bluuebunny/crossref_metadata_2025 huggingface dataset:
Crossover shortage in potato is caused byStMSH4mutant alleles and leads to either highly uniform unreduced pollen or sterility
Authors: Clot Corentin R , Klein Dennis , Koopman Joey , Schuit Cees , Engelen Christel J M , Hutten Ronald C B , Brouwer Matthijs , Visser Richard G F , Jurani Martina , van Eck Herman J
Published: November 2023

The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes. However, if CO shortage is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced male gametes, essentially composed of nonrecombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, CO shortage, a recessive trait previously referred to as desynapsis, was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the CO shortage locus and identified StMSH4, an essential component of the class I CO pathway, as the most likely candidate gene. A 7 base-pair insertion in the second exon of StMSH4 was found to be associated with CO shortage in our mapping population. We also identified a second allele with a 3,820 base-pair insertion and confirmed that both alleles cannot complement each other. Such nonfunctional alleles appear to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove alleles associated with CO shortage from their germplasm to improve fertility or to use them to produce highly uniform unreduced male gametes in alternative breeding schemes.
Physically motivated moment-tensor decomposition for mining-induced seismicity
Authors: Rigby Alex
Published: November 2023

Compared to existing schemes, the decomposition of moment tensors for mining-induced seismic events into closing-crack and double-couple components has the advantage that each can be interpreted in terms of a physical source process (excavation convergence and slip/shear, respectively). Obviously, not every moment tensor permits such a decomposition, and we translate existing bounds on those that do to the Hudson source-type plot. For moment tensors falling within these bounds, it has previously been noted that there will be a infinite set of possible decompositions in general. We derive an implicit equation defining this set and suggest physically motivated criteria that can be used to select a single decomposition from it. Furthermore, for moment tensors falling outside the source-type bounds, we present a simple geometric scheme for determining the closest moment tensor within them (which can then be decomposed). To demonstrate the methods developed in this paper, we apply them to two catalogues of mining-induced seismicity.
“More than just checking the box”: community-based organizations on their role in Medicaid redesigns
Authors: Tsering Dolma , Stauffer Claire M , Gittzus Jordan A , Byhoff Elena , Taylor Lauren A
Published: November 2023

New York and Massachusetts 1115 Medicaid demonstration waivers aimed to prioritize social determinants of health and engage community-based organizations to improve health outcomes. This is an evaluation of community-based organizations' public comments regarding their participation in social services delivery within the 1115 waivers. Both states solicited public comments on waiver implementation to date and potential improvements. The research team extracted all publicly available comments (n = 359) made by direct service providers between November 2016 and April 2019. The sample was then limited to only comments that discussed social service provision and health care–social service partnerships (n = 58). Findings are presented in 2 stages: (1) concerns regarding delivery system reform incentive payments funding levels, timing, and flow and (2) perspectives on how states and Medicaid administrators could improve health care–community organization relationships. Resource-dependent, community-based organizations protested insufficient funding. Additional comments identified specific design, structure, and implementation aspects of the 1115 waiver that could improve partnerships. Despite 1115 waivers prioritizing social service integration, community-based organizations still feel underfunded and disenfranchised. Aligning with health care standards requires significant time and effort. Given resource constraints, the state must facilitate these investments. Community organizations’ feedback can also offer guidance on waiver strategies in other states.
Network of GRAS transcription factors in plant development, fruit ripening and stress responses
Authors: Neves Catarina , Ribeiro Beatriz , Amaro Rute , Expósito Jesús , Grimplet Jérôme , Fortes Ana Margarida
Published: November 2023

The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.
Comparative judicial federalism
Authors: Gordon Jeffrey Steven
Published: November 2023

How does judicial federalism affect an apex court’s articulation of constitutional rights? Despite the growth of scholarship on comparative judicial review, federalism, and rights, comparative judicial federalism is underexplored. Building on an emerging literature, this article tentatively suggests that the authoritative declaration of constitutional rights may vary with a country’s particular species of judicial federalism. It first develops a qualitative framework for comparative judicial federalism, that is, the relationship between local (state) and central (federal) courts. The framework is structured around judicial federalism’s three dimensions: institutional, jurisdictional, and jurisprudential. After justifying these three dimensions, the article deploys them to compare Australia and the United States. It posits that in one context—federal free-speech limits on the common law—Australia’s purportedly modest implied freedom of political communication could resemble the powerful Free Speech Clause of the First Amendment. The relative degree of integration of central and local courts may affect the scope of the federal free-expression norm as articulated by the apex court.
The More Sophisticated, the More Biased? Testing a New Measure of Political Sophistication on Biased Information Processing
Authors: Valli Chiara , Eugster Beatrice , Arlt Dorothee
Published: November 2023

