bluuebunny/crossref_metadata_2025 huggingface dataset:
The status of the southernmost part (Lake Pihkva) of large Lake Peipsi: A purification pond or polluter?
Authors: Haberman Juta , Haldna Marina , Laugaste Reet
Published: October 2017

Large Lake Peipsi (3555 km2) is divided between two countries, Estonia (44%) and Russia (56%). The southernmost part of the lake, Lake Pihkva, is almost entirely (99%) in Russia, and is continuously being polluted by the greatest inflow to Lake Peipsi, the insufficiently purified River Velikaya. Research on this lake (Lake Peipsi) in the growing season has been possible as a result of Estonian–Russian joint expeditions (2003–2010) in the month of August. Our study has demonstrated statistically significant variances in the hydrochemistry and zoo- and phytoplankton data between the lake parts. Several parameters used for characterizing the lake's ecosystem were considerably higher for Lake Pihkva than for the larger Lake Peipsi s.s. These include increases in TP concentration (3×); TN (2×); Chlorophyll a (3×); biomass of cyanobacteria (4×); Microcystis (4×); Aphanizomenon (5×); abundance of Chydorus sphaericus (5×); Keratella tecta (8×). However, several values were lower in Lake Pihkva than in Lake Peipsi: water transparency (3×); ratio between zoo- and phytoplankton biomasses (2×); cladoceran mean weight (3×); abundance of Eudiaptomus gracilis (1.5×); abundance of Kellicottia longispina (1.8×). Different natural conditions (topography, catchment area, relative depth) and different pollution loads in the lake parts have resulted in apparently different resistances in their ecosystems and different responses to human activity. At present, on the basis of TP data (up to 200 mg m−3), Lake Pihkva appears to act a polluter of adjacent lake part rather than a purification pond.
Contributions towards an ecosystem based management of Lake Titicaca
Authors: Vera Cartas J. , Pucheu K. S. , Torres Beristain B.
Published: October 2017

Lake Titicaca is the highest navigable lake in the world, shared between the countries of Bolivia and Peru. In recent years population growth and the pressure from several anthropogenic activities have increased degradation of the lake's environment. There has been international concern about the restoration and maintenance of this valuable ecosystem and the preservation of the natural services the lake provides to the human populations that depend on it. Several initiatives and projects have been carried out to solve the problems that the lake faces.

In this article, the Peruvian aquaculture and fisheries governmental policy in Lake Titicaca for the period 2007–2011 will be assessed. The policy aims to promote the sustainability and competitiveness of Lake Titicaca fisheries and aquaculture sectors. Financial and technically supported by the Spanish Agency for International Development Cooperation, this policy is implemented in association with a complex network of local, regional and national governmental, social, scientific and economic stakeholders. The article describes and analyzes the different components, projects and results of this national policy at the light of the ecosystem based management paradigm.

This national policy has contributed towards an ecosystem management of Lake Titicaca, solving human needs through fisheries and aquaculture activities while giving great importance to ecological integrity and promoting the cooperation among different governmental levels and research institutes. The continuity of the activities and projects supported by this policy might be at risk in the short term due to the dependency on international financing, the changes in the political administration at a national, regional and local level, as well as the instability and high human resource turnover in several partner institutions. A transversal aspect still pending in Lake Titicaca ecosystem management has to do with being a developing country/region which is still structuring new government policies for conservation and restoration.
Impact of climate change on the hydrology of shallow Lake Trasimeno (Umbria, Italy): History, forecasting and management
Authors: Ludovisi A. , Gaino E. , Bellezza M. , Casadei S.
Published: October 2017

Lake Trasimeno is the largest lake of the Italian Peninsula. Because of the small extent of its watershed, meteorological conditions have caused dramatic floods and droughts over the centuries. Although numerous attempts have been made to regulate the lake level since Etruscan or Roman times, the problems related to water level changes remain unsolved, and the recently adaptive management strategies seem to be ineffective in the current climatic conditions. This study evaluates past and future management scenarios with the aim of identifying effective strategies to limit the lake level fluctuations. A lumped hydrological model, which incorporates climate forcing and water regulation policies adopted currently and in the past, is calibrated and validated using a fifty-year data series. Future scenarios (present–2090) of water level change are simulated on the basis of IPCC (Intergovernmental Panel on Climate Change) regional projections for precipitation and temperature. Possible mitigation measures, such as those involving the enlargement of the catchment basin, the water diversion from nearby dams and the adoption of more restrictive rules on abstractions are also considered. The model indicates that critical prospects emerge if the intermediate or the maximum rates of change estimated by global climate models are assumed. Under these circumstances, currently feasible mitigation measures seem effective in preventing severe water shortage in the next decades, but ineffective in preventing the drainage of the lake in the second half of the century. We recommend that plans for water resource management should be put in place as a matter of urgency to ensure the conservation of the hydrologically vulnerable Lake Trasimeno.
Phytoplankton community structure shaped by key environmental factors in fish and shellfish farms in Daya Bay, South China
Authors: Zhang Xia , Huang Xiaoping , Huang Liangmin
Published: October 2017

