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The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Assessment of genomic conservation between humans and pigs at the functional level can improve the potential of pigs as a human biomedical model. To address this, we developed a deep learning-based approach to learn the genomic conservation at the functional level (DeepGCF) between species by integrating 386 and 374 functional profiles from humans and pigs, respectively. DeepGCF demonstrated better prediction performance compared with the previous method. In addition, the resulting DeepGCF score captures the functional conservation between humans and pigs by examining chromatin states, sequence ontologies, and regulatory variants. We identified a core set of genomic regions as functionally conserved that plays key roles in gene regulation and is enriched for the heritability of complex traits and diseases in humans. Our results highlight the importance of cross-species functional comparison in illustrating the genetic and evolutionary basis of complex phenotypes.

Objective To compare the clinical effects of coronary artery bypass grafting (CABG) between the left anterior small thoracotomy (LAST) and lower-end sternal splitting (LESS) approaches for coronary artery disease. Methods In total, 110 patients who underwent LAST from October 2015 to December 2020 in Tianjin Chest Hospital were selected as the observation group. Patients who underwent the LESS approach during the same period were analyzed. The propensity score was calculated by a logistic regression model, and nearest-neighbor matching was used for 1:1 matching. Results The length of hospital stay and ventilator support time were significantly shorter in the LAST than LESS group. The target vessels in the obtuse marginal branch and posterior left ventricular artery branch grafts were significantly more numerous in the LAST than LESS group, but those in the right coronary artery graft were significantly less numerous in the LAST group. Conclusions CABG using either the LAST or LESS approach is safe and effective, especially in low-risk patients. The LAST approach can achieve complete revascularization for multivessel lesions and has the advantages of less trauma and an aesthetic outcome. However, it requires a certain learning curve to master the surgical techniques and has specific surgical indications.

Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-window based tests have been proposed to address this problem. However, when the SNP density on the genotype panel is not homogeneous, genomic-window based tests can lead to the detection of spurious associations by declaring effects of genomic windows that explain a large proportion of genetic variance as significant. We propose two methods to solve this problem.

Dairy production is an important source of nutrients in the global food supply, but environmental impacts are increasingly a concern of consumers, scientists, and policy-makers. Many decisions must be integrated to support sustainable production-which can be achieved using a simulation model. We provide an example of the Ruminant Farm Systems (RuFaS) model to assess changes in the dairy system related to altered animal feed efficiency. RuFaS is a whole-system farm simulation model that simulates the individual animal life cycle, production, and environmental impacts. We added a stochastic animal-level parameter to represent individual animal feed efficiency as a result of reduced residual feed intake and compared High (intake = 94% of expected) and Very High (intake = 88% of expected) efficiency levels with a Baseline scenario (intake = 100% of expected). As expected, the simulated total feed intake was reduced by 6 and 12% for the High and Very High efficiency scenarios, and the expected impact of these improved efficiencies on the greenhouse gas emissions from enteric methane and manure storage was a decrease of 4.6 and 9.3%, respectively.

Low-cost genome-wide single-nucleotide polymorphisms (SNPs) are routinely used in animal breeding programs. Compared to SNP arrays, the use of whole-genome sequence data generated by the next-generation sequencing technologies (NGS) has great potential in livestock populations. However, sequencing a large number of animals to exploit the full potential of whole-genome sequence data is not feasible. Thus, novel strategies are required for the allocation of sequencing resources in genotyped livestock populations such that the entire population can be imputed, maximizing the efficiency of whole genome sequencing budgets. We present two applications of linear programming for the efficient allocation of sequencing resources. The first application is to identify the minimum number of animals for sequencing subject to the criterion that each haplotype in the population is contained in at least one of the animals selected for sequencing. The second application is the selection of animals whose haplotypes include the largest possible proportion of common haplotypes present in the population, assuming a limited sequencing budget. Both applications are available in an open source program LPChoose. In both applications, LPChoose has similar or better performance than some other methods suggesting that linear programming methods offer great potential for the efficient allocation of sequencing resources. The utility of these methods can be increased through the development of improved heuristics.