According to literature, biased information processing increases with political sophistication. The logic behind this relationship is that political sophisticates possess greater cognitive skills and knowledge to defend their prior beliefs. Although political sophistication can be understood as a multidimensional concept, existing research primarily uses general political knowledge as a proxy to assess it. Therefore, we introduce a more rigorous measure of sophistication that gauges individuals’ ability to justify their attitudes with substantive and well-elaborated arguments and put the classic measure of political sophistication to a test. We study these mechanisms in a direct-democratic setting via an online survey, in which 898 Swiss-German voters are exposed to a tailored counterargument on a political referendum. Our results indicate that individuals with higher levels of sophistication evaluate counter-attitudinal information less favorably and hold more stable opinions. While we did not find support for the hypothesis that sophistication leads to selective exposure to consonant information, our analysis points to a reverse mechanism: individuals with lower levels of sophistication exhibit a higher likelihood of exposure to dissonant views. Notably, these results align with the trends reported for general political knowledge and corroborate the validity of using general political knowledge as a proxy for political sophistication.
Naturally Acquired Transmission-Blocking Immunity Against Different Strains of Plasmodium vivax in a Malaria-Endemic Area in Thailand
Authors: Thongpoon Sataporn , Roobsoong Wanlapa , Nguitragool Wang , Chotirat Sadudee , Tsuboi Takafumi , Takashima Eizo , Cui Liwang , Ishino Tomoko , Tachibana Mayumi , Miura Kazutoyo , Sattabongkot Jetsumon
Published: November 2023

Background

Human immunity triggered by natural malaria infections impedes parasite transmission from humans to mosquitoes, leading to interest in transmission-blocking vaccines. However, immunity characteristics, especially strain specificity, remain largely unexplored. We investigated naturally acquired transmission-blocking immunity (TBI) against Plasmodium vivax, a major malaria parasite.

Methods

Using the direct membrane-feeding assay, we assessed TBI in plasma samples and examined the role of antibodies by removing immunoglobulins through protein G/L adsorption before mosquito feeding. Strain specificity was evaluated by conducting a direct membrane-feeding assay with plasma exchange.

Results

Blood samples from 47 patients with P vivax were evaluated, with 37 plasma samples successfully infecting mosquitoes. Among these, 26 showed inhibition before immunoglobulin depletion. Despite substantial immunoglobulin removal, 4 samples still exhibited notable inhibition, while 22 had reduced blocking activity. Testing against heterologous strains revealed some plasma samples with broad TBI and others with strain-specific TBI.

Conclusions

Our findings indicate that naturally acquired TBI is mainly mediated by antibodies, with possible contributions from other serum factors. The transmission-blocking activity of plasma samples varied by the tested parasite strain, suggesting single polymorphic or multiple targets for naturally acquired TBI. These observations improve understanding of immunity against P vivax and hold implications for transmission-blocking vaccine development.
LibCity-Dataset: a standardized and comprehensive dataset for urban spatial–temporal data mining
Authors: Wang Jingyuan , Jiang Wenjun , Jiang Jiawei
Published: November 2023

The LibCity-Dataset represents a significant contribution to the field of urban spatial-temporal data mining. This dataset uniquely integrates macro traffic state data with micro trajectory data, providing researchers with comprehensive and diverse urban spatial-temporal data. Specifically, we begin by collecting and processing existing open-source spatial-temporal data. Subsequently, we independently collected Beijing taxi trajectory data through third-party interfaces. This data bridges the gap in the scarcity of current open-source vehicle trajectory data. The distinctive aspect of the LibCity-Dataset lies in its innovative approach of standardizing the storage format, achieved through the implementation of atomic files. By adopting this standardized format, diverse data sources are harmonized, enabling effortless application of spatial-temporal prediction models across various datasets. The uniform storage format not only simplifies experimentation but also expedites the advancement of spatial-temporal prediction research, acting as a catalyst for further innovation. This Data Note provides a comprehensive insight into the creation methodology of the LibCity-Dataset, including data collection and processing methodology, data description, data validation, and usage notes. By facilitating open-source collaboration and setting a benchmark for standardization within the spatial-temporal prediction domain, this dataset aims to foster increased research cooperation and knowledge sharing. The open-source link of our dataset is https://drive.google.com/drive/folders/1g5v2Gq1tkOq8XO0HDCZ9nOTtRpB6-gPe.
High prevalence of Panton–Valentine Leucocidin among Staphylococcus coagulans isolated from dogs in Rio de Janeiro
Authors: Teixeira Izabel M , Guimarães Luciana , da Silva Isabella T , Fonseca Carolina , Assumpção Yasmim , Lima dos Santos Ana Luiza , Antunes Milena , Pesset Camilla , Ferreira Eliane , Penna Bruno
Published: November 2023

Aims

The purpose of this study was to characterize the capacity for biofilm formation, antimicrobial resistance rates, and search for genetic determinants of resistance and virulence in the species.

