bluuebunny/crossref_metadata_2025 huggingface dataset:
Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon
Authors: Sato Mitsuhiko P , Iwakami Satoshi , Fukunishi Kanade , Sugiura Kai , Yasuda Kentaro , Isobe Sachiko , Shirasawa Kenta
Published: November 2023

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.
Impact of a clinician-to-clinician electronic consultation in heart failure patients with previous hospital admissions
Authors: Garcia-Vega David , Mazón-Ramos Pilar , Portela-Romero Manuel , Rodríguez-Mañero Moisés , Rey-Aldana Daniel , Sestayo-Fernández Manuela , Cinza-Sanjurjo Sergio , González-Juanatey José R
Published: November 2023

Aims

To evaluate the impact of an outpatient care management programme that includes a clinician-to-clinician e-consultation on delay time in care, hospital admissions, and mortality in a high-risk group of patients with heart failure (HF) and previous episodes of HF hospitalization (HFH).

Methods and results

We selected 6444 HF patients who visited the cardiology service at least once between 2010 and 2021. Of these, 4851 were attended in e-consult, and 2230 had previous HFH. Using an interrupted time series regression model, we analysed the impact of incorporating e-consult into the healthcare model in the group of patients with HFH and evaluated the elapsed time to cardiology care, HF, cardiovascular (CV), and all-cause hospital admissions and mortality, calculating the incidence relative risk (iRR). In the group of patients with HFH, the introduction of e-consult substantially decreased waiting times to cardiology care (8.6 [8.7] vs. 55.4 [79.9] days, P < 0.001). In that group of patients, after e-consult implantation, hospital admissions for HF were reduced (iRR [95%CI]: 0.837 [0.840–0.833]), 0.900 [0.862–0.949] for CV and 0.699 [0.678–0.726] for all-cause hospitalizations. There was also lower mortality (iRR [95%CI]: 0.715 [0.657–0.798] due to HF, 0.737 [0.764–0.706] for CV and 0.687 [0.652–0.718] for all-cause). The improved outcomes after e-consultation implementation were significantly higher in the group of patients with previous HFH.

Conclusion

In patients with HFH, an outpatient care programme that includes an e-consult significantly reduced waiting times to cardiology care and was safe, with a lower rate of hospital admissions and mortality in the first year.
The case for assessing oracy in primary and secondary schools in England
Authors: Khan Sullivan Ameena , Thomas MacGregor Annabel
Published: November 2023

The recognition of the importance of supporting children to learn to, and through, talk (often referred to as ‘oracy’) increasingly has prominence in educational and political discourse. However in the past decade the assessment of spoken language has been removed from GCSE exams, and nothing has replaced this vital measure of communication at a fundamental point in young people's progression. This article argues that this has helped to ensure oracy - speaking and listening - remains on the periphery, when increasingly evidence indicates that it should be central to all children and young people's education.
The pace of mitochondrial molecular evolution varies with seasonal migration distance
Authors: Pegan Teresa M , Berv Jacob S , Gulson-Castillo Eric R , Kimmitt Abigail A , Winger Benjamin M
Published: November 2023

Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than “fast” species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.
Coordinated Regulation of Myonuclear DNA Methylation, mRNA, and miRNA Levels Associates With the Metabolic Response to Rapid Synergist Ablation-Induced Skeletal Muscle Hypertrophy in Female Mice
Authors: Ismaeel Ahmed , Thomas Nicholas T , McCashland Mariah , Vechetti Ivan J , Edman Sebastian , Lanner Johanna T , Figueiredo Vandré C , Fry Christopher S , McCarthy John J , Wen Yuan , Murach Kevin A , von Walden Ferdinand
Published: November 2023

The central dogma of molecular biology dictates the general flow of molecular information from DNA that leads to a functional cellular outcome. In skeletal muscle fibers, the extent to which global myonuclear transcriptional alterations, accounting for epigenetic and post-transcriptional influences, contribute to an adaptive stress response is not clearly defined. In this investigation, we leveraged an integrated analysis of the myonucleus-specific DNA methylome and transcriptome, as well as myonuclear small RNA profiling to molecularly define the early phase of skeletal muscle fiber hypertrophy. The analysis of myonucleus-specific mature microRNA and other small RNA species provides new directions for exploring muscle adaptation and complemented the methylation and transcriptional information. Our integrated multi-omics interrogation revealed a coordinated myonuclear molecular landscape during muscle loading that coincides with an acute and rapid reduction of oxidative metabolism. This response may favor a biosynthesis-oriented metabolic program that supports rapid hypertrophic growth.
Methadone prescribing by addiction specialists likely to leave communities without available methadone treatment
Authors: Joudrey Paul J , Halpern Dylan , Lin Qinyun , Paykin Susan , Mair Christina , Kolak Marynia
Published: November 2023

