Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs.

Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico-predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination.

Ambient heat exposure and kidney function in patients with chronic kidney disease: a post-hoc analysis of the DAPA-CKD trial.

BACKGROUND: Higher temperatures are associated with higher rates of hospital admissions for nephrolithiasis and acute kidney injury. Occupational heat stress is also a risk factor for kidney dysfunction in resource-poor settings. It is unclear whether ambient heat exposure is associated with loss of kidney function in patients with established chronic kidney disease. We assessed the association between heat index and change in estimated glomerular filtration rate (eGFR) in participants from the DAPA-CKD trial in a post-hoc analysis. METHODS: DAPA-CKD was a randomised controlled trial of oral dapagliflozin 10 mg once daily or placebo that enrolled participants aged 18 years or older, with or without type 2 diabetes, with a urinary albumin-to-creatinine ratio of 200-5000 mg/g, and an eGFR of 25-75 mL/min per 1·73 m2. In this post-hoc analysis, we explored the association between time-varying daily centre-level heat index (ERA5 dataset) and individual-level change in eGFR in trial participants using linear mixed effect models and case-time series. The DAPA-CKD trial is registered with ClinicalTrials.gov, NCT03036150. FINDINGS: Climate and eGFR data were available for 4017 (93·3%) of 4304 participants in 21 countries (mean age: 61·9 years; mean eGFR: 43·3 mL per 1·73 m2; median 28 months follow-up). Across centres, a heat index of more than 30°C occurred on a median of 0·6% of days. In adjusted linear mixed effect models, within each 120-day window, each 30 days' heat index of more than 30°C was associated with a -0·6% (95% CI -0·9% to -0·3%) change in eGFR. Similar estimates were obtained using case-time series. Additional analyses over longer time-windows showed associations consistent with haemodynamic or seasonal variability, or both, but overall estimates corresponded to an additional 3·7 mL per 1·73 m2 (95% CI 0·1 to 7·0) loss of eGFR per year in a patient with an eGFR of 45 mL per 1·73 m2 located in a very hot versus a temperate environment. INTERPRETATION: Higher ambient heat exposure is associated with more rapid eGFR decline in those with established chronic kidney disease. Efforts to mitigate heat exposure should be tested as part of strategies to attenuate chronic kidney disease progression. FUNDING: None.

Albumin-to-D-dimer ratios: A novel prognostic factor for evaluating first-line chemotherapy efficacy in advanced lung adenocarcinoma patients.

The prognosis of advanced lung adenocarcinoma (LUAD) remains unfavorable, with chemotherapy constituting a primary treatment modality. Discerning the efficacy of chemotherapy for advanced LUAD is imperative. Prior investigations have demonstrated the prognostic value of albumin and D-dimer individually for malignancies; however, the predictive capacity of albumin-to-D-dimer ratios (ADR) for advanced LUAD subjected to first-line platinum-based chemotherapy remains unexplored. A cohort of 313 patients with advanced LUAD was retrospectively examined in this study, spanning from January 2017 to January 2021. ADR threshold values were ascertained via receiver operating characteristic analysis, followed by the evaluation of the association between pretreatment ADR and clinicopathological characteristics, disease control rate (DCR), and overall response rate (ORR) pertinent to first-line chemotherapy. Prognostic factors for progression-free survival (PFS) were determined employing Cox univariate and multivariate analyses. Subsequently, survival data were illustrated utilizing the Kaplan-Meier method and scrutinized through the log-rank test across the entire and subgroup populations. ADR demonstrated a superior area under the curve (AUC) value relative to albumin and D-dimer individually and exhibited enhanced prognostic predictive capability compared to albumin-to-fibrinogen ratios (AFR) for advanced LUAD (AUC: 0.805 vs. 0.640, DeLong test: p<0.001). ADR yielded a cut-off value of 16.608. A greater proportion of non-smokers was observed within the high-ADR group (ADR>16.608) compared to the low-ADR group (ADR≤16.608). Patients in the high-ADR group displayed elevated BMI and Na+ levels and reduced neutrophil count, monocyte count, globulin, and alkaline phosphatase (all p<0.05). Notably, the high-ADR group exhibited heightened DCR (96.7% vs. 89.2%, p=0.008) and ORR rates (70.1% vs. 51.0%, p=0.001) relative to the low-ADR group. Multivariate analysis outcomes indicated that high ADR constituted an independent risk factor for PFS (hazard ratio: 0.24, p<0.001). Furthermore, patients in the high-ADR cohort displayed a significantly prolonged median PFS (254 vs. 142 days, p<0.0001) compared to their low-ADR counterparts. In subpopulations exhibiting favorable implications for PFS, as determined by multivariate analysis, high-ADR patients consistently demonstrated extended PFS durations relative to the low-ADR group (all p<0.0001). Collectively, our findings suggest that ADR constitutes a novel and promising prognostic indicator for advanced LUAD patients, surpassing the accuracy of albumin and D-dimer individually and AFR. ADR thus serves as a potent instrument for assessing treatment effects and PFS in advanced LUAD patients undergoing first-line chemotherapy.

