Phylogeographic analyses of an epiphytic foliose lichen show multiple dispersal events westward from the Hengduan Mountains of Yunnan into the Himalayas.

Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis.

The precision of epidemiological investigation of COVID-19 transmission in Shanghai, China.

BACKGROUND: Shanghai had a local outbreak of COVID-19 from January 21 to 24. Timely and precise strategies were taken to prevent further spread of the disease. We discussed and shared the experience of COVID-19 containment in Shanghai. PROCESS: The first two patients worked at two hospitals but no staff from the two hospitals were infected. The suspected case and his two close contacts were confirmed to be infected within 12 h. The testing rate of individuals was low. The scope of screening was minimized to two related districts and the close contact tracing was completed within 12 h, which were precise and cost-effective. CONCLUSIONS: Active monitoring, precise epidemiological investigation and timely nucleic acid testing help discover new cases, minimize the scope of screening, and interrupt the transmission.

New species and records of Pyxine (Caliciaceae) in China.

In this study, the diversity of Pyxine Fr. in China was assessed based on morphological and chemical traits and molecular data are inferred from ITS and mtSSU sequences. Nineteen species were recognised, including three that are new to science (i.e. P.flavicans M. X. Yang & Li S. Wang, P.hengduanensis M. X. Yang & Li S. Wang and P.yunnanensis M. X. Yang & Li S. Wang) and three records new to China were found (i.e. P.cognata Stirt., P.himalayensis Awas. and P.minuta Vain.). Pyxineyunnanensis is diagnosed by the small size of the apothecia, a white medulla of the stipe and the presence of lichexanthone. Pyxineflavicans is characterised by broad lobes, a pale yellow medulla of the stipe and the presence of atranorin. Pyxinehengduanensis can be distinguished by its pale yellow medulla, marginal labriform soralia and the absence of atranorin. Detailed descriptions of each new species are presented, along with a key to the known species of Pyxine in China.

Two New Species of Placolecis (Lichenized Ascomycota) from China.

Two new species of the lichen genus Placolecis are discovered in China, namely P. kunmingensis An. C. Yin & Li S. Wang and P. sublaevis An. C. Yin & Li S. Wang. The new combination P. loekoesiana (S.Y. Kondr., Farkas, J.J. Woo & Hur) An. C. Yin is proposed. Placolecis kunmingensis is characterized by having simple, spherical or ellipsoid, hyaline spores, and pear-shaped pycnidia; while P. sublaevis can be distinguished by its thallus forming larger aggregations with slightly flattened lobes at the thallus margin, and urn-shaped pycnidia. Descriptions, a phylogenetic tree and a key are provided for all the known Placolecis species in China.

Acceptance of Chemo-prophylaxis for Latent Tuberculosis Infection among High School/College Student Contacts of Tuberculosis Patients in Shanghai, China.

Student contacts of tuberculosis (TB) cases are susceptible to latent tuberculosis infection (LTBI), and chemo-prophylaxis can reduce the risk of active TB among them. This study aimed to assess the acceptance of chemo-prophylaxis for LTBI among students, and their concerns regarding TB and its preventive treatment. A total of 560 students contacts were included in the investigation. The extent of contact was categorized from high to low (4 levels) with 12.9% of the students being close contacts. About 87.0% of the students were willing to receive chemo-prophylaxis if diagnosed with, LTBI, whereas 73 students declined. Students with a higher level of knowledge about TB (aOR = 1.11) or close contact with TB patients (aOR = 4.30) were more likely to accept treatment. To conclude, education regarding TB transmission is necessary. Moreover, LTBI detection should be integrated into the current school-based TB contact investigation.

Complete mitochondrial genome of Sellanucheza jaegeri Golovatch, 2013 by next generation sequencing (Polydesmida: Paradoxosomatidae) and phylogenetic analysis in Diplopoda.

The mitogenome of Sellanucheza jaegeri was 15,623 bp long, revealed the same gene order to that of typical Polydesmida. Both the tRNASer(AGN) and tRNASer(UCN) lacked the DHU arms. No tandem repeat was found in two control regions. Phylogenetic analysis indicated that Sphaerotheriida was so antiquity that divided out earlier than others. We supported that Polydesmida had a relatively systematic affinity between Julida and Playtdesmida, and suggested that the interordinal phylogenetic relationships within Diplopoda should be further investigated.

Sequencing complete mitochondrial genome of Lanius sphenocercus sphenocercus (Passeriformes: Laniidae) using Illunima HiSeq 2500.

Using an Illumina platform, we sequenced the complete mitochondrial genome of Lanius sphenocercus sphenocercus to an average coverage of 1669.5×. We performed a de novo assembly using SOAPdenovo2 and obtained the total mitogenome with 16,833 bp in length. Most PCGs begin with the typical ATG start codon with the exception of COI gene, which use GTG as the initiation codon. Stop codons AGG, TAG, TAA, and AGA are present in the PCGs; exceptions are COII, COIII and ND4, which possess incomplete termination codons (T). But, the function of COII with incomplete stop codon T should be further investigated. The phylogeny revealed that genetic distance of Laniidae and Corvidae was closer than other species. Compared to other three shrike species, L. s. sphenocercus occupy a separate status in the genus Lanius.