Methadone treatment for opioid use disorder is not available in most suburban and rural US communities. We examined 2 options to expand methadone availability: (1) addiction specialty physician or (2) all clinician prescribing. Using 2022 Health Resources and Services Administration data, we used mental health professional shortage areas to indicate the potential of addiction specialty physician prescribing and the location of federally qualified health centers (ie, federally certified primary care clinics) to indicate the potential of all clinician prescribing. We examined how many census tracts without an available opioid treatment program (ie, methadone clinic) are (1) located within a mental health professional shortage area and (2) are also without an available federally qualified health center. Methadone was available in 49% of tracts under current regulations, 63% of tracts in the case of specialist physician prescribing, and 86% of tracts in the case of all clinician prescribing. Specialist physician prescribing would expand availability to an additional 12% of urban, 18% of suburban, and 16% of rural tracts, while clinician prescribing would expand to an additional 30% of urban, 53% of suburban, and 58% of rural tracts relative to current availability. Results support enabling broader methadone prescribing privileges to ensure equitable treatment access, particularly for rural communities.
Eudaimonic entertainment overcoming resistance: an update and expansion of narrative persuasion models
Authors: Moyer-Gusé Emily , Wilson Julia
Published: November 2023

A growing body of research reveals that entertainment narratives are persuasive across a variety of topics. Models of narrative persuasion highlight key mechanisms, but one limitation of this theorizing is that it has not directly considered the full range of entertainment narratives that exist. Viewers select media content to fulfill various needs—hedonic needs for pleasure and enjoyment or more eudaimonic needs gratified by appreciation and mixed affective responses. Narrative persuasion theorizing would benefit from explicitly considering eudaimonic entertainment narratives and how they may uniquely lead to persuasion. Doing so will expand on existing narrative persuasion mechanisms and identify contingencies regarding when and for whom distinct types of entertainment narratives may persuade. This article builds on the entertainment overcoming resistance model by advancing a set of testable propositions regarding narrative persuasion by meaningful entertainment and offering an agenda for future research in this area.
Function identification of miR159a, a positive regulator during poplar resistance to drought stress
Authors: Fu Tiantian , Wang Chun , Yang Yuzhang , Yang Xiaoqian , Wang Jing , Zhang Lichun , Wang Zeqi , Wang Yanwei
Published: November 2023

Drought seriously affects the growth and development of plants. MiR159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress responses. However, studies of its function in woody plants are still lacking. Here, the expression of miR159a was significantly upregulated after drought treatment in poplar, and the overexpression of miR159a (OX159a) significantly reduced the open area of the stomata and improved water-use efficiency in poplar. After drought treatment, OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type lines. MYB was the target gene of miR159a, as verified by psRNATarget prediction, RT–qPCR, degradome sequencing, and 5′ rapid amplification of cDNA ends (5′ RACE). Additionally, miR159a–short tandem target mimic suppression (STTM) poplar lines showed increased sensitivity to drought stress. Transcriptomic analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite synthesis. Moreover, drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a lines. This investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area, increasing the number and total area of xylem vessels, and enhancing water-use efficiency, and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.
Gauging the threat: exposure and attraction of sooty albatrosses and white-chinned petrels to fisheries activities in the Southern Indian Ocean
Authors: Banda Shamiso , Pistorius Pierre , Collet Julien , Corbeau Alexandre , Weimerskirch Henri , Pajot Adrien , Keys Danielle Z , Orgeret Florian
Published: November 2023

Bycatch risk assessments typically rely on spatial overlaps between seabirds and fishing vessels but should also consider seabirds’ position in the attraction spectrum. Investigating seabird-fishery interactions in relation to habitat use is vital for species-specific risk assessments. To address this, we studied interactions between sooty albatrosses (SA) and white-chinned petrels (WCP) with fisheries. GPS data from 20 SA and 18 WCP individuals from Marion Island were analysed alongside Automatic Identification System-derived boat locations over two breeding seasons. We calculated encounter and attraction rates and correlated them with marine habitat characteristics. SA interactions occurred in deeper, warmer waters compared to their foraging habitat when vessels were absent, with 20% of individuals encountering and only 5% being attracted to boats. In contrast, WCP interactions occurred in shallow, warm South African shelf waters, consistent with their typical foraging habitats, with 72% encountering and 56% attracted to boats. These results highlight the need for continued reinforcement of mitigation measures for WCP. Despite the low attraction rates for SA, ongoing vigilance is required due to their smaller population size, which heightens the potential impact of illegal fisheries. The comparison of species along an attraction spectrum contributes to refining risk assessments and informs species-specific conservation strategies.
Advances in robotic lung transplantation: development and validation of a new surgical technique in animal models
Authors: Ascanio Fernando , Royo-Crespo Iñigo , Rosado Joel , Sánchez Leire , Romero Laura , Durán-Rey David , Sánchez-Margallo Francisco , Jauregui Alberto
Published: November 2023

