bluuebunny/crossref_metadata_2025 huggingface dataset:
Death for the Coral Reefs
Authors: Salvat Bernard
Published: April 2009

Coral reefs are being destroyed world-wide by fishermen and shell collectors, by developers and above all by direct extraction for building materials. In numbers of plants and animals the coral ecosystem is one of the richest in the world, but it is also extremely fragile. The author, who is Chairman of the Coral Group set up by the IUCN Survival Service and Ecology Commissions, describes the methods used to extract coral and the disastrous effects on the reefs. As a result of the Group's recommendations French Polynesia has decided to stop coral extraction from March 1981.
Bali's Endangered White Starling
Authors: van der Zon A.P.M.
Published: April 2009

Bali's endemic white starling, Rothschild's starling, is one of Indonesia's most endangered animals, along with the Javan and Sumatran rhinos. It is almost entirely confined to one reserve, in the north-west of the island, which has been severely reduced and disturbed in the 30 years since it was created. Only 13,000ha of the original 20,000ha of monsoon forest now survives, and estimates of starling numbers are 200 birds or even fewer. Capture for sale has also contributed to the bird's decline. The author urges the need for proper management of the reserve.
Parrot on the Way to Extinction
Authors: Jones Carl G.
Published: April 2009

With numbers down to under ten birds and no evidence of successful breeding since 1975, the endemic echo parakeet in Mauritius seems doomed to extinction very soon. The main reasons are the destruction and degradation of the native forest on which these fruit-eating parrots depend and competition with introduced macaque monkeys and another parakeet, aided by cyclones that have defoliated and stripped trees of their fruit. All attempts at captive breeding have failed and numbers are now too low to consider translocation.
Elephant Survivors
Authors: Hall-Martin Anthony
Published: April 2009

Three small elephant populations have survived in South Africa despite near extermination in the recent past. In Tongaland a group of fewer than 30 bulls survives by keeping contact with the population in a nearby reserve; in the Knysna, where there were 13 in 1920, there are now 12; and in the Addo Bush 11 survivors in 1931 had increased to only 18 in 1953, but to 102 in 1979. The author tells the story of each group, discusses the reasons for the different status of each, and describes what is being done to conserve them.
The Craft, the Trade and the Elephants
Authors: Martin Esmond Bradley
Published: April 2009

Carved ivory objects are widely sold in India, and up to 90 per cent to foreigners, either in exports or tourists’ accompanied luggage, which is a loophole in the government's otherwise complete ban on exports made from Indian ivory. Partly because of this ban, which has probably reduced elephant poaching in India, the ivory trade depends on imported African ivory, and the rise in price in recent years has been so steep that most carvers cannot affort to buy it. As a result the larger traders are turning to other crafts, and carvers are being re-trained to work in wood. This sad decline of an ancient skilled craft may, however, ease some of the pressure on both Indian and African elephants.
Birds That Vanish While We Turn Our Backs
Authors: Stuart Simon N.
Published: April 2009

Thirteen forest bird species are seriously threatened in East Africa – one, a bush shrike, may already be extinct. But the very small surviving area of forest is being rapidly destroyed, and soil eroded. If the tree-felling can be stopped it could both save the rare birds and stop the erosion. The author's study of these forest birds was aided by the FPS Oryx 100% Fund.
Translocating Crocodiles
Authors: Morgan-Davies A.M.
Published: April 2009

The state of Borno, in Nigeria, is trying to increase its dwindling crocodile populations. In 1976 the State wildlife authorities confiscated fifteen crocodiles that were being illegally kept, and used them to augment a low population in a game reserve. This proved successful, and in 1979 they followed it with another successful translocation, this time of 20 crocodiles born and bred in Kyarimi Park Zoo of which the author was Curator. The latest news is that a third translocation is planned from a record batch of 112 bred in the Kyarimi Park Zoo.
Range Extension for an Endangered Marmoset
Authors: Mittermeier Russell A. , Coimbra-Filho Adelmar F. , Constable Isabel D.
Published: April 2009

During a field expedition in eastern Brazil the authors found a new population of the endangered buffy-headed marmoset Callithrix flaviceps in the state of Tinas Gerais where it was not previously known. This was in a privately protected forest that also has an important population of the endangered woolly spider monkey Brachyteles arachnoides and other monkeys.
A Plea for Libya's Gazelles
Authors: Essghaier Mohamed F.A.
Published: April 2009

Hunting in modern vehicles has seriously reduced the Libyan gazelle populations. The author, who has been studying them, believes that the future for the three species is gravely threatened unless the Government takes strong measures to enforce the protection laws.
First Field Study of the Yellow-tailed Woolly Monkey
Authors: Luna Mariella Leo
Published: April 2009

After spending five months in Peru on the first field study of this rare monkey, which until 1974 was thought to be extinct (Oryx 13,1), the author believes that habitat destruction is the greatest threat to its survival, and that action to protect it now and provide refuges is urgent.
Caimans and Crocodiles – a Tale of Destruction
Authors: Medem Federico
Published: April 2009

