The effectiveness of digital twins in promoting precision health across the entire population: a systematic review.

Digital twins represent a promising technology within the domain of precision healthcare, offering significant prospects for individualized medical interventions. Existing systematic reviews, however, mainly focus on the technological dimensions of digital twins, with a limited exploration of their impact on health-related outcomes. Therefore, this systematic review aims to explore the efficacy of digital twins in improving precision healthcare at the population level. The literature search for this study encompassed PubMed, Embase, Web of Science, Cochrane Library, CINAHL, SinoMed, CNKI, and Wanfang Database to retrieve potentially relevant records. Patient health-related outcomes were synthesized employing quantitative content analysis, whereas the Joanna Briggs Institute (JBI) scales were used to evaluate the quality and potential bias inherent in each selected study. Following established inclusion and exclusion criteria, 12 studies were screened from an initial 1321 records for further analysis. These studies included patients with various conditions, including cancers, type 2 diabetes, multiple sclerosis, heart failure, qi deficiency, post-hepatectomy liver failure, and dental issues. The review coded three types of interventions: personalized health management, precision individual therapy effects, and predicting individual risk, leading to a total of 45 outcomes being measured. The collective effectiveness of these outcomes at the population level was calculated at 80% (36 out of 45). No studies exhibited unacceptable differences in quality. Overall, employing digital twins in precision health demonstrates practical advantages, warranting its expanded use to facilitate the transition from the development phase to broad application.PROSPERO registry: CRD42024507256.

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.

Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.

Boson-peak-like anomaly caused by transverse phonon softening in strain glass.

Strain glass is a glassy state with frozen ferroelastic/martensitic nanodomains in shape memory alloys, yet its nature remains unclear. Here, we report a glassy feature in strain glass that was thought to be only present in structural glasses. An abnormal hump is observed in strain glass around 10 K upon normalizing the specific heat by cubed temperature, similar to the boson peak in metallic glass. The simulation studies show that this boson-peak-like anomaly is caused by the phonon softening of the non-transforming matrix surrounding martensitic domains, which occurs in a transverse acoustic branch not associated with the martensitic transformation displacements. Therefore, this anomaly neither is a relic of van Hove singularity nor can be explained by other theories relying on structural disorder, while it verifies a recent theoretical model without any assumptions of disorder. This work might provide fresh insights in understanding the nature of glassy states and associated vibrational properties.

[Locking plate external fixation combined with membrane induction technology for the treatment of open and comminuted tibial fractures with bone defects].

OBJECTIVE: To explore clinical effect of locking plate external fixation combined with membrane induction technology in treating open and comminuted tibial fractures with bone defects. METHODS: Totally 92 patients of open and comminuted tibial fractures with bone defects were chosen form January 2018 to July 2019, and randomly divided into external fixation group and internal fixation group, 46 patients in each group. In external fixation group, there were 29 males and 17 females, aged from 25 to 62 years old, with an average of (37.45±10.92) years old;according to AO classification, 15 patients were type A, 22 patients were type B and 9 patients were type C;according to Gustilo classification, 21 patients were typeⅡ, 10 patients were type ⅢA, 10 patients were type ⅢB, 5 patients were type Ⅲ C;treated by fracture reduction with locking plate external fixation. In internal fixation group, there were 31 males and 15 females, aged from 23 to 60 years old, with an average of(36.88±10.64) years old;according to AO classification, 18 patients were type A, 20 patients were type B and 8 patients were type C; according to Gustilo classification, 22 patients were typeⅡ, 11 patients were type ⅢA, 7 patients were type ⅢB, 6 patients were type Ⅲ C;treated by traditional open reduction with plate internal fixation. Operation time, intraoperative blood loss, incision length, hospital stay, fracture healing time and lower limb full weight-bearing time and postoperative complications between two groups were observed and compared, bone mineral density, osteocalcin, blood calcium and phosphorus before operation and 1 month after operation. RESULTS: All patients were followed up from 12 to 18 months with an average of (14.92±2.46) months. Operation time, intraoperative blood loss, incision length, hospital stay, fracture healing time and lower limb full weight-bearing time of external fixation group were significantly better than that of internal fixation group(P<0.05). Postoperative bone mineral density, osteocalcin, blood calcium and phosphorus at 1 month in external group were higher than that of internal fixation group (P<0.05). Four patients in external fixation group occurred complications, 13 patients in internal fixtaion group, and occurrence rate of complications in external fixation group (8.70%) was lower than that of internal fixtaion group (28.26%)(χ2=4.618, P=0.032). CONCLUSION: Locking plate external fixation combined with membrane induction technology in treating open and comminuted tibial fractures with severe post-traumatic bone defects has advantages of less trauma, reliable fixation, shorter fracture healing time, and could improve bone metabolic activity with less postoperative complications.

