Phenotypic relationship and repeatability of methane emissions and performance traits in beef cattle using a GreenFeed system

Rumen methanogenesis results in the loss of 6% to 10% of gross energy intake in cattle and globally is the single most significant source of anthropogenic methane (CH4) emissions. The purpose of this study was to analyze greenhouse gas traits recorded in a commercial feedlot unit to gain an understanding into the relationships between greenhouse gas traits and production traits. Methane and carbon dioxide (CO2) data recorded via multiple GreenFeed Emission Monitoring (GEM), systems as well as feed intake, live weight, ultrasound scanning data, and slaughter data were available on 1,099 animals destined for beef production, of which 648 were steers, 361 were heifers, and 90 were bulls. Phenotypic relationships between GEM emission measurements with feed intake, weight traits, muscle ultrasound data, and carcass traits were estimated. Utilization of GEM systems, daily patterns of methane output, and repeatability of GEM system measurements across averaging periods were also assessed. Methane concentrations varied with visit number, duration, and time of day of visit to the GEM system. Mean CH4 and CO2 varied between sex, with mean CH4 of 256.1 g/day ± 64.23 for steers, 234.7 g/day ± 59.46 for heifers, and 156.9 g/day ± 55.98 for young bulls. A 10-d average period of GEM system measurements were required for steers and heifers to achieve a minimum repeatability of 0.60; however, higher levels of repeatability were observed in animals that attended the GEM system more frequently. In contrast, CO2 emissions reached repeatability estimates >0.6 for steers and heifers in all averaging periods greater than 2-d, suggesting that cattle have a moderately consistent CO2 emission pattern across time periods. Animals with heavier bodyweights were observed to have higher levels of CH4 (correlation = 0.30) and CO2 production (correlation = 0.61), and when assessing direct methane, higher levels of dry matter intake were associated with higher methane output (correlation = 0.31). Results suggest that reducing CH4 can have a negative impact on growth and body composition of cattle. Methane ratio traits, such as methane yield and intensity were also evaluated, and while easy to understand and compare across populations, ratio traits are undesirable in animal breeding, due to the unpredictable level of response. Methane adjusted for dry matter intake and liveweight (Residual CH4) should be considered as an alternative emission trait when selecting for reduced emissions within breeding goals.

A non-human primate model of acute liver failure suitable for testing liver support systems

Acute hepatic failure is associated with high morbidity and mortality for which the only definitive therapy is liver transplantation. Some fraction of those who undergo emergency transplantation have been shown to recover native liver function when transplanted with an auxiliary hepatic graft that leaves part of the native liver intact. Thus, transplantation could have been averted with the development and use of some form of hepatic support. The costs of developing and testing liver support systems could be dramatically reduced by the availability of a reliable large animal model of hepatic failure with a large therapeutic window that allows the assessment of efficacy and timing of intervention. Non-lethal forms of hepatic injury were examined in combination with liver-directed radiation in non-human primates (NHPs) to develop a model of acute hepatic failure that mimics the human condition. Porcine hepatocyte transplantation was then tested as a potential therapy for acute hepatic failure. After liver-directed radiation therapy, delivery of a non-lethal hepatic ischemia-reperfusion injury reliably and rapidly generated liver failure providing conditions that can enable pre-clinical testing of liver support or replacement therapies. Unfortunately, in preliminary studies, low hepatocyte engraftment and over-immune suppression interfered with the ability to assess the efficacy of transplanted porcine hepatocytes in the model. A model of acute liver failure in NHPs was created that recapitulates the pathophysiology and pathology of the clinical condition, does so with reasonably predictable kinetics, and results in 100% mortality. The model allowed preliminary testing of xenogeneic hepatocyte transplantation as a potential therapy.

Interhospital variability in localization techniques for small pulmonary nodules in children: A pediatric surgical oncology research collaborative study

BACKGROUND

Pulmonary nodules that are deep within lung parenchyma and/or small in size can be challenging to localize for biopsy. This study describes current trends in performance of image-guided localization techniques for pulmonary nodules in pediatric patients.

METHODS

A retrospective review was performed on patients < 21 years of age undergoing localization of pulmonary nodules at 15 institutions. Localization and resection success, time in interventional radiology (IR), operating room (OR) and total anesthesia time, complications, and technical problems were compared between techniques.

RESULTS

225 patients were included with an average of 1.3 lesions (range 1-5). Median nodule size and depth were 4 mm (range 0-30) and 5.4 mm (0-61), respectively. The most common localization techniques were: wire + methylene blue dye (MBD) (28%), MBD only (25%), wire only (14%), technetium-99 only (11%), coil + MBD (7%) and coil only (5%). Localization technique was associated with institution (p < 0.01); technique and institution were significantly associated with mean IR, OR, and anesthesia time (all p < 0.05). Comparing techniques, there was no difference in successful IR localization (range 92-100%, p = 0.75), successful resection (94-100%, p = 0.98), IR technical problems (p = 0.22), or operative complications (p = 0.16).

CONCLUSIONS

Many IR localization techniques for small pulmonary nodules in children can be successful, but there is wide variability in application by institution and in procedure time.

LEVEL OF EVIDENCE

Retrospective review, Level 3.

Evaluation of partial body weight for predicting body weight and average daily gain in growing beef cattle

Information on body weight and average daily gain (ADG) of growing animals is key not only to monitoring performance, but also for use in genetic evaluations in the pursuit of achieving sustainable genetic gain. Accurate calculation of ADG, however, requires serial measures of body weight over at least 70 days. This can be resource intensive and thus alternative approaches to predicting individual animal ADG warrant investigation. One such approach is the use of continuously collected individual animal partial body weights. The objective of the present study was to determine the utility of partial body weights in predicting both body weight and ADG; a secondary objective was to deduce the appropriate length of test to determine ADG from partial body weight records. The dataset used consisted of partial body weights, predicted body weights and recorded body weights recorded for 8,972 growing cattle from a range of different breed types in 35 contemporary groups. The relationships among partial body weight, predicted body weight and recorded body weight at the beginning and end of the performance test were determined and calculated ADG per animal from each body weight measure were also compared. On average, partial body weight explained 90.7 ± 2.0% of the variation in recorded body weight at the beginning of the postweaning gain test and 87.9 ± 2.9% of the variation in recorded body weight at its end. The GrowSafe proprietary algorithm to predict body weight from the partial body weight strengthened these coefficients of determination to 95.1 ± 0.9% and 94.9 ± 0.8%, respectively. The ADG calculated from the partial body weight or from the predicted body weight were very strongly correlated (r = 0.95); correlations between these ADG values with those calculated from the recorded body weights were weaker at 0.81 and 0.78, respectively. For some applications, ADG may be measured with sufficient accuracy with a test period of 50 days using partial body weights. The intended inference space is to individual trials which have been represented in this study by contemporary groups of growing cattle from different genotypes.

Altered Brain Structure in Infants with Turner Syndrome

Turner syndrome (TS) is a genetic disorder affecting approximately 1:2000 live-born females. It results from partial or complete X monosomy and is associated with a range of clinical issues including a unique cognitive profile and increased risk for certain behavioral problems. Structural neuroimaging studies in adolescents, adults, and older children with TS have revealed altered neuroanatomy but are unable to identify when in development differences arise. In addition, older children and adults have often been exposed to years of growth hormone and/or exogenous estrogen therapy with potential implications for neurodevelopment. The study presented here is the first to test whether brain structure is altered in infants with TS. Twenty-six infants with TS received high-resolution structural MRI scans of the brain at 1 year of age and were compared to 47 typically developing female and 39 typically developing male infants. Results indicate that the typical neuroanatomical profile seen in older individuals with TS, characterized by decreased gray matter volumes in premotor, somatosensory, and parietal-occipital cortex, is already present at 1 year of age, suggesting a stable phenotype with origins in the prenatal or early postnatal period.

Genetic parameter estimations and genomic insights for teat and udder structure in young and mature Canadian Angus cows

Poor teat and udder structure, frequently associated with older cows, impact cow production and health as well as calf morbidity and mortality. However, producer culling, for reasons including age, production, feed availability, and beef markets, creates a bias in teat (TS) and udder scores (US) assessed and submitted to the Canadian Angus Association for genetic evaluations toward improved mammary structure. In addition, due to the infancy of the reporting program, repeated scores are rare. Prior to the adoption of genetic evaluations for TS and US in Canadian Angus cattle, it is imperative to verify that TS and US from young cows are the same traits as TS and US estimated on mature cows. Genetic parameters for TS and US from all cows (n = 4,192) and then from young cows (parities 1 and 2) and from mature cows (parity ≥ 4) were estimated using a single-trait animal model. Genetic correlations for the traits between the two cow age groups were estimated using a two-trait animal model. Estimates of heritability (posterior SD [PSD]) were 0.32 (0.07) and 0.45 (0.07) for young TS and US and 0.27 (0.07) and 0.31 (0.07) for mature TS and US, respectively. Genetic correlation (PSD) between the young and mature traits was 0.87 (0.13) for TS and 0.40 (0.17) for US. Genome-wide association studies were used to further explore the genetic and biological commonalities and differences between the two groups. Although there were no genes in common for the two USs, 12 genes overlapped for TS in the two cow age groups. Interestingly, there were also 23 genes in common between TS and US in mature cows. Based on these findings, it is recommended that producers collect TS and US on their cow herd annually.