Pressure Dependence of the Structural and Superconducting Properties of the Bi-Based Superconductor Bi2Pd3Se2.

The structural and superconducting properties of the Bi-based compound Bi2Pd3Se2 were investigated over a wide pressure range. The prepared Bi2Pd3Se2 sample was a superconductor with a superconducting transition temperature, Tc, of approximately 3.0 K, which differed from a previous report (Tc of less than 1.0 K). At ambient pressure, the powder X-ray diffraction (XRD) pattern of the Bi2Pd3Se2 sample was consistent with that previously reported for Bi2Pd3Se2. The Rietveld method was used to refine the crystal structure, which had a space group of C2/m (No. 12), as reported previously. This compound showed no clear anomaly due to the charge-density-wave (CDW) transition, as seen from the temperature dependence of magnetic susceptibility. However, the temperature dependence of electrical resistivity indicated a clear anomaly, presumably because of the CDW transition in the low-pressure range; the CDW transition temperature was approximately 230 K. The XRD patterns of the Bi2Pd3Se2 sample were measured at 0.160-22.7 GPa, and the patterns were well analyzed by both the Le Bail and Rietveld refinement methods, showing no structural phase transitions in the above pressure range. The pressure dependence of Tc of Bi2Pd3Se2 was recorded based on the temperature dependence of the electrical resistance, which showed an almost constant Tc at 0-13.7 GPa, and the Tc-pressure (p) behavior was fully discussed.

Detection of Pig Movement and Aggression Using Deep Learning Approaches.

Motion and aggressive behaviors in pigs provide important information for the study of social hierarchies in pigs and can be used as a selection indicator for pig health and aggression parameters. However, relying only on visual observation or surveillance video to record the number of aggressive acts is time-consuming, labor-intensive, and lasts for only a short period of time. Manual observation is too short compared to the growth cycle of pigs, and complete recording is impractical in large farms. In addition, due to the complex process of assessing the intensity of pig aggression, manual recording is highly influenced by human subjective vision. In order to efficiently record pig motion and aggressive behaviors as parameters for breeding selection and behavioral studies, the videos and pictures were collected from typical commercial farms, with each unit including 8~20 pigs in 7~25 m2 space; they were bred in stable social groups and a video was set up to record the whole day's activities. We proposed a deep learning-based recognition method for detecting and recognizing the movement and aggressive behaviors of pigs by recording and annotating head-to-head tapping, head-to-body tapping, neck biting, body biting, and ear biting during fighting. The method uses an improved EMA-YOLOv8 model and a target tracking algorithm to assign a unique digital identity code to each pig, while efficiently recognizing and recording pig motion and aggressive behaviors and tracking them, thus providing statistics on the speed and duration of pig motion. On the test dataset, the average precision of the model was 96.4%, indicating that the model has high accuracy in detecting a pig's identity and its fighting behaviors. The model detection results were highly correlated with the manual recording results (R2 of 0.9804 and 0.9856, respectively), indicating that the method has high accuracy and effectiveness. In summary, the method realized the detection and identification of motion duration and aggressive behavior of pigs under natural conditions, and provided reliable data and technical support for the study of the social hierarchy of pigs and the selection of pig health and aggression phenotypes.

Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig.

BACKGROUND: As pre-cut and pre-packaged chilled meat becomes increasingly popular, integrating the carcass-cutting process into the pig industry chain has become a trend. Identifying quantitative trait loci (QTLs) of pork cuts would facilitate the selection of pigs with a higher overall value. However, previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts, neglecting the investigation of QTLs influencing these traits. This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips. Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values (GEBVs) for pork cuts. RESULTS: We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes, respectively. Specifically, we found that HMGA1, VRTN and BMP2 were associated with body length and weight. Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones, VRTN primarily affects the number of vertebrates, and BMP2 primarily affects the length of vertebrae and the size of hind leg bones. The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population, divided by the square root of the trait's heritability. The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693. Notably, ribs, boneless picnic shoulder, tenderloin, hind leg bones, and scapula bones exhibited prediction accuracies exceeding 0.600. Employing better models, increasing marker density through genotype imputation, and pre-selecting markers significantly improved the prediction accuracy of GEBVs. CONCLUSIONS: We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes. These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection. Additionally, we have constructed the first reference populations for genomic selection of pork cuts in pigs.