In coastal cultural regions of Dapeng Cove (southwest of Daya Bay), the composition, abundance and community structure of phytoplankton, as well as physicochemical variables, were investigated to identify factors driving seasonal changes. During summer, local phytoplankton biomass was low, probably because of nutrient depletion. In September, sudden heavy rainfalls resulted in a substantial increase in nitrogen. As a result, a disturbance-tolerant diatom, Skeletonema costatum, increased rapidly. Organic matter associated with freshwater runoff, fishery activities and settled algal cells increased consumption of dissolved oxygen (DO), especially in fish farms. It was suggested that heavy rainfall events was probably a trigger of low oxygen level and exerted a major effect on nutrient cycling and the phytoplankton community. In winter, phytoplankton community was characterized by dinoflagellates, which are adapted to well-mixed conditions. Spring blooms composed of Pseudonitzschia delicatissima and P. pungens were triggered by warm temperature and increasing light intensity. Excessive ammonium levels in March probably contributed to bloom initiation. Dissolved inorganic nitrogen (DIN) and total phosphorus (TP) concentrations in fish farms were significantly higher than that in bivalve cultures and control sites although phytoplankton abundance in fish farms was not. We suggest that intense fish culture farming exerts more pressure on the ambient environment than shellfish farming.
Spatio-temporal changes of hydro-chemical parameters in the estuarine part of the River Ganges under altered hydrological regime and its impact on biotic communities
Authors: Manna R. K. , Satpathy B. B. , Roshith C. M. , Naskar M. , Bhaumik Utpal , Sharma A. P.
Published: October 2017

Hooghly estuary, the lowermost part of River Ganges in India, following the construction of Farakka barrage in 1975, witnessed improved freshwater inflow in the estuarine stretch of the river with significant impact on the salinity regime, water transparency, suspended sediments and nutrient load leading to alternations in the distribution and abundance of fish and other biotic organisms like plankton and benthos. A detailed seasonal study was conducted in Hooghly estuary during 2010–2012 to evaluate the spatio-temporal changes in selected physico-chemical parameters like temperature, transparency, pH, free CO2, dissolved oxygen, specific conductivity, total alkalinity, total hardness, salinity, available nutrients like nitrate, phosphate and silicate under the present hydrological regime in determining the distribution of fish and other aquatic organisms. The salinity based zonation during pre-Farakka period apparently stands modified with a downward shift of freshwater zone. Accordingly, distribution and abundance of biotic communities like plankton and fish now present a completely different scenario from the past.
Aquatic Coleoptera response to environmental factors of freshwater ecosystems in Changbai Mountain, northeast China
Authors: Dong Baili , Geng Chunnu , Cai Yongjiu , Ji Lanzhu
Published: October 2017

Aquatic Coleoptera (beetles) play a key role in freshwater ecosystems and are considered as a suitable bioindicator. Despite being widely distributed in China, there are few aquatic Coleoptera-based methods to assess ecological quality and environmental conditions. Changbai Mountain, with its distinct temperate and boreal forest ecosystems, provides an excellent opportunity to explore the influence of environmental features on aquatic beetles along altitude gradients. The objectives of the study were to investigate community structure and to determine the dominant factors controlling aquatic beetles in the montane environment. Study results showed that there were 8 families, 40 genera, and 72 aquatic beetle species on Changbai Mountain, and that Dytiscidae, Hydrophilidae and Haliplidae were the dominant families. Seven sensitive species of aquatic beetles could be considered as the candidate of indicator for environmental monitoring. Canonical correspondence analysis showed that water pH, concentrations of total organic matter and total phosphorus in sediment, water conductivity and water temperature had a significant impact on the community structure of aquatic beetles, and that water pH was the most important factor. Our results suggested that water quality played a key role in species richness of aquatic beetles, and that therefore they could be considered as an indicator organism of freshwater ecosystem health.
Remote sensing assessment of sediment variation in the Pearl River Estuary induced by Typhoon Vicente
Authors: Ye Haibin , Chen Chuqun , Tang Shilin , Tian Liqiao , Sun Zhaohua , Yang Chaoyu , Liu Fenfen
Published: October 2017

A MODIS-based algorithm was developed to investigate the impact of Typhoon Vicente on the total suspended solid concentration in the Pearl River Estuary. This algorithm used two high resolution bands at 645 nm and 555 nm to map the concentrations. Regression between the remote sensing reflectance and in situ total suspended solid concentration showed good correlation (R2 = 0.91), indicating that the algorithm was valid for the high turbid waters in the Pearl River Estuary. MODIS-derived maps showed different total suspended solid concentration anomalies in different sub-regions of the estuary during the passage of Typhoon Vicente. In western inlets, the increase of total suspended solids (maximum values of 22.20 g m−3 before and 55.71 g m−3 after the typhoon) was possibly related to the larger rainfall discharge from the Pearl River. In Lingdingyang, the increase of total suspended solids (maximum values of 19.60 g m−3 before and 44.59 g m−3 after the typhoon) might be the result of typhoon-induced resuspension. In the southeastern portion of the Estuary, due to the typhoon-induced current, a significant decrease of total suspended solid area (decreased by 10 g m−3) was observed. Different changes were observed in different sub-regions under the influence of the typhoon, implying the complicated hydrological environment is an important feature in the Pearl River Estuary.
Lake Vänern: A historical outline
Authors: Drotz Marcus K. , Wängberg Sten-Åke , Jakobsson Eva , Gustavsson Eva , Nilsson Lars Göran
Published: October 2017

