Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km2, and >90% of 651 species had ranges >105 km2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.
The Wilms’ tumor suppressor gene (WT1) has been identified as an oncogene in many malignant diseases such as leukaemia, breast cancer, mesothelioma and lung cancer. However, the role of WT1 in non-small-cell lung cancer (NSCLC) carcinogenesis remains unclear. In this study, we compared WT1 mRNA levels in NSCLC tissues with paired corresponding adjacent tissues and identified significantly higher expression in NSCLC specimens. Cell proliferation of three NSCLC cell lines positively correlated with WT1 expression; moreover, these associations were identified in both cell lines and a xenograft mouse model. Furthermore, we demonstrated that up-regulation of Cyclin D1 and the phosphorylated retinoblastoma protein (p-pRb) was mechanistically related to WT1 accelerating cells to S-phase. In conclusion, our findings demonstrated that WT1 is an oncogene and promotes NSCLC cell proliferation by up-regulating Cyclin D1 and p-pRb expression.
Understanding how neuronal diversity is achieved within the cerebral cortex remains a major challenge in neuroscience. The advent of human embryonic stem cells (hESCs) as a model system provides a unique opportunity to study human corticogenesis in vitro and to identify the mechanisms that promote neuronal differentiation to achieve neuronal diversity in human brain. The transcription factor Fezf2 is necessary and sufficient for the specification of subcerebral projection neurons in mouse. However, its function during human corticogenesis is poorly understood. This study reports the differentiation of a hFezf2-YFP hESC reporter line into corticofugal projection neurons capable of extending axons toward the spinal cord upon transplantation into neonatal mouse brains. Additionally, we show that triple inhibition of the TGFß/BMP/Wnt-Shh pathway promotes the generation of hFezf2-expressing cells in vitro. Finally, this study unveils the isolation of two novel and distinct populations of hFezf2-YFP expressing cells reminiscent of the distinct Fezf2-expressing neuronal subtypes in the developing mouse brain. Overall our data suggest that the directed differentiation of hESCs into corticofugal neurons provides a useful model to identify the molecular mechanisms regulating human corticofugal differentiation and survival.
Programmed cell death (PCD) is a genetically-based cell death mechanism with vital roles in eukaryotes. Although there is limited consensus on similar death mode programs in prokaryotes, emerging evidence suggest that PCD events are operative. Here we present cell death events in a cyanobacterium living endophytically in the fern Azolla microphylla, suggestive of PCD. This symbiosis is characterized by some unique traits such as a synchronized development, a vertical transfer of the cyanobacterium between plant generations, and a highly eroding cyanobacterial genome. A combination of methods was used to identify cell death modes in the cyanobacterium. Light- and electron microscopy analyses showed that the proportion of cells undergoing cell death peaked at 53.6% (average 20%) of the total cell population, depending on the cell type and host developmental stage. Biochemical markers used for early and late programmed cell death events related to apoptosis (Annexin V-EGFP and TUNEL staining assays), together with visualization of cytoskeleton alterations (FITC-phalloidin staining), showed that all cyanobacterial cell categories were affected by cell death. Transmission electron microscopy revealed four modes of cell death: apoptotic-like, autophagic-like, necrotic-like and autolytic-like. Abiotic stresses further enhanced cell death in a dose and time dependent manner. The data also suggest that dynamic changes in the peptidoglycan cell wall layer and in the cytoskeleton distribution patterns may act as markers for the various cell death modes. The presence of a metacaspase homolog (domain p20) further suggests that the death modes are genetically programmed. It is therefore concluded that multiple, likely genetically programmed, cell death modes exist in cyanobacteria, a finding that may be connected with the evolution of cell death in the plant kingdom.
Motivation: Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.
Supplementary material is available at Bioinformatics online.
Objective: To screen mutations in FERM domain-containing protein 7 (FRMD7) gene in two Chinese families with X-linked idiopathic congenital nystagmus (XLICN). Methods: Common ophthalmic data and peripheral blood of two Chinese XLICN families (families A and B) were collected after informed consent. Genomic DNA was prepared from the peripheral blood of members of the two families and from 100 normal controls. Mutations in the FRMD7 gene were determined by directly sequencing polymerase chain reaction (PCR) products. Results: We identified a novel mutation c.980_983delATTA compound with c.986C>A mutation in the 11th exon of FRMD7 in family B, and a previously reported splicing mutation c.782G>C (p.R261G) in family A. The mutations were detected in patients and female carriers, while they were absent in other relatives or in the 100 normal controls. Conclusions: Our results expand the spectrum of FRMD7 mutations in association with XLICN, and further confirm that the mutations of FRMD7 are the underlying molecular mechanism for XLICN.
