Machine Learning-Aided Ultra-Low-Density Single Nucleotide Polymorphism Panel Helps to Identify the Tharparkar Cattle Breed: Lessons for Digital Transformation in Livestock Genomics.

Cattle breed identification is crucial for livestock research and sustainable food systems, and advances in genomics and artificial intelligence present new opportunities to address these challenges. This study investigates the identification of the Tharparkar cattle breed using genomics tools combined with machine learning (ML) techniques. By leveraging data from the Bovine SNP 50K chip, we developed a breed-specific panel of single nucleotide polymorphisms (SNPs) for Tharparkar cattle and integrated data from seven other Indian cattle populations to enhance panel robustness. Genome-wide association studies (GWAS) and principal component analysis were employed to identify 500 SNPs, which were then refined using ML models-AdaBoost, bagging tree, gradient boosting machines, and random forest-to determine the minimal number of SNPs needed for accurate breed identification. Panels of 23 and 48 SNPs achieved accuracy rates of 95.2-98.4%. Importantly, the identified SNPs were associated with key productive and adaptive traits, thus attesting to the value and potentials of digital transformation in livestock genomics. The ML-aided ultra-low-density SNP panel approach reported here not only facilitates breed identification but also contributes to preserving genetic diversity and guiding future breeding programs.

Impact of the Korea Early Childhood Home-visiting Intervention (KECHI) on child health and development and maternal health: a randomised controlled trial protocol.

INTRODUCTION: Randomised controlled trials (RCTs) of early childhood home-visiting interventions led by nurses have been conducted mainly in Western countries, whereas such trials have been limited in non-Western cultures, including Asia. In South Korea, a national nurse home visit programme (Korea Early Childhood Home-visiting Intervention (KECHI)) was developed in 2020 and launched throughout the country. We designed a pragmatic RCT to evaluate the effectiveness of KECHI on child health and development and maternal health. METHODS AND ANALYSIS: Eligible participants will be pregnant women at <37 weeks of gestation with risk factor scores of 2 or over, who are sufficiently fluent in Korean to read and answer the questionnaire written in Korean and live in districts where the KECHI services are available. Eight hundred participants will be recruited from the general community and through the District Public Health Centres. The participants will be randomised 1:1 to KECHI plus usual care or usual care. KECHI encompasses 25-29 home visits, group activities and community service linkage. Participants will complete assessments at baseline (<37 weeks gestation), 6 weeks, 6 months, 12 months, 18 months and 24 months post partum. The six primary outcomes will be (1) home environment (assessed by Infant/Toddler Home Observation for Measurement of the Environment), (2) emergency department visits due to injuries, (3) child development (assessed using Korean Bayley Scales of Infant and Toddler Development-III), (4) breastfeeding duration, (5) maternal self-rated health and (6) community service linkage. ETHICS AND DISSEMINATION: This trial has received full ethical approval from the Institutional Review Board of the Seoul National University Hospital. Written consent will be obtained from the participants. The results will be reported at conferences, disseminated through peer-reviewed publications and used by the Korean government to expand the KECHI services. TRIAL REGISTRATION NUMBER: NCT04749888.

The Destiny of the Subscapularis Tendon after Arthroscopic Supraspinatus Repair.

Background: The purpose of this study was to identify the changes in untreated subscapularis in patients who underwent supraspinatus repair and to evaluate the factors related to the changes in the subscapularis. Methods: A cohort of patients who underwent isolated supraspinatus repair with preservation of the subscapularis was reviewed. Changes in the subscapularis, including any newly formed lesion and aggravation of an existing lesion, were evaluated 12 months postoperatively on magnetic resonance imaging along with an examination to identify causative factors after supraspinatus repair. Clinical scores were compared between patients with and without subscapularis changes. Results: A total of 528 patients were reviewed. Changes in the subscapularis, including newly formed lesions and aggravation of an existing lesion, were shown in 90 patients (17.0%). Upon regression analysis, changes in the subscapularis were associated with the initial existence of a subscapularis lesion (grade I: p = 0.042, grade II: p = 0.025), an accompanying biceps lesion (p = 0.038), and a retear of the repaired supraspinatus (p = 0.024). No significant differences were shown in clinical scores between patients with and without subscapularis changes after supraspinatus repair. Conclusions: Untreated asymptomatic subscapularis may undergo morphological changes even after repair of the torn supraspinatus. Preoperative subscapularis lesions, biceps long head pathology, and retears of the repaired supraspinatus were associated with subscapularis pathology in patients who underwent supraspinatus repair.