In Latin America crocodilians are being poached and smuggled in thousands every year for their skins, and their future is bleak. Dr Medem, who is Colombia's foremost conservationist and reptile specialist, believes that only international efforts can save the caimans and crocodiles and that first Colombia must be persuaded to join the CITES Convention.
The Railway and a Rare Colobus Monkey
Authors: Rodgers W.A. , Homewood K.M. , Hall John B.
Published: April 2009

The Tanzania-Zambia railway now bisects the Magombera Forest Reserve in Tanzania, and as a result the most viable surviving population of the rare endemic Iringa red colobus is seriously threatened. The railway has facilitated tree-felling, settlement and cultivation, and the colobus habitat is already seriously damaged. The authors conducted a survey of the forest in 1979, and recommended that the southern part, which has a viable colobus population, be included in the neighbouring Selous Game Reserve, thus giving that part the stronger protection of a game reserve, and that the local people be compensated by the release to them of a small area of the Selous.
Tigers and Leopards in Russia's Far East
Authors: Prynn David
Published: April 2009

Russian settlement of the Far East inevitably reduced numbers of Siberian tigers and leopards, whose magnificent skins were a major lure for the settlers. But in the 1880s tigers were numerous, and tracks often seen in the streets of Vladivostok; many were shot. Today there may be 200 or so, which is probably as many as at any time since 1914. Now fully protected, they appear to have adjusted to the timber mills and the secondary forest, and are often seen on roads and near gardens. Their main strongholds are two reserves, both likely to be enlarged. The leopard, however, is seriously endangered, and depends for survival on two reserves in the Ussuri region which are being combined to create one huge reserve 200 miles long.
An endemic gecko in the Caribbean
Authors: Dodd C. Kenneth , Ortiz R. Pedro R.
Published: April 2009

When the Monito gecko was first discovered in 1974 on Isla Monito in the Caribbean it was apparently threatened by introduced rats. In 1982 a survey by the authors showed that the species is indeed rare and is restricted to two small areas of the tiny island but further work is needed to establish the reasons; the rats are the most obvious, but as yet unproven, cause. Meanwhile the gecko has been listed as endangered by the USA. This alone will not help but it is a start in the conservation of the species.
Rediscovery of a rare Indian turtle
Authors: Groombridge B. , Moll E.O. , Vijaya J.
Published: April 2009

While information was being gathered for Part 1 of the new IUCN Amphibia-Reptiha Red Data Book, dealing with crocodilians and chelonians (Groombridge, 1982), it became evident that one small terrestrial emydid turtle, Heosemys silvatica, was known to science by only two museum specimens, both collected i n 1911 in hill rain forest in south-west India (Henderson, 1912). The apparent rarity of the species, and the extent to which rain forests in south-west India have been destroyed or modified, led to concern for the species's survival and made a survey of the type locality a matter of priority. The species was included, with ‘Indeterminate’ status, in the new Red Data Book. This paper is a pre liminary report of a brief field survey initiated by the first author and carried out between 26 October and 5 November 1982.
In vitro effect of lentinan on the activation of immunological cells in Cyprinus carpio
Authors: Liu Zhang , Li-Ping Cao , Wei-Dong Ding , Jeney Galina , Pao Xu , Chuan-Xi Xiong , Guo-Jun Yin
Published: April 2009

Macrophages from the head kidney (HK) and peripheral blood leucocytes were isolated fromCyprinus carpio by Percoll gradient density centrifugation, cultured in vitro and exposed to different concentrations of the immunomodulator lentinan. To evaluate the immunostimulating effects of lentinan, proliferation of the peripheral blood leucocytes, respiratory burst of macrophages and interleukin-1β (IL-1β) gene mRNA expression of macrophages were investigated by MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide], NBT (nitroblue tetrazolium) reduction, Griess reaction and real-time polymerase chain reaction (PCR). Results showed that proliferation of peripheral blood leucocytes after 24 h incubation by the induction of lentinan at 100 and 1000 μg/ml was markedly stimulated. Lentinan at 1, 100 and 1000 μg/ml could significantly induce superoxide anions in macrophages. Production of nitric oxide by HK macrophages after 96 h incubation by lentinan showed that it had no conspicuous effect on nitrogen burst activity of macrophages. Moreover, it inhibited the nitrogen burst activity at higher doses. The expression of IL-1β in the HK macrophages after 24 h of polysaccharide stimulation showed that lentinan stimulated IL-1β expression in the head kidney in carp. Lentinan can modulate the immune response of C. carpio.
Auxin regulation in the interaction between Rice stripe virus and rice
Authors: Jin-Guang Yang , Wen-Ting Wang , Xin-Lun Ding , Li-Juan Guo , Zhen-Xing Fang , Li-Yan Xie , Qi-Ying Lin , Zu-Jian Wu , Lian-Hui Xie
Published: April 2009