Although Lake Vänern is the largest freshwater reservoir in Western Europe, it remains relatively unknown to the scientific community outside of Scandinavia. Therefore, we aim to give a brief outline of the lake and its geological history, in particular the landscape transformation, resource utilization, pollution history, and environmental development of the region. The landscape around Lake Vänern was shaped into its present form during the latest glaciations some 10,000 years ago. Large variation exists in its tributaries, with forest in the north and agricultural areas in the south. Human influence on the landscape was relatively small until the mid-18th century. Later, in the mid-19th century, the agriculture, forestry and shipping industries underwent large transformations as the towns around the lake grew and the economy changed. Development of fishing equipment, processes and changes in catching methods industrialized the fishing industry after mid-20th century. In the 1960s the lake was considered to be one of the most heavily mercury-polluted lakes in the world. After the passing of the first national environmental protection law in Sweden the lake turned into a success story: It has been declared to be healthy. However, old pollution still affects the fishing industry. With this new focus on the environment, the scientific community started to be interested in the lake. The lake has also played a very important role as the largest hydropower reservoir in Sweden. Here, too, the environmental question is in focus and the effects of the water regulation are still under debate. The result has been loss of biodiversity and an increased risk of an inflow of invasive species from international shipping. However, still many questions remain to be answered regarding the lake and effect of ongoing climate change on the sustainable development of the lake region.
Sustainability aspects of water regulation and flood risk reduction in Lake Vänern
Authors: Nyberg Lars , Evers Mariele , Dahlström Margareta , Pettersson Andreas
Published: October 2017

A modern feature of flood risk management is to integrate ecological, economic and social aspects in risk prevention and mitigation. Risk-reducing measures can be in conflict with ecosystem functions and complicate upstream/downstream relations. Flood risks are also influenced by processes in the catchment, such as changes in climate and land-use, or increases of vulnerable urban areas. Lake Vänern in Sweden has high ecological and social values but is also flood-prone, which in this article has been analyzed from a perspective of sustainable development. Lake Vänern and the Göta älv River are used for drinking water supply, shipping, hydropower production, fishing, tourism, as a recipient for industries and wastewater plants, etc. The flood risks are connected to landslide and industrial risks. One interest at stake is the drinking water supply for 800,000 persons in the Gothenburg region. According to climate scenarios, flood risks will increase in the 21st century due to increased precipitation. Recent studies in the region were used to identify relevant interests and values connected to Lake Vänern. The study reveals differing interests in relation to water level regimes. From a flood protection perspective (risks around the lake and downstream to Gothenburg) a low and stable water level is beneficial. For shipping and hydropower, a stable medium-high water level is wanted, whereas from an ecosystem and landscape development perspective larger water level amplitudes are optimal. One out of a few reasons for this is the need to prevent a massive increase in vegetation in coastal areas. There are good reasons to have a broad decision-support, representing different values and interests, when the permanent water regulation scheme will be decided. This study also addresses the potential to reconcile the concept of flood risk management with that of a sustainable development.
Tintinnids (Ciliophora: Choreotrichia) of the Suez Canal and their transmigration process between the Red Sea and the Mediterranean Sea
Authors: El-Serehy Hamed A. , Al-Misned Fahad A. , Abdel-Rahman Nasser S. , Al-Rasheid Khaled A.
Published: October 2017

On its route from the Mediterranean in the north to the Red Sea in the south, the Suez Canal crosses three different lakes which represent different habitats, and in some cases, hinder the migration of the fauna and flora from one sea to the other. Tintinnid species–specific abundance was determined at monthly intervals from 10 stations in the Suez Canal. A total of 18 species were recorded in the canal water, all Indo-Pacific in origin. Six of these species have been introduced to the Mediterranean, while 11 are new geographical records for the Suez Canal. Most species exhibited a seasonal cycle with low winter and high spring and summer densities. Tintinnid affinities and differences between the eastern Mediterranean and the Red Sea were discussed in the light of the results of distribution studies of the eighteen species of Tintinnid carried out over a complete year. These observations point to the role of the canal as a selective barrier and/or as a link in the migration of Tintinnid protozoa. While cases of migration from one sea to the other are more likely to occur in either direction, those concerning species of Indo-Pacific origin are more successful and numerous. Meanwhile, the Suez Canal acts as a local endemic habitat by itself.
Transport of harmful marine microalgae via ship's ballast water: Management and mitigation with special reference to the Arabian Gulf region
Authors: Hallegraeff Gustaaf M.
Published: October 2017

