Exploring potential relationships between acoustic indices and ecosystem functions: a test on insect herbivory.

Biodiversity loss is a global concern. Current technological advances allow the development of novel tools that can monitor biodiversity remotely with minimal disturbance. One example is passive acoustic monitoring (PAM), which involves recording the soundscape of an area using autonomous recording units, and processing these data using acoustic indices, for example, to estimate the diversity of various vocal animal groups. We explored the hypothesis that data obtained through PAM could also be used to study ecosystem functions. Specifically, we investigated the potential relationship between seven commonly used acoustic indices and insect leaf herbivory, measured as total leaf damage and as the damage from three major insect feeding guilds. Herbivory was quantified on seedlings in 13 plots in four subtropical forests in south China, and acoustic data, representing insect acoustic complexity, were obtained by recording the evening soundscapes in those same locations. Herbivory levels correlated positively with the acoustic entropy index, commonly reported as one of the best-performing indices, whose high values indicate higher acoustic complexity, likely due to greater insect diversity. Relationships for specific feeding guilds were moderately stronger for chewers, indicating that the acoustic indices capture some insect groups more than others (e.g., chewers include soniferous taxa such as crickets, whereas miners are mostly silent). Our findings suggest that the use of PAM to monitor ecosystem functions deserves to be explored further, as this is a research field with unexplored potential. Well-designed targeted studies could help us better understand how to best use novel technologies to monitor ecosystem functions.

Relation between endothelial nitric oxide synthase genetic polymorphisms and pulmonary arterial hypertension in newborns with congenital heart disease.

OBJECTIVE: To investigate whether endothelial nitric oxide synthase (eNOS) rs1799983, rs2070744, and rs61722009 gene polymorphisms are associated with pulmonary arterial hypertension (PAH) in South Fujian newborns with congenital heart disease (CHD). METHODS: Genotyping for the eNOS rs1799983, rs2070744, and rs61722009 polymorphisms was performed using Sanger sequencing in 50 newborns with PAH secondary to CHD [CHD PAH (+)], 52 newborns with CHD without PAH [CHD PAH (-)], and 60 healthy controls. RESULTS: The genotype and allele frequency distributions of eNOS rs1799983, rs2070744, and rs61722009 were similar between CHD and healthy controls (P > .05). The frequencies of the eNOS rs1799983 G/T allele were 85% and 15% in the CHD PAH (+) group and 96.15% and 3.85% in the CHD PAH (-) group, the frequency of the T allele was higher in the CHD PAH (+) group than in the CHD PAH (-) group(P< .05), and patients with the GT/TT genotypes of eNOS rs1799983 may present higher PAH (OR = 4.412, 95%CI:1.411-13.797, P= .011). Newborns with the GT/TT genotypes had decreased plasma NO production compared to newborns with the GG genotype (P< .01), and NO levels in the CHD PAH (+) group were significantly lower than those in the CHD PAH (-) group (P < .05). CONCLUSION: The T allele could be a risk factor for PAH in newborns with CHD in South Fujian through decreased levels of nitric oxide production by the endothelium.

Estimating species pools for a single ecological assemblage.