The expression of the YUCAA1 gene and the amount of endogenous indole acetic acid (IAA) in rice (Oryza sativa subsp. japonica) plants and rice suspension cells infected by Rice stripe virus (RSV) were investigated by real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and high-performance liquid chromatography, respectively. The results showed that the expression of the YUCAA1 gene and the amount of endogenous IAA increased at various times (16, 32, 48 and 64 h) after infection of rice suspension cells by RSV. In rice plants infected with RSV, the expression of the YUCAA1 gene and the amount of endogenous IAA increased, in comparison with healthy rice plants, at 4–8 days after infection, and decreased at 12 and 16 days. These results indicated that RSV infection could regulate auxin biosynthesis in rice. Additionally, the expression of the RSV gene CP increased 2.9 times in rice plants after they were treated with a KPSC buffer to deplete the endogenous auxins, and decreased 45% after treatment with 30 μmol/l IAA. All of these results suggest that auxin may play a role in RSV replication in rice plants.
Research progress in techniques for detecting genetically modified organisms
Authors: Wen-Tao Xu , Wei-Bin Bai , Yun-Bo Luo , Yan-Fang Yuan , Kun-Lun Huang
Published: April 2009

The techniques used to detect genetically modified organisms (GMO), including qualitative polymerase chain reaction (PCR), quantitative PCR, enzyme-linked immunosorbent assay (ELISA) and many others, are systematically described and discussed. The application progress of GMO in species-specific detection, endogenous genes, standard substances and restraining factors influencing detection are reviewed. The ongoing problems and development prospects of detection techniques of GMO are also pointed out.
Establishment and evaluation of real-time PCR for West Nile virus detection
Authors: Li-Jun Shi , Mao-Min Lu , Gang Li , Cheng-Yao Li , Jin-Gang Zhang
Published: April 2009

A rapid real-time polymerase chain reaction (RT-PCR) for detecting West Nile virus (WNV) was established. Primers were designed according to the sequence of the capsid protein gene of WNV by Primer Premier 5.0. In this way, an inexpensive assay using the intercalating dye SYBR Green I was developed and validated. The amplifying curve showed that this method could successfully amplify 102 copies/μl of the WNV gene, while reference to Japanese encephalitis virus (JEV) and blank control were all negative. Tenfold successive dilutions of positive WNV DNA were used to measure the sensitivity of RT-PCR. The assay system showed high reproducibility with coefficient of variation (CV) <2%. Thus the newly established RT-PCR assay was shown to be a rapid, sensitive and specific test for detecting WNV.
Real-time PCR assay for sensitive organ detection and epidemic investigation of Turbot reddish body iridovirus
Authors: Cheng-Long Wu , Cheng-Yin Shi , Jie Huang , Xiao-Yu Kong
Published: April 2009

A rapid and sensitive real-time polymerase chain reaction (PCR) assay coupled with SYBR Green I chemistry was developed for the quantitative detection of Turbot reddish body iridovirus (TRBIV) isolated from farmed turbot (Scophthalmus maximus). A 152 bp DNA fragment from the TRBIV major capsid protein (MCP) gene was involved in the real-time PCR (RT-PCR) assay using the Roter Gene 3000 sequence detection system. The PCR mixture contained a fluorescent dye, SYBR Green I, which exhibited fluorescence enhancement when bound to double-stranded (ds) DNA. The enhancement of fluorescence was proportional to the initial concentration of the template DNA. The positive control plasmid, pUCm-T/TRBIV MCP, containing the target sequence, was quantified to make a standard curve for sample detection after serial tenfold dilution. Linear coefficient correlations between the cycle threshold (CT) value and logarithmic positive plasmid concentration were close to one (R2=0.9952) and the detection limit of the assay was 102 copies of positive plasmids. The quantitative detection of virus in different tissues from TRBIV-infected fish showed that the spleen and kidney contained the largest number of viral particles (5.23×106 and 2.18×106 viral genome copies/mg tissue, respectively), while no viral DNA was detected in the muscular tissue. The molecular epidemic investigation of TRBIV showed that many cultured turbots were infected and TRBIV has become epidemic in turbot farms located along the Shandong peninsula. The virus number varied from 1.27×102 to 2.33×106 viral genome copies/mg tissue in spleens of infected turbot. These results suggest that the RT-PCR assay reported here can be used as a rapid, sensitive and quantitative method for TRBIV.
Growth and identification of human amniotic fluid stem cells and analysis of their influencing factors
Authors: Han Wang , Zhong-Ying Dou , Hua-Yan Wang
Published: April 2009