Measuring genetic connectedness between herds based on high density SNP markers.

The accuracy of genetic evaluations in different herds is affected by the degree of genetic connectedness among herds. In this study, we explored the application of high density SNP markers in the assessment of genetic connectedness by comparing the genetic connectedness based on pedigree data and genomic data. Six methods, including PEVD (prediction error variance of differences between estimated breeding values), PEVD (x), VED (variance of estimated difference between the herd effects), CD (generalized coefficient of determination), r (prediction error correlation) and CR (connectedness rating), were implemented to measure the genetic connectedness based on different relationship matrices (A, G, Gs, G0. 5 and H). Our results from both simulated data and SNP chip data indicated that, except for the PEVD (x) and VED methods, the genetic connectedness obtained by PEVD, CD, r and CR based on G. Gs and G0.5 matrices (using genome information only) were superior to those based on A matrix (using pedigree information only). Generally, for most approaches, the genetic connectedness based on H matrix (using both pedigree and genome information) was somewhere between A matrix and G matrices. CD could overestimate the degree of genetic connectedness as it was still very high when CR and r were close to 0. The method r could not accurately reflect the true genetic connectedness of the populations. It generated 0.01 of genetic connectedness for all three pig breeding farms, which were actually genetically different with each other. With increasing of heritability, the degree of genetic connectedness obtained by all methods were increased as well. However, in the case of heritability 0.1, PEVD based on A matrix performed better than based on G matrix, suggesting that traits with medium and high heritability are more suitable for the assessment of genetic connectedness compared to traits with low heritability. Our findings indicated that high-density SNP markers have advantages over pedigree analysis for the measurement of genetic connectedness, and CR is a robust and reliable method to assess genetic connectedness. Further, CR is easily calculated and less affected by heritability of trait. PEVD is good supplement to quantify the prediction errors of estimated breeding values under the specific genetic connectedness. In comparison, G matrix can reflect genetic connectedness better than its extensions Gs and G0.5 matrix.

The Identification of Mutation in BMP15 Gene Associated with Litter Size in Xinjiang Cele Black Sheep.

The Bone Morphogenetic Protein 15 (BMP15) gene is known to have multiple single-nucleotide polymorphism sites associated with sheep fecundity. This study used gene sequence analysis and mutation detection assays for BMP15 by using 205 blood samples of ewes with known lambing records. Sequence analysis showed that mutation B1 missed the CTT base in exon 1 at positions 28-30, leading to a leucine deletion in the BMP15 protein. Litter size of ewes differed significantly between BB and B+ genotypes of B1 (p < 0.05); however, the differences between wild genotype (++) and homozygous (BB) or wild genotype (++) and heterozygous (B+) were not significant (p > 0.05). Another mutation, T755C, is a T-to-C base change at position 755 of exon 2, resulting in leucine replacement by proline at this position of the BMP15 protein (p.L252P). Two genotypes were identified in the flock: heterozygous (E+) and wild-type genotype (++). Ewes with heterozygous (E+) p.L252P had significantly larger litter sizes than those with the wild-type genotype (p < 0.05). Comprehensive analysis suggests that p.L252P is a mutation that affects fecundity in Cele black sheep.