Association between maternal HIV infection and low birth weight and prematurity: a meta-analysis of cohort studies.

BACKGROUND: To assess the association between maternal human immunodeficiency virus (HIV) infection and low birth weight (LBW)/prematurity (PTD), we conducted a meta-analysis of cohort studies of HIV infected and uninfected women. METHODS: Several English and Chinese databases were searched (updated to May 2015) to find the studies reporting infant outcomes associated with exposure to maternal HIV infection during pregnancy. Relevant articles were manually selected based on several inclusion and exclusion criteria. RESULTS: Fifty-two cohort studies including 15,538 (for LBW) and 200,896 (for PTD) HIV infected women met the inclusion criteria. There was significant heterogeneity among studies for maternal HIV infection associated with LBW/PTD (I(2) = 71.7%, P < 0.05, and I(2) = 51.8%, P < 0.05 for LBW and PTD, respectively). The meta-analysis demonstrated that the maternal HIV infection was significantly associated with both LBW (pooled odds ratio (OR): 1.73, 95% confidence interval (CI): 1.64, 1.82, P < 0.001) and PTD (pooled OR: 1.56, 95% CI: 1.49, 1.63, P < 0.001). No significant difference in the relationship between maternal HIV infection and adverse pregnancy outcomes was detected among the groups of different study periods. HIV infected women were at slightly higher risk of LBW in developing countries compared with women in developed countries (OR: 2.12 (95% CI: 1.81, 2.48) vs. 1.75 (95% CI: 1.44, 2.12)). Antiretroviral drugs usage did not significantly change the associations of maternal HIV exposure with LBW and PTD. CONCLUSIONS: HIV infected women were at higher risk of having a low birth weight infant or a preterm delivery infant compared with uninfected women. Such associations did not change significantly over time or were not significantly affected by the usage of antiretroviral drugs.

HIV-, HCV-, and co-infections and associated risk factors among drug users in southwestern China: a township-level ecological study incorporating spatial regression.

BACKGROUND: The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) are major public health problems. Many studies have been performed to investigate the association between demographic and behavioral factors and HIV or HCV infection. However, some of the results of these studies have been in conflict. METHODOLOGY/PRINCIPAL FINDINGS: The data of all entrants in the 11 national methadone clinics in the Yi Autonomous Prefecture from March 2004 to December 2012 were collected from the national database. Several spatial regression models were used to analyze specific community characteristics associated with the prevalence of HIV and HCV infection at the township level. The study enrolled 6,417 adult patients. The prevalence of HIV infection, HCV infection and co-infection was 25.4%, 30.9%, and 11.0%, respectively. Prevalence exhibited stark geographical variations in the area studied. The four regression models showed Yi ethnicity to be associated with both the prevalence of HIV and of HIV/HCV co-infection. The male drug users in some northwestern counties had greater odds of being infected with HIV than female drug users, but the opposite was observed in some eastern counties. The 'being in drug rehabilitation variable was found to be positively associated with prevalence of HCV infection in some southern townships, however, it was found to be negatively associated with it in some northern townships. CONCLUSIONS/SIGNIFICANCE: The spatial modeling creates better representations of data such that public health interventions must focus on areas with high frequency of HIV/HCV to prevent further transmission of both HIV and HCV.

Effect of habitat fragmentation on the schistosome-transmitting snail Oncomelania hupensis in a mountainous area of China.

The effect of habitat fragmentation on schistosome-transmitting snails was assessed in an intervention village and a control village in Sichuan Province, China. Snail habitats were fragmented by environmental management. After 2 years, the proportions of quadrats with snails in the fragmented habitats decreased from 9.35% to 2.41% in one patch (c3) and from 12.20% to 6.57% in another patch (c12), whilst the proportions in habitats without fragmentation did not alter significantly. Mean snail density decreased from 0.246 to 0.063 snails/0.11 m2 in patch c3 and from 0.356 to 0.177 snails/0.11 m2 in patch c12, whilst the mean snail density of other patches did not alter significantly. Most snails from the same patch and/or its remaining patches after fragmentation clustered together in the phylogenetic tree, except for c1, c3 and its remaining patches (c5, c6 and c11). Snail habitats in the study zone exhibited visible fragmentation. Habitat fragmentation could decrease the snail population size and limit migration and dispersal of snails between patches.

A longitudinal study of comparison of the Kato-Katz technique and indirect hemagglutination assay (IHA) for the detection of schistosomiasis japonica in China, 2001-2006.

