathy (IMPA) is common in dogs, and is monitored by serial arthrocenteses.

Hypothesis/Objectives

Plasma C‐reactive protein (CRP), interleukin‐6 (IL‐6), and CXCL8 (interleukin‐8) would serve as noninvasive markers of joint inflammation in IMPA.

Animals

Nine client‐owned dogs with idiopathic IMPA; 6 healthy controls.

Methods

Prospective study. Plasma CRP, IL‐6, and CXCL8 were measured by ELISA at baseline, 2, and 4 weeks during treatment with prednisone at 50 mg/m²/day. Arthrocenteses, the canine brief pain inventory (CBPI), and accelerometry collars were used to assess joint inflammation, lameness, and mobility at all 3 time points.

Results

C‐reactive protein concentrations were higher in IMPA dogs (median 91.1 μg/mL, range 76.7–195.0) compared with controls (median <6.3 μg/mL, <6.3–13.7; P = .0035), and were significantly lower at week 2 (10.6 μg/mL, <6.3–48.8) and week 4 (<6.3 μg/mL, <6.3–24.4; P < .001).C‐reactive protein was correlated with median CBPI scores (r = 0.68; P = .0004), joint cellularity (r = 0.49, P = .011), and mobility by accelerometry (r = −0.42, P = .048). Plasma IL‐6 concentrations were also higher in IMPA dogs (median 45.9 pg/mL), compared with controls (median <15.7 pg/mL; P = .0008). IL‐6 was lower in IMPA dogs by week 4 (<15.7 pg/mL; P = .0099), and was modestly correlated with CBPI scores (r = 0.47, P = .023). CXCL8 did not differ significantly between IMPA and healthy dogs.

Conclusions

Plasma CRP and IL‐6 might be useful surrogate markers of synovial inflammation and disease activity in dogs with IMPA.     

Asymmetric densitometric and mechanical adaptation of the left fifth metacarpal bone in racing greyhounds

The densitometric and mechanical structural properties of the left and right fifth metacarpal bones of 10 racing greyhounds with a fracture of the central tarsal bone and 10 without a fracture were investigated by dual energy x-ray absorptiometry and a servo-hydraulic materials testing machine. In all the greyhounds the bone mineral density of the left fifth metacarpal bone was significantly greater than that of the right (P<0.001), but there was no significant difference between the degree of asymmetry in bone mineral density in the two groups. The ultimate torque and energy-to-failure of the left fifth metacarpal bone of the greyhounds with a fracture of the right central tarsal bone were significantly higher than in the right fifth metacarpal bone and higher than in both the left and right fifth metacarpal bones of the greyhounds with no fracture (P<0.05). The ultimate torque and energy-to-failure were significantly related to bone mineral density (P<0.005), and 22 per cent of the variation in these structural properties could be explained by variations in bone mineral density. Fifth metacarpal remodelling in response to asymmetric cyclic loading is bone-specific, and structural properties are enhanced in the left fifth metacarpal of greyhounds with a fracture of the right central tarsal bone.     

Tarsometatarsal subluxation in dogs: partial arthrodesis by plate fixation

In a retrospective study of tarsometatarsal joint subluxation in eight dogs, secondary fractures were identified in six dogs, particularly of the fourth tarsal bone and the proximal fifth metatarsal bone. Common causes of tarsometatarsal joint injury included jumping or falling and direct trauma to the foot. Partial tarsal arthrodesis, with the use of bone-plate stabilization and cancellous bone grafting of joint spaces after removal of articular cartilage, led to progressive bone healing in all dogs. Implant breakage did not occur in any dog.     

Clinical assessment of left ventricular relaxation

Ventricular relaxation is altered in a number of cardiac disorders affecting domestic animals. Clinical determination of the ventricular relaxation rate can provide useful information regarding disease severity and response to therapy. We believe that the current gold standard for assessing left ventricular relaxation requires measurement of ventricular luminal pressure at end-expiration using a high-fidelity catheter. Ventricular pressure should be digitized at ≥200 Hz for the period of pressure fall between the minimum rate of change of ventricular pressure and 10 mm Hg above left ventricular end-diastolic pressure of the preceding beat. The rate of relaxation then should be determined from the digitized data by Marquardt nonlinear least squares parameter estimation using an exponential decay model with nonzero asymptote. The major disadvantage in using an invasive method for evaluating left ventricular relaxation is that it requires general anesthesia in animals that frequently are categorized as high-risk anesthetic patients. Noninvasive estimates of ventricular relaxation using echocardiographic parameters such as isovolumic relaxation time, peak early filling rate, and time from end-systole to peak filling rate provide a crude and nonspecific assessment of ventricular relaxation that can be obtained from conscious animals. Determinations of these echocardiographic indices are of limited usefulness in assessing changes in ventricular relaxation associated with disease progression or therapeutic intervention, unless concurrent estimates of left atrial pressure, mitral valve characteristics, and left ventricular compliance are available.     

Cardiac dysrhythmias associated with gastric dilatation-volvulus in the dog

Of 16 dogs treated medically and surgically for gastric dilatation-volvulus, 11 developed electrocardiographic evidence of ventricular dysrhythmias. Seven of these dogs had ventricular dysrhythmias for the first time during their hospitalization after surgery. The ventricular dysrhythmias included ventricular premature depolarizations, slow ventricular rhythms, paroxysmal ventricular tachycardia, ventricular tachycardia, and multifocal ventricular tachycardia. Two of these dogs had electrocardiographic evidence of atrial premature depolarizations at the time of hospitalization. Treatment with lidocaine hydrochloride or procainamide hydrochloride was successful in reestablishing sinus rhythm in 9 of the 11 dogs with ventricular dysrhythmias.     

Electrocardiographic interpretation of thiobarbiturate-induced dysrhthymias in dogs.

The cardiac dysrhythmia occuring most commonly during intravenous administration of thiamylal sodium is ventricular bigeminy (ventricular premature depolarization coupled to the preceding sinus beat). Electrocardiographic tracings obtained during thiamylal-induced dyshythmias must be interpreted accurately if an accurate prognosis is to be give. Ventricular bigeminy seemed to originate in the ventricle, distal to the bundle of His. When ventricular premature depolarization was late in diastole, occuring simultaneiously with the next sinus-conducted impulse, a fusion beat resulted. The resultant ventricular bigeminy appeared as: (1) alternating ventricular premature dipolarizations, (2) an electrical alternans, and (3) alternating preexcitation syndrome. This dysrhythmia was associated with palpable alternating strong and weak frmoral arterial pulse. The likelihood that ventricular dysrhythmias will be caused by thiamylal is closely related to dose, concentration, and rate of administration. In a 23-month period, clinical occurrence of ventricular bigeminy during induction of anesthesia with thiamylal was approximately 4%.