Bursal Acromial Resurfacing Improves Shoulder Biomechanics in a Cadaveric Model of Massive Rotator Cuff Tear.

PURPOSE: To investigate the effectiveness of bursal acromial resurfacing (acromiograft) on acromiohumeral distance, subacromial contact area, and pressure in a cadaveric model of massive rotator cuff tear. METHODS: Eight fresh-frozen cadaveric shoulders were tested using a customized shoulder testing system. Humeral head translation, subacromial contact pressure, and the subacromial contact area were evaluated across 4 conditions: (1) intact shoulder; (2) simulated massive rotator cuff tear, (3) 3-mm acromiograft condition, and (4) 6-mm acromiograft condition. The acromiografts were simulated using Teflon and a reported technique. The values were measured at 0°, 20°, and 40° abduction and 0°, 30°, 60°, and 90° external rotation for each abduction status. RESULTS: Compared with a massive cuff tear, the 6-mm acromiograft significantly reduced the superior translation of the humeral head at all abduction/external rotation angles (P < .05). The 3-mm acromiograft also decreased superior translation of the humeral head compared with massive cuff tear, but not all differences were significant. The 3- and 6-mm acromiografts significantly decreased the subacromial contact pressure and increased the subacromial contact area in almost all positions (P < .05). The 3-mm acromiograft maintained biomechanical properties similar to the intact condition, whereas the 6-mm acromiograft increased the contact area. CONCLUSIONS: This biomechanical study demonstrated that both 3- and 6-mm acromiografts using Teflon in a cadaveric model of a massive cuff tear resulted in recentering of the superiorly migrated humeral head, increased the subacromial contact area, and decreased the subacromial contact pressure. The 3-mm graft was sufficient for achieving the intended therapeutic effects. CLINICAL RELEVANCE: The acromiograft can normalize altered biomechanics and may aid in the treatment of massive cuff tears. Because grafting the acromion's undersurface is new with limited clinical outcomes, further observation is crucial. Using a Teflon instead of an acellular dermal matrix allograft for bursal acromial resurfacing could yield different results, requiring careful interpretation.

Trajectories of nursing hours over the course of hospitalization and estimated additional nurse staffing requirements to reduce the length of stay.

PURPOSE: The aims of this study are to examine the trajectories of nursing hours per patient day (NHPPD) over the course of hospitalization according to the patient's length of stay (LOS) and to estimate changes in the total nursing hours during hospitalization, average NHPPD, and the number of nurses additionally required when the LOS was reduced by 1 day. DESIGN: This retrospective longitudinal study analyzed patient data collected from a tertiary university hospital located in Seoul, South Korea. The study sample included 11,316 inpatients who were discharged between September 1 and October 31, 2022. METHODS: NHPPD over the course of each patient's hospitalization was estimated using the total score of the Korean Patient Classification System-1 (KPCS-1), which nurses evaluated and recorded every day from admission to discharge. The NHPPD trajectories were examined using linear mixed models to analyze repeated KPCS-1 measurements and control for the effects of patient characteristics. The changes in the average NHPPD when LOS was reduced by 1 day were estimated using maximum and minimum estimations. The impact of a 1-day reduction in LOS on staffing requirements was calculated as the number of nurses additionally required to work each shift and to be hired. FINDINGS: The average LOS was 5.6 days, and the short (1-6 days) and medium (7-14 days) LOS groups accounted for 78.9% and 14.3% of patients, respectively. The NHPPD trajectories showed a "rise-peak-decline" pattern. Patients in the short LOS group received the most NHPPD on day 1 (day of admission) or day 2, whereas the NHPPD for patients in the medium LOS group peaked on days 3-6. After peaking, the NHPPD tended to decrease toward the end of hospitalization, with the least NHPPD on the day of discharge, followed by the day before discharge. When LOS was reduced by 1 day, the average NHPPD was estimated to increase by 7.7-50.0% in the maximum estimation, and 0.9-12.5% in the minimum estimation. In response to a 1-day reduction, 1.10-7.44 nurses were additionally required to care for 100 patients each shift and 5.28-35.70 additional nurses needed to be hired in the maximum estimation. In the minimum estimation, these values were 0.13-1.85 additional nurses per shift and 0.65-8.90 additional nurses to be hired, respectively. CONCLUSIONS: Since NHPPD exhibited a "rise-peak-decline" trajectory, reducing the LOS by 1 day was estimated to increase the average NHPPD and lead to additional staffing requirements. The additional nurse requirement for a 1-day reduction was not constant; instead, it increased with each day subtracted from an already shorter LOS. CLINICAL RELEVANCE: Sufficient nurse staffing is necessary to provide increased NHPPD as a result of shortened LOS. Changes in the LOS should be considered when determining nurse staffing requirements.