Pervasive introgression facilitated domestication and adaptation in the Bos species complex.

Species of the Bos genus, including taurine cattle, zebu, gayal, gaur, banteng, yak, wisent and bison, have been domesticated at least four times and have been an important source of meat, milk and power for many human cultures. We sequence the genomes of gayal, gaur, banteng, wisent and bison, and provide population genomic sequencing of an additional 98 individuals. We use these data to determine the phylogeny and evolutionary history of these species and show that the threatened gayal is an independent species or subspecies. We show that there has been pronounced introgression among different members of this genus, and that it in many cases has involved genes of considerable adaptive importance. For example, genes under domestication selection in cattle (for example, MITF) were introgressed from domestic cattle to yak. Also, genes in the response-to-hypoxia pathway (for example, EGLN1, EGLN2 and HIF3a) have been introgressed from yak to Tibetan cattle, probably facilitating their adaptation to high altitude. We also validate that there is an association between the introgressed EGLN1 allele and haemoglobin and red blood cell concentration. Our results illustrate the importance of introgression as a source of adaptive variation and during domestication, and suggest that the Bos genus evolves as a complex of genetically interconnected species with shared evolutionary trajectories.

The regulation of glucose on milk fat synthesis is mediated by the ubiquitin-proteasome system in bovine mammary epithelial cells.

Glucose as one of the nutrition factors plays a vital role in the regulation of milk fat synthesis. Ubiquitin-proteasome system (UPS) is a vital proteolytic pathway in all eukaryotic cells through timely marking, recognizing and degrading the poly-ubiquitinated protein substrates. Previous studies indicated that UPS plays a considerable role in controlling the triglyceride (TG) synthesis. Therefore, the aim of this study is to confirm the link between high-glucose and UPS and its regulation mechanism on milk fat synthesis in BMEC (bovine mammary epithelial cells). We incubated BMEC with normal (17.5 mm/L) and high-glucose (25 mm/L) with and without proteasome inhibitor epoxomicin and found that, compared with the control (normal glucose and without proteasome inhibitor), both high-glucose concentration and proteasome inhibitor epoxomicin could increase the accumulation of TG and poly-ubiquitinated proteins, and reduce significantly three proteasome activities (chymotrypsin-like, caspase-like, and trypsin-like). In addition, high-glucose concentration combined with proteasome inhibitor further enhanced the increase of the poly-ubiquitinated protein level and the decrease of proteasome activities. Our results suggest that the regulation of high-glucose on milk fat synthesis is mediated by UPS in BMEC, and high-glucose exposure could lead to a hypersensitization of BMEC to UPS inhibition which in turn results in increased milk fat synthesis.

[Detecting selection signatures on X chromosome in pig through high density SNPs].

In the process of domestic pig breeding, many important economic traits were subject to strong artificial se-lection pressure. With the availability of high density single nucleotide polymorphism (SNP) markers in farm animals, selection occurring in those traits could be traced by detecting selection signatures on genome, and the genes experiencing selection can also be further mined based on selection signatures. Due to the special characteristic of X chromosome, many approaches of genetic analysis fitted for autosome are not plausible for X chromosome. Fortunately, detecting selection signature provides an effective tool to settle such situation. In this study, the Cross Population Extend Haplotype Homozygosity Test (XP-EHH) was implemented to identify selection signatures on chromosome X in three pig breeds (Landrace, Songliao, and Yorkshire) using high density SNPs, and the genes located within selection signature regions were revealed through bioinformatic analysis. In total, 29, 13, and 15 selection signature regions, with 3.59, 4.92, and 4.07 SNPs on average in each region, were identified in Landrace, Songliao, and Yorkshire, respectively. Some overlaps of selection signature regions were observed between Songliao and Landrace, and between Landrace and Yorkshire, while no overlaps between Yorkshire and Songliao were found. Bioinformatic analysis revealed that many genes in the selection signature regions were related to reproduction and immune traits, and some of them have not been reported in pigs, which might serve as important candidate genes in future study.