Amniotic fluid stem (AFS) cells isolated from human amniotic fluid were cultured and the factors affecting the primary culture of these cells were investigated. The isolated AFS cells express both embryonic stem cell markers, such as Oct-4, and adult stem cell markers, such as CD29, and possess a high proliferation capability. Moreover, isolated AFS cells were able to differentiate into Nestin-positive and α-actin-positive cells. There were several factors, including the date of gestation, the level of blood contamination and the volume of amniotic fluid, which could significantly affect the attachment time and numbers of AFS cells in primary culture. The results showed that the cell attachment time (4.7±0.6 days) during the second trimester of gestation was significantly different from that during the third trimester of gestation (6±0.5 days) (P<0.05), suggesting that cells collected from the fluid during the third trimester of gestation needed a longer attachment time. Blood contamination could significantly affect the cell attachment time. The attachment time of the brown-coloured fluid group (10.8±0.3 days) was significantly different from the blood-cell-free fluid group (6±0.5 days) and the blood-cell group (6.3±0.6 days) (P<0.05). The volume of amniotic fluid influenced, to some extent, both cell attachment numbers and time. With the increase in amniotic fluid volume, cell attachment numbers significantly increased (P<0.05), and cell attachment time extended, but not significantly (P>0.05). The present studies systematically examined the factors that influence the primary culture of human AFS cells and provided useful data on AFS cell research. Additionally, the isolated AFS cells maintain the capacity for differentiation into other cell types and are able to become seed cells for clinical applications.
Upper ocean heat content in the Nordic seas
Authors: Di Iorio Daniela , Sloan Caitlin
Published: April 2009

Seven years of temperature profiles are obtained from the Argo float project and are used to study the vertically integrated heat content for the Nordic seas which is broken up into the Norwegian Basin, Greenland Sea, Lofoten region, and Iceland Plateau. The World Ocean Atlas 2005 (WOA05) is used as the climatological baseline for temperature and hence heat content. Temporally and spatially averaged temperature profiles within the Norwegian and Iceland basins show good agreement between the Argo and WOA05 data sets. For the Greenland and Lofoten basins, the WOA05 data show cooler surface temperatures (by 1–2°C) but still lie within 1 standard deviation of each other over the 7‐year period. The Argo float data show circulation within each of the basins that is counterclockwise, and some of the floats eventually disperse toward the outer edges of the basins. Vertically integrated heat content from 0 to 1200 m shows similar characteristics as the WOA05 results including the timing and strength of the seasonal variability. The anomalous heat content for the Greenland and Norwegian sea basins is calculated in depth bins of 400 m. The Greenland Sea shows a warming trend over the 7 years of study, which corresponds to a temperature increase of (4.1 ± 0.3) × 10−2 °C/yr. The Norwegian Sea basin shows interannual variability in heat content for the surface layer (0–400 m) that may be related to the North Atlantic Oscillation (NAO). During an NAO+ phase, the Norwegian Basin shows a warm phase, and during an NAO− phase, the Norwegian Basin is in a cold phase; the correlation is small (r = 0.32) but different from zero correlation only at the 90% level, implying that the variability in the AHC may be due to (1) local atmospheric forcing and hence changes in heat loss, (2) atmospheric pressure differences that are not resolved by the NAO index, and (3) exchange of heat with the basin boundaries.
Sinking organic matter spreads the nitrogen isotope signal of pelagic denitrification in the North Pacific
Authors: Sigman Daniel M. , DiFiore Peter J. , Hain Mathis P. , Deutsch Curtis , Karl David M.
Published: April 2009

Culture studies of denitrifying bacteria predict that denitrification will generate equivalent gradients in the δ15N and δ18O of deep ocean nitrate. A depth profile of nitrate isotopes from the Hawaii Ocean Time‐series Station ALOHA shows less of an increase in δ18O than in δ15N as one ascends from abyssal waters into the denitrification‐impacted mid‐depth waters. A box model of the ocean nitrate N and O isotopes indicates that this is the effect of the low latitude nitrate assimilation/regeneration cycle: organic N sinking out of the surface spreads the high‐δ15N signal of pelagic denitrification into waters well below and beyond the suboxic zone, whereas the nitrate δ18O signal of denitrification can only be transmitted by circulation in the interior.
Fault friction parameters inferred from the early stages of afterslip following the 2003 Tokachi‐oki earthquake
Authors: Fukuda Jun'ichi , Johnson Kaj M. , Larson Kristine M. , Miyazaki Shin'ichi
Published: April 2009