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences.

High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

Genetic dissection of 26 meat cut, meat quality and carcass traits in four pig populations.

BACKGROUND: Currently, meat cut traits are integrated in pig breeding objectives to gain extra profit. However, little is known about the heritability of meat cut proportions (MCP) and their correlations with other traits. The aims of this study were to assess the heritability and genetic correlation of MCP with carcass and meat quality traits using single nucleotide polymorphism chips and conduct a genome-wide association study (GWAS) to identify candidate genes for MCP. RESULTS: Seventeen MCP, 12 carcass, and seven meat quality traits were measured in 2012 pigs from four populations (Landrace; Yorkshire; Landrace and Yorkshire hybrid pigs; Duroc, and Landrace and Yorkshire hybrid pigs). Estimates of the heritability for MCP ranged from 0.10 to 0.55, with most estimates being moderate to high and highly consistent across populations. In the combined population, the heritability estimates for the proportions of scapula bone, loin, back fat, leg bones, and boneless picnic shoulder were 0.44 ± 0.04, 0.36 ± 0.04, 0.44 ± 0.04, 0.38 ± 0.04, and 0.39 ± 0.04, respectively. Proportion of middle cuts was genetically significantly positively correlated with intramuscular fat content and backfat depth. Proportion of ribs was genetically positively correlated with carcass oblique length and straight length (0.35 ± 0.08 to 0.45 ± 0.07) and negatively correlated with backfat depth (- 0.26 ± 0.10 to - 0.45 ± 0.10). However, weak or nonsignificant genetic correlations were observed between most MCP, indicating their independence. Twenty-eight quantitative trait loci (QTL) for MCP were detected by GWAS, and 24 new candidate genes related to MCP were identified, which are involved with growth, height, and skeletal development. Most importantly, we found that the development of the bones in different parts of the body may be regulated by different genes, among which HMGA1 may be the strongest candidate gene affecting forelimb bone development. Moreover, as previously shown, VRTN is a causal gene affecting vertebra number, and BMP2 may be the strongest candidate gene affecting hindlimb bone development. CONCLUSIONS: Our results indicate that breeding programs for MCP have the potential to enhance carcass composition by increasing the proportion of expensive cuts and decreasing the proportion of inexpensive cuts. Since MCP are post-slaughter traits, the QTL and candidate genes related to these traits can be used for marker-assisted and genomic selection.

Metformin alleviates the cognitive impairment induced by benzo[a]pyrene via glucolipid metabolism regulated by FTO/FoxO6 pathway in mice.

Benzo[a]pyrene (B[a]P) is neurotoxic; however, the mechanism and prevention are still unclear. In this study, we assessed the intervention effect of metformin (MET) on cognitive dysfunction in mice induced by B[a]P from the perspective of glucolipid metabolism. Forty-two male healthy ICR mice were randomly categorized into 6 groups and were gavaged with B[a]P (0, 2.5, 5, or 10 mg/kg), 45 times for 90 days. The controls were gavaged with edible peanut oil, and the intervention groups were co-treated with B[a]P (10 mg/kg) and MET (200 or 300 mg/kg). We assessed the cognitive function of mice, observed the pathomorphological and ultrastructural changes, and detected neuronal apoptosis and glucolipid metabolism. Results showed that B[a]P dose-dependently induced cognitive impairment, neuronal damage, glucolipid metabolism disorder in mice, and enhanced proteins of fat mass and obesity-associated protein (FTO) and forkhead box protein O6 (FoxO6) in the cerebral cortex and liver, which were alleviated by the MET intervention. The findings indicated the critical role of glucolipid metabolism disorder in the cognitive impairment in mice caused by B[a]P and the prevention of MET against B[a]P neurotoxicity by regulating glucolipid metabolism via restraining FTO/FoxO6 pathway. The finding provides a scientific basis for the neurotoxicity and prevention strategies of B[a]P.

Pressure Dependence of Superconductivity in a Charge-Density-Wave Superconductor Bi2Rh3Se2.