Genome-wide association study for T lymphocyte subpopulations in swine.

BACKGROUND: Lymphocytes act as a major component of the adaptive immune system, taking very crucial responsibility for immunity. Differences in proportions of T-cell subpopulations in peripheral blood among individuals under same conditions provide evidence of genetic control on these traits, but little is known about the genetic mechanism of them, especially in swine. Identification of the genetic control on these variants may help the genetic improvement of immune capacity through selection. RESULTS: To identify genomic regions responsible for these immune traits in swine, a genome-wide association study was conducted. A total of 675 pigs of three breeds were involved in the study. At 21 days of age, all individuals were vaccinated with modified live classical swine fever vaccine. Blood samples were collected when the piglets were 20 and 35 days of age, respectively. Seven traits, including the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8-, CD4-CD8+, CD4-CD8- and the ratio of CD4+ to CD8+ T cells were measured at the two ages. All the samples were genotyped for 62,163 single nucleotide polymorphisms (SNP) using the Illumina porcineSNP60k BeadChip. 40833 SNPs were selected after quality control for association tests between SNPs and each immune trait considered based on a single-locus regression model. To tackle the issue of multiple testing in GWAS, 10,000 permutations were performed to determine the chromosome-wise and genome-wise significance levels of association tests. In total, 61 SNPs with chromosome-wise significance level and 3 SNPs with genome-wise significance level were identified. 27 significant SNPs were located within the immune-related QTL regions reported in previous studies. Furthermore, several significant SNPs fell into the regions harboring known immunity-related genes, 14 of them fell into the regions which harbor some known T cell-related genes. CONCLUSIONS: Our study demonstrated that genome-wide association studies would be a feasible way for revealing the potential genetics variants affecting T-cell subpopulations. Results herein lay a preliminary foundation for further identifying the causal mutations underlying swine immune capacity in follow-up studies.

Comparison of five methods for genomic breeding value estimation for the common dataset of the 15th QTL-MAS Workshop.

BACKGROUND: Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB and BayesCπ, to the common dataset provided by the 15th QTL-MAS Workshop to evaluate and compare their predictive performances. RESULTS: For the 1000 progenies without phenotypic values, the correlations between GEBVs by different methods ranged from 0.812 (GBLUP and BayesCπ) to 0.997 (TABLUP and BayesB). The accuracies of GEBVs (measured as correlations between true breeding values (TBVs) and GEBVs) were from 0.774 (GBLUP) to 0.938 (BayesCπ) and the biases of GEBVs (measure as regressions of TBVs on GEBVs) were from 1.033 (TABLUP) to 1.648 (GBLUP). The three Bayesian methods and TABLUP had similar accuracy and bias. CONCLUSIONS: BayesA, BayesB, BayesCπ and TABLUP performed similarly and satisfactorily and remarkably outperformed GBLUP for genomic breeding value estimation in this dataset. TABLUP is a promising method for genomic breeding value estimation because of its easy computation of reliabilities of GEBVs and its easy extension to real life conditions such as multiple traits and consideration of individuals without genotypes.

Genome-wide association analyses of the 15th QTL-MAS workshop data using mixed model based single locus regression analysis.

BACKGROUND: The mixed model based single locus regression analysis (MMRA) method was used to analyse the common simulated dataset of the 15th QTL-MAS workshop to detect potential significant association between single nucleotide polymorphisms (SNPs) and the simulated trait. A Wald chi-squared statistic with df =1 was employed as test statistic and the permutation test was performed. For adjusting multiple testing, phenotypic observations were permutated 10,000 times against the genotype and pedigree data to obtain the threshold for declaring genome-wide significant SNPs. Linkage disequilibrium (LD) in term of D' between significant SNPs was quantified and LD blocks were defined to indicate quantitative trait loci (QTL) regions. RESULTS: The estimated heritability of the simulated trait is approximately 0.30. 82 genome-wide significant SNPs (P < 0.05) on chromosomes 1, 2 and 3 were detected. Through the LD blocks of the significant SNPs, we confirmed 5 and 1 QTL regions on chromosomes 1 and 3, respectively. No block was detected on chromosome 2, and no significant SNP was detected on chromosomes 4 and 5. CONCLUSION: MMRA is a suitable method for detecting additive QTL and a fast method with feasibility of performing permutation test. Using LD blocks can effectively detect QTL regions.

