A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation

Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.

[Immunogenicity, safety and immune persistence of the sequential booster with the recombinant protein-based COVID-19 vaccine (CHO cell) in healthy people aged 18-84 years]

Objective: To evaluate the immunogenicity, safety, and immune persistence of the sequential booster with the recombinant protein-based COVID-19 vaccine (CHO cell) in healthy people aged 18-84 years. Methods: An open-label, multi-center trial was conducted in October 2021. The eligible healthy individuals, aged 18-84 years who had completed primary immunization with the inactivated COVID-19 vaccine 3 to 9 months before, were recruited from Shangyu district of Shaoxing and Kaihua county of Quzhou, Zhejiang province. All participants were divided into three groups based on the differences in prime-boost intervals: Group A (3-4 months), Group B (5-6 months) and Group C (7-9 months), with 320 persons per group. All participants received the recombinant COVID-19 vaccine (CHO cell). Blood samples were collected before the vaccination and after receiving the booster at 14 days, 30 days, and 180 days for analysis of GMTs, antibody positivity rates, and seroconversion rates. All adverse events were collected within one month and serious adverse events were collected within six months. The incidences of adverse reactions were analyzed after the booster. Results: The age of 960 participants was (52.3±11.5) years old, and 47.4% were males (455). The GMTs of Groups B and C were 65.26 (54.51-78.12) and 60.97 (50.61-73.45) at 14 days after the booster, both higher than Group A's 44.79 (36.94-54.30) (P value<0.05). The GMTs of Groups B and C were 23.95 (20.18-28.42) and 27.98 (23.45-33.39) at 30 days after the booster, both higher than Group A's 15.71 (13.24-18.63) (P value <0.05). At 14 days after the booster, the antibody positivity rates in Groups A, B, and C were 91.69% (276/301), 94.38% (302/320), and 93.95% (295/314), respectively. The seroconversion rates in the three groups were 90.37% (272/301), 93.75% (300/320), and 93.31% (293/314), respectively. There was no significant difference among these rates in the three groups (all P values >0.05). At 30 days after the booster, antibody positivity rates in Groups A, B, and C were 79.60% (238/299), 87.74% (279/318), and 90.48% (285/315), respectively. The seroconversion rates in the three groups were 76.92% (230/299), 85.85% (273/318), and 88.25% (278/315), respectively. There was a significant difference among these rates in the three groups (all P values <0.001). During the sequential booster immunization, the incidence of adverse events in 960 participants was 15.31% (147/960), with rates of about 14.38% (46/320), 17.50% (56/320), and 14.06% (45/320) in Groups A, B, and C, respectively. The incidence of adverse reactions was 8.02% (77/960), with rates of about 7.50% (24/320), 6.88% (22/320), and 9.69% (31/320) in Groups A, B, and C, respectively. No serious adverse events related to the booster were reported. Conclusion: Healthy individuals aged 18-84 years, who had completed primary immunization with the inactivated COVID-19 vaccine 3 to 9 months before, have good immunogenicity and safety profiles following the sequential booster with the recombinant COVID-19 vaccine (CHO cell).

[Research and development of an intelligent platform for respiratory therapy]

In recent years, the incidence of respiratory diseases has increased year on year. This has become a major global public health issue. To effectively treat respiratory diseases and improve the quality of life and prognosis of patients, the intelligent platform of respiratory therapy was established. Through real-time monitoring patients' important physiological indicators and integrating medical information, visual management, and intelligent decision making can be realized to provide personalized respiratory treatment and rehabilitation programs for critically ill patients. The platform can also provide reliable data support for medical research and further promote the development of the field of respiratory disease treatment. In the future, the platform will continue to improve the level and efficiency of clinical treatment, and truly solve practical problems for patients.

The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection

Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.

[Efficacy and safety of epidermal growth factor receptor tyrosine kinase inhibitors combined with chemotherapy as first-line treatment for epidermal growth factor receptor-mutant advanced non-small cell lung cancer]

Objective: To observe the clinical efficacy and safety of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) combined with chemotherapy as first-line treatment for EGFR mutant advanced non-small cell lung cancer (NSCLC). Methods: It was a retrospective, single-arm real-world study and a total of 39 patients with stage ⅢB to Ⅳ EGFR mutant NSCLC diagnosed in Cancer Hospital of Chinese Academy of Medical Sciences from July 2018 to December 2020 were collected. There were 16 males and 23 females, the age ranged from 25 to 73 years, with a median age of 53 years. All patients received EGFR-TKIs synchronously combined with pemetrexed and platinum-containing chemotherapy for 4-6 cycles as first-line treatment, followed by EGFR-TKI monotherapy with or without pemetrexed maintenance therapy. The objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS) and adverse reactions were evaluated. Median follow-up time was 18.6 months (95%CI: 16.2-21.0 months). The Kaplan-Meier method was used for survival analysis. Results: The ORR was 61.5% (24/39), the DCR was 94.9% (37/39) and the median PFS was 16.4 months (95%CI: 12.1-20.7 months). The main adverse reactions were liver function injury (59.0%, 23/39), myelosuppression (43.6%, 17/39), skin reaction (25.6%, 10/39), gastrointestinal reaction (17.9%, 7/39), fatigue (12.8%, 5/39) and kidney injury (5.1%, 2/39). Most of the patients had grade 1-2 adverse reactions, and the rate of grade 3 adverse events were 12.8%(5/39), which were effectively alleviated after symptomatic support treatment, no grade 4 serious adverse events occurred. Conclusion: EGFR-TKIs synchronously combined with chemotherapy followed by EGFR-TKI monotherapy with or without pemetrexed maintenance therapy has a certain therapeutic effect and fairly good safety, which can prolong PFS in patients with EGFR mutated advanced NSCLC.

Population Structure and Genetic Diversity in the Natural Distribution of Neolamarckia cadamba in China

Neolamarckia cadamba (Roxb.) Bosser is a fast-growing deciduous tree species and belongs to the Neolamarckia genus of the Rubiaceae family. This species has great economic and medical values in addition to being an important timber species for multiple industrial purposes. However, few studies have examined the genetic diversity and population structure in the natural distribution of this species in China. Here, we applied both the haploid nrDNA ITS (619 bp for aligned sequences) and mtDNA (2 polymorphic loci) markers to investigate 10 natural populations (239 individuals in total) that covered most of the distribution of the species in China. The results showed that the nucleotide diversity was π = 0.1185 ± 0.0242 for the nrDNA ITS markers and π = 0.00038 ± 0.00052 for the mtDNA markers. The haplotype diversity for the mtDNA markers was h = 0.1952 ± 0.2532. The population genetic differentiation was small (Fstn = 0.0294) for the nrDNA ITS markers but large (Fstm = 0.6765) for the mtDNA markers. There were no significant effects of isolation by distance (IBD), by elevation, and by two climatic factors (annual average precipitation and tem perature). A geographic structure among populations (Nst<Gst) was absent. Phylogenetic analysis showed a highly genetic mixture among individuals of the ten populations. Pollen flow was substantially greater than seed flow (mp/ms ≫ 1.0) and played a dominant role in shaping population genetic structure. The nrDNA ITS sequences were neutral and all local populations did not undergo demographic expansion. The overall results provide fundamental information for the genetic conservation and breeding of this miraculous tree.

Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.

Postoperative outcomes and recurrence patterns of intermediate-stage hepatocellular carcinoma dictated by the sum of tumor size and number

BACKGROUND

The selection criteria for Barcelona Clinic Liver Cancer (BCLC) intermediate-stage hepatocellular carcinoma (HCC) patients who would truly benefit from liver resection (LR) remain undefined.

AIM

To identify BCLC-B HCC patients more suitable for LR.

METHODS

We included patients undergoing curative LR for BCLC stage A or B multi-nodular HCC (MNHCC) and stratified BCLC-B patients by the sum of tumor size and number (N + S). Overall survival (OS), recurrence-free survival (RFS), recur-rence-to-death survival (RTDS), recurrence patterns, and treatments after recurrence in BCLC-B patients in each subgroup were compared with those in BCLC-A patients.

RESULTS

In total, 143 patients who underwent curative LR for MNHCC with BCLC-A (n = 25) or BCLC-B (n = 118) were retrospectively analyzed. According to the N + S, patients with BCLC-B HCC were divided into two subgroups: BCLC-B1 (N + S ≤ 10, n = 83) and BCLC-B2 (N + S > 10, n = 35). Compared with BCLC-B2 patients, those with BCLC-B1 had a better OS (5-year OS rate: 67.4% vs 33.6%; P < 0.001), which was comparable to that in BCLC-A patients (5-year OS rate: 67.4% vs 74.1%; P = 0.250), and a better RFS (median RFS: 19 mo vs 7 mo; P < 0.001), which was worse than that in BCLC-A patients (median RFS: 19 mo vs 48 mo; P = 0.022). Further analysis of patients who developed recurrence showed that both BCLC-B1 and BCLC-A patients had better RTDS (median RTDS: Not reached vs 49 mo; P = 0.599), while the RTDS in BCLC-B2 patients was worse (median RTDS: 16 mo vs not reached, P < 0.001; 16 mo vs 49 mo, P = 0.042). The recurrence patterns were similar between BCLC-B1 and BCLC-A patients, but BCLC-B2 patients had a shorter recurrence time and a higher proportion of patients had recurrence with macrovascular invasion and/or extrahepatic metastasis, both of which were independent risk factors for RTDS.

CONCLUSION

BCLC-B HCC patients undergoing hepatectomy with N + S ≤ 10 had mild recurrence patterns and excellent OS similar to those in BCLC-A MNHCC patients, and LR should be considered in these patients.

Evolutionary Divergence between Toona ciliata and Toona sinensis Assayed with Their Whole Genome Sequences

Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was cultivated as an economic and nutritious tree for more than 2000 years. The two species differ in flower and leaf morphological traits, reproductive systems, and range size of natural distribution. To reveal the potential molecular basis of these divergences, we examined the similarities and differences in their whole genome sequences. Results indicate that T. ciliata had a higher number of expanded gene families than T. sinensis. The whole genome duplication (WGD) occurred before their speciation. The long-terminal repeats (LTRs) insertion was earlier in the T. ciliata genome (3.2985 ± 2.5007 Mya) than in the T. sinensis genome (3.1516 ± 2.2097 Mya). Twenty-five gene families in the T. ciliata genome were detected to be under positive selection compared with background branches of ten different land species. The T. ciliata genome was highly collinear with the T. sinensis genome, but had low collinearity with the genomes of more distant species. These genomic and evolutionary divergences are potentially associated with the differences between T. ciliata and T. sinensis in terms of their reproductive systems and ecological adaptation.

[Modified mattress inversion suturing with double barbed sutures used for totally laparoscopic esophagojejunostomy overlap anastomosis after radical total gastrectomy]

Objective: To explore the advantages and safety of a modified mattress inversion suturing using double barbed sutures compared with the traditional overlap method in totally laparoscopic esophagojejunostomy overlap anastomosis. Methods: A retrospective cohort study was conducted. The inclusion criteria were as follows: (1) patients were aged 18 - 80 years old; (2) adenocarcinoma was preoperatively confirmed by pathological analysis; (3) patients had undergone a complete laparoscopic radical total gastrectomy; (4) patients had undergone esophagojejunostomy using the overlap method; (5) patients received a grade of I-III on the American Society of Anesthesiologists physical status classification system; (6) patients' complete follow-up data had been collected. Patients with a history of other malignant tumors, multi-origin tumors, emergency surgery, non-R0 radical resection or distant metastasis were excluded. The clinical data of 89 gastric cancer patients who underwent total laparoscopic radical total gastrectomy in the Department of Gastrointestinal Surgery in the Sixth Affiliated Hospital of Sun Yat-sen University from January 2019 to December 2020 were collected. These patients were grouped according to the esophagojejunostomy method used. Of 89 patients, 32 received modified mattress inversion suturing with double barbed sutures to close the common opening of esophagojejunostomy (the modified anastomosis group), while 57 received traditional overlap anastomosis in which the common opening was closed by barbed suture (the traditional anastomosis group). The operation conditions (incision length, conversion to laparotomy, duration of esophagojejunostomy) and postoperative recovery (time to commencement of a liquid diet, duration of postoperative hospital stay, anastomotic leakage, anastomotic stenosis, and anastomotic bleeding) were compared between the two groups. Results: There was no significant difference in the baseline data of the two groups for any parameter (all P>0.05). All patients received complete laparoscopic radical gastrectomy without conversion to laparotomy. There were no significant differences in the length of the median incision, the proportion of food intake on the first day after surgery, or in the incidence of anastomotic complications such as anastomotic leakage, anastomotic stenosis, and anastomotic bleeding between the two groups (P>0.05). Compared with the traditional anastomosis group, patients in the modified anastomosis group had shorter anastomosis time [26 (19-62) minutes vs. 36 (20-50) minutes, Z=-2.546, P=0.011] and postoperative hospital stay [7 (6-12) days vs. 9 (7-42) days, Z=-4.202, P<0.001]. The differences were statistically significant (all P<0.05). In a subgroup analysis of tumor TNM stage III, Siewert type II and neoadjuvant chemotherapy patients, there was no significant difference in the incidence of anastomotic complications between the modified group and the traditional group. However, the postoperative hospital stay duration in the modified anastomosis group was less than in the traditional anastomosis group. The duration of anastomosis in Siewert type II patients was also shorter in the modified anastomosis group than in the traditional anastomosis group [26 (19-62) minutes vs. 38 (21-50) minutes, Z=-2.105, P=0.035], and the difference was statistically significant (all P<0.05). Conclusion: Complete laparoscopic esophagojejunostomy using modified mattress inversion suturing with double barbed sutures is a safe and feasible anastomosis method to close the common opening of esophagojejunostomy, with shorter operation time, faster postoperative recovery and shorter hospital stay than the traditional method.