Mutation; Idiopathic congenital nystagmus; FERM domain-containing protein 7 (FRMD7)
Two new species, namely Ancistrocerus transpunctatus You and Li, sp. n. and Ancistrocerus deqinensis You and Li, sp. n. are described and illustrated from Yunnan, China. A key to the Oriental species of the genus Ancistrocerus is provided.
Hymenoptera; Vespidae; Eumeninae; Ancistrocerus; new species; China
The specification of neuronal subtypes in the cerebral cortex proceeds in a temporal manner; however, the regulation of the transitions between the sequentially generated subtypes is poorly understood. Here, we report that the forkhead-box transcription factor Foxg1 coordinates the production of neocortical projection neurons through the global repression of a default gene program. The delayed activation of Foxg1 was necessary and sufficient to induce deep-layer neurogenesis, followed by a sequential wave of upper-layer neurogenesis. A genome-wide analysis revealed that Foxg1 binds to mammalian-specific non-coding sequences to repress over 12 transcription factors expressed in early progenitors, including Ebf2/3, Dmrt3, Dmrta1 and Eya2. These findings reveal an unexpected prolonged competence of progenitors to initiate corticogenesis at a progressed stage during development and identify Foxg1 as a critical initiator of neocorticogenesis through spatiotemporal repression, a system that balances the production of non-radially and radially migrating glutamatergic subtypes during mammalian cortical expansion.
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis.
This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying.
We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support.
ChEMBL; Bioactivity; Semantic web; Resource Description Framework; Linked Data
To establish a ultra-pressure liquid chromatography (UPLC) method for the determination of 5 phenolic acids including neochlorogenic acid, chlorogenic acid, caffeic acid, cryptochlorogenic acid, and cynarin in fried Fructus xanthii from different production sites and its dispensing granule.
Materials and Methods:
An Acquity BEH C18 chromatographic column (100 mm × 2.1 mm,1.7 μm) was used to perform the determination, which was maintained at 40°C throughout the analysis. Mobile phase was composed of methanol and water containing 0.1% phosphoric acid (v/v) with flow rate at 0.4 mL/min under gradient elution, and detection wavelength was set to 325 nm for monitoring the separation.
Neochlorogenic acid, chlorogenic acid, caffeic acid, cryptochlorogenic acid, and cynarin have shown good linearity (r2≥0.9997) within 0.959–239.75, 0.9408–235.2, 0.1638–40.95, 0.6744–67.44, and 0.47–117.5 μg/mL, and their average recoveries were 100.09%, 99.98%, 101.74%, 99.83%, and 99.63%, respectively.
The UPLC method established in this study was rapid, and of good accuracy, repeatability and resolution, and hence can assist in the control quality of fried Fructus xanthii as well as its dispensing granule in an efficient manner.
Dispensing granule; fried Fructus xanthii; phenolic acids; ultra-pressure liquid chromatography; Xanthium sibiricum Part
The Greater Mekong Subregion (GMS), comprised of six countries including Cambodia, China's Yunnan Province, Lao PDR, Myanmar (Burma), Thailand and Vietnam, is one of the most threatening foci of malaria. Since the initiation of the WHO's Mekong Malaria Program a decade ago, malaria situation in the GMS has greatly improved, reflected in the continuous decline in annual malaria incidence and deaths. However, as many nations are moving towards malaria elimination, the GMS nations still face great challenges. Malaria epidemiology in this region exhibits enormous geographical heterogeneity with Myanmar and Cambodia remaining high-burden countries. Within each country, malaria distribution is also patchy, exemplified by ‘border malaria’ and ‘forest malaria’ with high transmission occurring along international borders and in forests or forest fringes, respectively. ‘Border malaria’ is extremely difficult to monitor, and frequent malaria introductions by migratory human populations constitute a major threat to neighboring, malaria-eliminating countries. Therefore, coordination between neighboring countries is essential for malaria elimination from the entire region. In addition to these operational difficulties, malaria control in the GMS also encounters several technological challenges. Contemporary malaria control measures rely heavily on effective chemotherapy and insecticide control of vector mosquitoes. However, the spread of multidrug resistance and potential emergence of artemisinin resistance in Plasmodium falciparum make resistance management a high priority in the GMS. This situation is further worsened by the circulation of counterfeit and substandard artemisinin-related drugs. In most endemic areas of the GMS, P. falciparum and P. vivax coexist, and in recent malaria control history, P. vivax has demonstrated remarkable resilience to control measures. Deployment of the only registered drug (primaquine) for the radical cure of vivax malaria is severely undermined due to high prevalence of glucose-6-phosphate dehydrogenase deficiency in target human populations. In the GMS, the dramatically different ecologies, diverse vector systems, and insecticide resistance render traditional mosquito control less efficient. Here we attempt to review the changing malaria epidemiology in the GMS, analyze the vector systems and patterns of malaria transmission, and identify the major challenges the malaria control community faces on its way to malaria elimination.