A genome-wide association study identifies two novel promising candidate genes affecting Escherichia coli F4ab/F4ac susceptibility in swine.

Enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbria is the major pathogenic bacteria causing diarrhoea in neonatal and post-weaning piglets. Previous studies have revealed that the susceptibility to ETEC F4ab/F4ac is an autosomal Mendelian dominant trait and the loci controlling the F4ab/F4ac receptor are located on SSC13q41, between markers SW207 and S0283. To pinpoint these loci and further validate previous findings, we performed a genome-wide association study (GWAS) using a two generation family-based population, consisting of 301 piglets with phenotypes of susceptibility to ETEC F4ab/F4ac by the vitro adhesion test. The DNA of all piglets and their parents was genotyped using the Illumina PorcineSNP60 BeadChip, and 50,972 and 50,483 SNPs were available for F4ab and F4ac susceptibility, respectively, in the association analysis after quality control. In summary, 28 and 18 significant SNPs (p<0.05) were detected associated with F4ab and F4ac susceptibility respectively at genome-wide significance level. From these significant findings, two novel candidate genes, HEG1 and ITGB5, were firstly identified as the most promising genes underlying F4ab/F4ac susceptibility in swine according to their functions and positions. Our findings herein provide a novel evidence for unravelling genetic mechanism of diarrhoea risk in piglets.

[Expression of a novel metastasis-inducing protein human anterior gradient-2 (AGR2) in breast cancer and its clinical and prognostic significance].

OBJECTIVE: To investigate the expression of a novel metastasis-inducing protein human anterior gradient-2 (AGR2) in breast cancer and its clinical and prognostic significance. METHODS: AGR2 expression was assessed in 160 cases of breast cancer and 20 cases of benign breast diseases by immunohistochemistry using tissue chip technology. In addition the expression of ERa, PR and c-erbB-2 in breast cancer was also evaluated. Follow-up information of 5-year duration was available in 127 patients with breast cancer. Kaplan-Meier analysis and COX regression model were used to analyze the correlation between AGR2 expression and the follow-up clinical data. RESULTS: The expression of AGR2 was significantly higher in breast cancers than that in benign diseases (68.3% vs. 25.0% , P < 0.01). There was a negative correlation between AGR2 expression and the histological grade of breast cancer (P <0.05) , whereas positive correlations was found between the expression of AGR2 and ERalpha (P <0.05), and between the expression of AGR2 and PR (P <0.01). In the subgroup of ERalpha-positive breast cancer, Logistic regression model demonstrated AGR2 and TNM stage were important factors affecting lymph node metastasis (both P < 0.01). Kaplan-Meier analysis demonstrated that a positive expression of AGR2 was associated with poor overall survival and relapse-free survival (both P <0.01). Moreover, COX regression model confirmed the expression of AGR2 as an independent prognostic factor among patients with ERa-positive breast cancer (P <0.01). CONCLUSIONS: The abnormal expression of AGR2 may play a role in the pathogenesis and progression of breast cancer. The metastasis-inducing capability of AGR2 may be partly regulated through the ER pathway. Therefore, AGR2 may be a useful molecular marker for prognostication for patient with hormone-responsive breast cancer.

[Effect of paeoniflorin on hepatic immunopathogenesis in mice with Schistosoma japonicum infection].