The potential for transport of non-indigenous marine microalgae via ship's ballast water has been amply demonstrated, and nearly all known harmful algal bloom species have been documented in viable form from ship's ballast water. Ballast water uptake needs to be strongly discouraged during harmful algal bloom events. Efficacy of ballast water exchange in removing harmful microalgal cells is limited, since this nearly always leaves behind a viable inoculum. The precise location of ballast water exchange needs to be carefully chosen, and retention of dinoflagellate cysts and diatom spores in ballast tank sediments is of special concern. The only fully effective ballast water treatment for microalgae is the application of biocides, but heat treatment also offers considerable promise especially in subtropical and tropical waters. To manage harmful algal blooms, other key environmental drivers such as eutrophication and climate change also need to be addressed. Effective monitoring for harmful algal species and their toxins remains the critical tool to protect human health, fisheries, aquaculture and desalination industries. Challenges and opportunities for ballast water management in the Arabian Gulf region are discussed.
Sea of Azov: A brief review of the environment and fishery
Authors: Diripasko O. A. , Bogutskaya N. G. , Dem’yanenko K. V. , Izergin L. V.
Published: October 2017

The Sea of Azov, bounded by Ukraine and Russia, is a unique brackish waterbody from many points of view despite its small size. Low water salinity, shallow waters, high summer temperatures, large riverine inputs of organic matter and minerals, and other factors lead to its very high biological productivity. The article reviews specific features of the Sea of Azov fish fauna and fisheries providing some historical and modern statistical data. An updated check-list of native and non-indigenous fish taxa permanently or occasionally inhabiting the Sea of Azov is included.
The fish community of Hamilton Harbour, Lake Ontario: Status, stressors, and remediation over 25 years
Authors: Boston C. M. , Randall R. G. , Hoyle J. A. , Mossman J. L. , Bowlby J. N.
Published: October 2017

Hamilton Harbour is a large (21 km2) protected harbour located at the western end of Lake Ontario that was designated as an Area of Concern in 1985 by the International Joint Commission. As part of the designation, the fish community was deemed “impaired.” One of the long-term goals of the Hamilton Harbour Remedial Action Plan is to rehabilitate the fishery to a state, at least in part, to what it was prior to the degrading effects of industrial and municipal pollution, habitat loss, and invasive species. Since the Area of Concern designation, the nearshore fish community has been monitored regularly via a federal boat electrofishing program (1988–2013) and more recently, by a trap net program (2006–2012). During the study period, the harbour underwent significant physical and biological change which was related to both lake-wide (e.g. Dreissenids) and localized harbour events (e.g. habitat restoration). The fish community was assessed temporally using two indices of ecosystem health, the Great Lakes Index of Biotic Integrity and Proportion of Piscivore Biomass, and species-specific catch trends at unaltered sites or sites modified by habitat restoration. Early on, the fish community was dominated by tolerant species characteristic of degraded, eutrophic environments and piscivore abundance was low. The fish community responded positively to ecosystem actions during the first decade that improved water quality, increased physical habitat and reduced invasive species, but further progress was confounded by the interactions with other factors in the last decade that included new invasive species and a decline in water quality. Fish community assessments in the last decade, using both the indices found that the fish community was still impaired and dominated by non-native and pollution tolerant species. The Index of Biotic Integrity was a suitable indicator of ecosystem health strengthened by a consistent assessment with the Proportion of Piscivore Biomass index. A science based refinement of the existing Index in the future would benefit the ability to assess nearshore fish assemblages in the context of conservation goals.
Evaluation of the Remedial Action Plan goal for dissolved oxygen in Hamilton Harbour: A goal based on habitat requirements for Cisco
Authors: Bowlby J. N. , Hiriart-Baer V. P. , Blukacz-Richards E. A. , Yerubandi R. R. , Doka S. E. , Long T. L. , O'Connor K. M.
Published: October 2017

The Hamilton Harbour Remedial Action Plan has adopted a dissolved oxygen goal for restoring habitat in the pelagic portion of Hamilton Harbour based on the ecological needs of Cisco (Coregonus artedii), a fish formerly abundant in Hamilton Harbour. The goal for dissolved oxygen is based on retaining an adequate volume of optimum Cisco habitat characterized as temperature <20°C and dissolved oxygen >6 mg l−1 during the June to September period. The goal also specifies minimum habitat requirements for when optimum conditions are not achieved, that being a smaller volume of refuge habitat with temperature <20°C and dissolved oxygen >3 mg l−1 for no more than 2 weeks per year. Weekly temperature and dissolved oxygen profiles during May to October, 1987 to 2012 in the center of Hamilton Harbour were assessed to evaluate optimum and refuge Cisco habitat relative to the Remedial Action Plan goal for dissolved oxygen. This goal was met only in 2009. However, this was fortuitous, based on a combination of cooler water temperatures in May and June and exchanges of cool oxygenated water from Lake Ontario. From 1987 to 2002 optimum habitat was estimated to be absent at least one week and up to seven weeks during June to September. Cisco could not have survived in Hamilton Harbour during six of these years when refuge habitat was absent for one or two weeks. Since 2003, Cisco habitat in Hamilton Harbour improved markedly, as some refuge habitat was always present. As well, the number of weeks with inadequate refuge habitat, and with no optimum habitat has declined. These improvements in Cisco habitat since 2003 were related to higher dissolved oxygen in the mid-depths of Hamilton Harbour.
Preliminary analysis of the intraseasonal air–sea interaction influenced by Xisha warm eddy
Authors: Li Jian , Zu Tingting , Zeng Lili , Li Ting , Chen Ju , Yao Jinglong
Published: October 2017