Respiratory Responses to Single Oral Administration of Taurine in Sprague-Dawley Rats.

Taurine is a nonessential amino acid that has been increasingly consumed due to its various beneficial biological effects. Excessive taurine intake has been linked to the positive regulation of inflammatory responses and endoplasmic reticulum stress through the modulation of intracellular calcium levels. However, research on the potential adverse effects of taurine consumption on the respiratory system is limited. To address this, we investigated the respiratory responses of 6-week-old male Sprague-Dawley rats to taurine administered orally at 0, 100, 200, and 400 mg/kg. Respiratory rate, tidal volume, and minute volume were monitored in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) Harmonized Tripartite Guideline S7A for Safety Pharmacology Studies for Human Pharmaceuticals. We found that taurine administration did not significantly alter respiratory rate or tidal volume; however, a significant increase in minute volume was observed 6 h after administration of 200 mg/kg taurine.

Editorial Commentary: Biceps Rerouting Augmentation Technique Restores Biomechanics, Improves Healing, and Has Many Advantages for Repair of Large and Massive Rotator Cuff Tears.

The biceps rerouting (BR) augmentation technique has emerged as a useful option for the repair of rotator cuff tears when the torn tendon does not cover the footprint or can only be reduced under excessive tension. BR offers several advantages over traditional methods. It is an all-inside joint procedure, eliminating the need for skin incisions other than those for the arthroscopic portal, thus reducing operative time and infection risk. It does not lead to donor-site morbidity, unlike superior capsular reconstruction. In addition, the rerouted long head of the biceps tendon serves as a depressor of the humeral head and an internal splint, protecting cuff healing. Finally, it provides a biceps tenodesis such that biceps-related symptoms are prevented postoperatively. Clinical studies have shown the efficacy of the BR technique, particularly in achieving low rates of retear. Although the BR technique is a nonanatomic reconstruction, its biomechanical impact effectively restores joint function to a state similar to the original. Considering these findings, the BR technique represents a significant advancement in managing large to massive rotator cuff tears, given its straightforward application and ability to re-establish joint biomechanics.

Searchable Blockchain-Based Healthcare Information Exchange System to Enhance Privacy Preserving and Data Usability.

Ensuring the security and usability of electronic health records (EHRs) is important in health information exchange (HIE) systems that handle healthcare records. This study addressed the need to balance privacy preserving and data usability in blockchain-based HIE systems. We propose a searchable blockchain-based HIE system that enhances privacy preserving while improving data usability. The proposed methodology includes users collecting healthcare information (HI) from various Internet of Medical Things (IoMT) devices and compiling this information into EHR blocks for sharing on a blockchain network. This approach allows participants to search and utilize specific health data within the blockchain effectively. The results demonstrate that the proposed system mitigates the issues of traditional HIE systems by providing secure and user-friendly access to EHRs. The proposed searchable blockchain-based HIE system resolves the trade-off dilemma in HIE by achieving a balance between security and the data usability of EHRs.

Online Classification of Unstructured Free-Living Exercise Sessions in People with Type 1 Diabetes.

Background: Managing exercise in type 1 diabetes is challenging, in part, because different types of exercises can have diverging effects on glycemia. The aim of this work was to develop a classification model that can classify an exercise event (structured or unstructured) as aerobic, interval, or resistance for the purpose of incorporation into an automated insulin delivery (AID) system. Methods: A long short-term memory network model was developed with real-world data from 30-min structured sessions of at-home exercise (aerobic, resistance, or mixed) using triaxial accelerometer, heart rate, and activity duration information. The detection algorithm was used to classify 15 common free-living and unstructured activities and relate each to exercise-associated change in glucose. Results: A total of 1610 structured exercise sessions were used to train, validate, and test the model. The accuracy for the structured exercise sessions in the testing set was 72% for aerobic, 65% for interval, and 77% for resistance. In addition, we tested the classifier on 3328 unstructured sessions. We validated the session-associated change in glucose against the expected change during exercise for each type. Mean and standard deviation of the change in glucose of -20.8 (40.3) mg/dL were achieved for sessions classified as aerobic, -16.2 (39.0) mg/dL for sessions classified as interval, and -11.6 (38.8) mg/dL for sessions classified as resistance. Conclusions: The proposed algorithm reliably identified physical activity associated with expected change in glucose, which could be integrated into an AID system to manage the exercise disturbance in glycemia according to the predicted class.

