Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Automated peritoneal dialysis is associated with better survival rates compared to continuous ambulatory peritoneal dialysis: a propensity score matching analysis

The impact of peritoneal dialysis modality on patient survival and peritonitis rates is not fully understood, and no large-scale randomized clinical trial (RCT) is available. In the absence of a RCT, the use of an advanced matching procedure to reduce selection bias in large cohort studies may be the best approach. The aim of this study is to compare automated peritoneal dialysis (APD) and continuous ambulatory peritoneal dialysis (CAPD) according to peritonitis risk, technique failure and patient survival in a large nation-wide PD cohort. This is a prospective cohort study that included all incident PD patients with at least 90 days of PD recruited in the BRAZPD study. All patients who were treated exclusively with either APD or CAPD were matched for 15 different covariates using a propensity score calculated with the nearest neighbor method. Clinical outcomes analyzed were overall mortality, technique failure and time to first peritonitis. For all analysis we also adjusted the curves for the presence of competing risks with the Fine and Gray analysis. After the matching procedure, 2,890 patients were included in the analysis (1,445 in each group). Baseline characteristics were similar for all covariates including: age, diabetes, BMI, Center-experience, coronary artery disease, cancer, literacy, hypertension, race, previous HD, gender, pre-dialysis care, family income, peripheral artery disease and year of starting PD. Mortality rate was higher in CAPD patients (SHR1.44 CI95%1.21-1.71) compared to APD, but no difference was observed for technique failure (SHR0.83 CI95%0.69-1.02) nor for time till the first peritonitis episode (SHR0.96 CI95%0.93-1.11). In the first large PD cohort study with groups balanced for several covariates using propensity score matching, PD modality was not associated with differences in neither time to first peritonitis nor in technique failure. Nevertheless, patient survival was significantly better in APD patients.

Continuous infusion of propofol in calves: bispectral index and hemodynamic effects

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Protecting the √SWAP operation from general and residual errors by continuous dynamical decoupling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Protecting the √SWAP operation from general and residual errors by continuous dynamical decoupling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gray Whales (Eschrichtius robustus) Off Sakhalin Island, Russia: Seasonal And Annual Patterns Of Occurrence

The annual return, seasonal occurrence, and site fidelity of Korean-Okhotsk or western gray whales on their feeding grounds off northeastern Sakhalin Island, Russia, were assessed by boat-based photo-identification studies in 1994-1998. A total of 262 pods were observed, ranging in size from 1 to 9 whales with an overall mean of 2.0'. Sixty-nine whales were individually identified, and a majority of all whales (71.0%) were observed in multiple years. Annual sighting frequencies ranged from 1 to 18 d, with a mean of 5.4 d. The percentage of whales re-identified from previous years showed a continuous annual increase, reaching 87.0% by the end of the study. Time between first and last sighting of identified individuals within a given year was 1-85 d, with an overall mean of 40.6 d. Annual calf proportions ranged from 4.3% (1997) to 13.2% (1998), and mother-calf separations generally occurred between July and September. The seasonal site fidelity and annual return of whales to this part of the Okhotsk Sea emphasize its importance as a primary feeding ground for this endangered population.

Least-cost Disjoint Paths with Dependent Cost Structure in Wavelength Continuous Optical WDM Networks

One of the important issues in establishing a fault tolerant connection in a wavelength division multiplexing optical network is computing a pair of disjoint working and protection paths and a free wavelength along the paths. While most of the earlier research focused only on computing disjoint paths, in this work we consider computing both disjoint paths and a free wavelength along the paths. The concept of dependent cost structure (DCS) of protection paths to enhance their resource sharing ability was proposed in our earlier work. In this work we extend the concept of DCS of protection paths to wavelength continuous networks. We formalize the problem of computing disjoint paths with DCS in wavelength continuous networks and prove that it is NP-complete. We present an iterative heuristic that uses a layered graph model to compute disjoint paths with DCS and identify a free wavelength.

Continuous/Cluster-Pinned Recording Media

We propose and theoretically investigate a new class of nanostructured magnetic recording films, cluster-pinned recording media. The films consist of magnetic clusters exchange coupled to a continuous hard layer with perpendicular anisotropy and low coercivity. Our calculations yield the coercivity and the cross-track correlation length as a function of film thickness and pinning density and strength. The mechanism is very similar to the Gaunt–Friedel pinning in bulk magnets, which differs from ordinary strong pinning by the selfconsistent dependence of wall curvature and coercivity on defect concentration. The main difference is the exponent for the coercivity as a function of the pinning strength, which is equal to 2 in the bulk but equal to 3/2 in thin films. The pinning strength is estimated for various regimes, and it is shown that the diminished domain-wall curvature reduces jitter.