The objective of this study was to describe a novel minimally invasive robotic video-assisted approach for lung transplantation, utilizing a minimally invasive technique with a subxiphoid incision, in an animal experimentation model. Two left robotic-assisted single lung transplants were performed in sheep using a robotic surgical system. A subxiphoid incision was made, and robotic ports were inserted into the thoracic cavity for dissection and anastomoses of the bronchus, artery, and pulmonary veins. The integrity of anastomoses was evaluated, and procedural details were recorded. Both animals survived the procedure, with a mean duration of 255 min and a mean console time of 201 min. Anastomoses were performed without complications, and the closed-chest approach with a subxiphoid incision proved successful in preventing gas leakage. The novel approach demonstrated improved exposure and workflow compared to existing techniques. The minimally invasive robotic video-assisted approach for lung transplantation utilizing a closed-chest technique with a subxiphoid incision appears safe and feasible in an animal experimentation model. Further studies in the clinical setting are warranted to establish its feasibility and safety in human lung transplantation. This approach has the potential to offer benefits over the traditional Clamshell incision in lung transplantation procedures.
Remembering Martial Law: An Eco-System of Truth Initiatives and the Emergence of Narrative Documentation in the Philippines
Authors: Destrooper Tine
Published: November 2023

In the Philippines, governmental and civil society actors installed a range of mechanisms to deal with violent legacies of the Marcos regime. Formal truth-telling mechanisms were, however, not part of the early transitional justice architecture, meaning that truth-seeking initially took place as part of other justice efforts. Nonetheless, more recently, a boom in truth, documentation and memorialization processes has resulted in a dynamic eco-system of formal and informal truth initiatives, dealing with Martial Law as well as other violent legacies. This article argues that this eco-system of truth initiatives underlines the importance and potential of foregrounding the dissemination of truths through a decentralized approach to truth-telling, as well as the potential of ‘narrative documentation’ in doing so. I then explore how this eco-systemic approach to truth-telling, and the narrative documentation used as part of it, can be a meaningful strategy in the face of ongoing disinformation campaigns.
Airway and Blood Monocyte Transcriptomic Profiling Reveals an Antiviral Phenotype in Infants With Severe Respiratory Syncytial Virus Infection
Authors: Chappin K , Besteman S B , Hennus M P , Wildenbeest J G , Mokry M , Bont L J , van der Vlist M , Calis J J A ,   PROMISE Investigators, Chappin Klasina , Wildenbeest Joanne , Bont Louis , van der Vlist Michiel , Calis Jorg , Nair Harish , Pollard Andrew , Beutels Philippe , Openshaw Peter , Nohynek Hannah , Teirlinck Anne , Paget John , Heikkinen Terho , Martinón-Torres Federico , Kragten Leyla , Giaquinto Carlo , Diez-Domingo Javier , Mikolajczyk Rafael , Vernhes Charlotte , Janimak Jim , Htar Tin Tin , Aerssens Jeroen , Kumar Veena , Ahani Bahar , Molero Eva
Published: November 2023

Background

Respiratory syncytial virus (RSV) infection is the primary cause of lower respiratory tract infections in children <5 years of age. Monocytes, especially in the respiratory tract, are suggested to contribute to RSV pathology, but their role is incompletely understood. With transcriptomic profiling of blood and airway monocytes, we describe the role of monocytes in severe RSV infection.

Methods

Tracheobronchial aspirates and blood samples were collected from control patients (n = 9) and those infected with RSV (n = 14) who were admitted to the pediatric intensive care unit. Monocytes (CD14+) were sorted and analyzed by RNA sequencing for transcriptomic profiling.

Results

Peripheral blood and airway monocytes of patients with RSV demonstrated increased expression of antiviral and interferon-responsive genes as compared with controls. Cytokine signaling showed a shared response between blood and airway monocytes while displaying responses that were more pronounced according to the tissue of origin. Airway monocytes upregulated additional genes related to migration and inflammation.

Conclusions

We found that the RSV-induced interferon response extends from the airways to the peripheral blood. Moreover, RSV induces a migration-promoting transcriptional program in monocytes. Unraveling the monocytic response and its role in the immune response to RSV infection could help the development of therapeutics to prevent severe disease.
Review and assessment of technical and legal challenges in application of unmanned aerial vehicles in monitoring and inspection of bridges
Authors: Adibfar Alireza , Razkenari Mohamad , Costin Aaron
Published: November 2023