BACKGROUND: The species pool concept was formulated over the past several decades and has since played an important role in explaining multi-scale ecological patterns. Previous statistical methods were developed to identify species pools based on broad-scale species range maps or community similarity computed from data collected from many areas. No statistical method is available for estimating species pools for a single local community (sampling area size may be very small as ≤ 1 km2). In this study, based on limited local abundance information, we developed a simple method to estimate the area size and richness of a species pool for a local ecological community. The method involves two steps. In the first step, parameters from a truncated negative trinomial model characterizing the distributional aggregation of all species (i.e., non-random species distribution) in the local community were estimated. In the second step, we assume that the unseen species in the local community are most likely the rare species, only found in the remaining part of the species pool, and vice versa, if the remaining portion of the pool was surveyed and was contrasted with the sampled area. Therefore, we can estimate the area size of the pool, as long as an abundance threshold for defining rare species is given. Since the size of the pool is dependent on the rarity threshold, to unanimously determine the pool size, we developed an optimal method to delineate the rarity threshold based on the balance of the changing rates of species absence probabilities in the sampled and unsampled areas of the pool. RESULTS: For a 50 ha (0.5 km2) forest plot in the Barro Colorado Island of central Panama, our model predicted that the local, if not regional, species pool for the 0.5 km2 forest plot was nearly the entire island. Accordingly, tree species richness in this pool was estimated as around 360. When the sampling size was smaller, the upper bound of the 95% confidence interval could reach 418, which was very close to the flora record of tree richness for the island. A numerical test further demonstrated the power and reliability of the proposed method, as the true values of area size and species richness for the hypothetical species pool have been well covered by the 95% confidence intervals of the true values. CONCLUSIONS: Our method fills the knowledge gap on estimating species pools for a single local ecological assemblage with little information. The method is statistically robust and independent of sampling size, as proved by both empirical and numerical tests.

Intermittent maternal hypoxia has an influence on regional expression of endothelial nitric oxide synthase in fetal arteries of rabbits.

BACKGROUND: Maternal hypoxia induces sustained fetal adaptations associated with changes in gene expression. We hypothesized that intermittent maternal hypoxia has an influence on regional expression of endothelial nitric oxide synthase (eNOS) in fetal arteries of New Zealand White rabbits. METHODS: Timed-pregnant New Zealand White rabbits (term = 30 ± 1 d) were randomly assigned to a normoxic control group (n = 5) or a hypoxia group (12% O2, n = 5) during days 10-29 of pregnancy. At the end of pregnancy (29 d gestation), blood samples were collected from mothers and fetuses. Carotid and femoral arteries of fetuses were extracted for eNOS mRNA and protein concentration and analysis of total NOS activities. RESULTS: Our data demonstrate that chronic intermittent maternal hypoxia significantly increased eNOS mRNA and protein concentrations and total NOS activities in carotid artery segments but decreased eNOS mRNA and protein concentrations and total NOS activities in femoral artery segments in the same fetuses. Vascular endothelial cells, but not smooth muscle cells, of fetal rabbits exhibited positive immunostaining for the eNOS protein. CONCLUSION: These observations suggest that chronic hypoxia can regulate regional expression of eNOS as an adaptive response to hypoxic stress in fetal arteries.

Overexpression of cystatin SN positively affects survival of patients with surgically resected esophageal squamous cell carcinoma.

BACKGROUND: Cystatin SN is a secreted protein and a cysteine proteinase inhibitor. It has been considered to be a tumor marker for gastrointestinal tract cancer in several functional researches. However, the clinicopathological and prognostic significance of Cystatin SN expression in esophageal squamous cell carcinoma (ESCC) has not been elucidated. METHODS: In our study, the expression of Cystatin SN was detected in 209 surgically resected ESCC tissues and 170 peritumoral normal esophageal mucosae by immunohistochemistry. The prognostic significance of Cystatin SN expression was analysed with Kaplan-Meier plots and the Cox proportional hazards regression models. RESULTS: The results showed that the immunostaining of Cystatin SN in ESCC tissues was less intense than that in the normal control tissue (P < 0.001). Compared with patients with low tumoral Cystatin SN expression, ESCC patients with tumors high-expression Cystatin SN exhibited increased disease-free survival (DFS) and overall survival (OS) (P < 0.001 and P < 0.001, respectively). Furthermore, the expression level of Cystatin SN could further stratify the ESCC patients by survival (DFS and OS) in the stage II subgroup (P < 0.001 and P < 0.001, respectively). Multivariate analyses showed that Cystatin SN expression, N status and differentiation were independent and significant predictors of survival. CONCLUSIONS: We concluded that ESCC patients whose tumors express high levels of Cystatin SN have favourable survival compared with those patients with low Cystatin SN expression. Tumoral Cystatin SN expression may be an independent predictor of survival for patients with resectable ESCCs.