OBJECTIVE: To investigate the mechanism of paeoniflorin in preventing hepatic granuloma formation and fibrosis in mice infected with Schistosoma japonicum. METHODS: Model of hepatic granuloma and fibrosis was established by infecting mice with S. japonicum cercariae. The infected mice were randomly divided into 4 groups: group A as model (infected control) group (15 mice), and paeoniflorin being given before, simultaneously and after praziquantel treatment as groups B, C and D. Each of the groups B, C and D was subdivided into 3 subgroups (15 mice each): low dose (paeoniflorin 2 ml, 30 mg/(kg x d) x 30 d), high dose(paeoniflorin 2 ml, 120 mg/(kg x d) x 30 d) and control (2 ml, 0.5% sodium carboxymethylcellulose x 30 d). In group B, paeoniflorin or sodium carboxymethylcellulose was orally administrated on 12 d after infection. In groups C and D, paeoniflorin or sodium carboxymethylcellulose was administrated on 42 d or 72 d after infection. Each of group B, C and D was orally given praziquantel 2 ml (500 mg/(kg x d) x 2 d) on 42 d after infection. On the 102nd day after infection, all animals were sacrificed by cervical dislocation. Serum hyaluronic acid (HA) was detected by radioimmunoassay; area of egg granuloma and degree of hepatic fibrosis were observed via HE and Masson stainings; the expression of transforming growth factor beta1 (TGF-beta1), alpha smooth muscle actin (alpha-SMA and collagen I (Col I) protein were measured by immunohistochemical method. RESULTS: In group B, the level of HA (0.719 +/- 0.239 microg/ml, 0.721 +/- 0.182 microg/ml) in low or high dose subgroups was significantly lower (F = 9.429, P < 0.01) than the control subgroup (1.049 +/- 0.286 microg/ml); the area of granuloma (0.066 +/- 0.005 mm2, 0.064 +/- 0.004 mm2) or the degree of hepatic fibrosis (2.067 +/- 0.458, 1.967 +/- 0.399) in low or high dose subgroups was significantly greater (F = 862.540, F = 29.738, P < 0.01) than the control (0.141 +/- 0.008 mm2, 3.467 +/- 0.834); the expression of alpha-SMA positive cells (2.933 +/- 0.594, 3.000 +/- 0.535) in low or high dose subgroups was significantly lower (F = 12.323, P < 0.01, P < 0.01) than its control (4.800 +/- 1.859); the expression of TGF-beta1 (0.256 +/- 0.057, 0.274 +/- 0.054) in low or high dose subgroups was significantly lower (F = 148.990, P < 0.01) than its control (0.552 +/- 0.047); the content of Col I (0.334 +/- 0.041, 0.339 +/- 0.042) in low or high dose subgroups was significantly lower (F = 180.881, P < 0.01) than its control (0.601 +/- 0.049). In groups C & D, no significant difference was found between the low or high dose subgroups or between the subgroups and their corresponding controls. CONCLUSION: Paeoniflorin can significantly reduce hepatic granuloma formation and fibrosis due to schistosome eggs, and decrease the expression of TGF-beta1, alpha-SMA in mice when it is given before praziquantel administration, which may associate with the activation of hepatic stellate cells and the expression of TGF-beta1 in liver tissue.

Prognostic significance of MMP-9 and TIMP-1 serum and tissue expression in breast cancer.

Tumor progression and metastasis contribute to the great majority of breast cancer deaths. Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are thought to be involved in tumor progression and metastasis. Thus, we determined whether the expression of MMP-9 and TIMP-1 is associated with prognosis in breast cancer patients. We measured serum MMP-9 and TIMP-1 by enzyme-linked immunosorbent assay in 60 breast cancer patients, 18 benign breast disease patients and 15 healthy controls. We also evaluated the expression of MMP-9 and TIMP-1 protein and mRNA in paraffin-embedded tumor tissues from the 60 breast cancer patients by immunohistochemistry and in situ hybridization. We then correlated serum and tissue levels of MMP-9 and TIMP-1 in breast cancer samples and their expression with patients' clinicopathologic characteristics. We found that serum levels of MMP-9 and TIMP-1 were significantly higher in breast cancer patients than in benign breast disease and in healthy controls. High serum levels of MMP-9 and TIMP-1 were associated with lymph node metastasis, higher tumor stage and lower relapse-free and overall survival (OS) rates. Compared to low expression, high tissue expression of MMP-9 protein was associated with lymph node metastasis and higher tumor stage; and high tissue expression of TIMP-1 was associated with a lower OS rate. Our findings suggest that MMP-9 and TIMP-1 may further be evaluated as biomarkers for predicting progression and prognosis of breast cancer.