Planning “Discrete” Movements Using a Continuous System: Insights from a Dynamic Field Theory of Movement Preparation

The timed-initiation paradigm developed by Ghez and colleagues (1997) has revealed two modes of motor planning: continuous and discrete. Continuous responding occurs when targets are separated by less than 60° of spatial angle, and discrete responding occurs when targets are separated by greater than 60°. Although these two modes are thought to reflect the operation of separable strategic planning systems, a new theory of movement preparation, the Dynamic Field Theory, suggests that two modes emerge flexibly from the same system. Experiment 1 replicated continuous and discrete performance using a task modified to allow for a critical test of the single system view. In Experiment 2, participants were allowed to correct their movements following movement initiation (the standard task does not allow corrections). Results showed continuous planning performance at large and small target separations. These results are consistent with the proposal that the two modes reflect the time-dependent “preshaping” of a single planning system.

Arthrospira platensis biomass with high protein content cultivated in continuous process using urea as nitrogen source

Aims: Arthrospira platensis has been studied for single-cell protein production because of its biomass composition and its ability of growing in alternative media. This work evaluated the effects of different dilution rates (D) and urea concentrations (N0) on A.similar to platensis continuous culture, in terms of growth, kinetic parameters, biomass composition and nitrogen removal. Methods and results: Arthrospira platensis was continuously cultivated in a glass-made vertical column photobioreactor agitated with Rushton turbines. There were used different dilution rates (0.040.44 day-1) and urea concentrations (0.5 and 5 mmol l-1). With N0 = 5 mmol l-1, the maximum steady-state biomass concentration was1415 mg l-1, achieved with D = 0.04 day-1, but the highest protein content (71.9%) was obtained by applying D = 0.12 day-1, attaining a protein productivity of 106.41 mg l-1 day-1. Nitrogen removal reached 99% on steady-state conditions. Conclusions: The best results were achieved by applying N0 = 5 mmol l-1; however, urea led to inhibitory conditions at D = 0.16 day-1, inducing the system wash-out. The agitation afforded satisfactory mixture and did not harm the trichomes structure. Significance and Impact of the Study: These results can enhance the basis for the continuous removal of nitrogenous wastewater pollutants using cyanobacteria, with an easily assembled photobioreactor.

Fast detection of the magnetic easy axis on steel sheet using the continuous rotational Barkhausen method

The magnetic behaviour of most commercial ferromagnetic steels is usually anisotropic presenting a magnetic easy axis. Changes in the direction of this axis can be related to mechanical changes and anomalies that occur in the fabrication process. The present work describes a method that uses a device with permanent magnets to create a precise rotational magnetic field. The device measures continuous Magnetic Barkhausen Noise signals related to the angle of magnetization, in order to determine the direction of the macroscopic magnetic easy axis. It also offers the possibility of obtaining real time parameters that quantify the magnetic anisotropy of the sample. (C) 2011 Elsevier Ltd. All rights reserved.

Glucose Control in Acute Myocardial Infarction: A Pilot Randomized Study Controlled by Continuous Glucose Monitoring System Comparing the Use of Insulin Glargine with Standard of Care

Background: This pilot study aimed to verify if glycemic control can be achieved in type 2 diabetes patients after acute myocardial infarction (AMI), using insulin glargine (iGlar) associated with regular insulin (iReg), compared with the standard intensive care unit protocol, which uses continuous insulin intravenous delivery followed by NPH insulin and iReg (St. Care). Patients and Methods: Patients (n = 20) within 24 h of AMI were randomized to iGlar or St. Care. Therapy was guided exclusively by capillary blood glucose (CBG), but glucometric parameters were also analyzed by blinded continuous glucose monitoring system (CGMS). Results: Mean glycemia was 141 +/- 39 mg/dL for St. Care and 132 +/- 42 mg/dL for iGlar by CBG or 138 +/- 35 mg/dL for St. Care and 129 +/- 34 mg/dL for iGlar by CGMS. Percentage of time in range (80-180 mg/dL) by CGMS was 73 +/- 18% for iGlar and 77 +/- 11% for St. Care. No severe hypoglycemia (<= 40 mg/dL) was detected by CBG, but CGMS indicated 11 (St. Care) and seven (iGlar) excursions in four subjects from each group, mostly in sulfonylurea users (six of eight patients). Conclusions: This pilot study suggests that equivalent glycemic control without increase in severe hyperglycemia may be achieved using iGlar with background iReg. Data outputs were controlled by both CBG and CGMS measurements in a real-life setting to ensure reliability. Based on CGMS measurements, there were significant numbers of glycemic excursions outside of the target range. However, this was not detected by CBG. In addition, the data indicate that previous use of sulfonylurea may be a potential major risk factor for severe hypoglycemia irrespective of the type of insulin treatment.