Respiratory Safety Pharmacological Testing with Single Intravenous Administration of Caffeine in Sprague-Dawley Rats.

As caffeine consumption continues to increase, both positive and negative effects are becoming evident. Caffeine directly affects the cardiovascular system, including heart function and rate. Thus, understanding the current respiratory safety pharmacological responses is of utmost importance. To elucidate the respiratory safety pharmacological characteristics of caffeine, male Sprague-Dawley rats, aged 6 weeks, were intravenously administered doses of 0, 2, 6, and 20 mg/kg of caffeine. Respiratory rate, tidal volume, and minute volume were subsequently measured. In this study, we observed a significant increase in respiratory rate and minute volume, but a remarkable reduction in tidal volume following the intravenous administration of caffeine at doses exceeding 6 mg/kg. These changes were evident within the timeframe of 0.25 to 1.5 h. The data we have collected can serve as valuable foundational scientific information for future research on caffeine, encompassing absorption, distribution, metabolism, excretion, and pharmacological core-battery experiments.

Varus-valgus alignment of humeral short stem in reverse total shoulder arthroplasty: does it really matter?

BACKGROUND: The utilization of short humeral stems in reverse total shoulder arthroplasty has gained attention in recent times. However, concerns regarding the risk of misalignment during implant insertion are associated with their use. METHODS: Eight fresh-frozen cadaveric shoulders were prepared for dissection and biomechanical testing. A bespoke humeral implant was fabricated to facilitate assessment of neutral, varus, and valgus alignments using a single stem, and 10° was established as the maximum permissible angle for misalignments. Shift in humerus position and changes in deltoid length attributable to misalignments relative to the neutral position were evaluated using a Microscribe 3DLx system. The impingement-free range of motion, encompassing abduction, adduction, internal rotation, and external rotation (ER), was gauged using a digital goniometer. The capacity for abduction was evaluated at maximal abduction angles under successive loading on the middle deltoid. A specialized traction system coupled with a force transducer was employed to measure anterior dislocation forces. RESULTS: Relative to the neutral alignment, valgus alignment resulted in a more distal (10.5 ± 2.4 mm) and medial (8.3 ± 2.2 mm) translation of the humeral component, whereas the varus alignment resulted in the humerus shifting more superiorly (11.2 ± 1.3 mm) and laterally (9.9 ± 0.9 mm) at 0° abduction. The valgus alignment exhibited the highest abduction angle than neutral alignment (86.2°, P < .001). Conversely, the varus alignment demonstrated significantly higher adduction (18.4 ± 7.4°, P < .001), internal rotation (68.9 ± 15.0°, P = .014), and ER (45.2 ± 10.5°, P = .002) at 0° abduction compared to the neutral alignments. Anterior dislocation forces were considerably lower (23.8 N) in the varus group compared to the neutral group at 0°ER (P = .047). Additionally, abduction capability was markedly higher in varus alignment at low deltoid loads than the neutral alignment (5N, P = .009; 7.5 N, P = .007). CONCLUSIONS: The varus position enhances rotational range of motion (ROM) but increases instability, while the valgus position does not significantly impact ROM or instability compared to the neutral position.

Distributed Detour Routing Scheme for Link Failure with Minimized Overhead in LEO Satellite Networks.