[Real-world study on the efficacy and prognostic predictive biomarker of patients with metastatic non-small cell lung cancer treated with programmed death-1/programmed death ligand 1 inhibitors]

Objective: To describe the actual efficacy of programmed death-1 (PD-1)/ programmed-death ligand 1 (PD-L1) inhibitors in patients with metastatic non-small cell lung cancer (NSCLC) and explore potential prognostic predictive biomarkers. Methods: Patients with metastatic NSCLC who were treated with PD-1/PD-L1 inhibitors at Cancer Hospital, Chinese Academy of Medical Sciences from January 2016 to December 2019, either as monotherapy or in combination with other agents, were consecutively enrolled into this study. We retrospectively collected the data of demographics, clinical information and pathologic assessment to evaluate the therapeutic efficacy and conduct the survival analysis. Major endpoint of our study is progression-free survival (PFS). Secondary endpoints include objective response rate (ORR), disease control rate (DCR) and overall survival (OS). Results: The ORR of 174 patients who underwent PD-1/PD-L1 inhibitor was 28.7%, and the DCR was 79.3%. Immune-related adverse events (irAEs) occurred in 23 patients (13.2%). Brain metastasis, line of treatment, and treatment patterns were associated with the ORR of metastatic NSCLC patients who underwent immunotherapy (P<0.05). After a median follow-up duration of 18.8 months, the median PFS was 10.5 months (ranged from 1.5 to 40.8 months) while the median OS was not reached. The 2-year survival rate was estimated to be 63.0%. The pathologic type was related with the PFS of metastatic NSCLC patients who underwent immunotherapy (P=0.028). Sex, age, brain metastasis and autoimmune diseases were associated with OS (P<0.05). Analysis of the receptor characteristic curve (ROC) of neutrophil/lymphocyte ratio (NLR) predicting ORR of immunotherapy in metastatic NSCLC showed that the areas under the curve of NLR before immunotherapy (NLR(C0)), NLR after one cycle of immunotherapy (NLR(C1)) and ΔNLR were 0.600, 0.706 and 0.628, respectively. Multivariate logistic regression analysis showed that NLR(C1) was an independent factor of the ORR of metastatic NSCLC patients who underwent immunotherapy (OR=0.161, 95% CI: 0.062-0.422), and the efficacy of combination therapy was better than that of single agent (OR=0.395, 95% CI: 0.174-0.896). The immunotherapy efficacy in patients without brain metastasis was better than those with metastasis (OR=0.291, 95% CI: 0.095-0.887). Multivariate Cox regression analysis showed that NLR(C1) was an independent influencing factor of PFS of metastatic NSCLC patients after immunotherapy (HR=0.480, 95% CI: 0.303-0.759). Sex (HR=0.399, 95% CI: 0.161-0.991, P=0.048), age (HR=0.356, 95% CI: 0.170-0.745, P=0.006) were independent influencing factors of OS of metastatic NSCLC patients after immunotherapy. Conclusions: PD-1/PD-L1 inhibitors are proved to be efficacious and have tolerable toxicities for patients with metastatic NSCLC. Patients at advanced age could still benefit from immunotherapy. Brain metastasis is related to compromised response. Earlier application of immunotherapy in combination with other modalities enhances the efficacy without elevating risk of irAEs. NLR(C1) is an early predictor of clinical outcome. The OS of patients younger than 75 years may be improved when treated with immunotherapy.

A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis

Neolamarckia cadamba is an important tropical and subtropical tree for timber industry in southern China and is also a medicinal plant because of the secondary product cadambine. N. cadamba belongs to Rubiaceae family and its taxonomic relationships with other species are not fully evaluated based on genome sequences. Here, we report the complete sequences of mitochondrial genome of N. cadamba, which is 414,980 bp in length and successfully assembled in two genome circles (109,836 bp and 305,144 bp). The mtDNA harbors 83 genes in total, including 40 protein-coding genes (PCGs), 31 transfer RNA genes, 6 ribosomal RNA genes, and 6 other genes. The base composition of the whole genome is estimated as 27.26% for base A, 22.63% for C, 22.53% for G, and 27.56% for T, with the A + T content of 54.82% (54.45% in the small circle and 54.79% in the large circle). Repetitive sequences account for ~ 0.14% of the whole genome. A maximum likelihood (ML) tree based on DNA sequences of 24 PCGs supports that N. cadamba belongs to order Gentianales. A ML tree based on rps3 gene of 60 species in family Rubiaceae shows that N. cadamba is more related to Cephalanthus accidentalis and Hymenodictyon parvifolium and belongs to the Cinchonoideae subfamily. The result indicates that N. cadamba is genetically distant from the species and genera of Rubiaceae in systematic position. As the first sequence of mitochondrial genome of N. cadamba, it will provide a useful resource to investigate genetic variation and develop molecular markers for genetic breeding in the future.

Mating system and population structure in the natural distribution of Toona ciliata (Meliaceae) in South China

Most initially perfect flowers of Toona ciliata Roem subsequently develop into functionally unisexual flowers and their relative positions in the same inflorescence could enhance the outcrossing system in this species. Here we investigated the mating system of this species. We used eight nuclear microsatellite markers and investigated the progeny of 125 mother trees from six populations naturally distributed in South China, with sample sizes ranging from 64 to 300 seeds. The multilocus outcrossing rate was 0.970 ± 0.063, and the single locus outcrossing rate was 0.859 ± 0.106, indicating the pattern of predominant outcrossing. Selfing was present in one population, but biparental inbreeding occurred in five populations. Inbreeding was absent in maternal parents, and correlations of selfing among families or among loci were generally insignificant. Positive correlation of paternity at multiple loci was significant in four populations, but was not consistent with the results at single loci. Population substructure occurred in male similarity between outcrosses only in one population. Population genetic differentaitaion was significant (F_st = 34.5%) and the effects of isolation-by-distance at the eight loci were significant among the six populations. These results provide evidence that self-comptability and inbreeding naturally occur in T. ciliata and indicate that inbreeding avoidance is necessary during genetic improvement and breeding of this endangered tree species.