A study of the Xisha eddy is a good supplement to comprehend the local oceanic and atmospheric currents. Our work aims at analyzing the intraseasonal Air–Sea interaction process during the occurring of the Xisha warm eddy. Using a Complex Empirical Orthogonal Function statistical technique, we found an eddy that propagated southwestward along the continental slope of the northwestern South China Sea, at a similar phase speed to that of Rossby waves, at 0.12 m s−1. Intraseasonal variability in spring is related to the ocean-to-atmosphere interaction, and involves the cloud-radiation effects on surface sea temperature, as well as its impact on lower-level convergence over the South China Sea. This process, induced by the warm eddy, results in abnormal surface sea temperature, downward shortwave/longwave radiation flux, surface latent heat flux, and wind changes. We used composite results and the Weather Research and Forecasting Model to explore how the observed surface sea temperature anomalies influence precipitation in the South China Sea. The results showed that the atmospheric transport of heat and moisture improved with respect to the surface sea temperature max and the air active events have caused lower atmosphere instability, along with the lower pressure and enhanced precipitation frequency in spring.
Using eutrophication and ecological indicators to assess ecosystem condition in Poyang Lake, a Yangtze-connected lake
Authors: Zhang Yanhui , Yang Guishan , Li Bing , Cai Yongjiu , Chen Yuwei
Published: October 2017

Poyang Lake, the largest freshwater lake in China, has been facing shrinkage and environmental problems in recent years, making it imperative to assess the status of its ecosystem. In this study, such an assessment was conducted based on the trophic status index, phytoplankton biomass, the ratio of zooplankton biomass to phytoplankton biomass, eco-exergy, structural eco-exergy, and ecological buffer capacity to total phosphorus for phytoplankton. First, the spatial and temporal variations of the ecosystem status in Poyang Lake were assessed based on these six indicators. Then, cluster analysis was utilized to classify the 15 sites based on the various indicators and to identify the most influential indicators. The results showed that the ecological status of Poyang Lake was affected not only by eutrophication but also by hydrological characteristics. All of the 15 sites had deteriorated to a certain degree. An analysis of the relative spatial ecological status showed that the status of the water in the rivers was superior to the status of water in the central lake. Furthermore, the relative ecological status was found to be best in summer and second best in autumn with ecological status deteriorating in winter. There was no significant correlation between eco-exergy and trophic status index, but a very strong relationship was found between eco-exergy and macrozoobenthos biomass with an R2 of 0.92, indicating that macrozoobenthos contributed greatly to the eco-exergy.
Hamilton Harbour over the last 25 years: Insights from a long-term comprehensive water quality monitoring program
Authors: Hiriart-Baer V. P. , Boyd D. , Long T. , Charlton M. N. , Milne J. E.
Published: October 2017

Hamilton Harbour was identified by the International Joint Commission as a problem area in 1978 and later identified as an Area of Concern in 1985. In response to its Remedial Action Plan, the harbour has been systematically monitored since 1987. In this study, we present the long-term water quality record (1987 to 2012) of Hamilton Harbour, focusing on the parameters and seasonal intervals of particular importance to the Remedial Action Plan beneficial use impairments. The long-term summer records showed that total phosphorus concentrations decreased in the first decade and have remained relatively unchanged since 1998, while an increasing trend in Secchi disc depth was observed until 2005 only to be reversed since then. No significant changes in chlorophyll a concentrations have been observed since 1987 despite significant changes in total phosphorus. Hypoxia in the hypolimnion of Hamilton Harbour remains a common occurrence and despite long-term trend improvements there has been little change over the last decade. Spring conditions have also changed, and higher conductivity values and chlorophyll a concentrations have been measured in recent years. A strong correlation between spring hypolimnetic dissolved organic carbon concentrations and dissolved oxygen depletion rates was found suggesting the organic material load to the harbour is an important controlling factor for hypoxia. Finally, the data suggest that the hypolimnetic accumulation rate of soluble reactive phosphorus in the summer has increased since 1987, most notably since the early 2000s. However, it is only since 2008 that this translated into an increasing trend in hypolimnetic soluble reactive phosphorus concentrations. These data suggest that conditions have recently changed in Hamilton Harbour and that sediment phosphorus release may delay water quality improvements for many years following reductions in total phosphorus loadings. Further research is needed to understand the implications to the Remedial Action Plan water quality goals.
Characteristics of vertical exchange process in the Pearl River estuary
Authors: Hong Bo , Gong Wenping , Peng Shiqiu , Xie Qiang , Wang Dongxiao , Li Haobo , Xu Hongzhou
Published: October 2017