Increasing collaboration between China and India in the environmental sciences to foster global sustainability.

As the two largest countries by population, China and India have pervasive effects on the ecosphere. Because of their human population size and long international boundary, they share biodiversity and the threats to it, as well as crops, pests and diseases. We ranked the two countries on a variety of environmental challenges and solutions, illustrating quantitatively their environmental footprint and the parallels between them regarding the threats to their human populations and biodiversity. Yet we show that China and India continue to have few co-authorships in environmental publications, even as their major funding for scientific research has expanded. An agenda for collaboration between China and India can start with the shared Himalaya, linking the countries' scientists and institutions. A broader agenda can then be framed around environmental challenges that have regional patterns. Coordinated and collaborative research has the potential to improve the two countries' environmental performance, with implications for global sustainability.

Factors determining the survival of nasopharyngeal carcinoma with lung metastasis alone: does combined modality treatment benefit?

BACKGROUND: Nasopharyngeal carcinoma (NPC) with lung metastasis alone has been reported as a relatively favorable prognostic group, and combined modality treatment might be indicated for selected cases. However, the prognostic factors determining survival of this group and the indication of combined therapy have not been thoroughly studied. METHODS: We retrospectively reviewed 246 patients of NPC with lung metastasis(es) alone presented at diagnosis or as the first failure after primary treatment from 1993 to 2008 in an academic tertiary hospital. Univariate and multivariate survival analyses of post-metastasis survival (PMS) and overall survival (OS) were carried out to determine the prognostic factors. RESULTS: The 3-year, 5-year, and 10-year of PMS and OS for the whole cohort were 34.3%, 17.0%, 8.6% and 67.8%, 45.4%, 18.5%, respectively. The median PMS (45.6 months vs. 23.7 months) and OS (73.7 months vs. 46.2 months) of patients treated with combined therapy was significantly longer than that of those treated with chemotherapy alone (P < 0.001). Age, disease-free interval (DFI) and treatment modality were evaluated as independent prognostic factors of OS, while only age and treatment modality retain their independent significance in PMS analysis. In stratified survival analysis, compared to chemotherapy alone, combined therapy could benefit the patients with DFI > 1 year, but not those with DFI ≤ 1 year. CONCLUSIONS: Age ≤ 45 years, DFI > 1 year, and the combined therapy were good prognostic factors for NPC patients with lung metastasis(es) alone. The combination of local therapy and the basic chemotherapy should be considered for these patients with DFI > 1 year.

Extinction debt in local habitats: quantifying the roles of random drift, immigration and emigration.

We developed a time-dependent stochastic neutral model for predicting diverse temporal trajectories of biodiversity change in response to ecological disturbance (i.e. habitat destruction) and dispersal dynamic (i.e. emigration and immigration). The model is general and predicts how transition behaviours of extinction may accumulate according to a different combination of random drift, immigration rate, emigration rate and the degree of habitat destruction. We show that immigration, emigration, the areal size of the destroyed habitat and initial species abundance distribution (SAD) can impact the total biodiversity loss in an intact local area. Among these, the SAD plays the most deterministic role, as it directly determines the initial species richness in the local target area. By contrast, immigration was found to slow down total biodiversity loss and can drive the emergence of species credits (i.e. a gain of species) over time. However, the emigration process would increase the extinction risk of species and accelerate biodiversity loss. Finally but notably, we found that a shift in the emigration rate after a habitat destruction event may be a new mechanism to generate species credits.

The Prognostic Value of Peripheral Benzodiazepine Receptor in Patients with Esophageal Squamous Cell Carcinoma.

