Cold exposure impacts DNA methylation patterns in cattle sperm.

DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.

High-throughput screening to evaluate optimum coagulation conditions via colloidal stability analysis.

Current methods of optimizing the coagulant dosage in wastewater treatment processes typically rely on the use of labor- and material-intensive jar testers, which are inadequate when coagulation processes require frequent adjustments due to variations in properties of the incoming feed. Analytical centrifuges (ACs) employ an integrated optics system that simultaneously monitors the position of the boundary between two separating phases in multiple samples of fairly low volumes (∼2 mL) - thus it was expected that ACs would be ideally suited to study the stability and settling kinetics of coagulation treatment processes. In this study, wastewater samples from a biogas generation facility (known as centrate) were collected in February 2022 (Batch A) and July 2022 (Batch B). A comprehensive screening of the treatment performance for Batch B was conducted at three pHs (5, 6, and 7) and nine concentrations of ferric chloride (0-500 mg-Fe3+/L) - it was found that the front-tracking profiles measured by the integrated optics system could be used to identify the minimal coagulation conditions needed to transition from slow to rapid settling. While the settling velocity was found to be well correlated with the instability index, a dimensionless number between 0 and 1 (where values closer to 1 indicate better separation), it was determined that the percentage of COD removal from the centrate samples increased up to an instability index of approximately 0.5 and then plateaued. Finally, it was found that the front-tracking profiles could be used to estimate the volume of sludge produced at various coagulation conditions. Thus, the results from this study establish ACs as an important screening tool for rapid evaluation of treatment performance while consuming minimal material and time - in this study, a total of 132 screening experiments were conducted using approximately ∼11 L of centrate and ∼6 hours of operator time.

Lumicitabine, an orally administered nucleoside analog, in infants hospitalized with respiratory syncytial virus (RSV) infection: Safety, efficacy, and pharmacokinetic results.

Respiratory syncytial virus (RSV) infection is the leading cause of infant hospitalizations and mortality. Lumicitabine, an oral nucleoside analog was studied for the treatment of RSV. The phase 1b and phase 2b studies reported here assessed the safety, pharmacokinetics, and pharmacodynamics of lumicitabine in infants/neonates hospitalized with RSV. In the phase 1b study, infants (≥1 to ≤12 months) and neonates (<28 days) received a single-ascending or multiple-ascending doses (single loading dose [LD] then 9 maintenance doses [MD] of lumicitabine, or placebo [3:1]). In the phase 2b study, infants/children (28 days to ≤36 months old) received lumicitabine 40/20 mg/kg, 60/40 mg/kg LD/MD twice-daily or placebo (1:1:1) for 5 days. Safety, pharmacokinetics, and efficacy parameters were assessed over 28 days. Lumicitabine was associated with a dose-related increase in the incidence and severity of reversible neutropenia. Plasma levels of ALS-008112, the active nucleoside analog, were dose-proportional with comparable mean exposure levels at the highest doses in both studies. There were no significant differences between the lumicitabine groups and placebo in reducing viral load, time to viral non-detectability, and symptom resolution. No emergent resistance-associated substitutions were observed at the RSV L-gene positions of interest. In summary, lumicitabine was associated with a dose-related increase in the incidence and severity of reversible neutropenia and failed to demonstrate antiviral activity in RSV-infected hospitalized infants. This contrasts with the findings of the previous RSV-A adult challenge study where significant antiviral activity was noted, without incidence of neutropenia. Trial registration ClinicalTrials.gov Identifier: NCT02202356 (phase 1b); NCT03333317 (phase 2b).

Fouling of virus filtration membranes by monoclonal antibody feeds with low aggregate content.

Membrane fouling by monoclonal antibodies (mAbs) is one of the main challenges in virus-filtration processes. Previous publications attributed membrane fouling to the presence of mAb aggregates in the solution, which block the membrane pores. This fouling mechanism can be solved by a prefilter; however, it was shown that there are mAbs that severely foul the membranes (reduce permeability by 90% and more) even after prefiltering the aggregates, while other mAbs foul the membrane weakly (reduce permeability by ~10% and less). Unfortunately, the differences between the fouling- and the nonfouling mAbs have never been convincingly explained. To get a deeper insight on these differences, we measured the fouling of chemically modified Isoprene-Styrene-4-vinylpyridine (ISV) membranes (TeraPore Technologies) by 8 mAbs exhibiting different hydrophobicity and charge. The results show that mAb solutions with low concentration of aggregates foul ISV membranes via an adsorptive mechanism, and the adsorption is driven mainly by hydrophobic forces between the mAb and the membrane. The charge of the mAbs plays a secondary role in fouling. We want to emphasize that the conclusions pertain to ISV membranes; the insights presented in this paper can potentially be used to engineer new surface chemistries to mitigate fouling of other virus-filtration and/or ultrafiltration membranes.