The structural and superconducting properties of a Bi-based compound, Bi2Rh3Se2, are investigated over a wide pressure range. Bi2Rh3Se2 is a superconductor with a superconducting transition temperature, Tc, of 0.7 K. This compound is in a charge-density-wave (CDW) state below 240 K, which implies the coexistence of superconducting and CDW states at low temperatures. Here, the superconducting properties of Bi2Rh3Se2 are studied from the perspective of the temperature dependence of electrical resistance (R) at high pressures (p's). The pressure dependence of Tc of Bi2Rh3Se2 shows a slow increase in Tc at 0-15.5 GPa, and the Tc slowly decreases with pressure above 15.5 GPa, which is markedly different from that of normal superconductors because the value of Tc should simply decrease owing to the decrease in density of states (DOS) on the Fermi level, N(εF), driven by a simple shrinkage of the lattice under pressure. To ascertain the origin of such a dome-like Tc-p behavior, the crystal structure of Bi2Rh3Se2 was explored over a wide pressure range of 0-20 GPa on the basis of powder X-ray diffraction; no structural phase transitions or simple shrinkage of the lattice was observed. This result implies that the increase in Tc against pressure cannot simply be explained from a structural point of view. In other words, a direct relation between superconductivity and crystal structure was not found. On the other hand, the CDW transition became ambiguous at pressures higher than 3.8 GPa, suggesting that the Tc had been suppressed by the CDW transition in a low pressure range. Thus, the findings suggest that for Bi2Rh3Se2, Tc is enhanced through the suppression of CDW transition, which may be reasonable because the CDW-ordered state restrains the charge fluctuation to weaken the electron-phonon coupling and opens the gap to decrease the density of states on the Fermi level. The obtained dome-like Tc-p behavior indicates the possibility of Bi2Rh3Se2 being an exotic superconductor.

Lightweight Structural Biomaterials with Excellent Mechanical Performance: A Review.

The rational design of desirable lightweight structural materials usually needs to meet the strict requirements of mechanical properties. Seeking optimal integration strategies for lightweight structures and high mechanical performance is always of great research significance in the rapidly developing composites field, which also draws significant attention from materials scientists and engineers. However, the intrinsic incompatibility of low mass and high strength is still an open challenge for achieving satisfied engineering composites. Fortunately, creatures in nature tend to possess excellent lightweight properties and mechanical performance to improve their survival ability. Thus, by ingenious structure configuration, lightweight structural biomaterials with simple components can achieve high mechanical performance. This review comprehensively summarizes recent advances in three typical structures in natural biomaterials: cellular structures, fibrous structures, and sandwich structures. For each structure, typical organisms are selected for comparison, and their compositions, structures, and properties are discussed in detail, respectively. In addition, bioinspired design approaches of each structure are briefly introduced. At last, the outlook on the design and fabrication of bioinspired composites is also presented to guide the development of advanced composites in future practical engineering applications.

Genomic prediction in pigs using data from a commercial crossbred population: insights from the Duroc x (Landrace x Yorkshire) three-way crossbreeding system.

BACKGROUND: Genomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB) animals and to improve the performance of commercial crossbred (CB) animals. Most current predictions are based solely on PB performance. Our objective was to explore the potential application of genomic selection of PB animals using genotypes of CB animals with extreme phenotypes in a three-way crossbreeding system as the reference population. Using real genotyped PB as ancestors, we simulated the production of 100,000 pigs for a Duroc x (Landrace x Yorkshire) DLY crossbreeding system. The predictive performance of breeding values of PB animals for CB performance using genotypes and phenotypes of (1) PB animals, (2) DLY animals with extreme phenotypes, and (3) random DLY animals for traits of different heritabilities ([Formula: see text] = 0.1, 0.3, and 0.5) was compared across different reference population sizes (500 to 6500) and prediction models (genomic best linear unbiased prediction (GBLUP) and Bayesian sparse linear mixed model (BSLMM)). RESULTS: Using a reference population consisting of CB animals with extreme phenotypes showed a definite predictive advantage for medium- and low-heritability traits and, in combination with the BSLMM model, significantly improved selection response for CB performance. For high-heritability traits, the predictive performance of a reference population of extreme CB phenotypes was comparable to that of PB phenotypes when the effect of the genetic correlation between PB and CB performance ([Formula: see text]) on the accuracy obtained with a PB reference population was considered, and the former could exceed the latter if the reference size was large enough. For the selection of the first and terminal sires in a three-way crossbreeding system, prediction using extreme CB phenotypes outperformed the use of PB phenotypes, while the optimal design of the reference group for the first dam depended on the percentage of individuals from the corresponding breed that the PB reference data comprised and on the heritability of the target trait. CONCLUSIONS: A commercial crossbred population is promising for the design of the reference population for genomic prediction, and selective genotyping of CB animals with extreme phenotypes has the potential for maximizing genetic improvement for CB performance in the pig industry.