Intelligent transportation systems (ITSs) initiated a paradigm shift in the operation and management of transportation infrastructure by automating data collection, processing, and management. The drive toward using robotics to automate operational tasks in infrastructure management has gained significant momentum in recent years, with the introduction of unmanned aerial vehicles (UAVs), widely known as drones, being a notable milestone in this endeavor. UAVs reduced cost, time, and labor for tasks such as bridge monitoring while accelerating speed and precision such as structural scanning. Although not explicitly classified within the existing ITS categories, UAVs are becoming widely acknowledged as a valuable tool for improving the intelligent operation and management of transportation systems. Their potential to gather and transmit data in real time offers new opportunities for more accurate and timely decision-making as well as improved safety and efficiency within transportation infrastructure. Nevertheless, significant concerns remain regarding the use of UAVs, particularly in busy highways or densely populated metropolitan areas. Engineering and technical challenges, privacy and safety concerns, potential liabilities, and audio-visual disturbance for the public are among the issues that have impeded the widespread adoption and full integration of UAVs as complementary tools for ITS. This paper conducts a comprehensive review of the potential applications of UAVs for infrastructure and bridge structural health monitoring, while also evaluating the challenges associated with their utilization in this context. Furthermore, the paper discusses the ramifications of these challenges and emphasizes the areas that necessitate further attention and investigation by future research.
Digital twin in transportation infrastructure management: a systematic review
Authors: Yan Bin , Yang Fan , Qiu Shi , Wang Jin , Cai Benxin , Wang Sicheng , Zaheer Qasim , Wang Weidong , Chen Yongjun , Hu Wenbo
Published: November 2023

The concept of digital twin (DT) has emerged as a trend in various industries development, enabling the creation of virtual models of physical objects. We conduct a systematic review of the DT technology in the field of transportation infrastructure management from the aspects of concept definition, whole life cycle application, advanced technology, and equipment utilization, as well as the challenges. We begin with an introduction that defines DT and its components, while also distinguishing it from building information modeling and cyber-physical systems. We explore the diverse applications of DT throughout its lifecycle and highlight the significance of DT in structural monitoring, infrastructure operation and maintenance, and dataset expansion. We further investigate the advanced techniques and equipment associated with DT components, focusing on the importance of virtual parts, data acquisition, transmission, multi-source data fusion processing, and data security as well as dynamic updating of models for effective integration and utilization of DT in transportation infrastructure management. We identify key challenges faced by DT in transportation infrastructure management and propose future trends in the study. This comprehensive review serves as a valuable resource for researchers, practitioners, and decision-makers in understanding the potential of DT technology in transportation infrastructure management.
In-vitro polymicrobial oral biofilm model represents clinical microbial profile and disease progression during implant-related infections
Authors: Dini Caroline , Costa Raphael Cavalcante , Bertolini Martinna , Shibli Jamil Awad , Feres Magda , Klein Marlise Inêz , de Avila Érica Dorigatti , Souza João Gabriel Silva , Barão Valentim Adelino Ricardo
Published: November 2023

Aim

Clinically relevant in-vitro biofilm models are essential and valuable tools for mechanistically dissecting the etiopathogenesis of infectious diseases and test new antimicrobial therapies. Thus, the aim of this study was to develop and test a clinically relevant in-vitro oral polymicrobial biofilm model that mimics implant-related infections in terms of microbial profile.

Methods and Results

For this purpose, 24-well plate system was used to model oral biofilms, using three different microbial inoculums to grow in-vitro biofilms: (1) human saliva from periodontally healthy patients; (2) saliva as in inoculum 1 + Porphyromonas gingivalis strain; and (3) supra and subgingival biofilm collected from peri-implant sites of patients diagnosed with peri-implantitis. Biofilms were grown to represent the dynamic transition from an aerobic to anaerobic community profile. Subsequently, biofilms were collected after each phase and evaluated for microbiological composition, microbial counts, biofilm biomass, structure, and susceptibility to chlorhexidine (CHX). Results showed higher live cell count (P < .05) for biofilms developed from patients’ biofilm inoculum, but biomass volume, dry weight, and microbiological composition were similar among groups (P > .05). Interestingly, according to the checkerboard DNA–DNA hybridization results, the biofilm developed from stimulated human saliva exhibited a microbial composition more similar to the clinical subgingival biofilm of patients with peri-implantitis, with proportions of the main pathogens closer to those found in the disease. In addition, biofilm developed using saliva as inoculum was shown to be susceptible to CHX with significant reduction in bacteria compared with biofilms without exposure to CHX (P < .05).

Conclusion

The findings suggested that the in-vitro polymicrobial biofilm developed from human saliva as inoculum is a suitable model and clinically relevant tool for mimicking the microbial composition of implant-related infections.
108 Potential of Accelerometers to Remotely Detect Bovine Ephemeral Fever in Heifers Using Pattern Recognition
Authors: Trieu Ly Ly , Bailey Derek W , Cao Huiping , Son Tran Cao , Trotter Mark G , O'Connor Lauren , Tobin Colin T
Published: November 2023