FOCUS may detect wall motion abnormalities in patients with ACS.

BACKGROUND: Chest pain is a common presentation to the Emergency Department (ED) with roughly 6 million visits a year. The primary diagnostic modality for the identification of acute coronary syndrome (ACS) is the electrocardiogram (ECG), which is used to screen for electrocardiographic findings representing acute coronary occlusion. It is known that the ischemia generated by an acutely occluded coronary vessel generates a wall motion abnormality which can be visualized by echocardiogram; however, emergency physician-performed focused cardiac ultrasound (FOCUS) currently does not have a formal role in the diagnosis of OMI within the emergency department. PURPOSE: We sought to define the characteristics of FOCUS performed by emergency physicians of variable training levels in the identification of RWMA in patients presenting to the emergency department with high suspicion for ACS before undergoing cardiac catheterization or formal echocardiography. We also explored whether RWMA was associated with OMI in these patients. METHODS: We performed a structured, retrospective review of adult patients presenting to a large, academic, tertiary care center with suspected ACS from July 1st, 2019, and October 24th, 2020. Patients were included if they underwent FOCUS in the ED during the time-period above for suspected ACS looking for RWMA and FOCUS images were stored and reviewable in our middleware software. The primary outcome was the accuracy, sensitivity, and specificity of FOCUS compared to formal echocardiography for the detection of RWMA. Secondary outcomes were sensitivity of FOCUS compared to formal echocardiography for detection of RWMA in patients with and without cardiac catheterization proven OMI and sensitivity and specificity of FOCUS operators based on training. RESULTS: FOCUS for RWMA performed by emergency physicians had a sensitivity of 94% (95% CI, 82-98), specificity 35% (95% CI, 15-61), and overall accuracy of 78% (95% CI, 66-87). Of all subjects, 82% underwent urgent or emergency coronary angiography, of which 71% had OMI at the time of coronary angiography of the procedure. FOCUS identified RWMA in 87% of patients with coronary angiography proven OMI. Residents (PGY-1 - PGY-3) (n = 31) were able to detect RWMA with a sensitivity of 86% (95% CI, 64-96), a specificity of 56% (95% CI, 23-85%), and an accuracy of 77 (95% CI, 58-90%). Emergency ultrasound fellows and attendings (n = 34) were able to detect RWMA with a sensitivity of 85% (95% CI, 64-95%), a specificity of 75% (95% CI, 36-96%), and an accuracy of 82% (95% CI, 65-93%). CONCLUSIONS: Our retrospective study concludes FOCUS performed by emergency physicians may be used to detect RWMA in patients with high concern for acute coronary syndrome. This may have its greatest utility in patients presenting without STEMI where the ECG is felt to be equivocal, but the clinician has high concern for OMI, in which the presence of RWMA might result in emergent cath lab activation, though this requires further study. The presence of RWMA in such cases may help to rule in OMI as a cause; however, the absence of RWMA should exclude OMI. Further research is necessary to confirm these findings.

Point-of-care ultrasound diagnosis of a pyogenic liver abscess in the emergency department.

Pyogenic liver abscess (PLA) is a rarely encountered condition in the emergency department (ED) that necessitates a timely diagnosis by the emergency physician. An early ED diagnosis is challenging as the presenting symptoms of PLA are often variable and nonspecific. The rapid bedside diagnosis of PLA with point-of-care ultrasound (POCUS) performed by emergency physicians has not been investigated thoroughly. This case report describes the expeditious identification and ED management of PLA by implementing emergency physician-performed POCUS as the initial diagnostic modality.

Genome wide association study of passive immunity and disease traits in beef-suckler and dairy calves on Irish farms.