5.32 W ultraviolet laser generation at 266†nm using sum-frequency method with CsB3O5 crystal.

Ultraviolet (UV) beam generation at 266 nm using the sum-frequency (SFG) method with CsB3O5 (CBO) crystals was first suggested in 1997 [Opt. Lett.22, 1840 (1997).10.1364/OL.22.001840]; however, there has been no further research in the past 25 years. Herein, by sum-frequency mixing in CBO crystals, we obtained a high conversion efficiency picosecond (ps) and a high-power nanosecond (ns) 266 nm UV beam output. First, a ps laser device with simultaneously radiated wavelengths of 1064 and 355 nm and repetition frequency of 10 Hz was used as the fundamental laser source, and the conversion efficiency from 1064 + 355 nm to 266 nm reached 20.35%. We then used a 1064 nm ns laser with a high output power and repetition frequency of 10 kHz as the pump source. We accurately modified the optimal phase matching direction of the CBO crystal, and the achieved output power at 266 nm reached 5.32 W.

Efficacy and mechanism of lipoic acid in the treatment of reproductive injury caused by perfluorooctanoic acid.

Environmental pollutants, including perfluorooctanoic acid (PFOA), cause severe reproductive damage to humans and animals. Lipoic acid (LA) is a strong antioxidant that alleviates the oxidative damage caused by heavy metals, environmental toxicants, chemical poisons, etc. Therefore, the present study investigated the curative effect and mechanism of LA in treating spermatogenesis dysfunction caused by PFOA. A rat reproductive injury model was established by gavage of PFOA for consecutive 30 days and then rats were treated with different doses of LA for 42 days. The effects were assessed by ELISA, western blotting, H&E staining and immunofluorescence staining. The results demonstrated that LA had ameliorating effects on PFOA-induced reproductive injury in rats, it increased the sperm counts, and the levels of serum succinate dehydrogenase, lactate dehydrogenase, glutathione peroxidase and superoxide dismutase returned to normal levels following LA treatment. In addition, LA promoted the expression of estradiol, reduced the expression of serum sex hormones, such as follicle-stimulating hormone, androgen receptor (AR) and malondialdehyde in the testes, and restored the structure of seminiferous tubules. Its therapeutic mechanisms include regulating the testicular oxidative stress pathway and hypothalamic-pituitary-testis axis.

Recombination map construction method using ONT sequence.

Although meiotic recombination is a key step shared by eukaryotes, the rate of recombination varies at different taxonomic levels. The construction of high-resolution genome-wide recombination maps will help us understand the variability patterns of recombination rates and their molecular basis. ONT sequencing technology has the characteristics of long read length, high throughput, and reasonable cost, and can be used as a data source for the construction of whole-gene recombination landscapes. In order to construct the genome-wide recombination map of an individual conveniently and accurately, we developed a method to construct the recombination landscape based on the third-generation sequencing technology, Oxford Nanopore Sequencing. Here we detail a step-by-step approach to efficiently and accurately construct genome-wide recombination maps using ONT pooled sequencing data. The main contents include compression homopolymers and alignment; acquisition of high-quality variants; estimation of recombinant molecules by the sliding window method; and construction of recombinant maps. The results of simulation data validation show that our method has high sensitivity and specificity at moderate heterozygous variant density and sequencing depth. This method provides a new way of constructing high-resolution individual genome recombination maps using long read sequences, and has important reference significance for the study of recombination rate variation.

Quantification and visualization of meat quality traits in pork using hyperspectral imaging.

Accurate and rapid determination of meat quality traits plays key roles in food industry and pig breeding. Currently, most of the spectroscopic instruments developed for meat quality determination can only obtain the spectral average value of the sample, so it is difficult to evaluate the spatial variation of meat quality traits. In this study, we evaluated the predictive potential of 14 meat quality traits based on large-scale VIS/NIR hyperspectral images collected by SpecimIQ. When predictions were based solely on hyperspectral data, the prediction accuracy (R2cv) for the majority of meat qualities ranged from 0.60 to 0.70. After adding texture information, the prediction accuracy of all traits is improved by different magnitudes (R2cv increases from 1.5% to 16.4%). Finally, the best model was utilized to visualize the spatial distribution of Fat (%) and Moisture (%) to assess their homogeneity. These results suggest that hyperspectral imaging has great potential for predicting and visualizing various meat qualities, as well as industrial applications for automated measurements.