Methods and results

Strains were collected from asymptomatic and infected dogs. Identification was conducted using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), antimicrobial susceptibility using disk diffusion and PCR targeting mecA. Biofilm formation was evaluated on a microtiter plate assay. A total of 27 strains were selected for whole-genome sequencing. We identified 111 Staphylococcus coagulans. The highest number was obtained from infected dogs. The highest resistance rates were observed for penicillin, gentamicin, and ciprofloxacin/erythromycin. Twelve strains were characterized as resistant to methicillin. All isolates had the ability to form biofilm and were strong producers. Among Methicillin Resistant Staphylococcus coagulans (MRSC), SCCmec types IIIA, and Vc were identified. Acquired resistance genes, such as aac(6′)-aph(2′'), tet(K), blaZ, qacG, qacJ, and erm(C) were found. Different virulence genes were identified. Of note, Panton–Valentine Leucocidin was highly prevalent among the isolates.

Conclusion

Staphylococcus coagulans had a high isolation rate among infected dogs and demonstrated significant resistance to commonly used antibiotics such as penicillin and gentamicin.
431 Awardee Talk: Phenomics and Phenotyping in Animal Breeding
Authors: Steibel Juan P
Published: November 2023

Genomic prediction is now a mature technology for animal breeding and genetics and many breeders’ associations and livestock, and poultry genetics companies have adopted high-through genotyping for routine breeding value prediction and for assisting in selection decisions. In this context, more research efforts in breeding and genetics are focusing more on genome annotation and phenotyping. In animal breeding, the term phenomics is almost exchangeable with high-throughput phenotyping and automated phenotyping, i.e., the recording of high dimensional phenotypic data on an organism-wide scale. High throughput phenotyping is achieved through using a variety of sensors. The sensors generate raw data that must be captured, processed, cleaned, and modeled to produce meaningful phenotypes. Animal breeders are used to working with large amounts of data. However, high throughput phenomics usually produces data that may quickly overwhelm storage and processing capabilities of even the most prepared data analysis teams. Moreover, the black-box nature of many algorithms used to process raw sensor data into actionable phenotypes usually require thorough validation and checking. Animal breeders may build on prior lessons learned processing and modeling high-throughput genotypes and traditional phenotypes and we also need to adopt new practices commonly used in the field of machine learning and computer science. Finally, high throughput phenomics will produce novel phenotypes that will require different modeling or revisiting traditional models. In this talk I will share my views on all these points, and I will illustrate them using literature data and data from my own research related to computer vision, modeling of social genetic effects and modeling of social interactions.
142 Genotype-By-Environment Interactions in Dairy Cattle Raised in California and New England
Authors: Santana Bruna , Miles Asha , Tiezzi Francesco , Fragomeni Breno O
Published: November 2023

Genotype-by-environmental interactions (G x E) have been reported to cause sire reranking in dairy populations. However, the effects of such interactions are not included in the current US national dairy genetic evaluation. Phenotypes collected from animals across the country are considered the same trait, disregarding interactions between genetic effects and region or other environmental factors. Variations in production systems may interact with the genotypes of the animals, leading to distinct phenotypes. Separating data into regions could change decision-making on bull selection, which is the most important step of a breeding program. The goal of this study is to evaluate the extent of genotype-by-environment interaction between the state of California and the region of New England in the US Holstein Population. Data from Holstein cows in the aforementioned regions collected from 2010 to 2020 were provided by the Council on Dairy Cattle Breeding. The genetic evaluation models used for the national evaluation were modified to account for New England and California phenotypes as separated yet correlated traits. The mixed model accounted for additive genetic, sire-by-herd interaction, and permanent environmental effects as random, and for the management group, age of parity, birth year, and parity as fixed effects. In some scenarios, sire-by-herd interaction and permanent environment were removed due to convergence problems. Variance components were estimated using AIREML under the Method R procedure. Such a method allows computing variance components for large databases by splitting the data into several random groups. Ten random samples of data containing 100,000 records were used for each analysis. The scenarios included single trait for each state, single trait with both states, and two-trait with separated states. Breeding values from the top 100 bulls in each region were compared with evaluate potential sire reranking. Heritabilities varied across regions for all three traits (Table 1). California presented lower heritability than New England across methods. The genetic correlations on the two-trait analysis averaged at 0.96, 0.92, and 0.95 for yield, fat, and protein, respectively. The Spearman correlation coefficient between breeding values of the bulls with more than 200 daughters was 0.87 for milk yield, suggesting that the reranking is unimportant. The genetic correlations suggested that GxE between the two regions is small and that the traits should not be split in the current genetic evaluation. In conclusion, no critical effect of genotype-by-environment interaction was observed, even though top bulls may differ across regions. The next step of this project is to evaluate GxE for somatic cell score and to include genomic information in the evaluations. Finally, a genome-wide association study across the two regions will be performed to investigate changes in genomic regions associated with the phenotypes.
102 Development of a Bacteriophage-Based Feed Additive to Prevent Bovine Liver Abscesses
Authors: Mathieu Jacques , Laverde Jenny , Schwarz Cory , Tikhonova Marina , Miller Megan , Burdick Sanchez Nicole C , Carroll Jeffery A , Broadway Paul R , Alvarez Pedro
Published: November 2023