Calves with lower concentrations of immunoglobulin G (IgG) in their blood, have a greater risk of developing diseases. There is a lack of knowledge on genetic markers known to be associated with immunological variability or disease resistance. Therefore, the objective of this study was to identify SNP markers associated with passive immunity measures (serum IgG, serum protein, albumin, globulin and total protein concentrations, total solids Brix percentage, zinc sulphate turbidity units) and disease (pneumonia, diarrhoea, crude illness) traits in Irish commercial beef-suckler and dairy calves through genome wide association studies (GWAS). Genotyping was performed on DNA samples from beef-suckler (n = 698) and dairy (n = 1178) calves, using the IDBv3 chip. Heritability of passive immunity associated traits (range 0.02-0.22) and the disease traits (range 0.03-0.20) were low-to-moderate. Twenty-five and fifteen SNPs approached genome wide significance (P < 5 × 10-5) for the passive immunity and the disease traits, respectively. One SNP "ARS-BFGL-BAC-27914" reached Bonferroni genome wide significance (P < 1.15 × 10-6) for an association with serum IgG concentration in beef calves. Further work will evaluate these SNPs in larger cattle populations and assess their contribution to genomic selection breeding strategies, aimed towards producing more disease resistant livestock.

A mobile app to capture EPA assessment data: Utilizing the consolidated framework for implementation research to identify enablers and barriers to engagement.

INTRODUCTION: Mobile apps that utilize the framework of entrustable professional activities (EPAs) to capture and deliver feedback are being implemented. If EPA apps are to be successfully incorporated into programmatic assessment, a better understanding of how they are experienced by the end-users will be necessary. The authors conducted a qualitative study using the Consolidated Framework for Implementation Research (CFIR) to identify enablers and barriers to engagement with an EPA app. METHODS: Structured interviews of faculty and residents were conducted with an interview guide based on the CFIR. Transcripts were independently coded by two study authors using directed content analysis. Differences were resolved via consensus. The study team then organized codes into themes relevant to the domains of the CFIR. RESULTS: Eight faculty and 10 residents chose to participate in the study. Both faculty and residents found the app easy to use and effective in facilitating feedback immediately after the observed patient encounter. Faculty appreciated how the EPA app forced brief, distilled feedback. Both faculty and residents expressed positive attitudes and perceived the app as aligned with the department's philosophy. Barriers to engagement included faculty not understanding the EPA framework and scale, competing clinical demands, residents preferring more detailed feedback and both faculty and residents noting that the app's feedback should be complemented by a tool that generates more systematic, nuanced, and comprehensive feedback. Residents rarely if ever returned to the feedback after initial receipt. DISCUSSION: This study identified key enablers and barriers to engagement with the EPA app. The findings provide guidance for future research and implementation efforts focused on the use of mobile platforms to capture direct observation feedback.

Serial Point-of-care Echocardiography Performed by an Emergency Physician to Guide Thrombolytic Management of Massive Pulmonary Embolism.

Massive pulmonary embolism (PE) is a life-threatening condition with a high mortality burden. The rapid diagnosis of PE can be supported with focused cardiac ultrasound (FOCUS) by identifying signs of right ventricular dysfunction (RVD). This case report describes a patient with hemodynamically unstable massive PE who received systemic thrombolytic therapy. Emergency physicians performed serial FOCUS examinations to assess the resolution of RVD in guidance of clinical management.

Fast, Easy, and Good: Assessing Entrustable Professional Activities in Psychiatry Residents With a Mobile App.