Bovine Ephemeral Fever (BEF), an arthropod-borne rhabdovirus, is widespread in tropical and subtropical rangelands. It affects cattle with symptoms of fever, lameness, and inappetence, and can be a major economic impact. The goal of this study was to determine if accelerometer data can be used to identify the behavior patterns that occur when heifers become ill from BEF. The study was conducted from 24 August to 2 October 2016 in Rockhampton, Queensland, Australia. Eight heifers were monitored with 3-axis accelerometer sensors attached to collars. During the study, two heifers (1,402 and 1,413) were observed with BEF by the manager on 12 September and 1 October 2016, respectively. In this study, we demonstrated the potential of accelerometer data to autonomously detect the pattern and recognize when the heifers become sick by applying two different approaches, cosine similarity (CS) and deviation from previous behavioral patterns. Movement intensity (MI) and movement variation (MV) were calculated from accelerometer data using 1-minute epochs and then averaged into hour periods. Cosine similarity is a cosine of the angle between two data instances (MI or MV) that can be used to quantify their similarity. The time of illness detection by a veterinarian was compared with CS between the day of prediction and the average of 3 days before the prediction. Deviation is a measurement to calculate the sum or sum squares of the absolute difference of MI or MV between a day of prediction and the mean of 3 days before prediction for each corresponding hour. This approach is based on a hypothesis that when a heifer is sick, the heifer is likely less active during times it is normally active. When the heifer became ill with BEF, there were no similarities between the day of prediction and its 3 previous days resulting in a small CS value and potential illness detection, while there was a large difference between the day of prediction and its 3 previous days resulting in a high deviation value and a potential BEF detection metric. To determine how large deviation is or how small CS is to be considered abnormal behavior, the concept of outliers was evaluated using boxplots. A CS or deviation is an outlier if it is distant from other values of an individual animal. Our approaches show that heifer 1402 had behavioral changes one day before the manager observed BEF, and heifer 1413 had behavioral changes on the same day the manager observed BEF. This case study demonstrates the potential of using accelerometer data to detect disease autonomously. However, more research is to minimize false positives that may occur from other similar diseases, abnormal weather events or cyclical changes in behavior such as ostrus.
46 Next Generation Breeding Technologies Using Genome Editors to Address Animal Welfare and One-Health Challenges
Authors: Telugu Bhanu
Published: November 2023

Modern animal breeding based on marker-assisted selection, genomic selection, artificial insemination, and embryo transfer have led to a significant improvement in the performance of domestic animals, and are the basis for a regular supply of high quality animal derived food. However, the current strategy of breeding animals over multiple generations to introduce novel traits is not realistic in responding to the unprecedented challenges faced by animal agriculture. The vast majority of arable land around the world is already under production, with land use being further restricted by urbanization, production of biofuels, and climate change. Production practices related to animal welfare such as castration and dehorning are often vilified and continue to influence public opinion. Finally, risks of global pandemics affecting animals, such as foot-and-mouth disease virus, or zoonotic diseases that affect both humans and animals alike (e.g., influenza) are One-Health challenges that need to be tackled. Addressing these pressing challenges requires next generation breeding technologies using genome editors such that permit replacement or transfer of alleles (genetic information) between individuals, lines, breeds, and even species. The animal science community envisions the genome editors, specifically CRISPR/Cas9 system, as essential tools for addressing livestock genetic engineering for agriculture, and One-Health challenges.
119 Pedigree and Population-Based Genomic Inbreeding Trends Over Time in Five Commercial Swine Breeding Populations
Authors: Putz Austin M , Huisman Abe , Steibel Juan P
Published: November 2023

Controlling inbreeding within a population is critical to maintain additive genetic variance and reduce negative consequences such as inbreeding depression in small, closed herds. Some breeding programs may utilize subjective standard operating procedures (SOPs) such as setting the minimum number of boars, limiting the number of matings per boar, and limiting the relationships among active boars. Software programs such as Matesel can control inbreeding within a population more precisely using evolutionary algorithms by optimizing the mating and selection process to constrain inbreeding at a given target degree or other metric specified (e.g., coancestry). The main problem has been the choice of what relationship matrix to use in constraining inbreeding in these programs. Furthermore, there are many different genomic inbreeding metrics that can be used to quantify inbreeding rates over time. The objective of the current research was to investigate the trends in the pedigree [PED, (A diagonal – 1) * 100] and two population-based genomic inbreeding metrics. One based on expected homozygosity (2pq, Ghom) and one based on drift (squared allele frequency changes, Gdrift). Data included nucleus animals born from 2017 through 2022 from five different genetic lines (lines A-E). Most parents and male selection candidates were genotyped using the commercial 50k SNP panel from GeneSeek. Pedigree was traced back at least 3 generations. A total of 80k animals were sampled from the total number of genotyped animals for computational reasons across line and birth year. Results show that in general, the maternal lines (A and B) showed the least rate of inbreeding over time (0.30 and 0.43% / year for A and B, respectively), while terminal lines were greater, especially line D (0.36 to 0.76% / year). Pedigree inbreeding in 2022 was between 1.48% (line A) to 3.80% (line D) after subtracting the average pedigree inbreeding in 2017. Population-based genomic measures of inbreeding showed a very small difference in line A (0.09%), larger Gdrift than Ghom in line B (1.37%), and larger Ghom than Gdrift in lines C, D, and E (2.87% to 4.38%). In general, the trend for PED and Gdrift was very similar for all lines, while Ghom tended to increase rapidly out of control in the three terminal lines (C-E) in later years. Future research will focus on integrating results from the diagonals of a variety of G matrices on an individual basis (e.g., VanRaden 1 and 2, runs-of-homozygosity, and a linkage-analysis matrix). Results showed the pedigree and genomic drift trends over time were similar, however, the genomic homozygosity trend was much greater in terminal lines.
128 Reviewing the Definition of Mortality in Broiler Chickens
Authors: Richter Jennifer , Bussiman Fernando , Hidalgo Jorge A , Breen Vivian , Misztal Ignacy , Lourenco Daniela
Published: November 2023