malaria; the Greater Mekong Subregion; epidemiology; Anopheles vectors; drug resistance; border malaria; elimination
Despite significant improvement in the malaria situation of the Greater Mekong Subregion (GMS), malaria control for the region continues to face a multitude of challenges. The extremely patchy malaria distribution, especially along international borders, makes disease surveillance and targeted control difficult. The vector systems are also diverse with dramatic differences in habitat ecology, biting behavior, and vectorial capacity, and there is a lack of effective transmission surveillance and control tools. Finally, in an era of heavy deployment of artemisinin-based combination therapies, the region acts as an epicenter of drug resistance, with the emergence of artemisinin resistant P. falciparum posing a threat to both regional and global malaria elimination campaigns. This problem is further exacerbated by the circulation of counterfeit and substandard artemisinin drugs. Accordingly, this Southeast Asian Malaria Research Center, consisting of a consortium of US and regional research institutions, has proposed four interlinked projects to address these most urgent problems in malaria control. The aims of these projects will help to substantially improve our understanding of malaria epidemiology, vector systems and their roles in malaria transmission, as well as the mechanisms of drug resistance in parasites. Through the training of next-generation scientists in malaria research, this program will help build up and strengthen regional research infrastructure and capacities, which are essential for sustained malaria control in this region.
malaria; the Greater Mekong Subregion; epidemiology; vector systems; drug resistance; counterfeit drugs
Anopheles sinensis is the most important vector of malaria in Southeast Asia, including China. Currently, the most effective measure to prevent malaria transmission relies on vector control through the use of insecticides, primarily pyrethroids. Extensive use of insecticides poses strong selection pressure on mosquito populations for resistance. Resistance to insecticides can arise due to mutations in the insecticide target site (target site resistance), which in the case of pyrethroids is the para-type sodium channel gene, and/or the catabolism of the insecticide by detoxification enzymes before it reaches its target (metabolic detoxification resistance). In this study, we examined deltamethrin resistance in An. sinensis from China and investigated the relative importance of target site versus metabolic detoxification mechanisms in resistance. A high frequency (>85%) of nonsynonymous mutations in the para gene was found in populations from central China, but not in populations from southern China. Metabolic detoxification as measured by the activity of monooxygenases and glutathione S-transferases (GSTs) was detected in populations from both central and southern China. Monooxygenase activity levels were significantly higher in the resistant than the susceptible mosquitoes, independently of their geographic origin. Stepwise multiple regression analyses in mosquito populations from central China found that both knockdown resistance (kdr) mutations and monooxygenase activity were significantly associated with deltamethrin resistance, with monooxygenase activity playing a stronger role. These results demonstrate the importance of metabolic detoxification in pyrethroid resistance in An. sinensis, and suggest that different mechanisms of resistance could evolve in geographically different populations.
Global climate change caused by greenhouse gas (GHG) emissions, which severely limits the development of human society and threatens the survival of humanity, has drawn the international community's long-term attention. Gathering the most important production factors in the region, an industrial park usually represents the development level of specific industries in the region. Therefore, the industrial park should be regarded as the base unit for developing a low-carbon economy and reducing GHG emissions. Focusing on a typical high-end industrial park in Beijing, we analyze the carbon sources within the system boundary and probe into the emission structure in view of life-cycle analysis. A GHG inventory is thereby set up to calculate all GHG emissions from the concerned park. Based on the results, suggestions are presented to guide the low-carbon development of the high-end industrial park.
The purpose of this study was to evaluate clinical outcomes following one-stage anterior radical debridement, interbody fusion, and sacral rod fixation for the treatment of lumbosacral segment tuberculosis.
From March 2004 to November 2008, 11 patients diagnosed with spinal tuberculosis received antituberculosis medications for two to three weeks before anterior radical debridement, autologous iliac bone grafting, and internal sacral rod fixation. Surgery was performed when the toxic symptoms of tuberculosis were controlled and erythrocyte sedimentation rates (ESR) decreased to 37.2 ± 9.6 mm/h (25–54 mm/h). Lumbosacral angle, visual analogue scale (VAS) pain, ESR, and neurological performance were assessed before and after surgery.