PROBLEM: Entrustable professional activities (EPAs) can be used to operationalize competency-based medical education. Mobile apps can efficiently capture feedback based on direct observation. To leverage the benefits of both, the authors developed an assessment tool that combines EPAs with mobile technology. APPROACH: The authors designed an app to collect EPA data based on direct observation using human-technology interface guidelines. Data collected in the app included: name of resident, the 13 end-of-training EPAs for psychiatry, entrustment ratings, and corrective narrative feedback. The app was implemented in an outpatient continuity clinic for second-year psychiatry residents over a 10-month period between September 2017 and June 2018. Ten faculty-resident dyads piloted the app. To assess the feasibility, utility, and validity of this intervention, the authors examined 3 outcomes: (1) utilization (mean time to complete each assessment; percentage of dyads who completed 10 assessments), (2) quality of the comments (proportion of comments that were behaviorally specific and actionable), and (3) correlation between entrustment level and resident experience (defined as days elapsed since the beginning of the experience). OUTCOMES: A total of 99 assessments were completed during the pilot. Mean time to complete an assessment was 76 seconds (standard deviation = 50 seconds, median = 67 seconds). Only 6 of the 10 dyads completed at least 10 assessments. Of all comments, 95% (94) were behaviorally specific and actionable and 91% (90) were corrective. Entrustment scores correlated moderately with resident experience (r = 0.43, P < .001). NEXT STEPS: The authors' EPA mobile app was efficient, generated high-quality feedback, and produced entrustment scores that improved as the residents gained experience. Challenges included uneven adoption. Looking forward, the authors plan to examine the enablers and barriers to adoption from an implementation science perspective.

Analysis of a large dataset reveals haplotypes carrying putatively recessive lethal and semi-lethal alleles with pleiotropic effects on economically important traits in beef cattle.

BACKGROUND: In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS: In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS: We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS: We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.

Respiratory syncytial virus-A dynamics and the effects of lumicitabine, a nucleoside viral replication inhibitor, in experimentally infected humans.

Background: Respiratory syncytial virus (RSV) causes high morbidity, with mortality rates approaching or exceeding that of influenza in adult and infant patient populations, respectively. Lumicitabine (ALS-008176 or JNJ-64041575) is an oral nucleoside analogue prodrug in clinical development to treat RSV infections. This prodrug converts to plasma-circulating ALS-8112, and then to the 5'-active nucleoside triphosphate (NTP) form within host cells. We conducted an RSV-A challenge study in healthy adults to evaluate lumicitabine's activity during an active RSV infection. Objectives: To develop a semi-mechanistic mathematical model describing RSV kinetics, and the pharmacokinetics (PK) and pharmacodynamics (PD) of lumicitabine during treatment. Methods: Nasopharyngeal viral load and concentrations of ALS-8112 and ALS-8144 (uridine metabolite) were measured frequently over the study duration. Population viral kinetic and PK/PD models were developed using NONMEM. The RSV life-cycle was described using a target-cell-limited model that included a physiological delay. Results: The estimated clearances of ALS-8112 and ALS-8144 were 54.2 and 115 L/h/70 kg, respectively. A semi-physiological model was linked to predict ALS-8112 conversion to active intracellular NTP. Extensive and rapid RSV reduction occurred after lumicitabine treatment (EC50 = 1.79 µM), with >99% viral inhibition at 2 h after loading dose. Simulated NTP exposures and time to EC50 attainment suggested that rapid therapeutic effects and reduced dosing frequency are achievable in adult and paediatric patients. Conclusions: The semi-mechanistic model characterizes RSV kinetics and the antiviral effectiveness of lumicitabine in an adult challenge population. This model is applicable to guide dose selection in adult and paediatric patients.

Population Pharmacokinetics of AL-335 and Its Two Main Metabolites (ALS-022399, ALS-022227) in Monotherapy and in Combination with Odalasvir and/or Simeprevir.

The aim of the current study was to characterize the time course of plasma concentrations of AL-335 and its main metabolites (ALS-022399 and ALS-022227) after oral administration in healthy and hepatitis C virus (HCV)-infected subjects, in monotherapy as well as in combination with simeprevir and/or odalasvir. AL-335, ALS-022399, and ALS-022227 plasma concentrations from subjects receiving 800 mg of AL-335 orally once daily (qd) as monotherapy or in combination were pooled and analyzed using a nonlinear mixed effect modeling approach. The typical values (between subject variability) of AL-335 and ALS-022399 apparent linear clearances were 3300 L/h (33.9%) and 1910 L/h (30.0%), respectively. ALS-022227 elimination was characterized as a nonlinear process, with typical values of Vmax,ALS-022227 and Km,ALS-022227 estimated to be 84,799 ng/h (14.9%) and 450.2 ng/mL, respectively. AL-335 and ALS-022399 plasma concentrations were increased more than 2-fold in presence of simeprevir and/or odalasvir, while the effect on ALS-022227 plasma concentrations was limited. The effect of simeprevir and/or odalasvir might be explained by their capacity to inhibit P-glycoprotein. Internal evaluation confirmed that the population pharmacokinetic model developed was deemed appropriate to describe the time course of AL-335, ALS-022399, and ALS-022227 plasma concentrations and their associated variability in both healthy and HCV-infected subjects, as well as the interaction effect of simeprevir and/or odalasvir over AL-335 and its metabolites in healthy subjects. This model can be used as a starting point to evaluate drug-drug interaction processes in HCV-infected patients and support the development of a direct-acting antiviral (DAA) combination.