Estimation of economic value for efficiency and animal health and welfare traits, teat and udder structure, in Canadian Angus cattle

The Canadian Angus Association recently developed genetic evaluations for teat and udder structure, which impact efficiencies, and animal health and welfare. Genetic selection tools are most effective incorporated into economic selection indexes. An important factor in the development of economic indexes is the estimation of the economic value and discounted gene expression coefficients, and thereby the economic weight, of each trait. Traditional estimation methods, interrogation of previous studies quantifying the impact of the traits and bioeconomic modelling, were reinforced using producer surveys that employed pairwise ranking methods. Estimates of discounted genetic expression coefficients, economic value and economic weight for teat and udder score in Canadian Angus cattle were 0.31 per sire, $52.47, and $16.91 per score change on a per calf born basis, respectively, indicating that functional traits such as teat and udder structure have a significant impact on profitability and should be included in genetic selection programmes. Limitations in previous studies illustrate the need for longitudinal studies on traits that impact efficiencies and animal health and welfare.

Genome-Wide Association Analysis of Neonatal White Matter Microstructure

A better understanding of genetic influences on early white matter development could significantly advance our understanding of neurological and psychiatric conditions characterized by altered integrity of axonal pathways. We conducted a genome-wide association study (GWAS) of diffusion tensor imaging (DTI) phenotypes in 471 neonates. We used a hierarchical functional principal regression model (HFPRM) to perform joint analysis of 44 fiber bundles. HFPRM revealed a latent measure of white matter microstructure that explained approximately 50% of variation in our tractography-based measures and accounted for a large proportion of heritable variation in each individual bundle. An intronic SNP in PSMF1 on chromosome 20 exceeded the conventional GWAS threshold of 5 x 10-8 (p = 4.61 x 10-8). Additional loci nearing genome-wide significance were located near genes with known roles in axon growth and guidance, fasciculation, and myelination.

Microcoil localization as an effective adjunct to thoracoscopic resection of pulmonary nodules in children

BACKGROUND/PURPOSE

Thoracoscopic excision of pulmonary nodules is often required for diagnostic or therapeutic purposes, however subpleural and sub-centimeter nodules can be difficult to visualize. Various CT-guided localization techniques have been described, though there is minimal published pediatric data regarding the use of microcoils. We hypothesize that microcoil localization facilitates thoracoscopic resection of pulmonary nodules in children.

METHODS

A multi-institutional retrospective review of children who underwent preoperative CT-guided localization of lung nodules was conducted from 2012 to 2019. A combination of methylene blue dye (MBD), wires, and microcoils were utilized for CT-guided localization. When microcoils were utilized, fluoroscopy assisted in lesion identification and resection.

RESULTS

Eighteen patients (mean age 13 years, range 2-21 years) underwent thoracoscopic resection of 24 preoperatively localized pulmonary nodules. Mean size and depth of the lesions were 5.5 mm and 10 mm, respectively. Microcoil placement was successful 95% of the time and assisted in lesion localization in 88% of cases. Wire localization was not a durable technique, as 3 of 5 wires became dislodged upon lung  isolation.

CONCLUSIONS

Preoperative CT-guided localization with microcoils can assist in fluoroscopic-guided resection of pulmonary nodules in children. This technique avoids the pitfall of wire dislodgement, and provides surgeons an additional technique to localize sub-centimeter, subpleural nodules.

TYPE OF STUDY

Retrospective Review.

LEVEL OF EVIDENCE

Level III.

A head-to-head comparison of ixekizumab vs. guselkumab in patients with moderate-to-severe plaque psoriasis: 24-week efficacy and safety results from a randomized, double-blinded trial

Background

Significantly more patients with moderate‐to‐severe plaque psoriasis treated with the interleukin (IL)‐17A inhibitor ixekizumab vs. the IL‐23p19 inhibitor guselkumab in the IXORA‐R head‐to‐head trial achieved 100% improvement in Psoriasis Area and Severity Index (PASI 100) at week 12.

Objectives

To compare skin and nail clearance and patient‐reported outcomes for ixekizumab vs. guselkumab, up to week 24.

Methods

IXORA‐R enrolled adults with moderate‐to‐severe plaque psoriasis, defined as static Physician’s Global Assessment ≥ 3, PASI ≥ 12 and involved body surface area ≥ 10%. Statistical comparisons were performed using the Cochran–Mantel–Haenszel test stratified by pooled site. Time‐to‐first‐event comparisons were performed using Kaplan–Meier analysis, and P‐values were generated using adjusted log‐rank tests stratified by treatment group. Cumulative days at clinical and patient‐reported responses were compared by ancova. The trial was registered with ClinicalTrials.gov (NCT03573323).

Results

Of the 1027 patients randomly assigned, 90% completed the trial (465 of 520 ixekizumab and 459 of 507 guselkumab). As early as week 2 and through week 16, more patients on ixekizumab achieved PASI 100 (P < 0·01). At week 24, ixekizumab was noninferior to guselkumab (50% vs. 52%, difference −2·3%), with no statistically significant difference in PASI 100 (P = 0·41). More patients receiving ixekizumab showed completely clear nails at week 24 (52% vs. 31%, P = 0·007). The median time to first PASI 50/75/90 and PASI 100 were 2 and 7·5 weeks shorter, respectively, for patients on ixekizumab vs. guselkumab (P < 0·001). Patients on ixekizumab also had a greater cumulative benefit, with more days at PASI 90 and 100, with Dermatology Life Quality Index of 0 or 1, and itch free (P < 0·05). The frequency of serious adverse events was 3% for each group, with no new safety signals.

Conclusions

Ixekizumab was noninferior to guselkumab in complete skin clearance and superior in clearing nails at week 24. Ixekizumab cleared skin more rapidly in patients with moderate‐to‐severe plaque psoriasis, with a greater cumulative benefit, than guselkumab. Overall, the safety findings were consistent with the known safety profile for ixekizumab.

What is already known about this topic?

Patients with plaque psoriasis desire both high levels of clearance and rapid onset of treatment effects.

Ixekizumab is a high‐affinity monoclonal antibody that selectively targets interleukin (IL)‐17A.

In the 12‐week report of the IXORA‐R study, ixekizumab demonstrated significantly higher efficacy at early timepoints than the IL‐23p19 inhibitor guselkumab, with more patients achieving 100% improvement in Psoriasis Area and Severity Index (PASI 100) and improved quality of life as early as week 4.

What does this study add?

Patients on ixekizumab vs. guselkumab achieved similar levels of skin clearance and superior efficacy in the resolution of nail psoriasis at week 24.

Patients on ixekizumab vs. guselkumab had a greater cumulative benefit, with more days at PASI 90 and 100, more days when psoriasis did not impact their quality of life, and more itch‐free days.

The safety profiles of both drugs were consistent with those in previous studies.

Linked Comment: Puig. Br J Dermatol 2021; 184:992–993.

Disease activity and treatment efficacy using patient-level Psoriasis Area and Severity Index scores from tildrakizumab phase 3 clinical trials

BACKGROUND

It is unclear whether primary efficacy outcomes in plaque psoriasis clinical trials represent residual disease during treatment.

OBJECTIVES

To evaluate supplementing dichotomous efficacy with residual disease activity.

METHODS

This post hoc analysis used pooled, patient-level data after tildrakizumab 100 mg (N = 616) or placebo (N = 309) treatment from reSURFACE 1/2 (NCT01722331/NCT01729754) phase 3 clinical trials of patients with moderate to severe plaque psoriasis.

RESULTS

Median baseline Psoriasis Area and Severity Index (PASI) was 17.9 for patients receiving tildrakizumab 100 mg. At Week 12, median PASI was 2.9, whereas dichotomous PASI 90 response rate was 36.9%, and absolute PASI <5.0, <3.0, and <1.0 were 64.0%, 50.8%, and 23.3%, respectively. At Week 28, median PASI was 1.7, whereas PASI 90 response rate was 51.9%, and absolute PASI <5.0, <3.0, and <1.0 were 75.3%, 62.8%, and 38.0%, respectively. Dermatology Life Quality Index and PASI scores were correlated through Week 28 (r = 0.51, p ≤ .0001).