The mobility of low Earth orbit (LEO) satellites causes the LEO satellite network to experience topology changes. Topology change includes periodic topology change that occurs naturally and unpredictable topology change that occurs due to instability of the inter-satellite link between satellites. Periodic and unpredictable topology change causes frequent topology change, requiring massive communications throughout the network due to frequent route convergence. LEO satellites have limited onboard power because they operate on batteries. The waste of limited satellite onboard resources shortens the lifespan of the satellite, and achieving stable end-to-end transmission is challenging for the network. In this regard, minimizing communication overhead is a fundamental consideration when designing a routing scheme. In this paper, we propose a distributed detour routing scheme with minimal communication overhead. This routing scheme consists of a rapid detour, selective flooding, and link recovery procedures. When a link failure occurs in the network, a rapid detour can detect link failure using only a precalculated routing table. Subsequently, selective flooding searches for the optimal detour point within the minimum hop region and flood to detour point. After link recovery, a procedure is defined to traverse the pre-detour path and switch it back to the original path. The simulation results show that the proposed routing scheme achieves a reduction of communication overhead by 97.6% compared with the n-hop flooding approach.

A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population.

The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published. The majority of these studies focused on pigs and cattle; the association between fatty acid composition and meat quality in chickens has rarely been reported. Therefore, this study investigated candidate genes associated with fatty acid composition in chickens. A genome-wide association study (GWAS) was performed on 767 individuals from an F2 crossbred population of Yeonsan Ogye and White Leghorn chickens. The Illumina chicken 60K significant single-nucleotide polymorphism (SNP) genotype data and 30 fatty acids (%) in the breast meat of animals slaughtered at 10 weeks of age were analyzed. SNPs were shown to be significant in 15 traits: C10:0, C14:0, C18:0, C18:1n-7, C18:1n-9, C18:2n-6, C20:0, C20:2, C20:3n-6, C20:4n-6, C20:5n-3, C24:0, C24:1n-9, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). These SNPs were mostly located on chromosome 10 and around the following genes: ACSS3, BTG1, MCEE, PPARGC1A, ACSL4, ELOVL4, CYB5R4, ME1, and TRPM1. Both oleic acid and arachidonic acid contained the candidate genes: MCEE and TRPM1. These two fatty acids are antagonistic to each other and have been identified as traits that contribute to the production of volatile fatty acids. The results of this study improve our understanding of the genetic mechanisms through which fatty acids in chicken affect the meat flavor.

Prediction of Retear After Arthroscopic Rotator Cuff Repair Based on Intraoperative Arthroscopic Images Using Deep Learning.

BACKGROUND: It is challenging to predict retear after arthroscopic rotator cuff repair (ARCR). The usefulness of arthroscopic intraoperative images as predictors of the ARCR prognosis has not been analyzed. PURPOSE: To evaluate the usefulness of arthroscopic images for the prediction of retear after ARCR using deep learning (DL) algorithms. STUDY DESIGN: Cohort study (Diagnosis); Level of evidence, 2. METHODS: In total, 1394 arthroscopic intraoperative images were retrospectively obtained from 580 patients. Repaired tendon integrity was evaluated using magnetic resonance imaging performed within 2 years after surgery. Images obtained immediately after ARCR were included. We used 3 DL architectures to predict retear based on arthroscopic images. Three pretrained DL algorithms (VGG16, DenseNet, and Xception) were used for transfer learning. Training and test sets were split into 8:2. Threefold stratified validation was used to fine-tune the hyperparameters using the training data set. The validation results of each fold were evaluated. The performance of each model in the test set was evaluated in terms of accuracy, area under the receiver operating characteristic curve (AUC), F1-score, sensitivity, and specificity. RESULTS: In total, 1138 and 256 arthroscopic images were obtained from 514 patients and 66 patients in the nonretear and retear groups, respectively. The mean validation accuracy of each model was 83% for VGG16, 89% for Xception, and 91% for DenseNet. The accuracy for the test set was 76% for VGG16, 87% for Xception, and 91% for DenseNet. The AUC was highest for DenseNet (0.92); it was 0.83 for VGG16 and 0.91 for Xception. For the test set, the specificity and sensitivity were 0.93 and 0.84 for DenseNet, 0.89 and 0.84 for Xception, and 0.70 and 0.80 for VGG16, respectively. CONCLUSION: The application of DL algorithms to intraoperative arthroscopic images has demonstrated a high level of accuracy in predicting retear occurrences.

The association of women's experience of abuse in childhood with depression during pregnancy and the role of emotional support as a moderator.