Being an estuary with the occasional appearance of hypoxia, the Pearl River estuary was selected to investigate its vertical exchange process by a validated 3-D numerical model. The concept of vertical exchange time was used to quantify the vertical exchange process and was calculated by adding a conservative tracer to the hydrodynamic model. The results revealed vertical exchange time has significant seasonal variation modulated by seasonally changed external forcing, and has similar structure with spatial variation in salinity. During the wet season, remarkably long vertical exchange times (>50 days) occurred at the lower estuary under 10 m depth, which was coincident with the frequently reported hypoxic zone. The entire Pearl River estuary was occupied by water mass with a vertical exchange time of <5 days during the dry season, which indicated the estuary's health condition during this period. Further analyses revealed the seasonal trend of vertical exchange time was closely related with salinity stratification and river runoff in which the lowest vertical exchange times can be estimated by linear regressions in certain stages. Tide modulated these exchange times in different time scales. Spring tide better mixed the water column and thus facilitated the vertical exchange process compared with neap tide. As a result, minimum vertical exchange time during spring tide was about 10 days shorter than that during neap tide. Flood-ebb tide also modulated vertical exchange time in the Pearl River estuary. Vertical exchange time varies with the tide and reached minimum and maximum values during valley and high tides, respectively.
Seasonal and spatial variability of surface chlorophyll inside mesoscale eddies in the South China Sea
Authors: Xiu Peng , Guo Mingxian , Zeng Lili , Liu Na , Chai Fei
Published: October 2017

Mesoscale eddies can influence biogeochemical cycles through both vertical nutrient or plankton flux and horizontal advection of nutrient or plankton in eddy periphery. In this study, we analyzed the seasonal and spatial variability of near-sea-surface chlorophyll-a concentrations and their corresponding modulation mechanisms by collocating satellite observations of eddies tracked during 1998–2007 in the South China Sea. We found that in winter, cyclonic eddies show significantly high chlorophyll-a in the eddy core relative to the periphery, suggesting regulation by an eddy-pumping mechanism. While in summer, chlorophyll-a values in the core of cyclonic eddies are comparable with those in the periphery, and dipole features of chlorophyll-a around cyclonic eddies are conspicuous, which is largely induced by horizontal eddy advection. For anticyclonic eddies, however, low chlorophyll-a in eddy cores compared with the periphery are consistently present over most of the year. The impact of eddy advection on chlorophyll-a distribution in anticyclonic eddies is not clear from the composite images in different seasons. Variability of chlorophyll-a to the west of the Luzon Strait and northwest of the Luzon Island demonstrate that phytoplankton biomass in these two regions is mainly controlled by an eddy-pumping mechanism. In the regions off the Vietnam coast, chlorophyll-a distributions are generally associated with horizontal eddy advection. This research highlights different mesoscale mechanisms affecting biological structures in the upper ocean, which can potentially disturb ocean biogeochemical cycling processes in the South China Sea.
Monitoring the effects of aquaculture effluents on benthic macroinvertebrate populations and functional feeding responses in a tropical highland headwater stream (Kenya)
Authors: Minoo Carolyne Musyoki , Ngugi Charles C. , Oyoo-Okoth Elijah , Muthumbi Agnes , Sigana Dorcus , Mulwa Rich , Chemoiwa Emily Jepyegon
Published: October 2017

Intensification of aquaculture may result in more fish culture waste being discharged into adjacent rivers and streams. Due to composition of such wastes, ecological conditions in waterbodies may be adversely affected. We determined the ecological consequences of freshwater land-based Tilapia farms on headwater streams using macroinvertebrate community attributes and functional feeding response in an upstream tributaries of a highland stream in Kenya. Nine aquaculture sites adjacent to tributaries of three headwater streams with different fish production volumes were sampled and monitored for macroinvertebrate abundance, richness, composition of Ephemeroptera, Plecoptera and Trichoptera, Oligochaetes and Chironomids (percentage Oligochaetes and Chironomids), species diversity as well as the functional feeding group responses. The total abundance of benthic macroinvertebrate consistently increased near discharge points and immediately downstream of the effluent outlets near the aquaculture farms. We observed positive correlations between macroinvertebrate attributes (except Ephemeroptera, Plecoptera and Trichoptera) with fish production at aquaculture facilities adjacent to the tributaries of the headwater streams. The proportion of Oligochaetes and Chironomids (percentage Oligochaetes and Chironomids) increased while that of Ephemeroptera, Plecoptera and Trichoptera at discharge points and downstream of the farms decreased. Also, relative abundance of scrapers and shredders decreased significantly, while significant increase of abundance was observed for deposit feeders, filter feeders and parasites with low predator population at discharge and downstream points. These consistent patterns indicated changes in ecosystem integrity and functioning, due to aquaculture effluents with particulate organic matter from fish food-derived wastes becoming a central source of energy in river benthic food webs.
Fish habitat and fisheries of Brahmaputra River in Assam, India
Authors: Bhattacharjya B. K. , Bhaumik U. , Sharma A. P.
Published: October 2017