All surgical procedures were performed successfully without intra or postoperative complication. There were no instances of spinal tuberculosis recurrence. Patients were followed-up for a mean of 19.6 months. The mean lumbosacral angle was significantly increased from the mean preoperative angle (12.9 ± 5.0°) both postoperatively (21.5 ± 6.1°) and at final follow-up (20.1 ± 5.2°) (both P <0.001). The mean VAS scores and ESR were significantly decreased from preoperative levels (7.3 ± 1.2 and 37.2 ± 9.6 mm/h, respectively) both postoperatively (1.5 ± 0.5 at month six and 10.4 ± 4.5 mm/h at month three, respectively) and at final follow-up (0.6 ± 0.5 and 10.5 ± 2.3 mm/h, respectively) (all P <0.001). Bone fusion occurred in all patients at a mean of nine months (range six to 12 months) after surgery. Three patients who had impaired neurological performance before surgery had normal neurological performance after surgery.
Our findings suggest that anterior radical debridement, interbody fusion, and sacral rod fixation can be an effective treatment option for lumbosacral segment tuberculosis.
Early ecologists identified a pyramidal trophic structure in terms of number, biomass and energy transfer. In 1943, the psychologist Maslow put forward a pyramid model to describe layers of human needs. It is indicated that the pyramid principle is universally applicable in natural, humanistic and social disciplines. Here, we report that a pyramid structure also exists in urban public health (UPH). Based on 18 indicators, the UPH states of four cities (Beijing, Tokyo, New York, and London) are compared from the point of view of five aspects, namely physical health, living conditions, social security, environmental quality, and education and culture. A pyramid structure was found in each city when focusing on 2000–2009 data. The pyramid of Beijing is relatively similar to that of Tokyo, and the pyramids of New York and London are similar to each other. A general development trend in UPH is proposed and represented by different pyramid modes. As a basic conjecture, the UPH pyramid model can be verified and developed with data of more cities over a longer period, and be used to promote healthy urban development.
urban public health; pyramid structure; development trend; balance; diversity
In this study, a rare disease with characteristics of spontaneous osteolysis of the bone is reported. The patient was an eight-year-old male, who was admitted with shortness of breath. The absence of the right clavicle was identified by radiography. However, the change to the right clavicle was not malignant, as indicated by bone scanography. The biopsy of the right cervical rib revealed a number of vascular fibrous tissues and vessels distending and shunting together; however, no cell proliferation was observed. In addition, no acid-fast bacillia or malignant cells were detected in the sample of pleural effusion from the patient. Low hemoglobin (93 g/l) and a slight elevation of alkaline phosphatase levels (133 U/l) were observed; however, the other laboratory examination results were normal. The follow-up investigation and radiotherapy results indicated that the osteolysis of the skull and the other portion of bone had not worsened. Although it has been reported that >15% of patients succumb to this disease, the patient reported in the current study was in a relatively stable condition.
ribs; maxillary bone; Gorham’s disease; radiotherapy; prognosis
In this paper, a novel direction of arrival (DOA) estimation algorithm called the Toeplitz fourth order cumulants multiple signal classification method (TFOC-MUSIC) algorithm is proposed through combining a fast MUSIC-like algorithm termed the modified fourth order cumulants MUSIC (MFOC-MUSIC) algorithm and Toeplitz approximation. In the proposed algorithm, the redundant information in the cumulants is removed. Besides, the computational complexity is reduced due to the decreased dimension of the fourth-order cumulants matrix, which is equal to the number of the virtual array elements. That is, the effective array aperture of a physical array remains unchanged. However, due to finite sampling snapshots, there exists an estimation error of the reduced-rank FOC matrix and thus the capacity of DOA estimation degrades. In order to improve the estimation performance, Toeplitz approximation is introduced to recover the Toeplitz structure of the reduced-dimension FOC matrix just like the ideal one which has the Toeplitz structure possessing optimal estimated results. The theoretical formulas of the proposed algorithm are derived, and the simulations results are presented. From the simulations, in comparison with the MFOC-MUSIC algorithm, it is concluded that the TFOC-MUSIC algorithm yields an excellent performance in both spatially-white noise and in spatially-color noise environments.