BACKGROUND: This study aimed to examine the prevalence of antenatal depression and experience of abuse during childhood, to analyze the association between having experienced childhood abuse and depression during pregnancy, and to explore the role of emotional support as a moderator of that association. METHODS: In total, 44,770 pregnant women were analyzed from the self-administered registry for risk assessment at community public health centers in Seoul, Republic of Korea, for home visiting service provision between 2015 and 2019. The Edinburgh Postnatal Depression Scale (EPDS) was applied for the assessment of depression. The adjusted effects of childhood abuse experience on antepartum depression according to emotional support as an effect moderator were estimated. RESULTS: Depression was present in 2,451 pregnant women (5.5%), and 1,506 (3.4%) reported having experienced physical, emotional, or sexual abuse in childhood. After adjustment of covariates, pregnant women who had experienced abuse during childhood had EPDS scores 2.79 points higher than pregnant women without such experiences, and those who lacked emotional support during adulthood had 4.96 points higher than their counterparts. The difference in EPDS scores based on childhood abuse experience among women who reported emotional support (2.86) was larger than the difference in EPDS scores among those with no emotional support (1.91) (P for interaction = 0.0106). CONCLUSIONS: The experience of abuse in early life and emotional support in later life are both independently important for understanding antenatal depression in Korean women. More comprehensive emotional support is needed for pregnant women who experienced abuse in childhood.

Analysis of ultrasonographic images using a deep learning-based model as ancillary diagnostic tool for diagnosing gallbladder polyps.

BACKGROUND: Accurately diagnosing gallbladder polyps (GBPs) is important to avoid misdiagnosis and overtreatment. AIMS: To evaluate the efficacy of a deep learning model and the accuracy of a computer-aided diagnosis by physicians for diagnosing GBPs. METHODS: This retrospective cohort study was conducted from January 2006 to September 2021, and 3,754 images from 263 patients were analyzed. The outcome of this study was the efficacy of the developed deep learning model in discriminating neoplastic GBPs (NGBPs) from non-NGBPs and to evaluate the accuracy of a computer-aided diagnosis with that made by physicians. RESULTS: The efficacy of discriminating NGBPs from non- NGBPs using deep learning was 0.944 (accuracy, 0.858; sensitivity, 0.856; specificity, 0.861). The accuracy of an unassisted diagnosis of GBP was 0.634, and that of a computer-aided diagnosis was 0.785 (p<0.001). There were no significant differences in the accuracy of a computer-aided diagnosis between experienced (0.835) and inexperienced (0.772) physicians (p = 0.251). A computer-aided diagnosis significantly assisted inexperienced physicians (0.772 vs. 0.614; p < 0.001) but not experienced physicians. CONCLUSIONS: Deep learning-based models discriminate NGBPs from non- NGBPs with excellent accuracy. As ancillary diagnostic tools, they may assist inexperienced physicians in improving their diagnostic accuracy.

Genome-wide association study for the free amino acid and nucleotide components of breast meat in an F2 crossbred chicken population.

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

Probabilistic establishment of speckle-associated inter-chromosomal interactions.

Inter-chromosomal interactions play a crucial role in genome organization, yet the organizational principles remain elusive. Here, we introduce a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results from various cell types. Our method successfully identifies two apparently hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively. Interestingly, we discover that nuclear speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). Validation using DNA Oligopaint fluorescence in situ hybridization (FISH) shows a strong but probabilistic interaction behavior between nuclear speckles and CSE-harboring genomic regions. Strikingly, we find that the likelihood of speckle-CSE associations can accurately predict two experimentally measured inter-chromosomal contacts from Hi-C and Oligopaint DNA FISH. Our probabilistic establishment model well describes the hub-like structure observed at the population level as a cumulative effect of summing individual stochastic chromatin-speckle interactions. Lastly, we observe that CSEs are highly co-occupied by MAZ binding and MAZ depletion leads to significant disorganization of speckle-associated inter-chromosomal contacts. Taken together, our results propose a simple organizational principle of inter-chromosomal interactions mediated by MAZ-occupied CSEs.

A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach.

Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult. In this study, we developed a method to quantify and classify colour using an F2 population crossed from two pure lines: White Leghorn and the Korean indigenous breed Yeonsan Ogye. Using red, green, and blue values in the cropped body region, we identified significant genomic regions on chromosomes 33:3 160 480-7 447 197 and Z:78 748 287-79 173 793. Furthermore, we identified two potential candidate genes (PMEL and MTAP) that might have significant effects on melanin-based plumage pigmentation. Our study presents a new phenotyping method using a computer vision approach and provides new insights into the genetic basis of melanin-based feather colouration in chickens.