Background: The peripheral benzodiazepine receptor (PBR) has previously been reported as an oncogene in prostate, breast and colorectal cancers, but its prognostic value, biological behavior and function in esophageal squamous cell carcinoma (ESCC) has not been investigated. Methods: qRT-PCR, western blotting and immunohistochemistry (IHC) were used to detect PBR expression in ESCC and matched non-cancerous tissues. Based on all of the significantly independent factors, a nomogram was established to predict the prognosis of ESCC patients. In addition, we performed comprehensive in vitro experiments to study the functions of PBR in cell growth, colony formation, and migration ability, as well as its relationship with epithelial-mesenchymal transition (EMT) related proteins in ESCC cells. Results: The mRNA and protein expression levels of PBR in ESCC were higher than those in adjacent non-tumor esophageal epithelial tissues. The IHC results demonstrated that PBR expression was an independent prognostic factor in ESCC survival, patients with higher PBR expression had a poorer survival than those with low expression, and PBR expression was significantly associated with lymphoid nodal status. Furthermore, a nomogram was established to reliably predict the probability of death in ESCC patients, with a Harrell's c-index of 0.696. In the vitro experiments, knocking down the expression of PBR inhibited proliferation, colony formation and migration of ESCC cells, and regulated EMT-associated proteins (up-regulation of E-cadherin, ZO-1 and ß-catenin and concomitant with down-regulation of Fibronectin and N-cadherin). Conclusions: PBR is an independent prognostic factor in ESCC, and it promotes ESCC progression and metastasis. Basing on PBR expression level, a nomogram is established and performs a well in predicting survival of ESCC patients.

Analysis of ERCC1, BRCA1, RRM1 and TUBB3 as predictors of prognosis in patients with non-small cell lung cancer who received cisplatin-based adjuvant chemotherapy: A prospective study.

Although adjuvant platinum-based chemotherapy has been demonstrated to improve survival in patients with completely resected non-small cell lung cancer (NSCLC), individualized approaches to therapy are urgently required to improve the treatment efficacy and reduce unnecessary toxicity. It was hypothesized in the present study that the protein levels of excision repair cross-complementation group 1 (ERCC1), breast cancer 1 (BRCA1), ribonucleotide reductase M1 (RRM1) and class III ß-tubulin (TUBB3) may influence the therapeutic effect of adjuvant cisplatin-based chemotherapy. The expression of ERCC1, BRCA1, RRM1 and TUBB3 in tissues obtained from 84 patients with NSCLC was analyzed in the present non-interventional study by immunohistochemistry prior to adjuvant chemotherapy. All patients received adjuvant cisplatin-based chemotherapy. The primary endpoint in the present study was disease free survival (DFS). Out of the 84 tumors, the expression of ERCC1, BRCA1, RRM1 and TUBB3 was identified in 46 (55%), 11 (13%), 73 (87%) and 76 (90%) tissues, respectively. A beneficial response to adjuvant cisplatin-based chemotherapy in DFS was associated with the absence of the expression of ERCC1 [hazard ratio (HR), 2.166; 95% confidence interval (CI), 1.049-4.474; P=0.037] and BRCA1 (HR, 2.419; 95% CI, 1.127-5.193; P=0.023), but not with the expression status of RRM1 (HR, 0.568; 95% CI, 0.234-1.379; P=0.212) or TUBB3 (HR, 1.874; 95% CI, 0.448-7.842; P=0.39). In addition, patients lacking the expression of ERCC1 and BRCA1 benefited more from adjuvant cisplatin-based chemotherapy compared with patients that expressed either ERCC1 or BRCA1 (HR, 3.102; 95% CI, 1.343-7.163; P=0.008). The expression of ERCC1 and BRCA1 was significantly associated with the DFS time in patients with NSCLC treated with adjuvant cisplatin-based chemotherapy, respectively. The combination of the ERCC1 and BRCA1 expression levels may be a promising prognostic prediction for adjuvant cisplatin-based chemotherapy.

Prognostic value of pre-operative serum uric acid levels in esophageal squamous cell carcinoma patients who undergo R0 esophagectomy.