CONCLUSIONS

Disease activity was more reliably estimated by PASI scores than percentage PASI improvement; this may partially explain efficacy disparities between clinical trials and practice. These results suggest supplementing dichotomous PASI improvement with PASI scores and consideration of patient treatment goals could facilitate clinical decisions.

Baseline patient-reported outcomes from UNITE: an observational, international, multicentre registry to evaluate hidradenitis suppurativa in clinical practice

Background

Hidradenitis suppurativa (HS) is a chronic, inflammatory, skin condition associated with many comorbidities and often has a substantial impact on patients’ lives.

Objectives

To evaluate symptom burden and health‐related quality of life (HRQoL) at baseline in patients with HS in an observational, real‐world, clinical setting using several tools including a validated HS‐specific instrument.

Methods

This study evaluated HRQoL data from the international UNITE HS disease registry. Administration of patient‐reported outcome (PRO) instruments and collection of data were executed per local regulations. All data were assessed using descriptive statistical methods.

Results

PRO data from 529 adults and 65 adolescents were evaluated. Most adults (64.5%) and adolescents (73.8%) were classified as Hurley Stage II with substantial disease burden at baseline. HS had a large effect (mean DLQI = 12.6) and moderate effect (mean CDLQI = 6.9) on the lives of adults and adolescents, respectively. Approximately 58% of adults and 41% of adolescents had anxiety scores beyond the normal range; 30% of adults and 16% of adolescents exhibited symptoms of depression. Based on HSSA and HSIA scores, approximately 30% of adults reported a substantial burden of multiple HS clinical symptoms and more than 45% reported a significant emotional impact of HS that adversely affected their intimate relationships. Only 60% of adults were employed and of those, 64% reported at least some degree of impairment while working because of HS.

Conclusions

Based on PROs collected from patients enrolled in the UNITE registry, a real‐world, clinical setting, HS has a significant negative impact on the everyday lives of patients affected by this disease.

Phase II Trial of Carfilzomib Plus Irinotecan in Patients With Small-cell Lung Cancer Who Have Progressed on Prior Platinum-based Chemotherapy

INTRODUCTION

The purpose of this study was to evaluate the efficacy and tolerability of carfilzomib plus irinotecan (C/I) in patients with relapsed small-cell lung cancer (SCLC).

PATIENTS AND METHODS

Patients with SCLC who progressed after 1 platinum-containing regimen for recurrent or metastatic disease were eligible. Patients were stratified as: sensitive (SS) (progressive disease > 90 days after chemotherapy) or refractory (RS) (progressive disease 30 to 90 days after chemotherapy) and received up to 6 cycles of C/I; imaging was performed every 2 cycles. The primary endpoint was 6-month overall survival (OS).

RESULTS

All 62 patients enrolled were evaluable for efficacy and adverse events. 6-month OS was 59% in the platinum SS and 54% in the platinum RS. The overall response rate was 21.6% (2.7% complete response, 18.9% partial response) in SS (n = 37) and 12.5% (all partial response) in RS (n = 25). The disease control rate was 68% (SS) and 56% (RS). Progression-free survival and OS were 3.6 months (95% confidence interval [CI], 2.6-4.6 months) and 6.9 months (95% CI, 4.3-12.3 months) in SS, and 3.3 months (95% CI, 1.8-3.9 months) and 6.8 months (95% CI, 4.1-11 months) in RS. Twenty-nine (47%) patients experienced ≥ grade 3 adverse events; 8 (12.9%) subjects had grade 4 toxicities. Three treatment-related deaths occurred: myocardial infarction (possible), lung infection (possible), and sepsis (probable).

CONCLUSION

In patients with relapsed SCLC, C/I was effective in the treatment of SS and RS. With 4.8% grade 5 toxicity, C/I is a viable option for relapsed patients with SCLC with performance status 0 to 1, particularly in platinum-resistant patients, or subjects who cannot receive immunotherapy.

Development of optimal genetic evaluations for teat and udder structure in Canadian Angus cattle

Despite their heritability and influence on female productivity, there are currently no genetic evaluations for teat and udder structure in Canadian Angus cattle. The objective of this study was to develop optimal genetic evaluations for these traits in the Canadian Angus population. Guidelines recommended by Beef Improvement Federation (BIF) were used to score teat and udder structure in 1,735 Canadian Angus cows from 10 representative herds. Cows scored ranged in parity from 1 to 13; however, >70% of cows were parity ≤4. Scores ranged from 1 (large, bottle shaped) to 9 (very small) for teats and from 1 (very pendulous) to 9 (very tight) for udders. Consistent with parity distribution, >70% of teat and udder scores were ≥6. Teat and udder scores (TS9 and US9, respectively) were modeled using a multiple trait animal model with random effects of contemporary group (herd-year-season) and additive genetic effect, and fixed effects of breed, parity group, and days between calving and scoring. To test good versus poor structure, a binary classification of 1 or 2 (TS2, US2) [comprised of scores 1 to 5 = 1 (poor structure) and scores 6 to 9 = 2 (good structure)] was created. Further, to assess the impact of grouping less frequently observed poor scores, a 1 to 7 scale (TS7, US7) was created by combining teat and udder scores 1 to 3. Analyses for teat and udder scores on scales TS9, US9, TS7, US7, and TS2, US2 were compared. In addition, both threshold and linear animal models were used to estimate variance components for the traits. Data treatment and models were evaluated based on correlation of resulting estimated breeding value (EBV) with corrected phenotypes, Spearman's rank correlation coefficient, average EBV accuracies (r), and deviance information criteria (DIC). TS9, US9 scales for teat and udder scores and linear models performed best. Estimates of heritability (SE) for teat and udder score were 0.32 (0.06) and 0.15 (0.04), respectively, indicating these traits were moderately heritable and that genetic improvement for teat and udder scores was possible. Estimates of phenotypic and genotypic correlations for teat and udder score were 0.46 (0.02) and 0.71 (0.09), respectively. Estimates of genotypic correlations with birth weight (BW), weaning weight (WW), and yearling weight (YW), ranged from -0.04 (0.10) to -0.20 (0.12), verifying the importance of selecting for improved teat and udder score as individual traits, alongside performance traits.

Abstract 4945: Project Survival: Engineering a phenomic and artificial intelligence driven precision medicine biomarker pipeline for pancreatic adenocarcinomas

Pancreatic cancer is a complex and dynamic disorder necessitating a comprehensive clinical design integrated with robust OMICS technologies and AI analytics to identify potential molecular and clinical signatures of diagnosis, progression, and treatment outcomes. Project Survival is a multisite prospective longitudinal study currently in the 4th year of a 6 year initiative of sampling and analysis of subjects in 6 categories: healthy volunteers with a first degree relative with pancreatic cancer (N=39), pancreatitis (N=34), pancreatic cystic neoplasm (N=52), suspicious pancreatic masses with pathology other than pancreatic cancer (N=22), early stage (N=66), locally advanced (N=123), and metastatic pancreatic cancer (N=99). All diseased patients are longitudinally sampled multiple times per year for sera, plasma, buffy coat, saliva, urine, and tumor/adjacent normal tissue. The BERG Interrogative Biology® platform is employed for multi-omic mass spectrometry analysis (metabolomics, lipidomics and proteomics) and applies artificial intelligence (bAIcis®, BERG Artificial Intelligence Clinical Information System) technologies. bAIcis® is harnessed to align the multi-omic profiles with longitudinal clinical information to infer probabilistic cause-and-effect relationships among molecular and clinical variables in a network-based model. Multiple longitudinal time points continue to be collected during the course of the six-year timeline enabling dynamic modeling. The value of this longitudinal study is in the epidemiological assessment of patient type progression to more advanced stages and identification of biomarkers and clinical features that align with the shifts observed in the patient populations. Collectively, we are incorporating patient progression with longitudinal sampling to investigate predictive signatures of disease advancement. Biomarker panels with AUC &gt; 0.7 will be pursued in a further prospective clinical study with a larger subject number. The integration of multi-omic analysis with artificial intelligence has identified several biomarker panels that meet numerous unmet needs for the identification and clinical stratification of pancreatic adenocarcinoma.

Citation Format: Eric Michael Grund, Michael A. Kiebish, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, John J. Crowley, Amy Stoll-D'Astice, Tori Singer, Corinne Decicco, Wendy Hori, Abena Darkwah, Lixia Zhang, Valerie Bussberg, Leonardo O. Rodrigues, Emily Y. Chen, Tomislav Dragovich, Manuel Hidalgo, Niven R. Narain, A James Moser. Project Survival: Engineering a phenomic and artificial intelligence driven precision medicine biomarker pipeline for pancreatic adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4945.