We use subdaily GPS time series of positions in the first 5 hours following the 2003 Tokachi‐oki earthquake (Mw = 8.0) located offshore of Hokkaido, Japan, to estimate frictional parameters for the afterslip zone on the subduction interface. The data show little motion immediately after the earthquake with sudden acceleration at about 1.2 hours after the main shock. This coincides with the largest aftershock (M = 7.4), followed by gradual deceleration. We assume that early afterslip is the response of a fault patch to instantaneous stress perturbations caused by the main shock and the largest aftershock. Early afterslip is modeled with a spring‐slider system obeying a rate‐ and state‐dependent friction law. We develop and apply an inversion method to estimate friction parameters, Dc, aσ, and (a − b)σ, where σ is effective normal stress. The estimated 95% confidence intervals of Dc, aσ, and (a − b)σ are 2.6 × 10−4 to 1.8 × 10−3 m, 0.29 to 0.43 MPa, and 0.214 to 0.220 MPa, respectively. Estimated Dc is 10 to 103 times larger than typical laboratory values. Estimated aσ and (a − b)σ values suggest that a and a − b are smaller than typical laboratory values and/or the pore pressure on the plate boundary is significantly elevated above the hydrostatic value. Our analyses show that the model can reproduce the observed GPS data and that the timing of the rapid acceleration of postseismic deformation is controlled by the frictional properties of the fault and stress change from the main shock, not by the timing of the largest aftershock.
Development of synthetic salinity from remote sensing for the Columbia River plume
Authors: Palacios Sherry L. , Peterson Tawnya D. , Kudela Raphael M.
Published: April 2009

The Columbia River plume (CRP) is an ecologically important source of nutrients, pollutants, and fresh water to the Oregon/Washington shelf. It is traditionally under‐sampled, with observations constrained to ships or moorings. High‐spatial‐ and temporal‐resolution observations afforded by satellites would increase sampling if the plume could be quantitatively detected in the imagery. Two empirical algorithms are presented using data from the Moderate Resolution Imaging Spectroradiometer (MODIS) to estimate sea surface salinity in the region of CRP. Salinity cannot be detected directly, so a proxy for fresh water is employed. Light absorption by chromophoric dissolved organic matter (aCDOM) is inversely proportional to salinity and linear because of conservative mixing of CDOM‐rich terrestrial runoff with surrounding ocean water. To estimate synthetic salinity, simple linear (salinity versus aCDOM) and multiple linear (salinity and temperature versus aCDOM) algorithms were developed from in situ measurements of aCDOM collected on the Coastal Ocean Processes–River Influences on Shelf Ecosystems cruises. These algorithms were applied to MODIS 250 m resolution data layers of sea surface temperature and absorption by colored dissolved and detrital matter (aCDM) estimated at 350 nm and 412 nm from the Garver‐Siegel‐Maritorena model version 1 algorithm. Validation of MODIS‐derived synthetic salinity with coincident in situ measurements revealed significant correlation during both downwelling (simple, β1 = 0.95 and r2 = 0.89; multiple, β1 = 0.92 and r2 = 0.89) and upwelling periods (simple, β1 = 1.26 and r2 = 0.85; multiple, β1 = 1.10 and r2 = 0.87) using the 412 nm data layer. Synthetic salinity estimated using the 350 nm data layer consistently overestimated salinity. These algorithms, when applied to aCDM at 412 nm, enable synoptic observations of CRP not permitted by ships or moorings alone.
Turbulent air‐sea fluxes in the Gulf of Guinea during the AMMA experiment
Authors: Bourras D. , Weill A. , Caniaux G. , Eymard L. , Bourlès B. , Letourneur S. , Legain D. , Key E. , Baudin F. , Piguet B. , Traullé O. , Bouhours G. , Sinardet B. , Barrié J. , Vinson J. P. , Boutet F. , Berthod C. , Clémençon Aurélien
Published: April 2009

Turbulent fluxes at the air‐sea interface were estimated in the framework of the African Monsoon Multidisciplinary Analysis (AMMA) international program. A specific flux measurement mast was designed so as to minimize aerodynamic flow distortion and vibrations. The mast was installed on the research vessel Atalante that cruised in the Gulf of Guinea during the onset of the African monsoon, in June–July 2006. Turbulent fluxes were calculated with an eddy covariance method and with a spectral method. Calculation of eddy correlation fluxes required a correction of flow distortion at turbulent scales, which was performed with a new statistical technique. Application of the spectral flux calculation method revealed that an imbalance term was required, in agreement with results from earlier experiments, and indicated that the value of the Kolmogorov constant (0.55) should not be modified. Bulk exchange coefficients calculated are in good agreement with earlier parameterizations in medium wind conditions.
Temporal and spatial variations of carbon monoxide over the western part of the Pacific Ocean
Authors: Yashiro Hisashi , Sugawara Satoshi , Sudo Kengo , Aoki Shuji , Nakazawa Takakiyo
Published: April 2009