BACKGROUND: The serum uric acid (SUA) is the end-product from the metabolic breakdown of purine nucleotides. It has been considered to be a prognostic factor for malignant tumor in several researches. However, its prognostic value in patients with esophageal squamous cell carcinoma (ESCC) has not been elucidated. METHODS: We retrospectively reviewed the records of 209 ESCC patients who underwent R0 esophagectomy. A receiver operating characteristic (ROC) curve analysis was used to determine the optimal cut-off value for pre-operative SUA levels and to divide the ESCC patients into two groups. Furthermore, we analyzed the pre-operative serum uric acid (SUA) levels and its relationship with the clinicopathological parameters and the prognosis of 209 ESCC patients. RESULTS: Optimal cut-off value for pre-operative SUA in ROC analysis was 304.5 µ mol/l (sensitivity 67.46%, specificity 65.06%). SUA low- or high-levels were associated with gender (P< 0.001), smoking status (P< 0.001), pN statues (P= 0.003) and TNM stage (P= 0.010). SUA levels, tumor differentiation and pTNM stage were independent predictors of ESCC patient survival in a multivariate analysis. CONCLUSIONS: The pre-operative level of SUA is an independent prognostic predictor in ESCC patients who undergo R0 esophagectomy and patients with higher SUA level may have an unfavorable survival probability.

Evidence of selection pressures of neuraminidase gene (NA) of influenza A virus subtype H5N1 on different hosts in Guangxi Province of China.

In the present study, the possible evidence of positive selection was analyzed for the neuraminidase (NA) sequences of Guangxi H5N1 strains of China. Based on an overall site-specific positive selection analysis, it was found that NA gene of H5N1 Guangxi strains underwent purifying selection and no significant positively selected sites were identified. For the branch-specific positive selection analysis, there was no positive selection evidence for the branches leading to different poultry hosts (chicken, duck and goose). Conclusively, positive selection seems not possible (if not rare) for the NA gene in influenza H5N1 subtype, at least for the samples found in Guangxi Province of China.

Global distribution patterns of highly pathogenic H5N1 avian influenza: environmental vs. socioeconomic factors.

In this report, we quantitatively analyzed the essential ecological factors that were strongly correlated with the global outbreak of highly pathogenic H5N1 avian influenza. The ecological niche modeling (ENM) was used to reveal the potential outbreak hotspots of H5N1. A two-step modeling procedure has been proposed: we first used BioClim model to obtain the coarse suitable areas of H5N1, and then those suitable areas with very high probabilities were retained as the inputs of multiple-variable autologistic regression analysis (MAR) for model refinement. MAR was implemented taking spatial autocorrelation into account. The final performance of ENM was evaluated using the areas under the curve (AUC) of receiver-operating characteristic. In addition, principal component analysis (PCA) was employed to reveal the most important variables and relevant ecological gradients of H5N1 outbreak. Niche visualization was used to identify potential spreading trend of H5N1 along important ecological gradients. For the first time, we combined socioeconomic and environmental variables as joint predictors in developing ecological niche modeling. Environmental variables represented the natural element related to H5N1 outbreak, whereas socioeconomic ones represented the anthropogenic element. Our results indicated that: (1) the high-risk hotspots are mainly located in temperate zones (indicated by ENM)-correspondingly, we argued that the "ecoregions hypothesis" was reasonable to some extent; (2) evaporation, humidity, human population density, livestock population density were the first four important factors (in descending order) that were associated with the H5N1 global outbreak (indicated by PCA); (3) influenza had a tendency to expand into areas with low evaporation (indicated by niche visualization). In conclusion, our study substantiates that both the environmental and socioeconomic variables jointly determined the global spreading trend of H5N1, but environmental variables played a more important role. Consequently, our study is consistent with the assumption that the natural element is more important than the anthropogenic element as the underlying ecological mechanisms explaining global H5N1 transmission.

Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339.

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain AF407339. We challenged a previous study which suggested only one recombination event in AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome AF407339, respectively. The first one has two parents AF333000 (minor) and AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents AF531433 (minor) and GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification.

Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection.