River Brahmaputra is a trans-boundary major river flowing through the northeastern state of Assam, India and is the lifeline of its natural fisheries. In the present article, we discuss eco-hydrobiology (including sediment quality and energy flow) of River Brahmaputra and its important tributaries in the state of Assam, India based on extensive synoptic studies conducted from April 1996 to March 1998, duly collated with past and present studies. Salient aspects of fisheries of the river system in the state (ichthyofauna, biogeography, conservation status, migratory and exotic fish species, trends in fish yield and species composition, fishing crafts and gear) are discussed in light of past and present studies conducted by the Indian Council of Agricultural Research-Central Indian Fisheries Research Institute and others. Fisheries of floodplain wetlands (beels) located in the Brahmaputra valley in the state and their interaction with the river system are also discussed.
Status, threats and conservation challenges to key aquatic fauna (Crocodile and Dolphin) in National Chambal Sanctuary, India
Authors: Singh Hari , Rao R. J.
Published: October 2017

The Chambal River in India supports a rich variety of fauna and flora including the endangered Ganges River Dolphin and Crocodile. Threats to the continued functioning of the Chambal River as a living system have reached a critical level due to the exponential expansion of human populations. Population status of Crocodiles and Dolphins in a 425 km stretch of the Chambal River was determined by surveys conducted every year during 2007 to 2010. The average number of Dolphins recorded during the surveys was 82.75 ± 09.1 yr−1 with an encounter rate of 0.19 km−1 (range 69–91), Gharial 916.25 ± 91.6 yr−1 with an encounter rate of 2.15 km−1 (range 870–996), and Mugger 235 ± 27.7 yr−1 with an encounter rate of 0.56 km−1 (range 194–301). Increasing demands for sand for development activities and water abstraction for irrigation and energy generation, coupled with mortality in fishing nets, are likely to affect these populations. Recommendations for management and research are made to ensure the effective conservation of these species in the Chambal River.
So far, yet so close: α-Catenin dimers help migrating cells get together
Authors: Machesky Laura , Braga Vania M.M.
Published: October 2017

Epithelial cells in tissues use their actin cytoskeletons to stick together, whereas unattached cells make active plasma membrane protrusions to migrate. In this issue, Wood et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201612006) show that the junction component α-catenin is critical in freely moving cells to promote adhesion and migration.
Singularizing successor cardinals by forcing
Authors: Adolf Dominik , Apter Arthur , Koepke Peter
Published: October 2017

We exhibit models of set theory, using large cardinals and forcing, in which successor cardinals can be made singular by some “Namba-like” further set forcing, in most cases without collapsing cardinals below that successor cardinal. For successors ofregularcardinals, we work from consistency-wise optimal assumptions in the ground model. Successors ofsingularcardinals require stronger hypotheses. Our partial orderings are different from Woodin’s stationary tower forcing, which requires much stronger hypotheses when singularizing successors of regular cardinals, and collapses cardinals above the cardinal whose cofinality is changed when singularizing successors of singular cardinals.
On the fundamental tone of immersions and submersions
Authors: Cavalcante Marcos , Manfio Fernando
Published: October 2017

In this paper we obtain lower bound estimates of the spectrum of the Laplace-Beltrami operator on complete submanifolds with bounded mean curvature, whose ambient space admits a Riemannian submersion over a Riemannian manifold with negative sectional curvature. Our main theorem generalizes many previously known estimates and applies for both immersions and submersions.
The 𝑠-multiplicity function of 2×2-determinantal rings
Authors: Miller Lance , Taylor William
Published: October 2017

This article generalizes joint work of the first author and I. Swanson to the

s
s

-multiplicity recently introduced by the second author. For

k
k

a field and

X
=
[

x

i
,
j

]

X = [ x_{i,j}]

an

m
×
n

m \times n

-matrix of variables, we utilize Gröbner bases to give a closed form the length
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="lamda left-parenthesis k left-bracket upper X right-bracket slash left-parenthesis upper I 2 left-parenthesis upper X right-parenthesis plus German m Superscript left ceiling s q right ceiling Baseline plus German m Superscript left-bracket q right-bracket Baseline right-parenthesis right-parenthesis">

λ
(
k
[
X
]

/

(

I
2

(
X
)
+

m

⌈
s
q
⌉

+

m

[
q
]

)
)

\lambda ( k[X] / (I_2(X) + \mathfrak {m}^{ \lceil sq \rceil } + \mathfrak {m}^{[q]} ))

, where

s
∈

Z

[

p

−
1

]

s \in {\mathbf Z}[p^{-1}]

,

q
q

is a sufficiently large power of

p
p

, and

m

\mathfrak {m}

is the homogeneous maximal ideal of

k
[
X
]

k[X]

. This shows this length is always eventually a polynomial function of

q
q

for all

s
s

.
Riesz bases of exponentials on unbounded multi-tiles
Authors: Cabrelli Carlos , Carbajal Diana
Published: October 2017

We prove the existence of Riesz bases of exponentials of

L
2

(
Ω
)

L^2(\Omega )