Systematic observations of atmospheric carbon monoxide (CO) have been carried out in the western part of the Pacific Ocean since February 1990. The average CO concentration showed a latitudinal gradient, with higher values in the northern hemisphere than in the southern hemisphere. A clear seasonal CO cycle was found nearly at all sampling locations, showing maximum and minimum concentrations in spring and summer, respectively. In the 30°–35°N latitude zone, the average CO concentration was higher and the seasonal amplitude was larger compared with other latitudes. The CO concentration also showed a large interannual variability mainly in association with forest fires. In particular, the forest fires in Siberia in 1998 and Indonesia in 1997–1998 contributed to a remarkable increase in the regional CO concentration, followed by a recovery that took several months to a year. A three‐dimensional atmospheric global chemical transport model (CHASER) was used to simulate the observed characteristics of the latitudinal distribution, seasonal cycle, and interannual variability relatively well. Tagged CO experiments with the model revealed that the contribution of CO emissions from various regions in the northern hemisphere to the CO concentrations at our sampling locations varied seasonally in association with Asian outflows and long‐range transport from Europe and North America. In the southern hemisphere, biomass burnings significantly affected the regional seasonal CO cycle, in addition to the effect of CO oxidation with OH. It was also found that CHASER underestimates the average CO concentration in the northern hemisphere and its interannual variability.
Flux‐gradient relationship of water vapor in the surface layer obtained from CASES‐99 experiment
Authors: Park Sang‐Jong , Park Soon‐Ung , Ho Chang‐Hoi , Mahrt Larry
Published: April 2009

The flux‐gradient relationship of water vapor Φq was obtained from the Cooperative Atmosphere‐Surface Exchange Study‐1999 (CASES‐99) field experiment, which was conducted on a flat and grassy field in the southeastern part of Kansas, USA, during October 1999. The CASES‐99 data include turbulence measurements of wind, temperature, and vapor density along with their time‐averaged values at various levels above the ground. Quality control of the data on the turbulent wind velocity, sonic temperature, and vapor density was performed prior to flux calculation. The turbulent sensible heat and latent heat fluxes were calculated using a 30‐min window, and they were subsequently corrected and checked for the fulfillment of the steady state and for turbulence intensity. Weak fluxes and through‐tower wind data were also excluded from the analysis. Vertical gradients of the mean values were obtained by differentiating functions fitted to the measured mean profiles. It was found that Φq is comparable to ΦT for weakly stable stratification and less than ΦT for strongly stable stratification. On the contrary, Φq was found to be larger than ΦT by approximately 20% for the neutral and unstable stratifications. The best fitting functions for water vapor are found to be Φq = 1.21(1 − 13.1z/L)−1/2 and Φq = 1.21(1 + 60.4z/L)1/3 for the unstable and stable stratifications, respectively.
Phase transition pathways of the hydrates of magnesium sulfate in the temperature range 50°C to 5°C: Implication for sulfates on Mars
Authors: Wang Alian , Freeman John J. , Jolliff Bradley L.
Published: April 2009

Dehydration/rehydration experiments were conducted on pure Mg‐sulfates and mixtures of epsomite with Ca‐sulfates, Fe‐sulfates, Fe‐oxide, and Fe‐hydroxide. The goal was to investigate the stabilities and phase transition pathways of Mg‐sulfate hydrates, under temperature and relative humidity conditions relevant to Mars, as a function of starting structure and coexisting species. Two pathways were found to form Mg‐sulfate monohydrates between 5°C and 50°C through dehydration of epsomite or hexahydrite. Two polymorphs of Mg‐sulfate monohydrates were characterized in this study. It is important to distinguish among these phases on Mars because they have different formation conditions that have the potential to provide additional information on surface and subsurface geologic processes. We found that Mg‐sulfates with moderate hydration states (especially starkeyite and amorphous Mg‐sulfates) can be very stable under current Martian surface conditions. On the basis of NIR spectral features, these phases are good candidates for polyhydrated sulfates identified on Mars by OMEGA and CRISM; thus, they may contribute to the high hydrogen concentrations found by the neutron spectrometer on the orbiting Odyssey spacecraft. Our experiments indicate that the maximum number of water molecules per SO4 held by the amorphous Mg‐sulfate structure is three. In addition, the amorphization rate of Mg‐sulfates is strongly dependent on temperature. The low temperature (approximately −80°C) in the early morning hours during the Martian diurnal cycle would slow the dehydration rate, which would favor the stability of starkeyite over amorphous Mg‐sulfates and would lead to a low abundance of the latter.
On the impact of surface heterogeneity on a realistic convective boundary layer
Authors: Huang Hsin‐Yuan , Margulis Steven A.
Published: April 2009

Turbulent interactions of momentum and scalars within the convective boundary layer (CBL) over a heterogeneous surface can have a strong influence on both local flow properties and regional weather and climate. Using realistic heterogeneous surface flux data as well as mean vertical soundings obtained from the Soil‐Moisture Atmosphere Coupling Experiment 2002 (SMACEX) as boundary and initial conditions in a large‐eddy simulation (LES) model, this research attempts to further our understanding of the impact of surface heterogeneity on a growing CBL in a realistic environment. On the basis of a newly proposed method, a set of realizations precisely replicating the basic statistics (mean and variance) and cross correlation of surface flux boundary conditions (relative to the actual fields at the SMACEX) are used for a series of LES experiments. The impacts of heterogeneity on two aspects of the CBL are discussed in this study: (1) the characteristic vertical profiles of CBL properties and (2) the vertical mixing scales of the CBL. Within the set of conditions examined in this study, the potential temperature is more sensitive to the surface heterogeneity scale than to specific humidity, and the variation of velocity (both horizontal and vertical) clearly reflects the impact of surface organization. The vertical profile of the coefficient of variation calculated from the potential temperature field is introduced to identify the thermal blending height, and a good agreement is obtained compared to the predicted values using formulations from the literature. A commonly used formulation for the momentum blending height was found to inadequately represent the vertical mixing. Another stability‐dependent formulation combining both shear and convective characteristics is shown to provide more reasonable results.
Flow regimes, bed morphology, and flow resistance in self‐formed step‐pool channels
Authors: Comiti F. , Cadol D. , Wohl E.
Published: April 2009