The wave of gene advance under diverse systems of mating

Mating systems will influence gene spread across the natural distribution of a plant species. Existing theories have not fully explored the role of mating systems on the wave of advance of an advantageous gene. Here, we develop a theory to account for the rate of spread of both advantageous and neutral genes under different mating systems, based on migration-selection processes. We show that a complex relationship exists between selfing rate and the speed of gene spread. The interaction of selfing with gametophytic selection shapes the traveling wave of the advantageous gene. Selfing can impede (or enhance) the spread of an advantageous gene in the presence (or absence) of gametophytic selection. The interaction of selfing with recombination shapes the spread of a neutral gene. Linkage disequilibrium, mainly generated by selfing, enhances the traveling wave of the neutral gene that is tightly linked with the selective gene. Recombination gradually breaks down the genetic hitchhiking effects along the direction of advantageous gene spread, yielding decreasing waves of advance of neutral genes. The stochastic process does not alter the pattern of selfing effects except for increasing the uncertainty of the waves of advance of both advantageous and neutral genes. This theory helps us to explain how mating systems act as a barrier to spread of adaptive and neutral genes, and to interpret species cohesion maintained by a low level of adaptive gene flow.

[Safety and immunogenicity analysis of recombinant （hansenula polymorpha) hepatitis B vaccine （CpG ODN adjuvant) among adults: the preliminary results of phase I clinical trial]

Objective: To evaluate the safety and immune effect of recombinant hepatitis B vaccine （CpG ODN adjuvant). Methods: On Oct. 26, 2016, we launched volunteer recruitment in Kaihua county, Quzhou city, Zhejiang Province. In the randomized, double-blind, controlled trial, a total of 48 subjects with negative HBV screening tests and normal hepatorenal function among 18 and 60 years old were selected and divided into two groups randomly, 24 cases each. The experimental group was given 250 μg of CpG ODN recombinant （Hansenula polymorpha) Hepatitis B vaccine and the control group was given 10 μg of commercial Hepatitis B vaccine with timed at 0, 1and 6 months. The inoculation reactions were compared the difference between the two groups after observed and recorded in time periods. We also collected serum before and after immunization to compare the two groups of anti-HBs positive rate, geometric mean concentration（GMC). Results: During the study period, the incidence of adverse events was 66.67%（16/24) in the experimental group and 54.17%（13/24) in the control group, with no significant difference（P=0.556). The severities of adverse events were level 1 or level 2, and no level 3 or above adverse reactions occurred. After full-course immunization, in the FAS data set, the anti-HBs GMC in the experimental group [2 598.56（1 127.90-5 986.90) mIU/ml] was higher than that in the control group[371.97（164.54-840.91) mIU/ml] In the PPS set, the GMC of test group was 7 808.21（3 377.00-18 052.00) mIU/ml, which was higher than that of the control group [843.22（213.80-3 325.90) mIU/ml]. The anti-HBs positive rate of FAS（PPS) was 95.83%（100.00%) in the experimental group and the control group; The anti-HBs strongly positive rate of FAS（PPS) was 79.17%（90.00%) in the experimental group and 33.33%（50.00%) in the control group, with statistically significant differences among the FAS set（P=0.003) and no statistically significance differences among the PPS set（P=0.074). Conclusion: CpG Hepatitis B Vaccine is safe and shows better immunogenicity than the control vaccine.

[Respiratory support for severe 2019-nCoV pneumonia suffering from acute respiratory failure: time and strategy]

Respiratory support is a very important technique for saving severe 2019-nCoV pneumonia patients who suffering respiratory failure, which can improve oxygenation, reduce mortality. Therefore, how to reasonable using respiratory support technique is the key point that relating success or failure. In this paper, the authors introduce their experience on treating severe 2019-nCoV pneumonia, it is hopeful for current fighting against 2019-nCoV in China.

[Post-marketing safety analysis of inactivated enterovirus A71 vaccines]

Objectives: To evaluate the safety of inactivated enterovirus A71(EV-A71) vaccines after large-scale immunization in the community. Methods: We selected EV-A71 susceptible people (healthy children) aged 6-59 months in vaccination clinics from 89 counties in Zhejiang Province between April 2016 and March 2018. All local and systematic adverse actions were collected by 30 min on-site inspection, within 3 days and 4-30 days follow-up. Chi-square test and Fisher's exact test were used to compare the difference of AEs incidence in various characteristics among two groups. Results: A total of 71 663 doses of vaccines were included for active safety analysis, which included 37 331 doses in boys and 34 332 doses in girls. Among all the doses, children aged 6 to 11 months, 12 to 23 months and 24 to 59 months were received 13 707, 32 639 and 25 317 doses respectively. The incidence of adverse reactions within 30 min, 3 days and 4-30 days were 0.33% (239 doses), 1.58% (1 133 doses) and 0.34% (244 doses) respectively. Adverse reactions within 3 days were 1 372 doses, with a incidence of 1.91%; among all the cases, 539 doses (0.75%) were grade 1, 677 doses (0.94%) were grade 2 and 156 doses (0.22%) were grade 3, no grade-4 adverse reaction was reported. The common local adverse reactions were redness, swelling and pruritus, with the incidence rates were 0.05% (39 doses), 0.02% (16 doses) and 0.02% (12 doses), respectively, while the most common systemic adverse reaction was pyrexia with an incidence of 1.19% (856 doses), followed by diarrhea and anorexia with the incidence rates were 0.15% (104 doses) and 0.13% (90 doses) respectively. Conclusion: Most adverse actions of EV-A71 vaccines were mild and moderate and majority of them were common adverse actions. No new adverse reactions were found in the study.

[The clinical and pathological features, biomarker characteristics and prognosis analysis of lung adenosquamous carcinoma]

Objective: Adenosquamous carcinoma of lung is an uncommon subtype with more aggressive behavior and poor prognosis than adenocarcinoma and squamous cell carcinoma. This study was aimed to investigate the clinicopathological characteristics and prognostic factors of lung adenosquamous carcinoma. Methods: The pathological features and follow-up data of 133 patients were collected and the prognostic factors of these patients were retrospectively analyzed. Results: Among the 133 patients, 81 cases (60.9%) smoked. Among the 62 patients whose percentage of histological components were identified, 45 cases had >50% adenocarcinoma components, and 17 cases had >50% squamous cell carcinoma components. 55 patients had lymph node metastasis at the first visit. All patients accepted at least one test of tumor driven gene mutation, and the results showed that the mutation rate of EGFR was 50.8% (67/132), the mutation rate of K-ras was 8.6% (11/128), the ALK-positive rate was 4.2% (2/48). The gender, smoking status, and the proportion of pathological components were the main influence factors of EGFR mutation status. The median overall survival was 28 months, the rates of 1-year, 3-year, and 5-year survival were 72.9%, 23.3%, and 9.0%, respectively. EGFR tyrosine kinase inhibitors (TKIs) treatment was an independent risk factor for prognose of these patients (P=0.024). Conclusions: Lung adenosquamous carcinoma is a rare subtype with high malignancy and poor prognosis. Early diagnosis and driven-mutation-based individualized therapy may improve the survival of patients with lung adenosquamous carcinoma.