The aim of this study was to determine the effects of dietary grape seed polyphenols (GSP) supplementation during the late gestation and lactation period on reproductive performance, antioxidative status in serum, nutrient composition, and Ig content in colostrum of multiparous sows. On day 80 of gestation, a total of 64 sows with similar body condition were allocated to a completely randomized block design with 4 dietary treatments (n = 16 sows per treatment): 1) basal diet (CON, control group); 2) basal diet supplemented with 200 IU/kg vitamin E (200VE, positive control group); 3) basal diet supplemented with 200 mg/kg GSP (200GSP); and 4) basal diet supplemented with 300 mg/kg GSP (300GSP). The trial lasted 56 d until the piglets were weaned on day 21 of lactation. Reproductive performance, parameters of antioxidative status, and levels of progesterone (P4) and estradiol (E2) in serum, nutrient composition, and Ig content in colostrum of sows were determined. The number of dead fetuses was reduced, and farrowing survival was significantly improved in the litters from 300GSP-fed (P < 0.05). Preweaning survivability significantly increased in the litters from sows fed 200GSP and 200VE (P < 0.05). The activity of superoxide dismutase and glutathione peroxidase (GSH-Px) in the serum was significantly increased in sows fed 200GSP and 300GSP (P < 0.05). The activity of GSH-Px in the serum also significantly increased in sows fed 200VE (P < 0.05). Sows fed 300GSP had the greatest levels of P4 and E2 in the serum, which was significantly greater than sows fed 200VE and CON (P < 0.05). No significant differences were found among treatments for the content of solids-not-fat, fat, protein, and lactose in colostrum (P > 0.05). However, sows fed GSP had greater IgM and IgG content in colostrum compared with sows fed 200VE and CON (P < 0.05). In conclusion, dietary GSP supplementation during late gestation and lactation improved the farrowing survival and preweaning survivability, enhanced the antioxidant status and hormone levels in serum, and increased the IgM and IgG content in colostrum of sows.

Due to the widespread applications of change detection technology in urban change analysis, environmental monitoring, agricultural surveillance, disaster detection, and other domains, the task of change detection has become one of the primary applications of Earth orbit satellite remote sensing data. However, the analysis of dual-temporal change detection (CD) remains a challenge in high-resolution optical remote sensing images due to the complexities in remote sensing images, such as intricate textures, seasonal variations in imaging time, climatic differences, and significant differences in the sizes of various objects. In this paper, we propose a novel U-shaped architecture for change detection. In the encoding stage, a multi-branch feature extraction module is employed by combining CNN and transformer networks to enhance the network's perception capability for objects of varying sizes. Furthermore, a multi-branch aggregation module is utilized to aggregate features from different branches, providing the network with global attention while preserving detailed information. For dual-temporal features, we introduce a spatiotemporal discrepancy perception module to model the context of dual-temporal images. Particularly noteworthy is the construction of channel attention and token attention modules based on the transformer attention mechanism to facilitate information interaction between multi-level features, thereby enhancing the network's contextual awareness. The effectiveness of the proposed network is validated on three public datasets, demonstrating its superior performance over other state-of-the-art methods through qualitative and quantitative experiments. [ABSTRACT FROM AUTHOR]