In the US, beef cattle feedlots commonly use antibiotic feed additives, such as tylosin and virginiamycin, to prevent liver abscesses, which can cause significant economic losses and animal welfare concerns. However, growing public and regulatory pressure to curb the proliferation of antibiotic resistant bacteria has prompted a need to reduce or eliminate their use. As an alternative, our group is working on a bacteriophage-based feed additive that targets Fusobacterium necrophorum, the primary cause of bovine liver abscesses, with the aim of reducing or eliminating the dependence on antibiotic feed additives. Using a combination of phage isolation techniques, we identified and characterized fifteen new F. necrophorum phages belonging to six genetically distinct groups. These phages exhibited a broad intraspecific host range and could infect various contemporary F. necrophorum strains isolated from different regions of the United States. All the phages were temperate, with dsDNA genomes ranging from around 36 kbp to 114 kbp. Almost all contemporary F. necrophorum isolates were found to have one or more active prophages upon bacterial genome sequencing and prophage induction. In vitro evolution resulted in the recovery of a potential virulent mutant, φBB37, which inhibited the growth of the high leukotoxin-producing F. necrophorum 8L1 strain for over 40 hours in vitro. Phage cocktails proved effective for up to 60 hours. After minimal optimization, most phages demonstrated high productivity (> 109 PFU/mL) and little yield variation during scale-up, highlighting their commercial potential. Unexpectedly, we discovered a previously unrecognized Fusobacterium species, Fusobacterium varium, is widely prevalent and frequently the most abundant member of the genus in cattle rumen. Previous studies on liver abscess control in cattle have almost exclusively focused on F. necrophorum, which may explain the lack of effectiveness observed. To elucidate the ecological role and potential pathogenicity of ruminal F. varium, we conducted genome sequencing and found these bovine strains to have multiple virulence factors and high similarity to human clinical isolates. However, phages with the ability to infect F. varium were plentiful in rumen fluid, with several demonstrating purely lytic activity. To assess the safety and in vivo dynamics of F. necrophorum and F. varium phage cocktails, a small-scale animal trial was recently conducted with ten cannulated cattle.
183 Assessment of Textural Characteristics and Instrumental Color of Commercially Available Whole-Muscle Jerky-Style Pet Treats
Authors: Romero Jorge , Carrera Hilary , Dunavant Justin , Berganza Ileana , Abascal-Ponciano Gerardo A , Sandoval Jorge L , Cho Sungeun , Starkey Jessica D , Starkey Charles
Published: November 2023

Textural and instrumental color quantitative data of consumables is often kept confidential by manufacturers, making it limited and difficult to find. These data are also important for product development and further sensory analysis to understand preferences and acceptability of purchasers. Between January 2019 and September 2020, 7,200 pet food products were launched worldwide. With a wide variety of pet treat brands and product types on the market, differentiation is necessary from a consumer purchase experience and physical characteristic preference perspective. The objective was to collect quantitative data on textural characteristics and instrumental color of whole-muscle jerky treats from 4 commercially available brands. Four whole muscle jerky treat brands were purchased for analyses: brand 1, brand 2, brand 3, and brand 4. Textural analyses included a three-point bend test for hardness (g), the maximum force required to break the sample; flexibility (mm), the displacement of the sample until it fractures; and stiffness (g per mm), resistance to bending; and the Warner-Bratzler test assessed firmness (g), the maximum force needed to shear the sample; and toughness (g per second), the peak positive area under the curve. Instrumental color was measured using a HunterLab MiniScan EZ spectrophotometer in terms CIE color space, L*, representing lightness on a range from black to white; a*, denoting redness ranging from green to red; and b*, representing yellowness ranging from blue to yellow. Data were analyzed as a 1-way ANOVA using the GLIMMIX procedure of SAS ver. 9.4, and least square means were separated using the PDIFF option. Brand 2 was significantly harder (P < 0.0001), and stiffer (P < 0.0001) than the rest of the brands, and Brand 4 was the most flexible (P = 0.0006). Brand 4 treats were the darkest, and brands 1 and 3 were among the brightest (P < 0.0001), although brand 3 was still similar to brand 2. Brand 3 expressed the greatest redness values and brand 4 the least (P < 0.0001). Brands 1, 2, and 3 were similar in yellowness and were all more yellow than brand 4 (P < 0.0001). When manufacturing pet treats, the goal is to achieve an appropriate texture, not soft enough to compromise its durability and integrity during manufacturing, packing, transportation, and retail, but soft enough to appeal to pet owners and dogs alike. These data will aid product developers by providing quantitative information that will eventually lead to corollary consumer sensory panel analysis to determine pet owner preferences and acceptability.
19 The Swine Gut Microbiome and Animal Production
Authors: Zhao Jiangchao
Published: November 2023