DOA estimation; fourth order cumulants; MUSIC-like; Toeplitz approximation; spatially-white noise; spatially-color noise
Industrial sector is one of the indispensable contributors in global warming. Even if the occurrence of ecoindustrial parks (EIPs) seems to be a good improvement in saving ecological crises, there is still a lack of definitional clarity and in-depth researches on low-carbon industrial parks. In order to reveal the processes of carbon metabolism in a low-carbon high-tech industrial park, we selected Beijing Development Area (BDA) International Business Park in Beijing, China as case study, establishing a seven-compartment- model low-carbon metabolic network based on the methodology of Ecological Network Analysis (ENA). Integrating the Network Utility Analysis (NUA), Network Control Analysis (NCA), and system-wide indicators, we compartmentalized system sectors into ecological structure and analyzed dependence and control degree based on carbon metabolism. The results suggest that indirect flows reveal more mutuality and exploitation relation between system compartments and they are prone to positive sides for the stability of the whole system. The ecological structure develops well as an approximate pyramidal structure, and the carbon metabolism of BDA proves self-mutualistic and sustainable. Construction and waste management were found to be two active sectors impacting carbon metabolism, which was mainly regulated by internal and external environment.
The Millennium Ecosystem Assessment (MA) framework was modified with a special focus on ecosystem service values. A case study of a typical low-carbon industrial park in Beijing was conducted to assess the ecological and economic benefits. The total economic value of this industrial park per year is estimated to be 1.37 × 108 RMB yuan, where the accommodating and social cultural services are the largest two contributors. Due to the construction of small grasslands or green roofs, considerable environmental regulation services are also provided by the park. However, compared with an ecoindustrial park, carbon mitigation is the most prominent service for the low-carbon industrial park. It can be concluded that low-carbon industrial park construction is an efficacious way to achieve coordinated development of society, economy, and environment, and a promising approach to achieving energy saving and carbon reduction.
Osteochondral fracture (OCF) of the lateral femoral condyle has a low incidence and old OCF is even more rarely seen; it is difficult to differentiate from late osteochondritis dissecans (OCD).
In this report, we present the case of a 20-year-old male patient with an old OCF of the lateral femoral condyle. The possible etiology of OCF is discussed, along with its clinical manifestation, diagnosis, and treatment. He underwent arthroscopically-assisted reduction and fixation with cannulated screws. Four months after the surgery, arthroscopy showed good osteochondral healing, and screws were removed. He had achieved good functional recovery by the follow-up visit.
Old OCF should be distinguished from OCD in clinical practice, and osteochondral bodies should be preserved as much as possible. Osteochondral reduction and fixation under arthroscopy was minimal and the clinical effect was good.
osteochondral fracture (OCF); arthroscopy; femoral condyle
Along with increasing concerns on environmental protection and global warming mitigation, new industrial organization modes such as “Ecoindustrial Park” and “Low Carbon Industrial Park” are emerging. Since ecoindustrial parks and low carbon industrial parks may offer multifaceted benefits to the users, it naturally follows that the sustainability assessment of the industrial parks ought to adopt a multicriteria methodology. In this paper, a multicriteria sustainable evaluation framework is proposed in combination with the life cycle analysis and applied to a low carbon and high end industrial park (LCHE) in Beijing, China. Results show that the LCHE industrial park can contribute to both energy-saving and greenhouse gas emission mitigations compared with other industrial parks. In terms of economic performance, although the economic profits are considerable, the investment per constructed area is relatively high. The results of sustainable analysis of the LCHE industrial park can thus shed light on future upgrading of industrial parks.
As the major source of greenhouse gas (GHG) emission, cities have been under tremendous pressure of energy conservation and emission reduction for decades. Community is the main unit of urban housing, public facilities, transportation, and other properties of city's land use. The construction of low-carbon community is an important pathway to realize carbon emission mitigation in the context of rapid urbanization. Therefore, an efficient carbon accounting framework should be proposed for CO2 emissions mitigation at a subcity level. Based on life-cycle analysis (LCA), a three-tier accounting framework for the carbon emissions of the community is put forward, including emissions from direct fossil fuel combustion, purchased energy (electricity, heat, and water), and supply chain emissions embodied in the consumption of goods. By compiling a detailed CO2 emission inventory, the magnitude of carbon emissions and the mitigation potential in a typical high-quality community in Beijing are quantified within the accounting framework proposed. Results show that emissions from supply chain emissions embodied in the consumption of goods cannot be ignored. Specific suggestions are also provided for the urban decision makers to achieve the optimal resource allocation and further promotion of low-carbon communities.