Safety, tolerability, and pharmacokinetics of AL-335 in healthy volunteers and hepatitis C virus-infected subjects.

BACKGROUND: The nucleotide analog AL-335 is a pangenotypic hepatitis C virus (HCV) nonstructural protein (NS)5B inhibitor being evaluated as treatment for chronic HCV infection. METHODS: This three-part randomized, double-blind study evaluated the safety and pharmacokinetics of single and multiple ascending oral doses of AL-335. Healthy volunteers (HVs) received single doses of AL-335 (100-1,200 mg) or placebo in a fasted or fed (400 mg) state. Non-cirrhotic subjects (HCV genotype [GT]1-4) and GT1-infected subjects with Child Pugh A cirrhosis received multiple doses of AL-335 (400, 800, 1,200 mg) or placebo once daily (QD) for 7 days. RESULTS: Forty-eight HVs and 64 subjects with HCV GT1-4 were randomized and received treatment. AL-335 was well tolerated in HVs and HCV-infected subjects with/without cirrhosis. AL-335 was rapidly absorbed and converted to the metabolites ALS-022399 and ALS-022227. ALS-022227 exposure increased less than dose-proportionally and was unaffected by food, while AL-335 and ALS-022399 exposure increased with food by 85% and 50%, respectively, in HVs. Rapid and dose-dependent reductions in HCV-RNA were observed in GT1-infected subjects. In non-cirrhotic, GT1-4-infected subjects receiving AL-335 800 mg QD, potent antiviral activity was observed, regardless of genotype (mean maximum reductions in HCV-RNA of 4.0-4.8 log10 IU/mL). The same dose in GT1-infected cirrhotic subjects resulted in a 3.5 log10 IU/mL mean maximum reduction in HCV-RNA. CONCLUSIONS: AL-335 was well tolerated when administered as single and multiple doses, with an acceptable pharmacokinetic profile. The drug also demonstrated potent antiviral activity in HCV GT1-4-infected subjects, including GT1-infected subjects with cirrhosis.

Characterizing the Pharmacokinetic Interaction Between Simeprevir and Odalasvir in Healthy Volunteers Using a Population Modeling Approach.

The aim of this study was to characterize the pharmacokinetic drug-drug interaction (DDI) between simeprevir (NS3/4A protease inhibitor) and odalasvir (NS5A inhibitor) after oral administration to support the design and dose selection of clinical studies with this combination for the treatment of chronic hepatitis C infection (HCV). Simeprevir and odalasvir plasma concentrations from 30 healthy subjects receiving these drugs in monotherapy as well as in combination were pooled and analyzed using a population pharmacokinetic modeling approach. Previous pharmacokinetic models developed to characterize the pharmacokinetics for each drug were used as starting point. The dual effect of simeprevir and odalasvir on their pharmacokinetic parameters was explored. Simulations were performed to assess the impact of the DDI on exposure parameters. In presence of odalasvir, the relative bioavailability of simeprevir increased by 26% and the apparent clearance was reduced following competitive inhibition depending on odalasvir plasma concentrations, with an inhibitory constant (Ki) estimated to be 1610 ng/mL. The apparent odalasvir clearance was reduced by simeprevir plasma concentrations following an Imax model, characterized by a maximum inhibitory effect of 46.7% and an IC50 of 257 ng/mL. Model-based simulations indicated that both Cmax and AUC24h increased for both drugs, when co-administered. The pharmacokinetic model adequately describes the time course of plasma concentrations and their variability when simeprevir and/or odalasvir were orally administered. This model can be used as a first step to predict the exposures of concomitant administration of simeprevir and odalasvir in HCV-infected subjects. Data from study AL355-602 (NCT02512562) were used for this analysis.

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle.

Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.