Recent studies have dramatically improved our understanding of the swine gut microbiome regarding its composition and correlations with animal phenotypes. However, many basic biological and ecological questions still remain to be answered. In addition, it is even challenging to translate basic gut microbiome research into industrial applications. During my presentation, I will first address several important ecological questions in two animal trials: a longitudinal study and a fecal microbiota transplantation experiment. Through big data analysis, we identified a probiotic candidate that correlates well with growth performance. We then re-analyzed two published data sets from other animal trials (isolated rearing and ZnO treatment). All four animal trials show a positive correlation between an F2 strain with growth performance. We isolated 200 F2 strains using a culturomics approach developed in my lab to establish a causal relationship between F2 and the host. After in vitro characterization of these isolates and whole genome sequencing, we conducted three animal trials to validate their probiotic effects and explore their underlying mechanisms. At the end of my presentation, I will discuss the future directions of animal gut microbiome.
208 Impact of Feeding a Novel Probiotic on Ruminal Fermentation, Methane Production, and Nutrient Utilization in Beef Cattle
Authors: Marenchino Ignacio Fernandez , Garcia Liza , Maderal Araceli B , Tarnonsky Federico , Podversich Federico , Vargas Juan , Cuervo Wilmer , Gomez-Salmoral Macarena , Ramirez-Sepulveda Vanesa , Blanchard Horacio , Novo Sabina , Schulmeister Tessa M , DiLorenzo Nicolas
Published: November 2023

The search for alternatives to mitigate enteric methane emissions remains a top priority to ensure the continued sustainability of the livestock industry. Exploration of new direct-fed microbials with potential in ruminant nutrition is an active and promising area of research. This study aimed to evaluate the effects of feeding a novel probiotic on ruminal fermentation parameters, in vitro methane production, and nutrient utilization in beef steers. A total of 12 ruminally cannulated American Aberdeen steers (348 ± 37 kg BW) were used in a 4 × 4 Latin square design, with each period lasting for 35 d. The steers were fed a basal diet comprised of 82% corn silage, 12% cotton gin trash, 5% cottonseed meal, and 1% vitamin and mineral supplement on a dry matter (DM) basis. Four treatments were used in this study: CTL (no additive), B2 (probiotic at a dosage of 2 × 109 CFU/animal/d), B10 (probiotic at a dosage of 10 × 109 CFU/animal/d), and B30 (probiotic at a dosage of 30 × 109 CFU/animal/d). Steers were housed in two pens and were sorted daily to receive the treatments individually in a carrier of corn silage (250 g/d). The experiment consisted of 4 periods, with 21 d of adaptation to the treatments, 7 d of measurements, and 7 d of washout between periods. During the study, two in vitro batch culture incubations were performed in each period collecting ruminal fluid from each animal individually (experimental unit): one on d 0 before steers received the treatments, and one after 21 d of adaptation. The incubations on day 0 were used as a baseline. The use of this probiotic did not affect (P > 0.05) in vitro ruminal fluid pH, volatile fatty acids, or acetate to propionate ratio. However, there was a cubic effect (P < 0.05) on in vitro organic matter digestibility with the inclusion of probiotic, and the greatest digestibility was observed in the B2 treatment. The concentration of ammonia nitrogen linearly increased (P < 0.05) with the inclusion of probiotic with CTL and B2 treatments showing the least values. While there was no effect (P > 0.05) on total gas production among treatments, methane production (CH4) was decreased (P < 0.05), showing a quadratic effect where the B2 treatment showed the least values. These results suggest that adding this novel probiotic to beef steers fed a corn silage-based diet at a dose of 2× 109 CFU per day (B2) may have positive results in reducing CH4 and improving digestibility. However, confirmation of these results will be required by in vivo methane emissions data.
65 Machine and Deep Learning Modelling Strategies for Body Weight Prediction of Cattle and Swine
Authors: Tulpan Dan
Published: November 2023

Machine Learning (ML) and Deep Learning (DL) are two sub-fields of that focus on creating predictive models from data. The algorithms used in ML and DL have been widely used in various livestock science studies, but it is uncommon for both ML and DL to be applied to the same problem. This talk presents examples where both ML and DL algorithms were successfully applied for prediction of body weight of cattle and swine. Often referred to as data-driven modelling, ML uses algorithms such as linear regression, Decision Trees, Artificial Neural Networks (ANNs) and Random Forests to generate predictive models from data. These models are then used to make predictions based on new input data. On the other hand, DL is a more advanced sub-field of AI that uses deep neural networks (a larger version of traditional ANNs) to make predictions. While the domain of application of DL is somewhat restricted to problems where datapoints have stronger relationships among them (e.g., digital images, text) DL algorithms can handle more complex relationships between input data and the target variable, making them ideal for solving more challenging problems. In the case of body weight prediction of cattle and swine, both ML and DL algorithms have been successfully used to make predictions. For example, ML algorithms have been used to predict body weight based on factors such as age, gender, and morphometric measurements. On the other hand, DL algorithms have been successfully for either direct predictions based on the relationship between body weight and other physiological parameters, such as feed intake or growth rate, or as an assistive technology for decluttering and segmentation of animal subjects from digital images with variable backgrounds. In conclusion, both ML and DL are useful tools in the field of livestock science, and both have been successfully used in the prediction of body weight of cattle and swine. However, the choice of which approach to use and its success rate will depend on the specific problem at hand and the complexity of the relationships between the input data and the target variable.
67 Leveraging Ai/Ml to Address Critical Challenges in Livestock Research
Authors: Clarke Jennifer
Published: November 2023