Safety of selective IL-23p19 inhibitors for the treatment of psoriasis

Psoriasis is a chronic disease that requires long‐term treatment. Consequently, understanding the safety and tolerability of any potential treatment over time is critical to effective prescribing. The biologic agents currently available for the treatment of psoriasis target a number of different inflammatory cytokines involved in psoriasis disease pathogenesis. The monoclonal antibodies tildrakizumab, guselkumab and risankizumab target the p19 subunit that is specific to interleukin (IL)‐23. This article reviews published data on the safety of these IL‐23p19 inhibitors in patients with psoriasis compared with other currently available biologic therapies. Data from randomized, placebo‐ and active‐controlled phase 3 clinical trials show tildrakizumab, guselkumab and risankizumab to have a favourable risk–benefit profile in patients with moderate to severe psoriasis. No significant safety concerns have been observed for any of these IL‐23p19 inhibitors in the data published to date. The most commonly reported adverse events (AEs) associated with these agents in phase 3 studies were upper respiratory tract infections. No increase was seen in rates of serious infections, malignancies or major adverse cardiovascular events, with no signals suggestive of an elevated risk of opportunistic infections, active tuberculosis or reactivation of latent tuberculosis infection, mucocutaneous Candida infections, triggering or worsening of inflammatory bowel disease, demyelinating disorders or suicidal ideation. Selectively targeting IL‐23p19 may help avoid AEs that have been associated with biologic agents with other mechanisms of action. Data from long‐term extension studies and patient registries will further establish the safety profile of IL‐23p19 inhibitors for the treatment of moderate to severe psoriasis in routine practice.

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

BACKGROUND

Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations.

METHODS

Illumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb.

RESULTS

Seven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals.

CONCLUSIONS

Our results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis.

Modeling heterotic effects in beef cattle using genome-wide SNP-marker genotypes

An objective of commercial beef cattle crossbreeding programs is to simultaneously optimize use of additive (breed differences) and non-additive (heterosis) effects. A total of 6,794 multibreed and crossbred beef cattle with phenotype and Illumina BovineSNP50 genotype data were used to predict genomic heterosis for growth and carcass traits by applying two methods assumed to be linearly proportional to heterosis. The methods were as follows: 1) retained heterozygosity predicted from genomic breed fractions (HET1) and 2) deviation of adjusted crossbred phenotype from midparent value (HET2). Comparison of methods was based on prediction accuracy from cross-validation. Here, a mutually exclusive random sampling of all crossbred animals (n = 5,327) was performed to form five groups replicated five times with approximately 1,065 animals per group. In each run within a replicate, one group was assigned as a validation set, while the remaining four groups were combined to form the reference set. The phenotype of the animals in the validation set was assumed to be unknown; thus, it resulted in every animal having heterosis values that were predicted without using its own phenotype, allowing their adjusted phenotype to be used for validation. The same approach was used to test the impact of predicted heterosis on accuracy of genomic breeding values (GBV). The results showed positive heterotic effects for growth traits but not for carcass traits that reflect the importance of heterosis for growth traits in beef cattle. Heterosis predicted by HET1 method resulted in less variable estimates that were mostly within the range of estimates generated by HET2. Prediction accuracy was greater for HET2 (0.37-0.98) than HET1 (0.34-0.43). Proper consideration of heterosis in genomic evaluation models has debatable effects on accuracy of EBV predictions. However, opportunity exists for predicting heterosis, improving accuracy of genomic selection, and consequently optimizing crossbreeding programs in beef cattle.

Development and validation of a small SNP panel for feed efficiency in beef cattle

The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.

A total-population multigenerational family clustering study of autoimmune diseases in obsessive-compulsive disorder and Tourette's/chronic tic disorders

The association between obsessive-compulsive disorder (OCD) and Tourette's/chronic tic disorders (TD/CTD) with autoimmune diseases (ADs) is uncertain. In this nationwide study, we sought to clarify the patterns of comorbidity and familial clustering of a broad range of ADs in individuals with OCD, individuals with TD/CTD and their biological relatives. From a birth cohort of 7 465 455 individuals born in Sweden between 1940 and 2007, we identified 30 082 OCD and 7279 TD/CTD cases in the National Patient Register and followed them up to 31 December 2013. The risk of 40 ADs was evaluated in individuals with OCD, individuals with TD/CTD and their first- (siblings, mothers, fathers), second- (half siblings) and third-degree (cousins) relatives, compared with population controls. Individuals with OCD and TD/CTD had increased comorbidity with any AD (43% and 36%, respectively) and many individual ADs. The risk of any AD and several individual ADs was consistently higher among first-degree relatives than among second- and third-degree relatives of OCD and TD/CTD probands. The risk of ADs was very similar in mothers, fathers and siblings of OCD probands, whereas it tended to be higher in mothers and fathers of TD/CTD probands (compared with siblings). The results suggest a familial link between ADs in general (that is, not limited to Streptococcus-related conditions) and both OCD and TD/CTD. Additional mother-specific factors, such as the placental transmission of antibodies, cannot be fully ruled out, particularly in TD/CTD.

The IASLC Lung Cancer Staging Project: A Renewed Call to Participation

Over the past two decades, the International Association for the Study of Lung Cancer (IASLC) Staging Project has been a steady source of evidence-based recommendations for the TNM classification for lung cancer published by the Union for International Cancer Control and the American Joint Committee on Cancer. The Staging and Prognostic Factors Committee of the IASLC is now issuing a call for participation in the next phase of the project, which is designed to inform the ninth edition of the TNM classification for lung cancer. Following the case recruitment model for the eighth edition database, volunteer site participants are asked to submit data on patients whose lung cancer was diagnosed between January 1, 2011, and December 31, 2019, to the project by means of a secure, electronic data capture system provided by Cancer Research And Biostatistics in Seattle, Washington. Alternatively, participants may transfer existing data sets. The continued success of the IASLC Staging Project in achieving its objectives will depend on the extent of international participation, the degree to which cases are entered directly into the electronic data capture system, and how closely externally submitted cases conform to the data elements for the project.

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Stature is affected by many polymorphisms of small effect in humans ¹ . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes^2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10^-8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP-seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.

Improved ethical guidance for the return of results from psychiatric genomics research

There is an emerging consensus that genomic researchers should, at a minimum, offer to return to individual participants clinically valid, medically important and medically actionable genomic findings (for example, pathogenic variants in BRCA1) identified in the course of research. However, this is not a common practice in psychiatric genetics research. Furthermore, psychiatry researchers often generate findings that do not meet all of these criteria, yet there may be ethically compelling arguments to offer selected results. Here, we review the return of results debate in genomics research and propose that, as for genomic studies of other medical conditions, psychiatric genomics researchers should offer findings that meet the minimum criteria stated above. Additionally, if resources allow, psychiatry researchers could consider offering to return pre-specified 'clinically valuable' findings even if not medically actionable-for instance, findings that help corroborate a psychiatric diagnosis, and findings that indicate important health risks. Similarly, we propose offering 'likely clinically valuable' findings, specifically, variants of uncertain significance potentially related to a participant's symptoms. The goal of this Perspective is to initiate a discussion that can help identify optimal ways of managing the return of results from psychiatric genomics research.

Correlation of Long-term Results of Imatinib in Advanced Gastrointestinal Stromal Tumors With Next-Generation Sequencing Results: Analysis of Phase 3 SWOG Intergroup Trial S0033

IMPORTANCE

After identification of activating mutations of the KIT gene in gastrointestinal stromal tumor (GIST)-the most common sarcomaof the gastrointestinal tract-a phase 2 study demonstrated efficacy of imatinib mesylate in patients with metastatic GIST harboring a KIT exon 11 mutation. Initial results of long-term follow-up have found a survival benefit in this subgroup of patients.

OBECTIVE

To assess the long-term survival of patients with GIST who were treated in SWOG study S0033 and to present new molecular data regarding treatment outcomes.

DESIGN, SETTING, AND PARTICIPANTS

In this follow-up of randomized clinical trial participants (from December 15, 2000, to September 1, 2001), patients were required to have advanced GIST that was not surgically curable. Postprotocol data collection occurred from August 29, 2011, to July 15, 2015. Using modern sequencing technologies, 20 cases originally classified as having wild-type tumors underwent reanalysis. This intergroup study was coordinated by SWOG, a cooperative group member within the National Clinical Trials Network, with participation by member/affiliate institutions. This follow-up was not planned as part of the initial study.