Short-Duration AL-335, Odalasvir, With or Without Simeprevir, in Patients With HCV GT1 or 3 Infection Without Cirrhosis.

This open-label, phase IIa study assessed the safety, pharmacokinetics, and efficacy of direct-acting antiviral agent (DAA) regimens in patients with chronic hepatitis C virus (HCV) infection. Multiple 6-12-week oral regimens of 400-800 mg once daily (QD) AL-335 + 50 mg QD/every other day odalasvir ± 75-150 mg QD simeprevir were evaluated in treatment-naïve, HCV genotype (GT)1/3-infected patients without cirrhosis. Safety/pharmacokinetic parameters, HCV-RNA, and sequencing data were assessed. Treatment regimens for later study cohorts were adjusted based on emerging data. In total, 112 patients were enrolled. Three serious treatment-emergent adverse events occurred, one of which (a Mobitz type 1 second-degree atrioventricular block [Wenckebach]) was possibly related to high odalasvir exposure and resulted in premature discontinuation of study drugs. No other clinically significant safety findings were identified. GT1-infected patients receiving 3-DAA for 6-8 weeks achieved 100% sustained virologic response 12 weeks and 24 weeks after the end of treatment (sustained virologic response [SVR12/24]). GT1-infected patients receiving 2-DAA or GT3-infected patients receiving 3-DAA had SVR12/24 less than 90%, whether treated for 8 weeks or 12 weeks. Virologic failure was associated with the emergence of generally persistent NS5A and/or transient NS5B resistance-associated substitutions in most patients. Pharmacokinetic characteristics of the three drugs were also elucidated. Conclusions: In treatment-naïve subjects without cirrhosis, AL-335 + odalasvir + simeprevir for 6-8 weeks was generally safe and highly efficacious against HCV GT1. However, inadequate efficacy was observed for the 2-DAA regimen in GT1-infected subjects and the 3-DAA regimen in GT3-infected subjects.

Pharmacokinetics, safety, and tolerability of the 2- and 3-direct-acting antiviral combination of AL-335, odalasvir, and simeprevir in healthy subjects.

This Phase I, open-label, two-group, fixed-sequence study evaluated the pharmacokinetics and safety of AL-335, odalasvir, and simeprevir in healthy subjects. Group 1 (n = 16) received AL-335 800 mg once daily (QD) (days 1-3, 11-13, and 21-23), simeprevir 150 mg QD (days 4-23), and odalasvir 150 mg (day 14) followed by 50 mg QD (days 15-23). Group 2 (n = 16) received the same AL-335 regimen as in Group 1 plus odalasvir 150 mg (day 4) followed by 50 mg QD (days 5-23) and simeprevir 150 mg QD (days 14-23). Blood samples were collected to determine plasma concentrations of AL-335 (prodrug) and its metabolites, ALS-022399 (monophosphate precursor) and ALS-022227 (parent nucleoside), odalasvir, and simeprevir. Thirty-two subjects were enrolled. Odalasvir and simeprevir given alone, or in combination, increased AL-335 area under plasma concentration-time curve over 24 hours (AUC 0-24 h) 3-, 4-, and 7- to 8-fold, respectively; ALS-022399 AUC 0-24 h increased 2-, 2-, and 3-fold, respectively. Simeprevir had no effect on ALS-022227 AUC 0-24 h, whereas odalasvir with/without simeprevir increased ALS-022227 AUC 0-24 h 1.5-fold. AL-335 had no effect on odalasvir or simeprevir pharmacokinetics. Odalasvir and simeprevir AUC 0-24 h increased 1.5- to 2-fold for both drugs when coadministered irrespective of AL-335 coadministration. Study medications were well tolerated with no serious adverse events. One subject prematurely discontinued study drugs (unrelated event). This study defined the preliminary pharmacokinetic and safety profiles of the combination of AL-335, odalasvir, and simeprevir in healthy subjects. These data support the further evaluation of this combination for the treatment of chronic hepatitis C virus infection.

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification.

A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) verification in Bos taurus cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 B. taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800) selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present), and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non-matching genotypes per animal, SNP duplicates, sex and breed prediction mismatches, parentage and progeny validation results, and other situations. The Animal QC pipeline make use of ICBF800 SNP set where appropriate to identify errors in a computationally efficient yet still highly accurate method.