Effects of ß-blockers therapy on the 28-day and 3-year survival rates of end-stage renal disease patients with cardiovascular disease: a retrospective cohort study.

Background: ß-blockers have been used in the treatment of end-stage renal disease (ESRD) patients and cardiovascular disease (CVD) patients, separately. However, the effects of ß-blockers on ESRD patients with CVD have not been fully investigated. This study sought to investigate the effects of ß-blockers therapy on the 28-day and 3-year survival rates of ESRD patients with pre-existing CVD who were admitted to the intensive care unit (ICU). Methods: After excluding patients without CVD, receiving a kidney transplant, not admitted to the ICU, and with missing baseline data, this cohort study included 1081 ESRD participants with CVD from the Medical Information Mark for Intensive Care III database. Baseline characteristics, including demographic data and clinical data, were collected. The outcomes were 28-day and 3-year survival rates of the patients. At the 28-day of ICU hospitalization, patients had a mean inpatient hospital stay of 24.7 days. At 3-year, the patients had a median survival time of 489.2 days. Univariate and multivariate Cox regression analyses were used to evaluate the effects of ß-blockers therapy on the 28-day and 3-year survival outcomes of ESRD patients with CVD. Results: The 28-day and 3-year survival rates were 82.8% and 37.9%, respectively. The mean age of the all patients was 68 years, and 642 were male. After adjusting for age, race, hyperlipidemia, dialysis, simplified acute physiological score (SAPS) II, sequential organ failure assessment (SOFA) score, glucocorticoid, hemoglobin, diabetes, hypertension, the 28-day survival rate of the ESRD patients with CVD requiring intensive care who received ß-blockers therapy was higher than that of the patients who did not receive the treatment. Similarly, after adjusting for age, race, hyperlipidemia, dialysis, SAPS II, SOFA score, glucocorticoid, hemoglobin, diabetes, hypertension, creatinine, the long-term survival rate of the patients who received ß-blockers therapy was also higher than that of those who did not. Conclusions: ß-blockers therapy was associated with increased 28-day and 3-year survival rates in ESRD patients with CVD requiring intensive care. Our findings may provide a theoretical basis for the prognostic impact of ß-blockers therapy among patients with ESRD and CVD who were admitted to the ICU.

Protocol to construct biomimetic carbon fiber composites with improved interfacial strength.

Weak interfacial strength restricts the mechanical properties of carbon fiber-reinforced composites. Here, inspired by natural hook-groove microstructure system (HGMS) of black kite (Milvus migrans), we detail the steps to construct a biomimetic HGMS based on dopamine-functionalized carbon fibers (CFs) and zinc oxide nanorods (ZnO NRs) using a two-step modification approach. We describe the fabrication of biomimetic carbon fiber composites using vacuum-assisted contact molding (VACM) and subsequent characterization using standard comprehensive mechanical tests techniques. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).

NanoCross: A pipeline that detecting recombinant crossover using ONT sequencing data.

Meiotic recombination is crucial for eukaryotes but varies among taxonomic scales (between individuals, groups, species, etc.) and genome resolutions. Studying how and why recombination rates change can help us understand the molecular basis and mechanisms of genetics and evolution. We introduce a genome-wide identification script called NanoCross, which uses ONT sequences to detect pooled gamete DNA cross recombination events. NanoCross first reduced sequencing errors and then constructed individual haplotypes based on homopolymer-filtered ONT sequences. Then, each molecule read is used to estimate cross recombination. In the case of moderate heterozygous variation density and sequencing depth, simulations revealed that our technique offers a good level of sensitivity and specificity. We constructed a high-resolution recombination map of wild boar genomes using NanoCross and compared it to recombination maps of male breeding pig populations. NanoCross provides us with a method and scripts for constructing a high-resolution individual genome recombination map utilizing long-read sequencing, as well as a novel approach for examining the variation in individual recombination rate. The source code and data mechanism are hosted on GitHub (https://github.com/zuoquanchen/NanoCross).

Origin, evolution, and tissue-specific functions of the porcine repetitive element 1.

BACKGROUND: The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues. RESULTS: We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function. CONCLUSIONS: The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions.