Island Locations Research Articles

English

A Genomic Islands (GI) is a chunk of DNA sequence in a genome whose origin can be traced back to other organisms or viruses. The detection of GIs plays an indispensable role in biomedical research, due to the fact that GIs are highly related to special functionalities such as disease-causing GIs - pathogenicity islands. It is also very important to visualize genomic islands, as well as the supporting features corresponding to the genomic islands in the genome. We have developed a program, Genomic Island Visualization (GIV), which displays the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs. GIV was implemented in C++, and was compiled and executed on Linux/Unix operating systems.AvailabilityGIV is freely available for non-commercial use at http://www5.esu.edu/cpsc/bioinfo/software/GIV

Simultaneous Formation of AlB2-Type and ThSi2-Type Nanoislands of Er Silicide by Using a Prepatterned Si(001) Substrate

We report the simultaneous growth of hexagonal AlB2-phase and tetragonal ThSi2-phase nanoislands of erbium silicide on the same silicon substrate. As a new technique, the patterned Si(001) surface with pits in a reverse-pyramid shape and {111} sidewalls is taken as the substrate template. The distribution of nanoislands reveals that the upward diffusion over surface steps plays an influential role on the location of islands. Si {111} facets on the pit sidewalls actually provide growth symmetry for the hexagonal islands. This work paves the way for exploring the intrinsic electrical transport properties of metal-semiconductor nanocontacts.

Modeling the potential spread of the recently identified non-native panther grouper (Chromileptes altivelis) in the Atlantic using a cellular automaton approach.

The Indo-pacific panther grouper (Chromileptes altiveli) is a predatory fish species and popular imported aquarium fish in the United States which has been recently documented residing in western Atlantic waters. To date, the most successful marine invasive species in the Atlantic is the lionfish (Pterois volitans/miles), which, as for the panther grouper, is assumed to have been introduced to the wild through aquarium releases. However, unlike lionfish, the panther grouper is not yet thought to have an established breeding population in the Atlantic. Using a proven modeling technique developed to track the lionfish invasion, presented is the first known estimation of the potential spread of panther grouper in the Atlantic. The employed cellular automaton-based computer model examines the life history of the subject species including fecundity, mortality, and reproductive potential and combines this with habitat preferences and physical oceanic parameters to forecast the distribution and periodicity of spread of this potential new invasive species. Simulations were examined for origination points within one degree of capture locations of panther grouper from the United States Geological Survey Nonindigenous Aquatic Species Database to eliminate introduction location bias, and two detailed case studies were scrutinized. The model indicates three primary locations where settlement is likely given the inputs and limits of the model; Jupiter Florida/Vero Beach, the Cape Hatteras Tropical Limit/Myrtle Beach South Carolina, and Florida Keys/Ten Thousand Islands locations. Of these locations, Jupiter Florida/Vero Beach has the highest settlement rate in the model and is indicated as the area in which the panther grouper is most likely to become established. This insight is valuable if attempts are to be made to halt this potential marine invasive species.

Resistive wall mode and neoclassical tearing mode coupling in rotating tokamak plasmas

A model system of equations has been derived to describe a toroidally rotating tokamak plasma, unstable to resistive wall modes (RWMs) and metastable to neoclassical tearing modes (NTMs), using a linear RWM model and a nonlinear NTM model. If no wall is present, the NTM growth shows the typical threshold/saturation island widths, whereas a linearly unstable kink mode grows exponentially in this model plasma system. When a resistive wall is present, the growth of the linearly unstable RWM is accelerated by an unstable island: a form of coupled RWM–NTM mode. Crucially, this coupled system has no threshold island width, giving the impression of a triggerless NTM, observed in high beta tokamak discharges. Increasing plasma rotation at the island location can mitigate its growth, decoupling the modes to yield a conventional RWM with no threshold width.

Quantum dot growth on a stripe-pattern

We study the development of the Asaro-Tiller-Grinfel'd instability on a thin strained film on top of a stripe-patterned substrate and the subsequent growth of self-organized quantum dots. We use a continuum model describing the evolution equation enforced by surface diffusion. We compute the elastic energy up to the first non-linear order and investigate the long time dynamics which describes the dot growth. We find different island locations depending on the substrate wavelength and thickness. As found in experiments, the instability long-time dynamics leads to islands located either on top or in the bottom of the pattern.

Space weather effects on Earth's environment associated to the 24–25 October 2011 geomagnetic storm

Space weather studies have increased due to human society dependence on spaceborne and terrestrial infrastructure vulnerable to its effects. In this paper, we present an interdisciplinary study of the effects of solar activity on the Earth's environment; specifically, we focus on the effects on the ionosphere and the geomagnetic field. A timeline of effects occurring on the Earth produced by one of the first relevant events of the present solar cycle (24–25 October 2011) is given. We have analyzed the solar wind shockwave from satellite data, the storm‐time development, the ionospheric effects at global and local scales using the National Center for Atmospheric Research Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model fed with geomagnetic field‐aligned current data from the Active Magnetosphere and Planetary Electrodynamics Response Experiment, and ground ionosonde data from both hemispheres, at Ebre Observatory and Port Stanley locations. We have compared observed geomagnetic variations at high latitudes with those modeled by the National Center for Atmospheric Research Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model. We have analyzed rapid geomagnetic variations (e.g., solar flare effect, storm commencement, Pi2) also on both hemispheres, at Ebre Observatory and Livingston Island locations. Finally, we have estimated geoelectric field and geomagnetically induced currents in the northeast of Spain (Catalonia) produced by this geomagnetic disturbance.

Reverse Bipaddle Posterior Interosseous Artery Perforator Flap

The reverse posterior interosseous artery perforator flap is useful for covering defects over the distal forearm, wrist, and hand, but some of its major limitations include short vascular pedicle, inadequate distal reach, difficult pedicle dissection, and risk of venous congestion. Some of these drawbacks have been overcome with refinements over the years, but the problems of donor-site morbidity and inability to reconstruct multiple subunits of the hand in a single stage remain. The authors developed a variant of the original distally based flap to extend its applications and minimize donor-site morbidity. Eleven cases of reverse bipaddle posterior interosseous artery perforator flap reconstruction were reviewed. Defect locations included the first web space, proximal thumb, dorsum of the hand, palm, wrist, and the radial or ulnar half of the hand. Eleven patients were successfully treated with the bipaddle posterior interosseous artery perforator flap with no major complications. In seven cases, the type A chain-like variant was used to cover defects involving two different units of the hand. In four patients, the type B "kiss" pattern was required to resurface a large defect of a single unit of the hand. In all type B cases, the donor site was closed directly. All patients were satisfied with their outcomes. The reverse bipaddle posterior interosseous artery perforator flap is an excellent method of covering large defects of the hand involving multiple subunits. The authors confirm its vascular reliability and highlight several recommendations for skin island location, pedicle dissection, and flap raising and insetting.

A Novel Method for CpG Islands Location Identification Based on Conditional Random Fields

A Novel Method for CpG Islands Location Identification Based on Conditional Random Fields

Upper Turonian–Santonian slope limestones of the Islands of Premuda, Ist and Silba (Adriatic Coast, Croatia)

Upper Turonian-Santonian limestones at three island locations (Ist, Silba and Premuda) in the southwestern part of the Adriatic carbonate platform, record slope deposition based on their sedimentological and palaeontological characteristics.These Upper Cretaceous successions consist of three vertically superimposed lithotypes: (1) pelagic mudstonespackstones, (2) laminated pelagic wackestones-packstones, and (3) bioclastic floatstones-rudstones to packstonesgrainstones with fossils of shallow marine organisms.According to the proximity of the shallow water carbonate platform interior the depositional setting of the slope deposits could be identified as relatively more proximal or distal. The proximal part is characterized by non laminated pelagic limestones with resedimented bioclastic limestones, while the more distal parts have both laminated and nonlaminated pelagic limestones with rare resedimented bioclastic limestones. The resedimented bioclastic limestones represent slope apron deposits. Locally, at Premuda Island, the slope apron includes blocks of laminated pelagic limestones. The depositional environments of the Ist and Premuda profiles could be interpreted as of more distal origin, while those of the Silba profile represents a more proximal part of the slope.

Bidding the CpG island goodbye

Experiments on seven vertebrates suggest that identifying the locations of islands of non-methylated DNA provides more insights into evolutionarily-conserved epigenetic regulatory elements than studies of CpG islands.

Historical reconstruction of mangrove expansion in the Gulf of Mexico: Linking climate change with carbon sequestration in coastal wetlands

There has been considerable interest in a recently recognized and important sink in the global carbon pool, commonly referred to as “blue carbon”. The major goal of this study was to determine the historical reconstruction of mangrove expansion (Avicennia germinans) into salt marshes (Spartina alterniflora) and its effects on carbon sequestration and soil chemistry in wetland soils of the northwestern Gulf of Mexico. We used bulk stable isotopic, chemical biomarker analyses, and aerial imagery analysis to identify changes in OC wetland sources, and radiotracers (137Cs and 210Pb) for chronology. Soil cores were collected at two sites at Port Aransas, Texas (USA), Harbor Island and Mud Island.Stable isotopic values of δ13C and δ15N of all soil samples ranged from −26.8 to −15.6‰ and 1.8–10.4‰ and showed a significant trend of increasing depletion for each isotope from bottom to surface soils. The most depleted δ13C values were in surface soils at the Mud Island (Mangrove 2) location. Carbon sequestration rates were greater in mangroves and for the Mud Island Mangrove 1 and the Marsh 1 sites ranged from 253 to 270 and 101–125 g C m−2 yr−1, respectively. Lignin storage rates were also greater for mangrove sites and for the Mud Island Mangrove 1 and the Marsh 1 ranged from 19.5 to 20.1 and 16.5 to 12.8 g lignin m−2 yr−1, respectively. Τhe Λ8 and Λ6 values for all cores ranged from 0.5 to 21.5 and 0.4 to 16.5, respectively, and showed a significant increase from bottom to surface sediments. If regional changes in the Gulf of Mexico are to persist and much of the marsh vegetation was to be replaced by mangroves, there could be significant increases on the overall storage and sequestration of carbon in the coastal zone.

Redefinition of the Terminus of the Middle America Trench

The terminus of the Middle America Trench has been traditionally represented as an arc, concave towards the continent. Tres Marias Islands are located at the terminus of the Middle America Trench in western Mexico, and their location is not only intriguing but also a key to the re-construction of the position of Baja California peninsula before separation from the North America plate. Previous re-constructions suggested various places around the location of Tres Marias Islands for the position of the tip of the peninsula, and several converge to a position that invades the area occupied by the islands, offering no explanation for the overlap. Before peninsular separation from North America, the Guadalupe trench followed a smooth curve; recreating the position of this paleo-trench yields a baseline for fixing the position of the peninsula, as well as the original position of the Tres Marias Islands fragment. A new tectonic view of the structure of the Middle America Trench terminus is proposed, replacing the traditional arc representation with a series of en echelon blocks, the northernmost terminates at the Tres Marias Escarpment. The long sides of the blocks correspond to previously identified geological faults in the Bahia de Banderas region, while their offshore continuation is supported by topographic observations. As a test of this model I show the corresponding re-construction of the position of Baja California prior to separation from the North America plate and the positional evolution of the peninsula and the Tres Marias fragment from Chron 4n.2 (7.90 Ma) to Chron 3n.4 (5.12 Ma).