INTERVENTIONS

Patients were randomized to 1 of 2 dose levels of imatinib mesylate, including 400 mg once daily (400 mg/d) vs 400 mg twice daily (800 mg/d), and were treated until disease progression or unacceptable toxic effects of the drug occurred.

MAIN OUTCOMES AND MEASURES

The primary end point was overall survival. Updated survival data were correlated with clinical and molecular factors, and patterns of postprotocol therapies were enumerated and described in long-term survivors.

RESULTS

Of 695 eligible patients (376 men [54.1%]; 319 women [45.9%]; mean [SD] age, 60.1 [14.0] years), 189 survived 8 years or longer, including 95 in the 400-mg/d dose arm and 94 in the 800-mg/d arm. The 10-year estimate of overall survival was 23% (95% CI, 20%-26%). Among 142 long-term survivors, imatinib was the sole therapy administered in 69 (48.6%), with additional systemic agents administered to 54 patients (38.0%). Resequencing studies of 20 cases originally classified as KIT/PDGFRA wild-type GIST revealed that 17 (85.0%) harbored a pathogenic mutation, most commonly a mutation of a subunit of the succinate dehydrogenase complex.

CONCLUSIONS AND RELEVANCE

A subset of patients with metastatic GIST experiences durable, long-term overall survival with imatinib treatment. Although this study provides guidance for management of GIST harboring the most common KIT and PDGFRA mutations, optimal management of other genotypic subtypes remains unclear.

TRIAL REGISTRATION

clinicaltrials.gov Identifier: NCT00009906.

Host conditioning and rejection monitoring in hepatocyte transplantation in humans

BACKGROUND & AIMS

Hepatocyte transplantation partially corrects genetic disorders and has been associated anecdotally with reversal of acute liver failure. Monitoring for graft function and rejection has been difficult, and has contributed to limited graft survival. Here we aimed to use preparative liver-directed radiation therapy, and continuous monitoring for possible rejection in an attempt to overcome these limitations.

METHODS

Preparative hepatic irradiation was examined in non-human primates as a strategy to improve engraftment of donor hepatocytes, and was then applied in human subjects. T cell immune monitoring was also examined in human subjects to assess adequacy of immunosuppression.

RESULTS

Porcine hepatocyte transplants engrafted and expanded to comprise up to 15% of irradiated segments in immunosuppressed monkeys preconditioned with 10Gy liver-directed irradiation. Two patients with urea cycle deficiencies had early graft loss following hepatocyte transplantation; retrospective immune monitoring suggested the need for additional immunosuppression. Preparative radiation, anti-lymphocyte induction, and frequent immune monitoring were instituted for hepatocyte transplantation in a 27year old female with classical phenylketonuria. Post-transplant liver biopsies demonstrated multiple small clusters of transplanted cells, multiple mitoses, and Ki67⁺ hepatocytes. Mean peripheral blood phenylalanine (PHE) level fell from pre-transplant levels of 1343±48μM (normal 30-119μM) to 854±25μM (treatment goal ≤360μM) after transplant (36% decrease; p<0.0001), despite transplantation of only half the target number of donor hepatocytes. PHE levels remained below 900μM during supervised follow-up, but graft loss occurred after follow-up became inconsistent.

CONCLUSIONS

Radiation preconditioning and serial rejection risk assessment may produce better engraftment and long-term survival of transplanted hepatocytes. Hepatocyte xenografts engraft for a period of months in non-human primates and may provide effective therapy for patients with acute liver failure.

LAY SUMMARY

Hepatocyte transplantation can potentially be used to treat genetic liver disorders but its application in clinical practice has been impeded by inefficient hepatocyte engraftment and the inability to monitor rejection of transplanted liver cells. In this study, we first show in non-human primates that pretreatment of the host liver with radiation improves the engraftment of transplanted liver cells. We then used this knowledge in a series of clinical hepatocyte transplants in patients with genetic liver disorders to show that radiation pretreatment and rejection risk monitoring are safe and, if optimized, could improve engraftment and long-term survival of transplanted hepatocytes in patients.

The IASLC Lung Cancer Staging Project: External Validation of the Revision of the TNM Stage Groupings in the Eighth Edition of the TNM Classification of Lung Cancer

INTRODUCTION

Revisions to the TNM stage classifications for lung cancer, informed by the international database (N = 94,708) of the International Association for the Study of Lung Cancer (IASLC) Staging and Prognostic Factors Committee, need external validation. The objective was to externally validate the revisions by using the National Cancer Data Base (NCDB) of the American College of Surgeons.

METHODS

Cases presenting from 2000 through 2012 were drawn from the NCDB and reclassified according to the eighth edition stage classification. Clinically and pathologically staged subsets of NSCLC were analyzed separately. The T, N, and overall TNM classifications were evaluated according to clinical, pathologic, and "best" stage (N = 780,294). Multivariate analyses were carried out to adjust for various confounding factors. A combined analysis of the NSCLC cases from both databases was performed to explore differences in overall survival prognosis between the two databases.

RESULTS

The databases differed in terms of key factors related to data source. Survival was greater in the IASLC database for all stage categories. However, the eighth edition TNM stage classification system demonstrated consistent ability to discriminate TNM categories and stage groups for clinical and pathologic stage.

CONCLUSIONS

The IASLC revisions made for the eighth edition of lung cancer staging are validated by this analysis of the NCDB database by the ordering, statistical differences, and homogeneity within stage groups and by the consistency within analyses of specific cohorts.

Antibiotic resistance among Helicobacter pylori clinical isolates in Lima, Peru

Objectives

Gastric carcinoma is the most common cancer and cause of cancer mortality in Peru. Helicobacter pylori, a bacterium that colonizes the human stomach, is a Group 1 carcinogen due to its causal relationship to gastric carcinoma. While eradication of H. pylori can help prevent gastric cancer, characterizing regional antibiotic resistance patterns is necessary to determine targeted treatment for each region. Thus, we examined primary antibiotic resistance in clinical isolates of H. pylori in Lima, Peru.

Materials and methods

H. pylori strains were isolated from gastric biopsies of patients with histologically proven H. pylori infection. Primary antibiotic resistance among isolates was examined using E-test strips. Isolates were examined for the presence of the cagA pathogenicity island and the vacA m1/m2 alleles via polymerase chain reaction.

Results

Seventy-six isolates were recovered from gastric biopsies. Clinical isolates showed evidence of antibiotic resistance to 1 (27.6%, n=21/76), 2 (28.9%, n=22/76), or ≥3 antibiotics (40.8%). Of 76 isolates, eight (10.5%) were resistant to amoxicillin and clarithromycin, which are part of the standard triple therapy for H. pylori infection. No trends were seen between the presence of cagA, vacA m1, or vacA m2 and antibiotic resistance.

Conclusion

The rate of antibiotic resistance among H. pylori isolates in Lima, Peru, is higher than expected and presents cause for concern. To develop more targeted eradication therapies for H. pylori in Peru, more research is needed to better characterize antibiotic resistance among a larger number of clinical isolates prospectively.

A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project

BACKGROUND

The Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequence information is an important part of achieving this goal as it facilitates efforts to associate specific DNA differences with phenotypic variation. These associations can be used to guide breeding decisions and provide valuable insight into the molecular basis of traits.

FINDINGS

We describe a dataset of 379 whole-genome sequences, taken primarily from key historic Bos taurus animals, along with the analyses that were performed to assess data quality. The sequenced animals represent ten populations relevant to beef or dairy production. Animal information (name, breed, population), sequence data metrics (mapping rate, depth, concordance), and sequence repository identifiers (NCBI BioProject and BioSample IDs) are provided to enable others to access and exploit this sequence information.

CONCLUSIONS

The large number of whole-genome sequences generated as a result of this project will contribute to ongoing work aiming to catalogue the variation that exists in cattle as well as efforts to improve traits through genotype-guided selection. Studies of gene function, population structure, and sequence evolution are also likely to benefit from the availability of this resource.

Age-related cataract in men in the selenium and vitamin e cancer prevention trial eye endpoints study: a randomized clinical trial

IMPORTANCE

Observational studies suggest a role for dietary nutrients such as vitamin E and selenium in cataract prevention. However, the results of randomized clinical trials of vitamin E supplements and cataract have been disappointing and are not yet available for selenium.

OBJECTIVE

To test whether long-term supplementation with selenium and vitamin E affects the incidence of cataract in a large cohort of men.