In recent years the scientific community has witnessed extraordinary growth in the development and application of techniques from Artificial Intelligence/Machine Learning (AI/ML) to address pressing societal challenges. Contrary to more traditional linear models, some AI/ML approaches suffer from a general lack of interpretability and in disciplines/industries where understanding biological relationships among predictor and predictand is important, utility and even trust in resulting predictions is a potential issue. Regardless, the livestock research community has shown considerable interest in the utilization of AI/ML methods, coupled with advanced cyberinfrastructure, to address large-scale data challenges from the use of sensors and internet of things (IoT) to solve problems related to animal identification, welfare, behavior detection, genome-to-phenome, and data quality concerns from large-scale non-research sources (to name a few). The effective application of AI/ML to problems in livestock research requires an understanding of what methods are available; the benefits and pitfalls of these methods; what resources are required including data and metadata, cyberinfrastructure, and interdisciplinary skills; best practices; and how AI/ML methods compare with alternative approaches. Awareness of the above-mentioned items is critical to avoid reproducibility issues and the possibility of using overly complex models for simple tasks. Each of these topics will be addressed, including a gentle introduction to AI/ML, in the context of examples from livestock research and a view towards future developments and application.
227 Evaluation of Beef Cattle Performance on Nontraditional Beef Cattle Finishing System Compared with Traditional Beef Cattle Finishing System
Authors: Guelker Lakan D , Karisch Brandi B , Rivera Daniel
Published: November 2023

While much research exists examining finishing cattle in conventional systems (confined cattle feeding, or feedlot systems), few data exist regarding finishing cattle in non-traditional systems, particularly in the micro-climates of the Gulf Coast. Non-traditional finishing systems feature additional variables and complexities versus feedlot finishing. The objective of this trial was to compare two non-traditional low input finishing cattle programs with a greater input traditional cattle finishing management program. Crossbred beef heifers [n = 12, initial body weight (BW) = 400 kg] were used to evaluate performance and cost of finishing beef cattle on limit-fed supplemental rations (CORN and SBH) compared with a totally mixed, free-choice ration (DIET). Animals were blocked by BW and randomly allotted to three treatments (CORN, n = 4; SBH, n = 4 and DIET n = 4). Two limit fed diets were combinations corn and a protein based mixing pellet (CORN) or soyhulls and a protein based mixing pellet (SBH), both fed at the rate of 1.9% of BW, while providing the heifers with free-choice access to bahiagrass (Paspalum notatum) forage during the summer months; DIET was a more conventional total mixed ration that provided both the concentrate and roughage component and included corn, soyhull pellets, mixing pellet, and cotton gin motes. Cattle were finished for 132 (n = 6) or 174 d (n = 6) and harvested at the MSU Meat Laboratory in Starkville located 235 miles from the trial location. Data were analyzed using MIXED procedure of SAS By design, dry matter intake during the entire finishing phase was greater (P = < 0.0001) for the free-choice DIET (10.8 kg. per day), compared with the limit fed diets (8.5 and 8.4 kg. per day). Overall average daily gain (ADG) was similar (P= 0.10) between both limit-fed diets (0.99 and 0.98 kg. per day for CORN and SBH). Average daily gain of cattle fed DIET (1.14 kg. per day) tended to be greater (P < 0.06) than both CORN and SBH diets. No differences were noted in G:F at any point during the study (P > 0.20). No differences (P > .0.05) were evident for slaughter weight, hot carcass weight, shrink, and dressing percentage among treatments. Total cost of gain for CORN and SOY were $1.74 and $1.65 cents per kilogram compared with DIET of $1.74 cents per kilogram (P = 0.76). Results indicate limit fed CORN and SBH diets could be a viable option to finish beef just as efficiently as a greater roughage total mixed ration (DIET).
80 Precision Nutrition to Enhance Poultry Performance and Health: the Role of Functional Amino Acids
Authors: Rochell Samuel J
Published: November 2023