Aims: To investigate the roles of neurotrophic factors on cognition in patients with Alzheimer's disease (AD) carrying Apolipoprotein E (APOE) ε4. Methods: Totals of 173 patients with AD were divided into APOE ε4 carrier and non‐carrier groups, and their demographics, cognition, and neurotrophic factors in cerebrospinal fluid (CSF) were compared. Multiple linear regression analyses were performed to assess correlations among APOE ε4, neurotrophic factors and cognition. Mediation analyses were conducted to assess the sequential associations among APOE ε4, nerve growth factor (NGF), and cognition. Results: Global cognition and multiple domains were impaired in the APOE ε4 carrier group (all p < 0.05). NGF level in the APOE ε4 carrier group was lower than that in the non‐carrier group (p = 0.016). NGF level showed significant correlations with both global and multiple domains cognitions. Specifically, NGF mediated the association between APOE ε4 and Animal Fluency Test score (β, −0.45; 95% CI [−0.96, −0.07]; p < 0.001) and Trail Making Test‐A (time) (β, 0.15; 95% CI [0.01, 0.33]; p < 0.001). Conclusion: APOE ε4 is associated with cognitive impairment, and those carrying APOE ε4 have decreased NGF level in CSF. Declined NGF level is correlated with compromised cognition. NGF mediates APOE ε4‐associated cognitive impairment. [ABSTRACT FROM AUTHOR]

Aims: This study aimed to comprehensively explore the nutrition and gait of AD patients at different stages and the relationship between them. Methods: A total of 85 AD patients were consecutively enrolled in this cross‐sectional study and divided into the mild cognitive impairment (MCI) due to AD (AD‐MCI) and the dementia due to AD (AD‐D) groups. Demographic information, nutritional status, and gait performance were compared between the two groups, and the correlation between nutritional status and gait performance was subsequently analyzed by Pearson and Spearman correlation analyses. Results: The AD‐D group had lower scores on Mini‐Nutritional Assessment (MNA) and MNAm scales, lower levels of urea nitrogen, folic acid, and vitamin B12 in blood, and higher homocysteine level than those in the AD‐MCI group (all p < 0.05). The AD‐D group had slower step speed, shorter step length, and shorter stride length than those in the AD‐MCI group (all p < 0.05). AD patients with decreased scores of MNA and MNAm scales, and declined levels of urea nitrogen and vitamin B12 in blood had reduced gait speed and gait cadence, and prolonged step length time and stride length time, whereas homocysteine showed the almost opposite results (all p < 0.05). In the AD‐MCI group, the score of scale was negatively correlated with the coefficient of variation (CV) of stride length, and the folic acid level was negatively correlated with the CV of stride length and cadence (all p < 0.05). Conclusions: AD patients at the dementia stage had worse nutritional status and gait performance than those at the MCI stage, which was associated with worse global cognition and activities of daily living. Poorer nutritional status was associated with higher gait variability in patients at the MCI stage and with poorer gait performance in patients at the dementia stage. Early identification and intervention of patients with nutritional risk or malnutrition may improve gait performance, thus reducing the risk of falling and cognitive decline, as well as the mortality. [ABSTRACT FROM AUTHOR]

Aims: To explore the roles of apolipoprotein E (APOE) ε4 on the neuropathology and neuroinflammation in Alzheimer's disease (AD) patients. Methods: AD patients were divided into the APOE ε4 carrier and the APOE ε4 non‐carrier groups according to APOE genotype. Demographic information, cognitive function, the levels of neuropathological proteins and neuroinflammatory factors in cerebrospinal fluid (CSF) were compared between the two groups, and their correlations were subsequently analyzed. Results: β amyloid protein (Aβ)1–42 level from the APOE ε4 carrier group was significantly lower than that from the non‐carrier group (p = 0.023), which was associated with worse cognitive function. The nitric oxide (NO) level was significantly elevated in the APOE ε4 carrier group compared to the non‐carrier group (p = 0.016), which was significantly and positively correlated with the Trail Making Test (TMT)‐A‐time (r = 0.21, p = 0.026) and TMT‐B‐time (r = 0.38, p < 0.01). Conclusion: APOE ε4 is associated with poorer cognition, particularly the early symptoms of memory, language, and attention. APOE ε4 is associated with lower Aβ1–42 level, and the more numbers of APOE ε4 are carried, the lower level of Aβ1–42 is measured. APOE ε4 is associated with elevated NO level, which is linked to the impaired attention and executive function. [ABSTRACT FROM AUTHOR]