DESIGN, SETTING, AND PARTICIPANTS

The Selenium and Vitamin E Cancer Prevention Trial (SELECT) Eye Endpoints Study was an ancillary study of the Southwest Oncology Group-coordinated SELECT, a randomized placebo-controlled 4-arm trial of selenium and vitamin E conducted among 35,533 men, 50 years and older for African American participants and 55 years and older for all other men, at 427 participating sites in the United States, Canada, and Puerto Rico. A total of 11,267 SELECT participants from 128 SELECT sites participated in the SELECT Eye Endpoints ancillary study.

INTERVENTIONS

Individual supplements of selenium (200 μg per day from L-selenomethionine) and vitamin E (400 IU per day of all rac-α-tocopheryl acetate).

MAIN OUTCOMES AND MEASURES

Incident cataract was defined as a lens opacity, age related in origin, and responsible for a reduction in best-corrected visual acuity to 20/30 or worse based on self-reports confirmed by medical record review. Cataract extraction was defined as the surgical removal of an incident cataract.

RESULTS

During a mean (SD) of 5.6 (1.2) years of treatment and follow-up, 389 cases of cataract were documented. There were 185 cataracts in the selenium group and 204 in the no selenium group (hazard ratio, 0.91; 95 % CI, 0.75-1.11; P = .37). For vitamin E, there were 197 cases in the treated group and 192 in the placebo group (hazard ratio, 1.02; 95 % CI, 0.84-1.25; P = .81). Similar results were observed for cataract extraction.

CONCLUSIONS AND RELEVANCE

These data from a large cohort of apparently healthy men indicate that long-term daily supplementation with selenium and/or vitamin E is unlikely to have a large beneficial effect on age-related cataract.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT00784225.

A randomized controlled trial of vitamin E and selenium on rate of decline in lung function

Background

The intake of nutrients with antioxidant properties is hypothesized to augment antioxidant defenses, decrease oxidant damage to tissues, and attenuate age-related rate of decline in lung function. The objective was to determine whether long-term intervention with selenium and/or vitamin E supplements attenuates the annual rate of decline in lung function, particularly in cigarette smokers.

Methods

The Respiratory Ancillary Study (RAS) tested the single and joint effects of selenium (200 μg/d L-selenomethionine) and vitamin E (400 IU/day all rac-α-tocopheryl acetate) in a randomized double-blind placebo-controlled trial. At the end of the intervention, 1,641 men had repeated pulmonary function tests separated by an average of 3 years. Linear mixed-effects regression models estimated the effect of intervention on annual rate of decline in lung function.

Results

Compared to placebo, intervention had no main effect on either forced expiratory volume in the first second (FEV₁) or forced expiratory flow (FEF_25–75). There was no evidence for a smoking by treatment interaction for FEV₁, but selenium attenuated rate of decline in FEF_25–75 in current smokers (P = 0.0219). For current smokers randomized to selenium, annual rate of decline in FEF_25–75 was similar to the annual decline experienced by never smokers randomized to placebo, with consistent effects for selenium alone and combined with vitamin E.

Conclusions

Among all men, there was no effect of selenium and/or vitamin E supplementation on rate of lung function decline. However, current smokers randomized to selenium had an attenuated rate of decline in FEF_25–75, a marker of airflow.

Trial registration

Clinicaltrials.gov identifier: NCT00241865.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0195-5) contains supplementary material, which is available to authorized users.

Retained surgical stents as a cause of biliary obstruction in pediatric liver transplants

BACKGROUND

Small-caliber plastic stents are sometimes placed across the hepaticojejunostomy in liver transplant recipients at the time of biliary reconstruction. These stents usually pass spontaneously, but they can be retained and, rarely, this may cause biliary obstruction.

OBJECTIVE

The purpose of this paper is twofold: to describe the appearance of biliary tract obstruction caused by retained surgical stents in pediatric liver transplants, and to report how these stents can be removed using interventional radiology techniques.

MATERIALS AND METHODS

Three pediatric patients presenting with biochemical and imaging evidence of biliary obstruction were encountered over a 6-month period. At percutaneous cholangiography all patients were found to have retained surgical stents which appeared to be causing biliary tract obstruction. Percutaneous snaring of the stents was undertaken.

RESULTS

All stents were successfully removed using interventional radiology techniques, and follow-up showed no evidence of recurrent obstruction.

CONCLUSION

Surgical stents in children undergoing hepaticojejunostomy may be retained and cause biliary obstruction. Radiologists involved with imaging these patients should be aware of this potential cause of biliary obstruction. This complication is amenable to interventional radiology techniques with good long-term results. There is no easy endoscopic or surgical treatment option in these patients.

Long-term central venous access in pediatric patients at high risk: conventional versus antibiotic-impregnated catheters

PURPOSE

To study selective use of antibiotic-impregnated catheters in children at increased risk of venous catheter-related infections (CRIs).

MATERIALS AND METHODS

From December 2008 to June 2009, 428 peripherally inserted central catheters (PICCs) were placed by the interventional radiology service of a large metropolitan children's hospital. This retrospective study analyzed demographic and outcome data for the 125 patients in this group at high risk for venous CRI. Patients at high risk were those with active systemic infection, previous complicated central venous access, intensive care unit (ICU) admission, intestinal failure, transplantation, complex congenital heart disease, or renal failure. Patients (age, 7.6 y ± 7.0; 73 male and 52 female) received a conventional or antibiotic-impregnated PICC, with 17 receiving more than one catheter.

RESULTS

Of the 146 of 428 qualifying patient encounters (34%), 53 patients received an antibiotic-impregnated PICC and 93 received a conventional PICC, representing 5,080 total catheter-days (CDs). The rates of CRIs per 1,000 CDs, including catheter exit site infections and catheter-related bloodstream infections, were 0.86 for antibiotic-impregnated PICCs and 5.5 for conventional PICCs (P = .036). A propensity-based model predicts 15-fold greater infection-free survival over the lifetime of the catheter in patients who receive an antibiotic-impregnated PICC (P < .001). Antibiotic-impregnated PICC recipients with active infection or ICU admission at the time of insertion had no catheter-associated infections, compared with 3.42 and 9.46 infections per 1,000 CDs, respectively, for patients who received conventional PICCs. Patients with intestinal failure had 1.49 and 10 infections per 1,000 CDs with antibiotic-impregnated versus conventional PICCs, respectively.

CONCLUSIONS

Antibiotic-impregnated long-term PICCs significantly improve infection-free catheter survival in pediatric patients at high risk.

Copy number variation in schizophrenia in Sweden

Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500 kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry--genome-wide screens for CNVs, common variation and exonic variation--are converging on similar sets of pathways and/or genes.

A phase 2 trial of R1507, a monoclonal antibody to the insulin-like growth factor-1 receptor (IGF-1R), in patients with recurrent or refractory rhabdomyosarcoma, osteosarcoma, synovial sarcoma, and other soft tissue sarcomas: results of a Sarcoma Alliance for Research Through Collaboration study

BACKGROUND

Insulin-like growth factor-1 receptor (IGF-1R) is implicated in the pathogenesis of rhabdomyosarcoma (RMS), osteosarcoma (OS), and synovial sarcoma (SS). The authors conducted a multi-institutional phase 2 trial of the monoclonal antibody R1507 in patients with various subtypes of recurrent or refractory sarcomas.

METHODS

Eligibility criteria included age ≥ 2 years and a diagnosis of recurrent or refractory RMS, OS, SS, and other soft tissue sarcomas. Patients received a weekly dose of 9 mg/kg R1507 intravenously. The primary endpoint was the best objective response rate using World Health Organization criteria. Tumor imaging was performed every 6 weeks × 4 and every 12 weeks thereafter.

RESULTS

From December 2007 through August 2009, 163 eligible patients from 33 institutions were enrolled. The median patient age was 31 years (range, 7-85 years). Histologic diagnoses included OS (n = 38), RMS (n = 36), SS (n = 23), and other sarcomas (n = 66). The overall objective response rate was 2.5% (95% confidence interval, 0.7%-6.2%). Partial responses were observed in 4 patients, including 2 patients with OS, 1 patient with RMS, and 1 patient with alveolar soft part sarcoma. Four additional patients (3 with RMS and 1 with myxoid liposarcoma) had a ≥ 50% decrease in tumor size that lasted for <4 weeks. The median progression-free survival was 5.7 weeks, and the median overall survival was 11 months. The most common grade 3/4 toxicities were metabolic (12%), hematologic (6%), gastrointestinal (4%), and general constitutional symptoms (8%).

CONCLUSIONS

R1507 is safe and well tolerated but has limited activity in patients with recurrent or refractory bone and soft tissue sarcomas. Additional studies to help identify the predictive factors associated with clinical benefit in selected histologies such as RMS appear to be warranted.