Mating system shifts a species' range

Understanding the ecological and evolutionary mechanisms that shape a species' range is an important goal in evolutionary biology. Evidence indicates that mating system is an effective predictor of the global range of native species or naturalized alien plants, but the mechanisms underlying this predictability are not elaborated. Here, we develop a theoretical model to account for the ranges of plants under different mating systems based on migration-selection processes (an idea proposed by Haldane). The model includes alternation of gametophyte and sporophyte generations in one life cycle and the dispersal of haploid pollen and diploid seeds as vectors for gene flow. We show that the interaction between selfing rates and gametophytic selection determines the role of mating system in shaping a species' range. Selfing restricts the species' range under gametophytic selection in nonrandom mating systems, but expands the species' range under the absence of gametophytic selection in any mating system. Gametophytic selection slightly restricts the species' range in random mating. Both logarithmic and logistic models of population demography yield similar conclusions in the case of fixed or evolving genetic variance. The theory also helps to explain a broader relationship between mating system and range size following biological invasion or plant naturalization.

Estimating the number of sexual events per generation in a facultatively sexual haploid population

In populations of facultatively sexual organisms, the proportion of sexually produced offspring contributed to each generation is a critical determinant of their evolutionary potential. However, estimating this parameter in natural populations has proved difficult. Here we develop a population genetic model for estimating the number of sexual events occurring per generation for facultatively sexual haploids possessing a biallelic mating-type locus (e.g., Chlamydomonas, ascomycete fungi). Our model treats the population as two subpopulations possessing opposite mating-type alleles, which exchange genes only when a sexual event takes place. Where mating types are equally abundant, we show that, for a neutral genetic marker, genetic differentiation between mating-type subpopulations is a simple function of the effective population size, the frequency of sexual reproduction, and the recombination fraction between the genetic marker and the mating-type locus. We employ simulations to examine the effects of linkage of markers to the mating-type locus, inequality of mating-type frequencies, mutation rate, and selection on this relationship. Finally, we apply our model to estimate the number of sexual reproduction events per generation in populations of four species of facultatively sexual ascomycete fungi, which have been jointly scored for mating type and a range of polymorphic molecular markers. Relative estimates are in line with expectations based on the known reproductive biology of these species.

[Trend analysis and clinicopathological characteristics of 198 young patients with advanced lung adenocarcinoma]

Objective: The aim of this study was to analyze the trend of incidence, clinicopathological characteristics and therapy of young (less than 40 years old) patients with advanced lung adenocarcinoma, and to identify the prognostic factors. Methods: The clinical data of 198 young patients with advanced lung adenocarcinoma were collected from the Cancer hospital and Institute of Chinese academy of Medical Sciences from January 2001 to June 2012. To analyze the trend of incidence, clinicopathological characteristics and therapy and evaluate the independent prognostic factors affecting survival time with Cox proportional hazards model. Results: From 2001 to 2012, the incidence of lung adenocarcinoma in young patients was increased year by year. Among the 198 patients, 92 were males and 106 were females. Their age was from 20 to 40 with a median age of 34 years. Most patients had poorly differentiated adenocarcinoma (46.7%) whereas 36.7% of the cases had moderately differentiated tumor. Among the 198 patients, there were 25 patients with stage ⅢB (12.6%) and 173 (87.4%) cases of stage Ⅳ cancer.The 1-, 3- and 5-year survival rates were 70.7%, 21.6% and 10.3%, respectively. Among the198 cases, patients who received epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) therapy, the median OS (25.6 months) was significantly longer than that of patients who never received EGFR-TKI therapy (13.3 months)(P<0.001). Since 2009, the number of cases detected for EGFR gene was gradually increased, and the median OS of patients diagnosed from 2010 to 2012 was 22 months, significantly higher than that of 16 months of patients diagnosed during 2001-2009 (P=0.019). The Cox regression analysis showed that the performance status, extra-pulmonary metastasis and whether received EGFR-TKI therapy were independent prognostic factors. Conclusions: The incidence rate of lung adenocarcinoma in young patients has an increasing trend. They have a high proportion of women and of poor differentiation. The patients can get benefits from EGFR-TKI therapy. Mutivariate Cox regression analysis shows that the performance status, extra-pulmonary metastasis and whether received EGFR-TKI therapy are independent prognostic factors for young patients with advanced lung adenocarcinoma.

High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens

Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G_st = 0.05 ± 0.049). The smallest divergence is among African populations (G_st = 0.0081 ± 0.0025), with increased divergence among non-African populations (G_st = 0.0217 ± 0.0109) and then among African and non-African populations (G_st = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

[Retrospective analysis of albumin-bound paclitaxel in the treatment of elderly patients with advanced non-small cell lung cancer]

OBJECTIVE

To observe the safety and short-term efficacy of sigle drug albumin-bound paclitaxel (ABP) in the treatment of elderly patients with advanced non-small cell lung cancer (NSCLC).

METHODS

A total of 23 elderly patients with advanced NSCLC who received weekly ABP regimen (130 mg/m(2)/week) in our hospital from October 2011 to March 2014 were retrospectively evaluated. The short-term efficacy, progression-free survival (PFS), and overall survival (OS) were analyzed.

RESULTS

The median treatment period was 4 cycles (2-10 cycles). Partial response, stable disease, progressive disease, overall response rate, and disease control rate were 26.1%, 43.5%, 30.4%, 26.1% and 69.6%, respectively. The median PFS was 5.33 months (95% CI: 2.95-7.70 months), while the median OS was 40.33 months (95% CI: 29.82-50.83 months). Major adverse events included leucopenia (82.6%), neutropenia (78.3%), nausea or vomiting (56.5%), fatigue (52.2%), peripheral neuropathy (26.1%), myalgia/arthralgia (30.4%), thrombocytopenia (13.0%) and arrhythmia (4.3%). The patients accompanied with chronic diseases had significantly higher incidence rate of peripheral neuropathy and myalgia/arthralgia compared with the patients without accompanied chronic diseases (50.0% vs. 9.1% and 66.7% vs. 9.1%, P<0.05 for both).

CONCLUSION

The weekly single drug ABP regimen is effective and well-tolerated in elderly patients with advanced NSCLC.

Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models

Copy-number variation (CNV) is an important form of DNA structural variation because a certain proportion of genomes in many eukaryotic species can contribute to such variations. Owing to the differences between CNVs and single nucleotide polymorphisms (SNPs) in size, mutation rate and maintaining mechanism, it is more realistic to characterize CNV evolution under the finite-allele and finite-site models. Here, we propose a method to test multiple CNVs neutrality under the finite-allele and finite-site models and the assumption of mutation-drift process. The statistical property of the method is evaluated through Monte Carlo simulations under the effects of the sample size, the scaled mutation rates, the number of CNVs, the population demographic change, and selection. Different from Tajima's D test, a bootstrap or a permutation approach is suggested to conduct a neutrality test. Application of this method is illustrated using the diploid CNV genotypes measured in discrete copy numbers in 11 HapMap phase III populations. The results show that the mutation-drift process can explain the variation of genome-wide CNVs among 1184 individuals (856 CNVs, ∼0.02Mb on average in size), irrespective of the historical demographic changes. Patterns from allele-frequency-spectrum analysis also support the hypothesis of neutral CNVs. Our results suggest that most human chromosomal changes in healthy individuals via unbalanced rearrangements of the segments with certain sizes are neutral.

[Expression and significance of p38 mitogen-activated protein kinase in oral lichen planus and oral squamous cell cacinoma]

OBJECTIVE

To assess the differences among the expressions of p38 mitogen activated protein kinases (MAPK), phospho-p38MAPK and nuclear factor kappa B (NF-κB) in oral lichen planus (OLP) and oral squamous cell carcinoma(OSCC).

METHODS

In the study, 53 cases of OLP, 45 of OSCC, and 18 controls were obtained and 4-μm-thick histological sections were prepared from formalin-fixed paraffin-embedded tissue blocks.The expressions of p38MAPK,phospho-p38MAPK and NF-κB were detected by immunohistochemistry staining. Furthermore, the expressions of p38MAPK and phospho-p38MAPK were detected using Western blotting analyses in the fresh tissues from 11 cases of OLP, 5 cases of OSCC, and 7 cases of the controls.

RESULTS

p38MAPK was over-expressed in the lamina propria, but lowly expressed in the epithelium in OLP group. Phospho-p38MAPK was lower expressed in OLP group than in OSCC and control groups.NF-κB was found over-expressed in the lamina propria in OLP group.p38MAPK was found expressed in all the samples in the 3 groups. The expression of phospho-p38MAPK was observed in 8 (8/11) OLP samples, 5 (5/5) OSCC samples and 4 (4/7) controls by Western blotting, but no significant differences were found within the 3 groups.

CONCLUSION

p38MAPK can be detected in normal oral mucosa, OLP and OSCC. Phospho-p38MAPK may be related to the onset and progression of OSCC. The role of p38MAPK in OLP is yet to be revealed.

Anti-tumor activity of dendritic cell-cytokine induced killer cells (DC-CIKs) sensitized to HER2 against HER-positive breast cancer cells

This study aimed to investigate the cytotoxicity of cytokine-induced killer cells (CIKs) and Her2 epitope peptide-sensitized dendritic cells (DCs), when co-cultured with Her2-positive MCF-7 cells. DCs were separated from the Her epitope peptide-sensitized peripheral blood; the Her epitope combines directly with the MHC-II molecule on the DC surface. The DCs were co-cultured with autologous CIKs. Lactate dehydrogenase (LDH) and ELISA kits were used to detect cytotoxicity of CIKs against MCF-7 breast cancer cells; IL-12 and IFN-γ levels were also analyzed in the supernatant of the culture medium. CIKs activated by DCs sensitized by anchored Her polypeptide antigen have greater cytotoxicity against MCF-7 than CIKs alone or non-anchored antigen sensitized DCs-CIKs (P < 0.01); the IL-12 and IFN-γ levels in the supernatant were higher than that of the control (P < 0.01). In conclusion, DCs anchored by polypeptide antigen alone or in combination with effector cells can be used to develop therapeutic DC vaccines against breast cancer.

The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome

The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7)  years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations

Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI) possess more significant zygotic LDs for the double-homozygotes (D_AABB) than any other significant zygotic LDs (D_AABb, D_AaBB, and D_AaBb), while non-Africa populations generally have more significant D_AaBb’s than any other significant zygotic LDs (D_AABB, D_AABb, and D_AaBB). Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for D_AABB and D_AaBb than for D_AaBB and D_AABb in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia), which helps to understand geographical genomic medicine.

Mating system as a barrier to gene flow

Understanding mating system as one of reproductive isolating barriers remains important although this barrier is classified in a different sense from behavioral, ecological, and mechanical isolating barriers. Selfing enhances incipient speciation while outcrossing facilitates species integrity. Here, I study how mating system affects gene exchanges between genetically diverging species in a hybrid zone. Results show that a predominant selfing species has a greater barrier to selective gene flow than does a predominant outcrossing species. Barrier to neutral gene flow convexly changes with the selfing rate due to linkage disequilibrium, with a maximum at around intermediate selfing rate. Asymmetric transient or steady-state barriers to neutral gene flow occur between two sides of a hybrid zone when the neutral gene is affected by its linked selective gene whose alternative alleles are adaptive to heterogeneous habitats. Selfing interacts with both a physical barrier and a density-dependent ecological regulation (a logarithmic model) to strengthen the barriers to neutral and selective gene flow. This theory helps to interpret incipient speciation driven by selfing or to explain the asymmetric gene flow or unequal genomic mixtures between closely related species caused by their asymmetric mating systems in natural hybrid zones.

Assessing postzygotic isolation using zygotic disequilibria in natural hybrid zones

Hybrid zones as windows on evolutionary processes provide a natural laboratory for studying the genetic basis and mechanisms of postzygotic isolation. One resultant pattern in hybrid zones is the Hardy-Weinberg disequilibrium (HWD) for a single locus or the linkage disequilibrium (LD) for multiple loci produced by natural selection against hybrids. However, HWD and the commonly used low-order gametic or composite digenic LD cannot fully reflect the pattern of the high-order genotypic interactions. Here we propose the use of zygotic LD to elucidate the selection mechanisms of postzygotic isolation, and its calculation is based on genotypic frequencies only, irrespective of the type of mating system. We numerically and analytically show that the maximum composite digenic LD is always greater than the maximum absolute zygotic LD under the linear-additive selection, but is comparable to or smaller than the maximum absolute zygotic LD under the strong epistatic selection. Selection mechanisms can be inferred by testing such differences. We analyze a previously reported mouse hybrid zone assayed with genome-wide SNPs, and confirm that the composite digenic LD cannot appropriately indicate all possible significant genotypic interactions for a given SNP pair. A large proportion of significant zygotic LDs, ∼75% in general in the mouse hybrid zone, cannot be revealed from the composite digenic LD analysis. Statistical tests indicate that epistatic selection occurred among multiple loci in the mouse hybrid zone. The results highlight that the joint patterns of the composite digenic and zygotic LDs can help to elucidate the selection mechanism that is potentially involved in postzygotic isolation.

Evolution of zygotic linkage disequilibrium in a finite local population

One crucial feature of zygotic linkage disequilibrium (LD) analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level) are more informative than gametic LD (haploid level) in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.

