Retrieval,alignment, and clustering of computational models based on semantic annotations

The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data.     

Evaluating rainstorm hazard prevention and mitigation capability in mountainous ecological scenic areas: A case study of the Qinling Mountains,China

Abstract

Mountainous areas have become tourism hotspots in recent years, at the same time, some tourism safety issues have been revealed. To study rainstorm hazard prevention and mitigation capabilities, four representative scenic areas in the Qinling Mountains of China were selected as research foci for this study. The similar weight method and the unascertained measure model were used to establish an evaluation index, and the weights of indices at all levels were determined. Rainstorm hazard prevention and mitigation capabilities in the four scenic areas and on defferent slopes were then evaluated quantitatively. The results found that : according to the rainstorm hazard prevention and mitigation capabilities, the rankings of these scenic areas from high to low were Taibai Mountain National Forest Park, Cuihua Mountain National Geopark, Huayang Scenic Area, and Jinsixia National Forest Park. The rainstorm hazard prevention and mitigation capability on the north of the Qinling Mountains were higher than on the south slope, and the difference was relatively large. Rainstorm hazard prevention and mitigation capabilities on the eastern and western Qinling Mountains were more similar. These conclusions could provide a reference for regional rainstorm hazard prevention and mitigation measures, as well as sustainable development.     

1953-2011年小兴安岭森林火灾含碳气体排放的估算

根据1953-2011年小兴安岭森林调查数据和森林火灾统计资料,结合野外火烧迹地调查与室内控制试验数据,估算了小兴安岭1953-2011年森林火灾的碳排放量和含碳气体排放量.结果表明: 1953-2011年小兴安岭森林火灾的总碳排放量为1.12×10⁷ t,年均排放量为1.90×10⁵ t,约占全国年均森林火灾碳排放量的1.7%;其中,含碳气体CO₂、CO、CH₄和非甲烷烃(NMHC)的排放量分别为3.39×10⁷、1.94×10₅、1.09×10⁵和7.46×10⁴ t,相应年均排放量5.74×10⁵、3.29×10⁴、1.85×10³、1.27×10³ t分别占全国年均森林火灾含碳气体排放量的1.4%、1.2%、1.7%和1.1%.不同林型的燃烧效率和单位过火面积的碳排放量均为针叶林＞阔叶林＞针阔混交林.最后提出了合理的林火管理措施.     

Excess iron-induced changes in the photosynthetic characteristics of sweet potato

Iron (Fe) is an essential nutrient for plant growth and development. In plant tissues, approximately 80% of Fe is found in photosynthetic cells. This study was carried out to determine the effect of different iron concentrations on the photosynthetic characteristics of sweet potato plants. The fluorescence transient of chlorophyll a (OJIP), chlorophyll index and gas exchange were measured in plants grown for seven days in Hoagland solution containing an iron concentration of 0.45, 0.90, 4.50 or 9.00 mM Fe (as Fe-EDTA). The initial and maximum fluorescence increased in the plants receiving 9.00 mM Fe. In the analysis of the fluorescence kinetic difference, L- and K-bands appeared in all of the treatments, but the amplitude was higher in plants receiving 4.50 or 9.00 mM Fe. In plants grown in 9.00 mM Fe, the parameters of the JIP-Test indicated a better efficiency in the capture, absorption and use of light energy, and although the chlorophyll index was higher, the net photosynthesis was lower. The overall data showed that sweet potato plants subjected to high iron concentrations may not exhibit the toxicity symptoms, but the light reactions of photosynthesis can be affect, which may result in a declining net assimilation rate.     

Red porgy (Pagrus pagrus) larval feeding performance and behavior at the onset of exogenous feeding

The feeding performance and behavior at the onset of exogenous feeding, 3 to 4 days after hatching (DAH), were studied in red porgy Pagrus pagrus larvae. Similar feeding efficiency and intensity were achieved for two feeding treatments (live or freeze-dried rotifers) suggesting that prey movement is not decisive for their detection and capture and demonstrating that at first feeding red porgy larvae can ingest inert food. Larvae feeding performance was not affected by a diet shift between treatments. Based on maximum rotifers consumption and gut evacuation time at 18 °C, the daily ration was estimated as 14.035 μg, considering 14 h of feeding and a 25% egg:female rotifer ratio. Larval swimming activity measured by video recording showed a close association with gut fullness and similar swimming patterns for 3 and 4 DAH larvae. However, 20.3% larger mouth gape and 54.6% higher swimming speed of the older larvae should provide a better feeding performance and more energy needed for growth.     

印加孔雀草入侵生态风险评估及其管理措施

【目的】印加孔雀草为菊科一年生草本植物,原产南美洲,现已在我国多个地区发现,局部呈现生态危害。分析印加孔雀草生态适应性特点,可以有针对地提出其风险指标体系和判断标准,确定其危险级别。【方法】对印加孔雀草的分布、危害情况及生物学特性进行调查,定性分析其生态适应性特点,定量分析评估其生态风险,确定其危险级别。【结果】根据风险指标体系准则层的赋值,其中入侵性R_1为83,适应性R_2为88,扩散性R_3为65,危害性R_4为84,计算得出印加孔雀草风险值(R)=8061,属于具有危害性和侵入性的物种。【结论】印加孔雀草为具有危害性和侵入性的物种,应严格禁止引入。由于该植物已经传入我国,应采取必要的应急措施,开展检疫、监测和灭除,防止其传入其他还未发生的地区。     

Interim Response of Wading Birds (Pelecaniformes and Ciconiiformes) and Waterfowl (Anseriformes) to the Kissimmee River Restoration Project,Florida, U.S.A

Success of the Kissimmee River Restoration Project will be evaluated in part by monitoring populations of wading birds (Pelecaniformes and Ciconiiformes) and waterfowl (Anseriformes). These two waterbird guilds were integral components of the pre‐channelization river–floodplain ecosystem, and both declined substantially following channelization. Restoration is expected to attract wading birds and waterfowl by reintroducing naturally fluctuating water levels, seasonal hydroperiods, and historic vegetation communities. Post‐construction aerial surveys (November 2001 to May 2008) within the Phase I restoration area indicate that the abundance and species richness of both wading birds and waterfowl have shown a positive restoration response thus far. Dry season abundance of aquatic wading birds and waterfowl has exceeded restoration expectations (≥30.6 birds/km² and ≥3.9 birds/km², respectively) each year since the completion of restoration Phase I in 2001. While there has been a significant positive restoration effect on waterfowl abundance, waterfowl species richness (n = 6) has not yet reached the restoration expectation of ≥13 species. Abundance of the terrestrial cattle egret (Bubulcus ibis), which increased dramatically after the majority of floodplain wetlands were converted to cattle pastures in the channelized system, has shown a significant negative response to restoration. It is anticipated that completion of the remaining phases of restoration (II/III), and implementation of the Kissimmee River Headwaters Revitalization water regulation schedule by 2019, will further increase and improve habitat for wading birds and waterfowl by reestablishing floodplain hydrology that more closely mimics historical conditions.     

Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ~3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D(2) distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D(2) distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.