We used a mobile bed flume with scaled grain size distribution, channel geometry, and flow to examine morphology and hydraulics of stepped channels. We hypothesized that (1) step geometry and flow resistance differs significantly as a function of the range of grain sizes present, (2) a transition from nappe to skimming flow occurs in stepped channels with mobile beds for conditions similar to stepped spillways, and (3) the partitioning of flow resistance changes significantly when flow passes from nappe to skimming conditions. Results support each of these hypotheses and help to illuminate the complexity of V‐Q relationships in stepped channels, in which a dramatic decrease in flow resistance and increase in velocity accompany the transition from nappe to skimming flow near step‐forming events. Therefore, a single flow resistance equation applicable to both ordinary and large floods may not be ideal in stepped channels. Nonetheless, models based on dimensionless velocity and unit discharge appear more robust compared to those based on the Darcy‐Weisbach friction factor.
Preventing the repetition: Or, what Los Angeles' experience in water management can teach Atlanta about urban water disputes
Authors: Feldman David L.
Published: April 2009

Southern California's water history is an epic story with larger‐than‐life characters and ambitions and abundant hubris. Students of water policy might reasonably ask: Does this story, while unique to greater Los Angeles, hold lessons for other metropolises experiencing water conflict caused by explosive growth? We examine this question by considering similarities between the challenges facing Atlanta, Georgia, one of the nation's fastest growing cities in the 21st century, with those of Los Angeles. We focus on junctures where important decisions regarding water were made and how these decisions continue to challenge both cities' futures. Atlanta's financial, cultural, and environmental imprint on its surrounding region share remarkable similarities with Los Angeles' influence trajectory: it is the largest city in the southeast, a principal transportation and business hub, and it is embroiled in water conflict with nearby communities and adjoining states.
Impact of historical land cover change on daily indices of climate extremes including droughts in eastern Australia
Authors: Deo R. C. , Syktus J. I. , McAlpine C. A. , Lawrence P. J. , McGowan H. A. , Phinn S. R.
Published: April 2009

There is growing scientific evidence that anthropogenic land cover change (LCC) can produce a significant impact on regional climate. However, few studies have quantified this impact on climate extremes and droughts. In this study, we analysed daily data from a pair of ensemble simulations using the CSIRO AGCM for the period 1951–2003 to quantify the impact of LCC on selected daily indices of climate extremes in eastern Australia. The results showed: an increase in the number of dry and hot days, a decrease in daily rainfall intensity and wet day rainfall, and an increase in the decile‐based drought duration index for modified land cover conditions. These changes were statistically significant for all years, and especially pronounced during strong El Niño events. Therefore it appears that LCC has exacerbated climate extremes in eastern Australia, thus resulting in longer‐lasting and more severe droughts.
Elasticity of phase‐X at high pressure
Authors: Mookherjee Mainak , Steinle‐Neumann Gerd
Published: April 2009

Using a plane‐wave pseudopotential method, we calculate the equation of state and elasticity of phase‐X [(K,Na)2Mg2Si2O7] up to 30 GPa, which encompasses its experimentally observed stability field. We find that the pressure‐volume results for anhydrous phase‐X are well represented by a third order Birch‐Murnaghan formulation, with K0 = 132 GPa, K′0 = 4.4 and V0 = 284.6 Å3 for the potassium (K) end member and K0 = 128 GPa, K′0 = 4.0 and V0 = 265.9 Å3 for the sodium (Na) end member. The full elastic constant tensor reveals significantly larger stiffness along the [001] direction than in the (100) plane. We attribute such stiffness to the 1800 angle of Si‐O‐Si units and their orientation parallel to the [001] direction. Assuming ideal behavior between Na and K phase‐X, the shear modulus softens with sodium content as G = [84 − 0.14 × Na(wt%)] GPa.
GreenPhylDB: A Gene Family Database for plant functional Genomics
Authors: Conte Matthieu , Laporte Marie-Angélique , Périn Christophe , Rouard Mathieu
Published: April 2009