Effect of high hydrostatic pressure on overall quality parameters of watermelon juice

High hydrostatic pressure as a kind of non-thermal processing might maintain the quality of thermo-sensitive watermelon juice. So, the effect of high hydrostatic pressure treatment on enzymes and quality of watermelon juice was investigated. After high hydrostatic pressure treatment, the activities of polyphenol oxidase, peroxidase, and pectin methylesterase of juice decreased significantly with the pressure ( P < 0.05). Inactivation of polyphenol oxidase and peroxidase could be fitted by two-fraction model and that of pectin methylesterase could be described by first-order reaction model. Titratable acidity, pH, and total soluble solid of juice did not change significantly ( P > 0.05). No significant difference was observed in lycopene and total phenolics after high hydrostatic pressure treatment when compared to the control ( P > 0.05). Cloudiness and viscosity increased with pressure ( P < 0.05) but did not change significantly with treatment time ( P > 0.05). a*- and b*-value both unchanged after high hydrostatic pressure treatment ( P > 0.05) while L*-value increased but the values had no significant difference among treated juices. Browning degree after high hydrostatic pressure treatment decreased with increase in pressure and treatment time ( P < 0.05). Through the comparison of total color difference values, high hydrostatic pressure had little effect on color of juice. The results of this study demonstrated the efficacy of high hydrostatic pressure in inactivating enzymes and maintaining the quality of watermelon juice.

Estimating animal abundance in ground beef batches assayed with molecular markers

Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources in a single product batch, which produces a high heterogeneity in capture probability. In order to estimate animal abundance through DNA profiling of ground beef constituents, two parameter-based statistical models were developed for incidence data. Simulations were applied to evaluate the maximum likelihood estimate (MLE) of a joint likelihood function from multiple surveys, showing superiority in the presence of high capture heterogeneity with small sample sizes, or comparable estimation in the presence of low capture heterogeneity with a large sample size when compared to other existing models. Our model employs the full information on the pattern of the capture-recapture frequencies from multiple samples. We applied the proposed models to estimate animal abundance in six manufacturing beef batches, genotyped using 30 single nucleotide polymorphism (SNP) markers, from a large scale beef grinding facility. Results show that between 411∼1367 animals were present in six manufacturing beef batches. These estimates are informative as a reference for improving recall processes and tracing finished meat products back to source.

Nanomagnet logic: progress toward system-level integration

Quoting the International Technology Roadmap for Semiconductors (ITRS) 2009 Emerging Research Devices section, 'Nanomagnetic logic (NML) has potential advantages relative to CMOS of being non-volatile, dense, low-power, and radiation-hard. Such magnetic elements are compatible with MRAM technology, which can provide input–output interfaces. Compatibility with MRAM also promises a natural integration of memory and logic. Nanomagnetic logic also appears to be scalable to the ultimate limit of using individual atomic spins.' This article reviews progress toward complete and reliable NML systems. More specifically, we (i) review experimental progress toward fundamental characteristics a device must possess if it is to be used in a digital system, (ii) consider how the NML design space may impact the system-level energy (especially when considering the clock needed to drive a computation), (iii) explain--using both the NML design space and a discussion of clocking as context—how reliable circuit operation may be achieved, (iv) highlight experimental efforts regarding CMOS friendly clock structures for NML systems, (v) explain how electrical I/O could be achieved, and (vi) conclude with a brief discussion of suitable architectures for this technology. Throughout the article, we attempt to identify important areas for future work.

Small-incision orbicularis-levator fixation technique: a modified double-eyelid blepharoplasty for treating trichiasis in young Asian patients

Upper-eyelid trichiasis often occurs with a single puffy eyelid or shallow eyelid crease in young Asian patients. This study presents a novel modified trichiasis correction method to simultaneously treat trichiasis and create a natural eyelid crease. It combines the modified small-incision debulking procedure and the orbicularis-levator fixation technique. The eyelash lift angle (LA), body curl angle (BCA) and end curl angle (ECA) were quantitatively analysed. A total of 90 patients (152 trichiasis eyelids) were followed up for approximately 22 months. The LA changed from 24.32° ± 9.21°-54.12° ± 10.32° in the nasal section of the eyelid (section 1), from 21.03° ± 11.34°-52.03° ± 10.56° in the middle section of the eyelid (section 2) and from 23.31° ± 8.12°-63.15° ± 8.43° in the temporal section of the eyelid (section 3). All patients were satisfied with the eyelid-fold appearance. In conclusion, for young Asian patients with upper-eyelid trichiasis, the small-incision orbicularis-levator fixation technique is able to acquire a stable up-curved position of the eyelashes and satisfactory aesthetic results.

Structural genomics: correlation blocks, population structure, and genome architecture

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level.

Non-majority magnetic logic gates: a review of experiments and future prospects for 'shape-based' logic

We discuss the experimental demonstration of non-majority, two-input, nanomagnet logic (NML) AND and OR gates. While gate designs still can incorporate the symmetric, rounded-rectangle magnets used in the three-input majority gate experiments by Imre (2006 Science 311 205-8), our new designs also leverage magnets with an edge that has a well-defined 'slant'. In rectangular and ellipsoid nanomagnets, the easy axis of the device coincides with its longer edge. For a magnet with a slanted edge, the easy and hard axes are 'tilted', and magnetic fields applied along the (geometrical) hard axis alone can set the easy axis magnetization state. This switching phenomenon can be employed to realize NML Boolean logic gates with both reduced footprints and critical path delays. Experimental demonstrations of two-input AND and OR gates are supported by corresponding micromagnetic simulations with temperature effects associated with a 300 K environment. Simulations suggest that the time evolution of experimentally demonstrated structures is correct, and that designs can also tolerate clock field misalignment. Additionally, simulations suggest that a slanted-edge 'compute magnet' can (i) be driven by two anti-ferromagnetically ordered lines of NML devices (for input) and (ii) drive an anti-ferromagnetically ordered line (for output). Both are essential if slanted-edge devices are to be used in NML circuits. We conclude with a discussion of extensibility and scaling prospects for shape-based computation with nanomagnets.

Species-area relationships explained by the joint effects of dispersal limitation and habitat heterogeneity

Species-area relationships (SARs) characterize the spatial distribution of species diversity in community ecology, but the biological mechanisms underlying the SARs have not been fully explored. Here, we examined the roles of dispersal limitation and habitat heterogeneity in shaping SARs in two large-scale forest plots. One is a 24-ha subtropical forest in Gutianshan National Nature Reserve, China. The other is a 50-ha tropical rain forest in Barro Colorado Island, Panama. Spatial point pattern models were applied to investigate the contributions of dispersal and habitat heterogeneity and their interactions to the formation of the SARs in the two sites. The results showed that, although dispersal and habitat heterogeneity each could significantly contribute to the SARs, each alone was insufficient to explain the SARs. Their joint effects sufficiently explained the real SARs, suggesting that heterogeneous habitat and dispersal limitation are two predominant mechanisms for maintaining the spatial distributions of the species in these two forests. These results add to our understanding of the ecological processes underlying the spatial variation of SARs in natural forest communities.