A new method for haplotype inference including full-sib information.

Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families, can be an alternative strategy in determining linkage phase and estimating haplotype frequencies. In the case of no possibility to obtain genotypes for parents, and only full-sib information being used, a new approach is suggested to infer phase and to reconstruct haplotypes. We present a maximum-likelihood method via an expectation-maximization algorithm, called FSHAP, using only full-sib information when parent information is not available. FSHAP can deal with families with an arbitrary number of children, and missing parents or missing genotypes can be handled as well. In a simulation study we compare FSHAP with another existing expectation-maximization (EM)-based approach (FAMHAP), the conditioning approach implemented in FBAT and GENEHUNTER, which is only pedigree based and assumes linkage equilibrium. In most situations, FSHAP has the smallest discrepancy of haplotype frequency estimation and the lowest error rate in haplotype reconstruction, only in some cases FAMHAP yields comparable results. GENEHUNTER produces the largest discrepancy, and FBAT produces the highest error rate in offspring in most situations. Among the methods compared, FSHAP has the highest accuracy in reconstructing the diplotypes of the unavailable parents. Potential limitations of the method, e.g., in analyzing very large haplotypes, are indicated and possible solutions are discussed.

Oral respiratory syncytial virus (RSV) DNA vaccine expressing RSV F protein delivered by attenuated Salmonella typhimurium.

Human respiratory syncytial virus (RSV) is a major viral pathogen of the lower respiratory tract of infants and young children worldwide. No effective prevention measure is available. Attenuated Salmonella strains expressing heterologous antigens can be delivered by the oral route, triggering efficient antigen-specific humoral, cellular, and mucosal immunity. In this study, we orally administered attenuated Salmonella strain SL7207, carrying the plasmid pcDNA3.1/F expressing the RSV F gene, to BALB/c mice and showed significant elevations of serum anti-RSV IgG and bronchoalveolar lavage secretory IgA as compared with the control group carrying empty plasmid (p<0.001). The ratio of IgG1 and IgG2a was 0.96. The experimental group also showed a stronger cytotoxic T cell response (p<0.01 at effector:target ratios of 100:1 and 50:1) and a higher stimulation index value of T cell proliferation (p<0.05) than the respective control group. RSV titers in the lung homogenates of the experimental group on day 3 and day 5 postchallenge were lower than in the control group (p<0.05). Histopathological analysis showed obvious differences in infiltration of inflammatory cells and pulmonary alveolar wall thickness (p<0.01) between the two groups. In summary, our results demonstrate the potential of orally administered SL7207-based DNA vaccines against RSV infection.

Methodology of mapping quantitative trait loci for ordinal traits of disease resistance in livestock.

Methodology of QTL mapping for ordinal traits of disease resistance based on the framework of a generalized linear model (GLM) was presented. The location and effect parameters of putative QTL were estimated using maximum likelihood method. The efficiency and power were compared with the linear model (LM). The factors influencing QTL detection efficiency (e.g. QTL effect and heritability) were simulated in our study too. Daughter design with multiple families was applied,and the number of segregating population was 500. Results showed that the threshold model has a certain advantage in location estimation and power of QTL mapping, and has efficiency and accuracy for ordinal traits. In addition,the accuracy of QTL mapping depends on the effect of putative quantitative trait loci and the value of heritability. With the increase of QTL effect and heritability, the accuracy of QTL mapping improves slightly.