Codon usage patterns of duck hepatitis A virus (HAV) were studied in the present study. The major trends of codon usage patterns were analyzed using principal component analysis on the basis of the relative synonymous codon usage values. Correlation analysis was utilized to reveal the associations of the first two major axes of PCA and nucleotide- or amino acid-relevant indices. Our results showed that compositional constraint and/or mutational pressure are major factors influencing codon usage bias patterns of HAV. However, the influence of natural selection is also prevalent, as indicated by strongly significant correlations between the hydrophobicity, aromaticity, aliphaticity and ionization and the first axis of PCA. Also, ionization could characterize the second axis of PCA. At last, maximum likelihood phylogenetic analysis shows that there are no remarkable geographic clustering patterns of HAV strains in the phylogenetic tree. However, through MANOVA test, there are significant differences on the codon usage patterns among HAV strains from different countries. In conclusion, both mutational pressure and natural selection are of equally great importance to codon usage patterns of duck HAV genomes.

Downregulated expression of PTK6 is correlated with poor survival in esophageal squamous cell carcinoma.

To investigate the clinical prognostic value of protein tyrosine kinase 6 (PTK6) in patients with esophageal squamous cell carcinoma (ESCC), quantitative RT-PCR and Western blotting were utilized to measure the mRNA and protein expression levels of PTK6 in 29 and eight pairs of ESCC and peritumoral normal esophageal tissues, respectively. Furthermore, the expression of PTK6 protein in 210 ESCCs was examined with immunohistochemistry (IHC), and its clinical value was analyzed using Kaplan-Meier plots and the Cox proportional hazards regression model. The results found that the expression levels of both PTK6 mRNA and protein in ESCC tissues were significantly lower than those in peritumoral normal esophageal tissues. Regarding the IHC analysis of ESCC, the cytoplasmic expression of PTK6 was significantly correlated with tumor grade (P < 0.001). Compared with patients with low PTK6 expression, ESCC patients with overexpression of PTK6 displayed preferable disease-free survival (DFS) and overall survival (OS) (P < 0.001 and P = 0.001, respectively), especially in stage II disease (P = 0.002 and P = 0.021, respectively). PTK6 was evaluated as an independent prognostic factor for ESCC using multivariate Cox regression analysis. All data demonstrated that the expression level of PTK6 is an independent prognostic factor in ESCCs. Low expression of PTK6 is correlated with poor DFS and OS in ESCCs.

Prognosticators and risk grouping in patients with lung metastasis from nasopharyngeal carcinoma: a more accurate and appropriate assessment of prognosis.

BACKGROUND: Lung metastases arising from nasopharyngeal carcinomas (NPC) have a relatively favourable prognosis. The purpose of this study was to identify the prognostic factors and to establish a risk grouping in patients with lung metastases from NPC. METHODS: A total of 198 patients who developed lung metastases from NPC after primary therapy were retrospectively recruited from January 1982 to December 2000. Univariate and multivariate analyses of clinical variables were performed using Cox proportional hazards regression models. Actuarial survival rates were plotted against time using the Kaplan-Meier method, and log-rank testing was used to compare the differences between the curves. RESULTS: The median overall survival (OS) period and the lung metastasis survival (LMS) period were 51.5 and 20.9 months, respectively. After univariate and multivariate analyses of the clinical variables, age, T classification, N classification, site of metastases, secondary metastases and disease-free interval (DFI) correlated with OS, whereas age, VCA-IgA titre, number of metastases and secondary metastases were related to LMS. The prognoses of the low- (score 0-1), intermediate- (score 2-3) and high-risk (score 4-8) subsets based on these factors were significantly different. The 3-, 5- and 10-year survival rates of the low-, intermediate- and high-risk subsets, respectively (P < 0.001) were as follows: 77.3%, 60% and 59%; 52.3%, 30% and 27.8%; and 20.5%, 7% and 0%. CONCLUSIONS: In this study, clinical variables provided prognostic indicators of survival in NPC patients with lung metastases. Risk subsets would help in a more accurate assessment of a patient's prognosis in the clinical setting and could facilitate the establishment of patient-tailored medical strategies and supports.