The use of nasal dilator strips as a placebo for trials evaluating continuous positive airway pressure

OBJECTIVES: The aim of the current study was to compare the objective and subjective effects of continuous positive airway pressure to the use of nasal dilator strips in patients with acromegaly and moderate to severe obstructive sleep apnea. METHODS: We studied 12 patients with acromegaly and moderate to severe obstructive sleep apnea (male/females = 8/4, age = 52 +/- 8 ys, body mass index = 33.5 +/- 4.6 Kg/m(2), apnea-hypopnea index = 38 +/- 14 events/h) who had been included in a randomized, crossover study to receive three months of treatment with continuous positive airway pressure and nasal dilator strips. All patients were evaluated at study entry and at the end of each treatment by polysomnography, and Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index and treatment satisfaction questionnaires. ClinicalTrials.gov: NCT01265121 RESULTS: The apnea-hypopnea index values decreased significantly with continuous positive airway pressure treatment but did not change with the use of nasal dilator strips. All of the subjective symptoms improved with both treatments, but these improvements were significantly greater with continuous positive airway pressure than with the nasal dilator strips. CONCLUSION: The use of nasal dilator strips had a much smaller effect on the severity of obstructive sleep apnea in patients with acromegaly and moderate to severe obstructive sleep apnea in comparison to the use of continuous positive airway pressure. Moreover, the improvement in several subjective parameters without any significant objective improvement in obstructive sleep apnea resulting from the use of nasal dilator strips is compatible with a placebo effect.

Continuous-wave watt-level Nd:YLF/KGW Raman laser operating at near-IR, yellow and lime-green wavelengths

A Nd:YLF/KGW Raman laser has been investigated in this work. We have demonstrated CW output powers at six different wavelengths, 1147 nm (0.70 W), 1163 nm (0.95 W), 549 nm (0.65 W), 552 nm (1.90 W), 573 nm (0.60 W) and 581 nm (1.10 W), with higher peak powers achieved under quasi-CW operation. Raman conversion of the 1053 nm fundamental emission is reported for the first time, enabling two new wavelengths in crystalline Raman lasers, 549 nm and 552 nm. The weak thermal lensing associated with Nd:YLF has enabled to achieve good beam quality, M-2 <= 2.0, and stable operation in relatively long cavities. (C) 2012 Optical Society of America

Toward the optimal dose metric in continuous renal replacement therapy

Purpose: There is no consensus on the optimal method to measure delivered dialysis dose in patients with acute kidney injury (AKI). The use of direct dialysate-side quantification of dose in preference to the use of formal blood-based urea kinetic modeling and simplified blood urea nitrogen (BUN) methods has been recommended for dose assessment in critically-ill patients with AKI. We evaluate six different blood-side and dialysate-side methods for dose quantification. Methods: We examined data from 52 critically-ill patients with AKI requiring dialysis. All patients were treated with pre-dilution CWHDF and regional citrate anticoagulation. Delivered dose was calculated using blood-side and dialysis-side kinetics. Filter function was assessed during the entire course of therapy by calculating BUN to dialysis fluid urea nitrogen (FUN) ratios q/12 hours. Results: Median daily treatment time was 1,413 min (1,260-1,440). The median observed effluent volume per treatment was 2,355 mL/h (2,060-2,863) (p<0.001). Urea mass removal rate was 13.0 +/- 7.6 mg/min. Both EKR (r(2)=0.250; p<0.001) and K-D (r(2)=0.409; p<0.001) showed a good correlation with actual solute removal. EKR and K-D presented a decline in their values that was related to the decrease in filter function assessed by the FUN/BUN ratio. Conclusions: Effluent rate (ml/kg/h) can only empirically provide an estimated of dose in CRRT. For clinical practice, we recommend that the delivered dose should be measured and expressed as K-D. EKR also constitutes a good method for dose comparisons over time and across modalities.