Mortality has been a trait of importance in livestock species, especially for poultry, as birds continue to become more efficient and grow larger, and mortality rates have shown an increase at the phenotypic level. Mortality at different stages may be due to different genetic, environmental, and biological factors; however, in most cases, selection can be based on overall mortality. This study aimed to investigate alternative models and trait definitions of mortality by exploring the classification of mortality into different life stages and including a maternal effect in the model. Data provided by Cobb-Vantress, Inc. included mortality records from three separate lines of chicken making up about three generations worth of data. The datasets included records for mortality (0-1) and weekly mortality (0-10) recorded on individuals during their first ten weeks of life. Due to low incidence levels of weeks seven through ten for weekly mortality, those birds were combined with those that survived the first six weeks. Three models with different trait definitions were considered in this study. They were compared against a benchmark model with overall survival as trait definition (M0). Each line was evaluated separately for each model investigated, and the traits under different definitions were treated as binary traits. Thus, threshold models were used to estimate variance components under a Bayesian approach via the Gibbs sampling algorithm implemented in Gibbsf90+ software. The first model and trait definition (M1) investigated was a single trait model with weekly mortality classified into a binary response to whether the bird died within the first six weeks of life (BMORT). The second model and trait definition (M2) investigated was a bivariate model that classified weekly mortality into early (EMORT; weeks 1 to 3) and late (LMORT; weeks 4 to 6) mortality. The heritabilities ranged from 0.11 to 0.19 for M1, 0.10 to 0.21 for EMORT, and 0.15 to 0.17 for LMORT. For both models investigated, heritabilities were greater than that of M0, ranging from 0.03 to 0.09. The second model was additionally run with the maternal effect (M3) composed of the additive maternal and maternal permanent environmental (mpe) effects to investigate any potential effect on the estimated variance components. The maternal heritability and the percentage of phenotypic variance explained by mpe ranged from 0.02 to 0.03 and 0.01 to 0.04, respectively. Including the maternal effect considerably decreased direct heritability for EMORT but not for LMORT, indicating the maternal effect plays an important role in early mortality. The genetic correlations between EMORT and LMORT were low, ranging from 0.23 to 0.44; therefore, it may be necessary to include both traits in the selection index to make better-informed decisions. Selecting against early and late mortality may help improve overall livability in broiler chickens.
125 Implementing a Genetic Evaluation Program for Acute Hepatopancreatic Necrosis Disease Resistance in Penaeus Vannamei (Pacific White Shrimp)
Authors: Ampofo Issabelle , Mai Hung , Dhar Arun , Greevers Daniel , Wright Harris , Fragomeni Breno O
Published: November 2023

This study aims to evaluate the feasibility of a genomic evaluation program for Acute hepatopancreatic necrosis disease (AHPND) resistance in a commercial population of Penaeus vannamei. AHPND is caused by a strain of Vibrio parahaemolyticus (VpAHPND) producing a binary toxin. It is a World Organization for Animal Health (WOAH, Paris, France)-listed bacterial disease that has caused severe economic losses to the shrimp industry worldwide in recent years. The working hypothesis of this study is that the genetic variation in a commercial P. vannamei population allows an efficient genetic and genomic selection program. To investigate the genetic parameters for AHPND resistance, a controlled challenge experiment was performed at the Shrimp Improvement System biosafety laboratory in Miami, Florida, following an immersion challenge protocol using 4.95 × 107 CFU/ mL bacteria and Specific Pathogen Free (SPF) P. vannamei post larvae (n = 2,400) representing 40 selected families. The bioassay was terminated at 3 days post-challenge. Each family consisted of 60 animals, with one-half of the families (n = 20) representing a fast-growth (FG) line and the remaining one-half (n = 20) representing a slow-growth (SG) line. Survival was recorded as a binary of dead or alive at the end of the three days challenge experiment. Variance components were estimated under an animal threshold binary model using a Gibbs sampler. Estimation of genetic parameters was done within lines and by combining all data records. The average hazard risk ratio (HRR) of survival was 80% greater for the FG line (average mortality 40%) than the SG line (average mortality 20%, P < 0.05) based on survival analysis with a 31% mortality rate combining all data records. The posterior mean estimates of heritabilities were 0.14 (± 0.06) for FG, 0.16 (± 0.07) for SG, and 0.38 (± 0.08), combining all records. Estimated breeding values (EBVs) based on the animal threshold binary model ranged from -0.76 to 1.01 on the liability scale. Spearmans’ rank correlation coefficient between the average EBV of parents and the average mortality rates of corresponding families was 0.98. The results suggest that a breeding program for AHPND resistance is feasible. Moreover, the heritabilities suggest that both lines will respond to mass selection due to the presence of additive genetic variation for APHND-survivability. The next step of this project is to genotype animals from every family and implement a genomic selection program. Additionally, high throughput laboratory results and histopathology scores will be introduced in the genetic evaluation as correlated traits.
138 Sire Differences for Blood Urea Nitrogen (BUN) in Hereford Cattle
Authors: Hurst Caleb W , Enns R Mark , Huffhines Craig , Stackhouse-Lawson Kim R , Speidel Scott E
Published: November 2023