From 2001 to 2006, about one-third of the residents aged 5-65 years were selected as the subjects in a schistosome-endemic village located in Jiangxi Province, China. Every 1 year, all participants were analyzed by the Kato-Katz parasitologic examination and indirect hemagglutination assay (IHA). Statistical analysis of the results showed the k indices ranged from 0.250 to 0.347 between the two methods. Assuming the Kato-Katz results as the gold standard reference, the specificity of the IHA was from 60% to 77%, the positive predictive value of this method was from 19% to 30%, and its sensitivity and negative predictive value were more than 97%. The IHA method is unsuitable for individual screening in endemic community with relatively high prevalence (e.g. with >10% or more prevalence). A search for a better diagnostic test that can be applied in field situations in China is essential and should be given high priority.

[The impact of incorrectly-measured variables when mixed with precisely measured variables on the study of validity in epidemiological research].

OBJECTIVE: To explore the impact of measurement error on the associated effects under the incorrectly-measured variables when mixed with precisely measured variables. METHODS: Based on the functions of measurement error, correlation of incorrectly-measured predictors and precisely measured explanatory variables, number of precisely measured explanatory variables and associated effect, the 'R Project for Statistical Computing' method is used to analyze the impact of measurement on the validity of a study. RESULTS: Under the scenario that the continuous response Y and the continuous explanatory Z are precisely measured but the continuous predictor X is incorrectly-measured, when focusing on inference about the effect of X on Y, the non-differential measurement error always makes the value of estimated effect less than the actual value, and the attenuation effect of measurement error more closely worsens the correlation of X and Z. Under a misclassification dichotomous predictor X with an additional precisely measured explanatory variable Z and focusing on inference about the effect of X on Y, the misclassification bias is not only related to the sensitivity and specificity of exposure measurement, but also to the correlation between X and Z and exposure proportion of X. The attenuation factor (AF) decreases gradually with the increasing correlation between X and Z. For instance, in the p = 0.5 scenario, AF is 1.419, and the estimated effect of dichotomous predictor X on continuous response Y is more than the actual effect. When it increases to 0.9, AF is 0.474, the estimated effect becomes less than the true effect. CONCLUSION: In the studies of the impact of measurement error in linear regression with additional precisely measured explanatory variables, the impact of measurement error on the associated effect is relatively complex, suggesting that it is necessary to control and to assess the measurement error bias in order to correctly interpret the results of a study.

Field comparison of immunodiagnostic and parasitological techniques for the detection of Schistosomiasis japonica in the People's Republic of China.

A total of 1,811 individuals from two villages located in the areas of China endemic for Schistosoma japonicum were analyzed by the Kato-Katz parasitologic examination, indirect hemagglutination assay (IHA), and enzyme-linked immunosorbent assay (ELISA). Statistical analysis of the results showed the kappa indices ranged from 0.106 to 0.234 between IHA and the stool examination and ranged from 0.037 to 0.134 between ELISA and the fecal examination. The sensitivity value of the IHA was 83.7% in Village A and 92.3% in Village B; the specificity value of the IHA was 55.8% in Village A and 67.3% in Village B. The sensitivity value of the ELISA was 88.4% in Village A and 96.2% in Village B; the specificity value of the ELISA was 38.4% in both Village A and Village B. A search for a good diagnostic test that can be applied in field situations in China should be given high priority.

[Study on the impact of exposure misclassification on the validity of a study].

OBJECTIVE: To explore the impact of misclassification in binary explanatory variables on the effects associated with 'exposure-disease'. METHODS: Based upon the functions of probabilities on misclassification, effects of association and proportions of exposure, the 'R Project for Statistical Computing' method was used to analyze the impact of misclassification on the validity of a study. RESULTS: To the linear model case, the effect of nondifferential misclassification serves as an attenuating bias. When r = 0.5, the bias is symmetric in both sensitivity and specificity but when r is not equal to 0.5, the bias is not symmetric in sensitivity and specificity. When misclassification is nondifferential, estimated odds ratio tends to be 1 while the exposure prevalence in the control tends to be 0 or 1. Bias seems to be very complex in differential misclassification than in nondifferential misclassification that can make OR tend to or be away from the null value. CONCLUSION: The impact of exposure misclassification on the effect associated with exposure--disease is complicated, hence necessary to understand, to control, and to assess bias of misclassification in order to correctly interpret the results of a study.

[A study on the screening of high-risk population of schistosomiasis using a quick inquiry discriminant method during the years of disasters].

OBJECTIVE: To seek a rapid, simple, but effective inquiry method for screening high risk population challenged by schistosomiasis. METHODS: Two embankment collapsed villages were selected in schistosomiasis epidemic area in Dongting Lake. Information on water exposure was collected through a retrospective study. Data was analyzed by stepwise discriminant analysis. RESULTS: A Fisher's function was established by stepwise discriminant analysis which including 5 variables out of 18. Two hundred and forty-six individuals were discriminated by the function with accuracy, sensitivity and specificity of predicting their current infection status with the results of 87.4%, 84.1% and 89.0% respectively. CONCLUSION: The inquiry method might serve as simple, rapid, economic and effective tool for diagnosis in screening high risk population challenged by schistosomiasis in lake communities.