Dietary amino acids drive the performance and meat yield of modern broiler strains, and as such, amino acids are among the most economically important nutrients in poultry feeds. At the same time, minimizing N excretion is an increasingly prevalent sustainability target for poultry producers across the world, and this goal is often pursued by feeding reduced crude protein diets. Moreover, poultry production has largely transitioned away from the use of in-feed antibiotic growth promoters, bringing attention to the impact of dietary protein and amino acid levels on the intestinal and overall health of broilers. In response to these dynamic scenarios, research from our lab and others has attempted to more precisely link dietary supply of essential and non-essential amino acids with their functional needs for broilers subjected to various pathogenic and environmental stressors. This presentation will address existing research and knowledge gaps related to functional amino acids in the context of precision nutrition to enhance poultry performance and health.
255 Effects of Dietary Valerate Glycerides on Serum Inflammatory Markers, Serum Metabolomic Profile, and Intestinal Mucosa Gene Expression in Weanling Pigs Infected with a Pathogenic Escherichia Coli
Authors: Kovanda Lauren L , Rengman Sofia , Tawde Snehal , Pos Jeroen , Kim Kwangwook , Liu Yanhong
Published: November 2023

Our previous work showed that dietary valerate glycerides reduced frequency of diarrhea and β-hemolytic coliforms in fecal cultures of pigs infected with F18+ Enterotoxigenic Escherichia coli (ETEC). However, the impact of these feed additives on the immune response and intestinal physiology of newly weaned pigs experiencing ETEC-associated diarrhea has not been evaluated. The present experiment aimed to determine the effects of dietary valerate glycerides on intestinal mucosa gene expression, systemic inflammatory status, and serum metabolomic profile of weanling piglets infected with F18+ ETEC. Sixty weaned piglets (6.97 ± 0.75 kg body weight; 21 days old) were randomly assigned to one of four dietary treatments: nursery basal diet (control), 0.075% or 0.1% monovalerin, or 0.1% trivalerin added to control. After a 7-day adaptation, all piglets were orally inoculated with F18+ ETEC (1010 CFU/3 mL) on d 0, d 1, and d 2 post-inoculation (PI). Serum samples were collected on d 0 prior to ETEC inoculation, d 3, d 6, and d 21 PI to analyze concentration of tumor necrosis factor-α (TNF-α), C-reactive protein (CRP), and haptoglobin. Serum samples from d 6 PI were submitted for untargeted metabolomics analysis at the West Coast Metabolomics Center. Six replicate pigs per treatment group were euthanized on d 7 PI to collect jejunal and ileal mucosa for gene expression analysis. Data were analyzed in RStudio by ANOVA in a linear mixed model with treatment as fixed effect and pig as random effect. Metabolomics analysis was performed using the online platform, MetaboAnalyst. Pigs fed trivalerin had reduced (P < 0.05) serum TNF-α on d 0 and d 6 PI compared with pigs in control. Whereas pigs supplemented with 0.1% monovalerin tended (P ≤ 0.10) to have decreased serum TNF-α on d 0 and d 3 PI, and less (P < 0.05) serum CRP on d 3 PI compared with pigs in control. No differences in serum concentrations of haptoglobin were detected among dietary treatments. Preliminary results for gene expression analysis indicate a tendency (P = 0.078) for increased mRNA expression of tight junction protein, ZO-1 in pigs fed 0.1% trivalerin compared with control. Among all valerate derivative treatments, significant fold changes [FC > 2, log2(FC) > 1] for individual metabolites were detected, where levels of adenosine, putrescine, and shikimic acid were decreased compared with the control group. No differential metabolomic profiles in serum were identified on d 6 PI as indicated by a lack of cluster separation using principal component analysis (PCA). In conclusion, valerate glycerides could regulate gene expression of the intestinal epithelium and systemic immune response of weanling piglets infected with F18+ ETEC.
275 Effects of Increased Nsp with Or Without Nspase Supplementation on Growth Performance, Intestinal Health, and Intestinal Microbiome of Nursery Pigs and Implications on Subsequent Phases of Production
Authors: Baker Jonathan T , Duarte Marcos Elias Elias , Kim Sung Woo , Gormley Alexa R , Jang Ki beom
Published: November 2023