Excess Nitrogen excretion is a growing concern worldwide within animal agriculture, and blood urea nitrogen (BUN; mg/dL) is known as a predictor of nitrogen excretion in cattle. The objective of this study was to determine sire differences in BUN within a population of Hereford steers. Steers (n = 74) were born between March and June of 2021 from a reference sire herd for The American Hereford Association in Western Nebraska. Sixteen different Hereford sires from The American Hereford Association reference sire program produced offspring used in this study. The steers entered an on-site feed intake unit and were fed a finishing diet consisting predominantly of corn, corn distiller grain, and corn silage. Animals were subjected to a 21-d warm-up period with a 55-d individual feed intake test period. Blood samples were collected on day 43 of the test period. Blood samples were then centrifuged to extract serum. The Urea Nitrogen (BUN) Colorimetric Detection Kit by Invitrogen was used for the assay. The average BUN concentration for all animals in this study was (0.492 ± 0.061 mg/dL). A generalized linear regression model was used to determine sire differences in BUN concentrations. Factors considered were sire and pen group. The sire with lowest least squared mean progeny BUN concentration estimate was (0.0362 ± 0.08 mg/dL; n = 4), and the highest was (0.605 ± 0.03 mg/dL; n = 7). Sire differences (P < 0.05; r2 = 0.36) were found to be important sources of variation as evidenced by its r2; however, pen group (P = 0.65; r2 < 0.05) appeared to have little impact on variation. The differences in sires indicate genetic differences could be leveraged to reduce excess nitrogen excretion in cattle populations.
145 The Relationship of Methane Emissions with Stayability in Angus Cattle
Authors: Torres-Quijada Isaac F , Speidel Scott E , Zuvich Miranda L , Raynor Edward J , Carvalho Pedro H V , Place Sara E , Stackhouse-Lawson Kim R , Enns R Mark
Published: November 2023

The dairy and beef industries have been identified as an important producer of methane emissions, yet little is known of its relationship to other economically relevant traits. Stayability (STAY) is a fertility and longevity-related trait with EPD (Expected Progeny Differences) representing predicted genetic differences in the probability of daughters remaining in the breeding herd until six years of age. Understanding the relationship between methane emissions and STAY might inform breeders of the consequences of selection on either trait. The objective of this study was to determine the relationship of methane emissions with STAY in Angus cattle (Bos Taurus) from Colorado State University’s John E. Rouse Beef Improvement Center located in southern Wyoming. A total of 123 animals (86 steers, 37 heifers) were sorted into four different pens where individual methane emissions were measured using a GreenFeed system (C-Lock, Rapid City, South Dakota). Stayability was evaluated using EPD values. A general linear model was used to calculate the regression of the average methane emission of each animal measured in grams/day (mean = 163.08, SD = 38.75, min = 87.72, max = 247.03) on STAY (mean = 0.59, SD = 0.69, min = -2.41, max = 2.36), including age in days (mean = 258.2, SD = 20.01, min = 200, max = 298) and pen as effects in the model. The regression of methane emission on STAY EPD was 0.52, however, it was not significant (P = 0.87). The effect of pen was significant (P < 0.001?). Age was significant, having an effect of 0.6794 (P = 3.93e-08). This suggests that younger individuals had decreased methane emissions. These preliminary results indicate that there is no significant relationship between methane emissions and STAY EPD.
140 Targhee Sire Benchmarking at the U.S. Sheep Experiment Station
Authors: Wilson Carrie S , Taylor J Bret B , Murphy Tom W , Stewart Whit C , Notter David R , Lewis Ronald M
Published: November 2023