지구온난화에 따른 제주도 내 참다래 개화일의 지리적 이동

제주도의 새로운 소득 과수인 참다래 '헤이워드'를 대상으로 IPCC의 미래 시나리오 기후조건에서 개화기 분포를 정밀하게 추정함으로써 도내 재배적지의 지리적 이동을 가시화 하였다. 개화기 예측을 위해 휴면시계모형과 발육속도모형을 각각 '헤이워드' 품종에 맞도록 조정하였으며, 시공간적으로 독립적인 자료(해남 2006-2009, 제주 2010-2011)에 의해 검증한 결과 개화일 추정오차는 RMSE = 2.5일(휴면시계모형)과 4.0일(발육속도모형)로 나타났다. 제주도의 현재평년(1981-2010) 기온 및 A1B 시나리오에 따른 10년 단위 미래 기온을 종관기상자료와 공간기후추정기술에 의해 상세 격자형 분포도로 제작하였다. 일별 기온분포도를 이용하여 휴면시계모형을 구동시켰으며 그 결과를 30m 해상도의 상세 개화일분포도로 가시화 하였다. 이 모의결과에 따르면 미래로 갈수록 현재평년에 비해 개화일이 앞당겨지는 한편, 저온요구도의 부족으로 개화불량인 지역이 늘어날 것으로 추정된다. 개화기에 근거한 재배적지의 면적은 가까운 미래에는 증가하지만 먼 미래로 갈수록 급격히 줄어들어 21세기 말에는 현재의 절반이 될 것이며, 같은 기간 재배적지는 해안지대로부터 해발 250m 정도 한라산 방향으로 이동할 것으로 예측된다. A kiwifruit cultivar 'Hayward' has been grown in Jeju Island where the current climate is suitable for growth and development of this crop. Prediction of the geographical shift in the phenology can help the kiwifruits growers to adapt to the local climate change in the future. Two phenology models (i.e., chill-day and DVS) were parameterized to estimate flowering date of kiwifruits 'Hayward' based on the data collected from field plots and chamber experiments in the southern coastal and island locations in South Korea. Spatio-temporally independent datasets were used to evaluate performance of the two models in predicting flowering date of 'Hayward'. Chill-day model showed better performance than DVS model (2.5 vs. 4.0 days in RMSE). Daily temperature data interpolated at a higher spatial resolution over Jeju Island were used to predict flowering dates of 'Hayward' in 2021-2100 under the A1B scenario. According to the model calculation under the future climate condition, the flowering of kiwifruits shall accelerate and the area with poor flowering might increase due to the warmer winter induced insufficient chilling. Optimal land area for growing 'Hayward' could increase for a while in the near future (2021-2030), whereas such areas could decrease to one half of the current areas by 2100. The geographic locations suitable for 'Hayward' cultivation would migrate from the current coastal area to the elevated mountain area by 250 m.

Projecting annual air temperature changes to 2025 and beyond: implications for vegetable production worldwide

SUMMARYData sets were accumulated of annual average maximum, minimum and mean air temperature from a range of sites worldwide, specifically from non-urban locations such as agricultural research institutes, universities and other rural or island locations for the period 1975–2011 or longer where data were available. The data sets were then analysed using linear regression to determine the rate and direction of change in temperature over the reference periods. This analysis was performed to provide vegetable scientists with likely future temperature change scenarios up to 2025 and 2050 (on the assumption that recent trends are maintained) so that breeding, agronomic and other related research programmes may better respond to potential challenges from abiotic and biotic stresses to vegetable production. Substantial variation was evident between sites and between time runs at specific sites. At some locations rapid increases in air temperature are projected, such as for sites in East Asia, but at other locations little change is evident; in rare cases, local cooling is shown. The implications of variability and change in air temperature in the context of constraints to vegetable production and the opportunities to exploit the range of genetic diversity available in climatically uncertain environments are discussed. It is believed that modern agricultural science can address successfully the problems raised by climate uncertainty, yet the lack of sufficient, immediate investment in horticultural disciplines worldwide places the world at severe risk of failing to attain effective food and nutritional security.

Differential Impact of Monsoon and Large Amplitude Internal Waves on Coral Reef Development in the Andaman Sea

The Andaman Sea and other macrotidal semi-enclosed tropical seas feature large amplitude internal waves (LAIW). Although LAIW induce strong fluctuations i.e. of temperature, pH, and nutrients, their influence on reef development is so far unknown. A better-known source of disturbance is the monsoon affecting corals due to turbulent mixing and sedimentation. Because in the Andaman Sea both, LAIW and monsoon, act from the same westerly direction their relative contribution to reef development is difficult to discern. Here, we explore the framework development in a number of offshore island locations subjected to differential LAIW- and SW-monsoon impact to address this open question. Cumulative negative temperature anomalies – a proxy for LAIW impact – explained a higher percentage of the variability in coral reef framework height, than sedimentation rates which resulted mainly from the monsoon. Temperature anomalies and sediment grain size provided the best correlation with framework height suggesting that so far neglected subsurface processes (LAIW) play a significant role in shaping coral reefs.