International genetic evaluations for feed intake in dairy cattle through the collation of data from multiple sources

Feed represents a large proportion of the variable costs in dairy production systems. The omission of feed intake measures explicitly from national dairy cow breeding objectives is predominantly due to a lack of information from which to make selection decisions. However, individual cow feed intake data are available in different countries, mostly from research or nucleus herds. None of these data sets are sufficiently large enough on their own to generate accurate genetic evaluations. In the current study, we collate data from 10 populations in 9 countries and estimate genetic parameters for dry matter intake (DMI). A total of 224,174 test-day records from 10,068 parity 1 to 5 records of 6,957 cows were available, as well as records from 1,784 growing heifers. Random regression models were fit to the lactating cow test-day records and predicted feed intake at 70 d postcalving was extracted from these fitted profiles. The random regression model included a fixed polynomial regression for each lactation separately, as well as herd-year-season of calving and experimental treatment as fixed effects; random effects fit in the model included individual animal deviation from the fixed regression for each parity as well as mean herd-specific deviations from the fixed regression. Predicted DMI at 70 d postcalving was used as the phenotype for the subsequent genetic analyses undertaken using an animal repeatability model. Heritability estimates of predicted cow feed intake 70 d postcalving was 0.34 across the entire data set and varied, within population, from 0.08 to 0.52. Repeatability of feed intake across lactations was 0.66. Heritability of feed intake in the growing heifers was 0.20 to 0.34 in the 2 populations with heifer data. The genetic correlation between feed intake in lactating cows and growing heifers was 0.67. A combined pedigree and genomic relationship matrix was used to improve linkages between populations for the estimation of genetic correlations of DMI in lactating cows; genotype information was available on 5,429 of the animals. Populations were categorized as North America, grazing, other low input, and high input European Union. Albeit associated with large standard errors, genetic correlation estimates for DMI between populations varied from 0.14 to 0.84 but were stronger (0.76 to 0.84) between the populations representative of high-input production systems. Genetic correlations with the grazing populations were weak to moderate, varying from 0.14 to 0.57. Genetic evaluations for DMI can be undertaken using data collated from international populations; however, genotype-by-environment interactions with grazing production systems need to be considered.

Overview: progression-free survival as an endpoint in clinical trials with solid tumors

Progression-free survival (PFS) is increasingly used as an important and even a primary endpoint in randomized cancer clinical trials in the evaluation of patients with solid tumors for both practical and clinical considerations. Although in its simplest form, PFS is the time from randomization to a predefined endpoint, there are many factors that can influence the exact moment of when disease progression is recorded. In this overview, we review the circumstances that can devalue the use of PFS as a primary endpoint and attempt to provide a pathway for a future desired state when PFS will become not just a secondary alternative to overall survival but rather an endpoint of choice.

A randomized controlled Alzheimer's disease prevention trial's evolution into an exposure trial: the PREADViSE Trial

OBJECTIVES

To summarize the ongoing prevention of Alzheimer's disease (AD) by vitamin E and selenium (PREADViSE) trial as an ancillary study to SELECT (a large prostate cancer prevention trial) and to present the blinded results of the first year as an exposure study.

DESIGN

PREADViSE was designed as a double blind randomized controlled trial (RCT).

SETTING

SELECT terminated after median of 5.5 years of exposure to supplements due to a futility analysis. Both trials then converted into an exposure study.

PARTICIPANTS

In the randomized component PREADViSE enrolled 7,547 men age 62 or older (60 if African American). Once the trial terminated 4,246 of these men volunteered for the exposure study. Demographics were similar for both groups with exposure volunteers having baseline mean age 67.3 ± 5.2 years, 15.3 ± 2.4 years of education, 9.8% African Americans, and 22.0% reporting a family history of dementia.

INTERVENTION

In the RCT men were randomly assigned to either daily doses of 400 IU of vitamin E or placebo and 200 µg of selenium or placebo using a 2x2 factorial structure.

MEASUREMENTS

In the RCT, participants completed the memory impairment screen (MIS), and if they failed, underwent a longer screening (based on an expanded Consortium to Establish a Registry in AD [CERAD] battery). CERAD failure resulted in visits to their clinician for medical examination with records of these examinations forwarded to the PREADViSE center for further review. In the exposure study, men are contacted by telephone and complete the telephone version of the memory impairment screen (MIS-T) screen. If they fail the MIS-T, a modified telephone interview of cognitive status (TICS-M) exam is given. A failed TICS-M exam also leads to a visit to their clinician for an in-depth examination and forwarding of records for a centralized consensus diagnosis by expert clinicians. A subgroup of the men who pass the MIS-T also take the TICS-M exam for validation purposes.

RESULTS

While this ancillary trial was open to all 427 SELECT clinical sites, only 130 (30.0%) of the sites chose to participate in PREADViSE. Staff turnover at the sites presented challenges when training persons unfamiliar with cognitive testing procedures to conduct the memory screens. In the RCT few participants (1.6%) failed the MIS screen and among those who passed this screen a significant practice effect was encountered. In the exposure study 3,581 men were reached by phone in year 1, 15.7% could not be reached after 5 calls, and of those contacted 6.0% refused the screen even after consenting to the procedures at their clinical site. Most notable is that the failure rate for the MIS-T increased fourfold to 7.2%. Of the 257 men who took the TICS-M, 84.0% failed and were asked to contact their physicians for a more detailed memory assessment, and approximately half of these had some form of dementia or cognitive impairment. Several of these dementia cases are not AD.

CONCLUSION

Partnering with SELECT led to an AD prevention trial conducted at a very reasonable cost by taking advantage of the experience and efficient clinical trial management found in a cancer cooperative group (Southwest Oncology Group or SWOG). Once unblinded, the RCT and exposure study data have the potential to yield new information on long term exposure to antioxidant supplements under controlled conditions.

Efficacy of adalimumab across subgroups of patients with moderate-to-severe chronic plaque psoriasis of the hands and/or feet: post hoc analysis of REACH

Background

The Randomized Controlled Evaluation of Adalimumab in Treatment of Chronic Plaque Psoriasis of the Hands and Feet (REACH) trial demonstrated that adalimumab was efficacious and well-tolerated for the treatment of hand and/or foot psoriasis through 28 weeks.

Objective

To evaluate the effects of patient baseline characteristics on efficacy of adalimumab treatment of hand and/or foot psoriasis.

Methods

Patients with moderate-to-severe chronic plaque psoriasis of the hands and/or feet were randomized 2: 1 to adalimumab or placebo during the 16 week, double-blind period of REACH. Primary endpoint was percentage of patients achieving Physician’s Global Assessment of the hands and/or feet of clear/almost clear at week 16. Post hoc analyses evaluated effects of baseline patient characteristics on the primary endpoint. Patients with nail psoriasis at baseline were assessed for association of Nail Psoriasis Severity Index (NAPSI) 50 response with efficacy outcomes at week 16.

Results

Seventy-two patients (49 adalimumab: 23 placebo) were analysed. Greater percentages of adalimumab-treated patients achieved the primary endpoint vs. placebo across all subgroups. Among 31 patients with nail psoriasis, a greater percentage of adalimumab-treated patients achieved NAPSI 50 (56.5%) vs. placebo (12.5%) at week 16. In adalimumab-treated patients, greater percentages of NAPSI 50 Responders vs. Non-responders achieved the primary endpoint, and had greater improvements in erythema, scaling, induration and fissuring, Dermatology Life Quality Index, and pain scores.

Conclusions

Adalimumab was efficacious in treating chronic plaque psoriasis of the hands and/or feet over 16 weeks, regardless of baseline characteristics. Marked improvement in nail psoriasis among adalimumab-treated patients correlated with significant improvements in skin disease and patient-reported outcomes.

Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production

Genetic selection for residual feed intake (RFI) is an indirect approach for reducing enteric methane (CH4) emissions in beef and dairy cattle. RFI is moderately heritable (0.26 to 0.43), moderately repeatable across diets (0.33 to 0.67) and independent of body size and production, and when adjusted for off-test ultrasound backfat thickness (RFI fat) is also independent of body fatness in growing animals. It is highly dependent on accurate measurement of individual animal feed intake. Within-animal repeatability of feed intake is moderate (0.29 to 0.49) with distinctive diurnal patterns associated with cattle type, diet and genotype, necessitating the recording of feed intake for at least 35 days. In addition, direct measurement of enteric CH4 production will likely be more variable and expensive than measuring feed intake and if conducted should be expressed as CH4 production (g/animal per day) adjusted for body size, growth, body composition and dry matter intake (DMI) or as residual CH4 production. A further disadvantage of a direct CH4 phenotype is that the relationships of enteric CH4 production on other economically important traits are largely unknown. Selection for low RFI fat (efficient, -RFI fat) will result in cattle that consume less dry matter (DMI) and have an improved feed conversion ratio (FCR) compared with high RFI fat cattle (inefficient; +RFI fat). Few antagonistic effects have been reported for the relationships of RFI fat on carcass and meat quality, fertility, cow lifetime productivity and adaptability to stress or extensive grazing conditions. Low RFI fat cattle also produce 15% to 25% less enteric CH4 than +RFI fat cattle, since DMI is positively related to enteric methane (CH4) production. In addition, lower DMI and feeding duration and frequency, and a different rumen bacterial profile that improves rumen fermentation in -RFI fat cattle may favor a 1% to 2% improvement in dry matter and CP digestibility compared with +RFI fat cattle. Rate of genetic change using this approach is expected to improve feed efficiency and reduce enteric CH4 emissions from cattle by 0.75% to 1.0% per year at equal levels of body size, growth and body fatness compared with cattle not selected for RFI fat.