With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as O. sativa and A. thaliana, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by phylogenetic analysis to infer orthologs and paralogs that will be particularly helpful to study genome evolution. Previously, each cluster has to be curated (i.e. properly named and classified) using different sources of information. A web interface for plant gene families’ curation was developed for that purpose. This interface, accessible on GreenPhylDB ("http://greenphyl.cirad.fr":http://greenphyl.cirad.fr), centralizes external references (e.g. InterPro, KEGG, Swiss-Prot, PIRSF, Pubmed) related to all gene members of the clusters and shows statistics and automatic analysis. We believe that this synthetic view of data available for a gene cluster, combined with basic guidelines, is an efficient way to provide reliable method for gene family annotations.
Direct submission system and literature annotation of rice genes in Oryzabase
Authors: Yamazaki Yukiko , Tsuchiya Rie , Asanuma Takao , Shidahara Yo , Sakaniwa Shingo
Published: April 2009

Oryzabase ("http://www.shigen.nig.ac.jp/rice/oryzabase/":http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date, literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown genes from journals. The machine extraction followed by manual annotation achieved promising results and increased efficiency in manual annotation. Furthermore a direct submission system where rice researchers can deposit new genes according to the standardized nomenclature ^2^ became operational in 2008. Recent advances will be introduced.[1] Kurata, N. and Y. Yamazaki., Oryzabase, An Integrated Biological and Genome Information Database for Rice. Plant Physiology (2006) 140, 12-17 [2] Susan R. McCouch, Gene Nomenclature System for Rice, Rice (2008) 1:72-84
Immunogenetic sequence annotation based on IMGT-ONTOLOGY
Authors: Jabado-Michaloud Joumana , Folch Géraldine , Bellahcene Fatena , Ehrenmann François , Duroux Patrice , Giudicelli Véronique , Lefranc Marie-Paule
Published: April 2009

IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).
Protein Ontology and Community Curation
Authors: Arighi Cecilia
Published: April 2009

The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways, complexes, or in disease modeling. This is useful for proteomics studies where isoforms and modified forms must be differentiated and for biological pathway/network representation where the cascade of events often depends on a specific protein modification. The PRO framework is designed to allow the community to curate any protein entities of interest and will provide a stable unique identifier to any protein type. PRO is manually curated starting with content derived from various data sources coupling with scientific literature. Only annotation with experimental evidence is included, and is in the form of relationship to other ontologies (such as Gene Ontology, Sequence Ontology, and PSI-MOD). We have developed a web-based curation editor for PRO community annotation. In the tutorial, we will first give a brief introduction to the ontology and its relevance to the research communities - OBO ontologies, MOD, pathway and other databases, and any resources that need references/links to protein types. We will show the components of the PRO entry report, and how to search the ontology. Then, we will walk through an example where we will teach the basic curation steps: accessing the web editor, entering the protein to be defined with source attribution, and adding functional annotation. We will provide the necessary tools and documentation so that the user will be able to start curating the protein types of interest. PRO URL: "http://pir.georgetown.edu/pro/":http://pir.georgetown.edu/pro/
Language Modeling as an Efficacious Early Language Intervention Approach With Young Children Demonstrating Complex Communication Needs
Authors: Solomon-Rice Patti , Soto Gloria
Published: April 2009

This article highlights evidence supporting the efficacy of adult language modeling and child imitation, including use of aided AAC modeling, during language intervention with young children demonstrating complex communication needs. First, four evidence-based language intervention approaches that incorporate adult language modeling and child imitation with young children demonstrating language delays are described. Second, two additional evidence-based language intervention approaches that incorporate aided AAC modeling during communication partner training, and direct clinical intervention with young children using aided AAC are further discussed. The article concludes with suggestions for strategies to use during language intervention with young children who use aided AAC.
Internet Resources for Augmentative and Alternative Communication in Early Intervention and Early Childhood Services
Authors: Robinson Nancy B.
Published: April 2009

The development and implementation of augmentative and alternative communication (AAC) tools for children in the earliest stages of communication and language development may include a range of communication modalities that include gesture, vocalization, actual objects, photos, picture icons, Speech Generating Devices (SGDs), and higher-tech AAC devices. Internet resources for AAC in early intervention settings include assessment tools, communication aids, early literacy supports, educational tools for professionals and families and much more. Some of the key resources that have been reviewed by a team of professionals through the Supporting Early Education Development Systems (SEEDS) Project in the Sacramento County Office of Education, Sacramento, California, are described.
Response to Intervention: Applications for AAC in Preschool Settings
Authors: Grether Sandra M.
Published: April 2009

Educators were previously encouraged to use IQ-achievement discrepancy to identify children with learning disabilities. The Individuals with Disabilities Education Improvement Act (IDEA, 2004) promotes an alternative method, “Response to Intervention” or RTI, to identify and provide early intervention to all children at risk for school failure. Recognition and Response (R & R) is the RTI model for preschool-aged children. Children with complex communication needs, who use augmentative and alternative communication (AAC), are at risk for failing in the preschool classroom and can benefit from the educational supports provided through R & R. This article discusses the levels of support provided by RTI and strategies and supports for achieving academic success for preschool children who use AAC.