This study aimed to investigate the effects of increased NSP from alternative feedstuffs in feeds with or without NSPase supplementation on growth performance, nutrient digestibility, intestinal health, immune status, and modulation of the intestinal microbiome of nursery pigs and the carryover effect from dietary nursery intervention on the subsequent phases of production. One hundred and sixty newly weaned pigs at 7.0 ± 0.3 kg BW were allotted in a 2 x 2 factorial arrangement with NSP level and NSPase supplementation serving as factors and sex as block. Pigs were assigned to one of 4 dietary treatments with the control having corn DDGS as the main source of NSP and HNSP having soy hulls and wheat bran replacing corn DDGS as the source of NSP. Pigs were fed for 37 d in 2 phases (19 d and 18 d, respectively) and housed in a pen of 4. Growth performance was measured at the end of each phase. At d 37, a pig representing the median BW within each pen from each treatment was euthanized for sampling jejunal mucosa, jejunal tissue, and ileal digesta to analyze intestinal health variables, oxidative stress products, and digesta viscosity. The remaining pigs were then fed a common diet for the subsequent grower and finisher phases to evaluate the carryover effect. At the end of the finisher phase, all pigs were euthanized to obtain carcass data. Data were analyzed using Mixed procedure of SAS 9.4. Overall, NSP level and type nor NSPase supplementation had an effect on growth performance; however, HNSP tended to have improved (P = 0.087) feed efficiency (0.52 to 0.53) in the grower period immediately following the nursery phase. Additionally, HNSP increased (P < 0.05) IgG (4.84 to 5.83 µg/mg of protein) in the jejunal mucosa and tended to increase (P = 0.096) the villus height in the jejunum (482.8 to 506.6 μm). The body weight of HNSP pigs was more uniform (P < 0.05; 8.7 to 11.6%) than the control at the end of the 120-day trial. No differences were observed in carcass traits however, the hot carcass weight of pigs in HNSP tended to be more uniform (P = 0.089; 6.4 to 10.00%) than the control. In conclusion, increased amounts of NSP from alternative feedstuffs does not further impair or damage the intestinal health and subsequent growth performance of nursery pigs and may aid the pig through generated metabolites and alterations to the intestinal microbiota as they are transitioned to the ensuing phases of production as evidenced by the increased uniformity at the end of the trial.
266 Interactive Effects of Dietary Isoleucine and Valine Ratios to Lysine in Response to Varying Leucine to Lysine Ratios on Hepatic Protein Expression in Commercial Broilers
Authors: Ventura Diego E , Almendares Cristopher I , Kriseldi Ruben , Corzo Alex , Adhikari Roshan , Lee Jason , Williams Chance , Starkey Charles , Starkey Jessica D
Published: November 2023

A central composite design (CCD) study was conducted to understand the relationship among dietary branched chain amino acid (BCAA) ratios and expression of proteins related to amino acid and protein metabolism in the liver of broilers. A total of 2,592 d-old Ross 344 × 708 male broilers were randomly placed in 144 floor pens. Each pen received 1 of 15 dietary treatments in a 23 CCD with 6 center points from 20 to 35 d of age, varying in digestible ratios of isoleucine:lysine (Ile:Lys; 52 to 75), valine:lysine (Val:Lys; 64 to 87), and leucine:lysine (Leu:Lys; 110 to 185). On d 35, 1 bird per pen was selected, euthanized, and liver tissue samples were collected for protein extraction and proteomic analysis via data independent acquisition protein sequencing with a timsTOF Pro 2 LC/MS/MS and Spectronaut 15 software. Dihydrolipoamide acetyltransferase (PDHX), aspartate aminotransferase (GOT2), branched-chain-amino-acid aminotransferase (BCAT1), diphosphomevalonate decarboxylase (MVD), acylamino-acid-releasing enzyme (APEH), and aspartate aminotransferase (GOT1) were identified and quantified. Protein quantification data were analyzed as a CCD using the RSREG procedure of SAS v. 9.4 with significance declared at P ≤ 0.10. When the individual AA effect in the response surface (RS) regression analysis was P ≤ 0.2, raw protein quantification data were analyzed as a 1-way ANOVA and the PDIFF option of SAS set at P ≤ 0.1 using the GLIMMIX procedure. The RS model for MVD and APEH expression were significant (P ≤ 0.0511). However, models for PDHX, GOT2, BCAT1, and GOT1 were not significant (P ≥ 0.1356) and the R2 values ≤ 0.25 for all proteins did not allow for prediction of protein expression means. No linear, quadratic, cross product, or individual BCAA ratio effects were observed for PDHX, GOT2, and BCAT1 (P ≥ 0.1977). A linear model for MVD and APEH protein expression (P ≤ 0.8030) and quadratic model for APEH (P ≤ 0.0552) were significant. MVD increased as Val:Lys ratio increased when Leu:Lys and Ile:Lys were fixed at 148 and 63 or 170 and 70, respectively (P ≤ 0.0926). Low Val:Lys ratio expressed the least hepatic APEH expression when Leu:Lys and Ile:Lys ratios were 148 and 63 or 125 and 70, respectably (P ≤ 0.0153). Hepatic MVD expression decreased as Leu:Lys ratio increased when Val:Lys and Ile:Lys were 75 and 63, respectably (P ≤ 0.0044). GOT1 expression was higher with 170 Leu:Lys ratio compared with 125, when Val:Lys and Ile:Lys ratio were 68 and 70, respectably (P ≤ 0.0460). APEH was greater with a low Ile:Lys ratio when Val:Lys and Leu:Lys were 68 and 125, respectably (P ≤ 0.0786). Varying concentrations of dietary BCAA and their interactions seem to alter hepatic protein expression and may help explain the mechanisms underlying their influence on broiler growth.