Risk of recurrent Helicobacter pylori infection 1 year after initial eradication therapy in 7 Latin American communities

IMPORTANCE

The long-term effectiveness of Helicobacter pylori eradication programs for preventing gastric cancer will depend on recurrence risk and individual and community factors.

OBJECTIVE

To estimate risk of H. pylori recurrence and assess factors associated with successful eradication 1 year after treatment.

DESIGN, SETTING, AND PARTICIPANTS

Cohort analysis of 1463 randomized trial participants aged 21 to 65 years from 7 Latin American communities, who were treated for H. pylori and observed between September 2009 and July 2011.

INTERVENTIONS

Randomization to 1 of 3 treatment groups: 14-day lansoprazole, amoxicillin, and clarithromycin (triple therapy); 5-day lansoprazole and amoxicillin followed by 5-day lansoprazole, clarithromycin, and metronidazole (sequential); or 5-day lansoprazole, amoxicillin, clarithromycin, and metronidazole (concomitant). Participants with a positive (13)C-urea breath test (UBT) 6 to 8 weeks posttreatment were offered voluntary re-treatment with 14-day bismuth-based quadruple therapy.

MEASUREMENTS

Recurrent infection after a negative posttreatment UBT and factors associated with successful eradication at 1-year follow-up.

RESULTS

Among participants with UBT-negative results who had a 1-year follow-up UBT (n=1091), 125 tested UBT positive, a recurrence risk of 11.5% (95% CI, 9.6%-13.5%). Recurrence was significantly associated with study site (P = .03), nonadherence to initial therapy (adjusted odds ratio [AOR], 2.94; 95% CI, 1.31-6.13; P = .01), and children in the household (AOR, 1.17; 95% CI, 1.01-1.35 per child; P = .03). Of the 281 with positive posttreatment UBT results, 138 completed re-treatment, of whom 93 tested UBT negative at 1 year. Among the 1340 who had a 1-year UBT, 80.4% (95% CI, 76.4%-83.9%), 79.8% (95% CI, 75.8%-83.5%), and 77.8% (95% CI, 73.6%-81.6%) had UBT-negative results in the triple, sequential, and concomitant groups, respectively (P = .61), with 79.3% overall effectiveness (95% CI, 77.1%-81.5%). In a single-treatment course analysis that ignored the effects of re-treatment, the percentage of UBT-negative results at 1 year was 72.4% (95% CI, 69.9%-74.8%) and was significantly associated with study site (P < .001), adherence to initial therapy (AOR, 0.26; 95% CI, 0.15-0.42; P < .001), male sex (AOR, 1.63; 95% CI, 1.25-2.13; P < .001), and age (AOR, 1.14; 95% CI, 1.02-1.27 per decade; P = .02). One-year effectiveness among all 1463 enrolled participants, considering all missing UBT results as positive, was 72.7% (95% CI, 70.3%-74.9%).

CONCLUSIONS AND RELEVANCE

One year after treatment for H. pylori infection, recurrence occurred in 11.5% of participants who had negative posttreatment UBT results. Recurrence determinants (ie, nonadherence and demographics) may be as important as specific antibiotic regimen in determining the long-term success of H. pylori eradication interventions. Study findings are relevant to the feasibility of programs for the primary prevention of gastric cancer in high-incidence regions of Latin America.

TRIAL REGISTRATION

clinicaltrials.gov Identifier: NCT01061437.

Patient income level and cancer clinical trial participation

PURPOSE

Studies have shown an association between socioeconomic status (SES) and quality of oncology care, but less is known about the impact of patient SES on clinical trial participation.

PATIENTS AND METHODS

We assessed clinical trial participation patterns according to important SES (income, education) and demographic factors in a large sample of patients surveyed via an Internet-based treatment decision tool. Logistic regression, conditioning on type of cancer, was used. Attitudes toward clinical trials were assessed using prespecified items about treatment, treatment tolerability, convenience, and cost.

RESULTS

From 2007 to 2011, 5,499 patients were successfully surveyed. Forty percent discussed clinical trials with their physician, 45% of discussions led to physician offers of clinical trial participation, and 51% of offers led to clinical trial participation. The overall clinical trial participation rate was 9%. In univariate models, older patients (P = .002) and patients with lower income (P = .001) and education (P = .02) were less likely to participate in clinical trials. In a multivariable model, income remained a statistically significant predictor of clinical trial participation (odds ratio, 0.73; 95% CI, 0.57 to 0.94; P = .01). Even in patients age ≥ 65 years, who have universal access to Medicare, lower income predicted lower trial participation. Cost concerns were much more evident among lower-income patients (P < .001).

CONCLUSION

Lower-income patients were less likely to participate in clinical trials, even when considering age group. A better understanding of why income is a barrier may help identify ways to make clinical trials better available to all patients and would increase the generalizability of clinical trial results across all income levels.

Patient income level and cancer clinical trial participation

PURPOSE

Studies have shown an association between socioeconomic status (SES) and quality of oncology care, but less is known about the impact of patient SES on clinical trial participation.

PATIENTS AND METHODS

We assessed clinical trial participation patterns according to important SES (income, education) and demographic factors in a large sample of patients surveyed via an Internet-based treatment decision tool. Logistic regression, conditioning on type of cancer, was used. Attitudes toward clinical trials were assessed using prespecified items about treatment, treatment tolerability, convenience, and cost.

RESULTS

From 2007 to 2011, 5,499 patients were successfully surveyed. Forty percent discussed clinical trials with their physician, 45% of discussions led to physician offers of clinical trial participation, and 51% of offers led to clinical trial participation. The overall clinical trial participation rate was 9%. In univariate models, older patients (P = .002) and patients with lower income (P = .001) and education (P = .02) were less likely to participate in clinical trials. In a multivariable model, income remained a statistically significant predictor of clinical trial participation (odds ratio, 0.73; 95% CI, 0.57 to 0.94; P = .01). Even in patients age ≥ 65 years, who have universal access to Medicare, lower income predicted lower trial participation. Cost concerns were much more evident among lower-income patients (P < .001).

CONCLUSION

Lower-income patients were less likely to participate in clinical trials, even when considering age group. A better understanding of why income is a barrier may help identify ways to make clinical trials better available to all patients and would increase the generalizability of clinical trial results across all income levels.

Practice effects in a longitudinal, multi-center Alzheimer's disease prevention clinical trial

Background

Practice effects are a known threat to reliability and validity in clinical trials. Few studies have investigated the potential influence of practice on repeated screening measures in longitudinal clinical trials with a focus on dementia prevention. The current study investigates whether practice effects exist on a screening measure commonly used in aging research, the Memory Impairment Screen (MIS).

Methods

The PREADViSE trial is a clinical intervention study evaluating the efficacy of vitamin E and selenium for Alzheimer’s disease prevention. Participants are screened annually for incident dementia with the MIS. Participants with baseline and three consecutive follow-ups who made less than a perfect score at one or more assessments were included in the current analyses (N=1,803). An additional subset of participants with four consecutive assessments but who received the same version of the MIS at baseline and first follow-up (N=301) was also assessed to determine the effects of alternate forms on mitigating practice. We hypothesized that despite efforts to mitigate practice effects with alternate versions, MIS scores would improve with repeated screening. Linear mixed models were used to estimate mean MIS scores over time.

Results

Among men with four visits and alternating MIS versions, although there is little evidence of a significant practice effect at the first follow-up, mean scores clearly improve at the second and third follow-ups for all but the oldest participants. Unlike those who received alternate versions, men given the same version at first follow-up show significant practice effects.

Conclusion

While increases in the overall means were small, they represent a significant number of men whose scores improved with repeated testing. Such improvements could bias case ascertainment if not taken into account.