The Targhee breed was developed at the U.S. Sheep Experiment Station (USSES) starting in 1926, and has become an established range breed used commercially in the Western U.S. Our objective was to benchmark the performance of industry-based (external) Targhee sires with those currently in use at USSES. Nineteen Targhee sires from 12 flocks were incorporated into the USSES breeding flock starting with the 2015 breeding season. Data were measured through 2022 for 3 production and 12 wool traits with a range of 180 to 1,967 records per trait. Externally sourced sires averaged 38.3 progeny (7 to 78), with 0 to 4 ram lambs (15 total) and 0 to 15 (106 total) ewe lambs retained per sire in the flock. They were ancestors of 984 grand-progeny. USSES sires averaged 25.0 progeny (5 to 52), with 0 to 1 ram lambs (2 total) and 0 to 8 (53 total) ewe lambs retained per sire. They had 275 grand-progeny. Pedigree data was used to compute the marginal genetic contributions for each sire to the current flock using ENDOG. External sires had a cumulative contribution of 31.9 percent (0.4 to 3.9) while the USSES sires contributed 1.4 percent (0.0 to 0.9). Using R, fixed effects examined were age of dam, lamb sex, lamb birth year, grazing group, and type of birth/rearing. Significant variation explained in a trait by main effects (P < 0.005), and their two-way interactions (P < 0.001), were included in the final linear mixed models fitted. Externally sourced and USSES sires were assigned to separate genetic groups to account for the anticipated differences in genetic base. Using WOMBAT, a univariate animal model was fitted to estimate variance components and predict estimated breeding values for each lamb trait. Selection of random effects was based on log-likelihood ratio tests. Final models fitted and estimated heritabilities are summarized in Table 1. Total litter weight at 120 days per ewe lambing (TW120) was evaluated using a repeated measures model with direct additive and permanent environmental random effects of the ewe. Genetic group solutions were not significantly different (P > 0.05) for any traits evaluated. Since both sire groups originated from the same population, this suggests significant selection divergence had not occurred between industry and USSES flocks. Incorporation of external Targhee sires increased the genetic diversity of the USSES flock. It also strengthened industry ties to the USSES flock, which will benefit the commercial genetic evaluation conducted by the National Sheep Improvement Program. USDA is an equal opportunity provider and employer.
160 Effect of Diets Containing Soybean Co-Products Formulated for High-Risk Stocker Cattle on Growth Performance, Morbidity and Mortality Associated with Respiratory Disease
Authors: Midkiff Kirsten A , Kegley Beth B , Cheek Robin A , Galloway Doug L , Reynolds Jana L , Shoulders Benjamin P , Powell Jeremy G
Published: November 2023

The objectives of this study were to determine the effect of including soybean co-products on growth performance and respiratory disease incidence in high-risk stocker cattle. For this study, crossbred beef bulls and steers [n = 272; initial body weight (BW) 230.9 ± 19.7 kg] were purchased from local auction markets at 3 time points (load 1: n = 93 cattle; load 2: n = 91 cattle; load 3: n = 88 cattle). On day 0, cattle were processed (ear tagged, vaccinated, dewormed, ear notched for identification of cattle persistently infected with bovine viral diarrhea virus, castrated intact bulls), stratified by BW and allocated randomly to 1 of 8 pens (0.45 ha). Pens were assigned randomly to 1 of 3 dietary treatments: 1) a control supplement containing no soy co-products (CON); 2) a supplement containing soybean meal (SBM); or 3) a supplement containing soy oil (SBO). All supplements were isonitrogenous and isoenergetic. Cattle were fed supplements (2.45 kg DM/day) and offered bermudagrass hay for ad libitum intake for a 42-day trial. Body weights were taken on days 14, 28, 41, and 42 of the trial. Each morning, cattle were observed for signs of morbidity. If presenting with symptoms, cattle were pulled and rectal temperatures were recorded; if temperature exceeded 40°C, calves were treated according to a standard protocol. Cattle were deemed chronic if they received 3 antibiotic treatments and had an overall average daily gain (ADG) of less than 0.5 kg/d. Statistical analyses were performed using SAS 9.4, with PROC MIXED used for BW, ADG, and antibiotic cost analysis. Body weights were analyzed with the repeated measure of day and for treatment, day, and treatment by day interaction. PROC GLIMMIX was used for morbidity and mortality analyses. There was no treatment by day interaction (P = 0.99) or main effect of treatment (P = 0.86), but there was a day effect (P < 0.0001) with BW increasing throughout the trial. Average daily gain was not affected by treatment (P ≥ 0.42; 0.81 kg/d for SBM, 0.79 kg/d for SBO, and 0.76 kg/day for CON). Overall morbidity and mortality were 71% and 1%, respectively, and were not affected by treatment (P = 0.62 and P = 0.99, respectively). Relapse rates and chronics were not affected by treatment (P = 0.52 and P = 0.51, respectively). Total cost of antibiotic treatments was not different (P = 0.8; $30.37 for SBO, $28.95 for CON, and $28.52 for SBM). While the inclusion of soybean co-products did not affect BW, respiratory disease incidence, or cost of antibiotic treatments in high-risk stocker cattle, further work will focus on haptoglobin, hemocytology, and antibody titer responses during the receiving period.