, provided that

Ω
⊂

R

d

\Omega \subset \mathbb {R}^d

is a measurable set of finite and positive measure, not necessarily bounded, that satisfies a multi-tiling condition and an arithmetic property that we call admissibility. This property is satisfied for any bounded domain, so our results extend the known case of bounded multi-tiles. We also extend known results for submulti-tiles and frames of exponentials to the unbounded case.
On the arithmetically Cohen-Macaulay property for sets of points in multiprojective spaces
Authors: Favacchio Giuseppe , Guardo Elena , Migliore Juan
Published: October 2017

We study the arithmetically Cohen-Macaulay (ACM) property for finite sets of points in multiprojective spaces, especially

(

P

1

)
n

(\mathbb P^1)^n

. A combinatorial characterization, the

(
⋆
)

(\star )

-property, is known in

P

1

×

P

1

\mathbb P^1 \times \mathbb P^1

. We propose a combinatorial property,

(

⋆
s

)

(\star _s)

with

2
≤
s
≤
n

2\leq s\leq n

, that directly generalizes the

(
⋆
)

(\star )

-property to

(

P

1

)
n

(\mathbb P^1)^n

for larger

n
n

. We show that

X
X

is ACM if and only if it satisfies the

(

⋆
n

)

(\star _n)

-property. The main tool for several of our results is an extension to the multiprojective setting of certain liaison methods in projective space.
Transseries as germs of surreal functions
Authors: Berarducci Alessandro , Mantova Vincenzo
Published: October 2017

We show that Écalle’s transseries and their variants (LE and EL-series) can be interpreted as functions from positive infinite surreal numbers to surreal numbers. The same holds for a much larger class of formal series, here called omega-series. Omega-series are the smallest subfield of the surreal numbers containing the reals, the ordinal omega, and closed under the exp and log functions and all possible infinite sums. They form a proper class, can be composed and differentiated, and are surreal analytic. The surreal numbers themselves can be interpreted as a large field of transseries containing the omega-series, but, unlike omega-series, they lack a composition operator compatible with the derivation introduced by the authors in an earlier paper.
Epithelial contribution to the profibrotic stiff microenvironment and myofibroblast population in lung fibrosis
Authors: Gabasa Marta , Duch Paula , Jorba Ignasi , Giménez Alícia , Lugo Roberto , Pavelescu Irina , Rodríguez-Pascual Fernando , Molina-Molina Maria , Xaubet Antoni , Pereda Javier , Alcaraz Jordi
Published: October 2017

The contribution of epithelial-to-mesenchymal transition (EMT) to the profibrotic stiff microenvironment and myofibroblast accumulation in pulmonary fibrosis remains unclear. We examined EMT-competent lung epithelial cells and lung fibroblasts from control (fibrosis-free) donors or patients with idiopathic pulmonary fibrosis (IPF), which is a very aggressive fibrotic disorder. Cells were cultured on profibrotic conditions including stiff substrata and TGF-β1, and analyzed in terms of morphology, stiffness, and expression of EMT/myofibroblast markers and fibrillar collagens. All fibroblasts acquired a robust myofibroblast phenotype on TGF-β1 stimulation. Yet IPF myofibroblasts exhibited higher stiffness and expression of fibrillar collagens than control fibroblasts, concomitantly with enhanced FAKY397 activity. FAK inhibition was sufficient to decrease fibroblast stiffness and collagen expression, supporting that FAKY397 hyperactivation may underlie the aberrant mechanobiology of IPF fibroblasts. In contrast, cells undergoing EMT failed to reach the values exhibited by IPF myofibroblasts in all parameters examined. Likewise, EMT could be distinguished from nonactivated control fibroblasts, suggesting that EMT does not elicit myofibroblast precursors either. Our data suggest that EMT does not contribute directly to the myofibroblast population, and may contribute to the stiff fibrotic microenvironment through their own stiffness but not their collagen expression. Our results also support that targeting FAKY397 may rescue normal mechanobiology in IPF.
Evaluation of tools for long read RNA-seq splice-aware alignment
Authors: Križanović Krešimir , Echchiki Amina , Roux Julien , Šikić Mile
Published: October 2017

Motivation

High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens up new possibilities. However, the high error rates common to these technologies set new bioinformatics challenges for the gapped alignment of reads to their genomic origin. In this study, we have explored how currently available RNA-seq splice-aware alignment tools cope with increased read lengths and error rates. All tested tools were initially developed for short NGS reads, but some have claimed support for long Pacific Biosciences (PacBio) or even Oxford Nanopore Technologies (ONT) MinION reads.

Results

The tools were tested on synthetic and real datasets from two technologies (PacBio and ONT MinION). Alignment quality and resource usage were compared across different aligners. The effect of error correction of long reads was explored, both using self-correction and correction with an external short reads dataset. A tool was developed for evaluating RNA-seq alignment results. This tool can be used to compare the alignment of simulated reads to their genomic origin, or to compare the alignment of real reads to a set of annotated transcripts. Our tests show that while some RNA-seq aligners were unable to cope with long error-prone reads, others produced overall good results. We further show that alignment accuracy can be improved using error-corrected reads.

Availability and implementation

https://github.com/kkrizanovic/RNAseqEval, https://figshare.com/projects/RNAseq_benchmark/24391

Supplementary information

Supplementary data are available at Bioinformatics online.