F(ST) in the cytonuclear system

Selection on nuclear (or organelle) sites inevitably affects the spatial distribution of a neutral organelle (or nuclear) allele via transient cytonuclear disequilibrium. Here I examine this effect in terms of F(st) for a neutral allele by bringing together cytonuclear genomes with contrasting modes of inheritance. The relationships between cytonuclear disequilibrium and increment in F(st) are explored and confirmed through Monte Carlo simulations. Results show that the transient increment in F(st) for a neutral allele is not only related to the vectors of seed and pollen dispersal but also to the mode of its inheritance. Such increments can be substantial under certain conditions. Seed dispersal is more effective than pollen dispersal in changing the transient increment. The cumulative effects from multiple selective nuclear sites can amplify the transient increment in F(st) for a neutral paternal or maternal organelle allele. Selection on selective organelle sites facilitates the transient increment in F(st) for a neutral nuclear allele. Partial selfing can significantly reinforce the transient increment in F(st). These theoretical insights highlight the roles of transient cytonuclear disequilibrium as a biological factor in evolving population differentiation and refine our practical interpretations of F(st) with cytonuclear markers.

Resveratrol reduces endothelial progenitor cells senescence through augmentation of telomerase activity by Akt-dependent mechanisms

BACKGROUND AND PURPOSE

Recent studies have shown that resveratrol increased endothelial progenitor cells (EPCs) numbers and functional activity. However, the mechanisms remain to be determined. Previous studies have demonstrated that increased EPC numbers and activity were associated with the inhibition of EPC senescence, which involves activation of telomerase. Therefore, we investigated whether resveratrol inhibits the onset of EPC senescence through telomerase activation, leading to potentiation of cellular activity.

EXPERIMENTAL APPROACH

After prolonged in vitro cultivation, EPCs were incubated with or without resveratrol. The senescence of EPCs were determined by acidic beta-galactosidase staining. The bromo-deoxyuridine incorporation assay or a modified Boyden chamber assay were employed to assess proliferative or migratory capacity, respectively. To further examine the underlying mechanisms of these effects, we measured telomerase activity and the phosphorylation of Akt by western blotting.

KEY RESULTS

Resveratrol dose dependently prevented the onset of EPCs senescence and increased the proliferation and migration of EPCs. The effect of resveratrol on senescence could not be abolished by eNOS inhibitor or by an oestrogenic receptor antagonist. Resveratrol significantly increased telomerase activity and Akt phosphorylation. Pre-treatment with the PI3K inhibitor, LY294002, significantly attenuated resveratrol-induced telomerase activity.

CONCLUSIONS AND IMPLICATIONS

Resveratrol delayed the onset of EPC senescence and this effect was accompanied by activation of telomerase through the PI3K-Akt signalling pathway. The inhibition of EPCs senescence by resveratrol might protect EPCs against dysfunction induced by pathological factors in vivo and improve EPC functional activities in a way that may be important for cell therapy.

Species diversity in local neutral communities

We extend the neutral theory of macroecology by deriving biodiversity models (relative species abundance and species-area relationships) in a local community-metacommunity system in which the local community is embedded within the metacommunity. We first demonstrate that the local species diversity patterns converge to that of the metacommunity as the size (scale) of the embedded local community increases. This result shows that in continuous landscapes no sharp boundaries dividing the communities at the two scales exist; they are an artificial distinction made by the current spatially implicit neutral theory. Second, we remove the artificial restriction that speciation cannot occur in a local community, even if the effects of local speciation are small. Third, we introduce stochasticity into the immigration rate, previously treated as constant, and demonstrate that local species diversity is a function not only of the mean but also of the variance in immigration rate. High variance in immigration rates reduces species diversity in local communities. Finally, we show that a simple relationship exists between the fundamental diversity parameter of neutral theory and Simpson's index for local communities. Derivation of this relationship extends recent work on diversity indices and provides a means of evaluating the effect of immigration on estimates of the fundamental diversity parameter derived from relative species abundance data on local communities.

Sex-ratio distortion driven by migration loads

The significance of migration load in driving the evolution of recipient populations has long been documented in population genetics, but its effects have not been linked to the formation of biased sex ratios in natural populations. In this study, we develop a single-locus model to demonstrate how the migration load can shape the primary and secondary sex ratios in dioecious plants where sexual dimorphism is determined by the sex chromosomes (the XX-XY or similar systems). Our results show that migration load can generate an array of sex ratios (from the female- to male-biased primary/secondary sex ratios), depending on the selection systems at the gametophyte and sporophyte stages and on the sex ratio in the migrating seeds. Ovule abortion and the purging of maladaptive genes from the immigrating pollen at the gametophyte stage can alter the primary sex ratio and indirectly alter the secondary sex ratio. The presence of maladaptive sex-linked genes from the migrating pollen and seeds of males facilitates the outcome of the female-biased secondary sex ratios, while the presence of maladaptive sex-linked genes from the migrating seeds of females can lead to the male-biased secondary sex ratios. The detrimental effects of the Y-chromosome from the migrating pollen and seeds can enhance the formation of female-biased primary and secondary sex ratios. These theoretical predictions highlight an alternative approach to the existing sex-ratio theories for interpreting the formation of biased sex ratios in the populations that are subject to the impacts of maladaptive genes from immigrants.

A general framework for marker-assisted selection

Early simulation studies have showed that the inclusion of epistatic components (especially the additive-by-additive effects) into marker-assisted selection (MAS) can improve selection efficiency for a short-term breeding program. In this study I extend Lande and Thompson's theory to incorporate both additive and non-additive effects into MAS with reference to the mass selection case. Four different indices are analytically examined in terms of the type of genetic components involved in the marker scores: phenotype-, general combining ability (GCA)-, and GCA and reciprocal effects-based marker scores. The phenotype-based marker index is applicable to any population of non-random mating, while the other three indices are applicable to the synthetic population derived from diallel crosses. All these indices may have higher selection efficiencies than the index with solely additive effects-associated markers as long as the detectable transient non-additive effects are present. The improvement in selection efficiency depends on the magnitude of non-additive variances and the proportion of them explained by markers. The index with the phenotype-based marker scores operates on the whole of the additive and non-additive effects, and has the largest selection efficiency. The indices with the GCA-based marker scores operate only on additive and additive-by-additive genetic variation and have relatively small selection efficiencies. Inclusion of the markers from organelle genomes can also increase selection efficiency, depending upon the proportion of the total genetic variation attributable to organelle genomes and the proportion of them explained by organelle genomic markers. Sharing of markers among different marker scores does not facilitate the improvement of selection efficiency.