Reconstructing palaeo-volcanic geometries using a Geodynamic Regression Model (GRM): Application to Deception Island volcano (South Shetland Islands, Antarctica)

This article describes a reconstruction made of the palaeo-volcanic edifice on Deception Island (South Shetland Islands, Antarctica) prior to the formation of its present caldera. Deception Island is an active Quaternary volcano located in the Bransfield Strait, between the South Shetland Islands and the Antarctic Peninsula. The morphology of the island has been influenced mainly by the volcanic activity but geodynamics and volcanic deformation have also contributed. A volcanic reconstruction method, the Geodynamic Regression Model (GRM), which includes a terrain deformation factor, is proposed. In the case of Deception Island, the directions of this deformation are NW–SE and NE–SW, and match both the observed deformation of the Bransfield Strait and the volcanic deformation monitored over the last 20years in the island, using Global Navigation Satellite System (GNSS) techniques. Based on these data, possible volcanic deformation values of 5–15mm/yr in these directions have been derived. A possible coastline derived from a current bathymetry is transformed, according to values for the chosen date, to obtain the palaeo-coastline of Deception Island of 100kyears ago. Topographic, geomorphologic, volcanological and geological data in a GIS system have been considered, for computation of the outside caldera slope, palaeo-coastline, palaeo-summit height and palaeo digital elevation model (DEM). The result is a 3D palaeo-geomorphological surface model of a volcano, reaching 640m in height, with an increase of 4km3 in volume compared to the current edifice, covering 4km2 more surface area and the method reveals the previous existence of parasite volcanoes. Two photorealistic images of the island are obtained by superposition of textures extracted from a current Quick Bird satellite image also. This technique for reconstructing the terrain of an existing volcano could be useful for analysing the past and future geomorphology of this island and similar locations.

Website application for calculating cesium-137 ingestion doses from consumption of locally grown foods in the Marshall Islands

Fallout deposition from the US nuclear weapons test program at Bikini and Enewetak Atolls (1946–1958) resulted in widespread nuclear fallout contamination of the northern Marshall Islands. About 85–90 % of the nuclear test-related dose delivered to resident populations is derived from ingestion of cesium-137 (137Cs) contained in locally grown tree-crop food products. The Lawrence Livermore National Laboratory has developed a series of interactive internet applications to provide the public with an open access platform to learn more about radiological conditions in the Marshall Islands. The ingestion dose calculator application described here is one such feature whereby users can calculate hypothetical ingestion doses from 137Cs based on interactive user input matched to environmental data on the activity concentration of 137Cs contained in food plants such as coconut, breadfruit, Pandanus, and arrowroot. Users are asked to enter a date, an island and atoll location, a plant food type, and a daily intake amount (highlighted by the number of portions eaten per day in estimated gram equivalents). The application computes the user daily dose and the user equivalent annualized dose, and then compares the results with default settings based on dietary models developed for the Marshall Islands from independent dietary surveys. The default diets are based on a local plus imported food diet (or IA diet model) and an imported foods unavailable diet (or IUA diet model). Environmental data are decay corrected to the date entered by the user using an effective half-life of 137Cs of 8.5 years (http://marshallislands.llnl.gov).

Multi-year investigations of aerosols from an island station, Port Blair, in the Bay of Bengal: climatology and source impacts

Abstract. Long-term measurements of spectral aerosol optical depth (AOD) using multi-wavelength solar radiometer (MWR) for a period of seven years (from 2002 to 2008) from the island location, Port Blair (11.63° N, 92.7° E, PBR) in the Bay of Bengal (BoB), along with the concurrent measurements of the size distribution of near-surface aerosols, have been analyzed to delineate the climatological features of aerosols over eastern BoB. In order to identity the contribution of different aerosol types from distinct sources, concentration weighted trajectory (CWT) analysis has been employed. Climatologically, AODs increase from January to reach peak value of ~0.4 (at 500 nm) in March, followed by a weak decrease towards May. Over this general pattern, significant modulations of intra-seasonal time scales, caused by the changes in the relative strength of distinctively different sources, are noticed. The derivative (α') of the Angstrom wavelength exponent α in the wavelength domain, along with CWT analysis, are used to delineate the different important aerosol types that influence this remote island. Corresponding changes in the aerosol size distributions are inferred from the numerical inversion of the spectral AODs as well from (surface) measurements. The analyses revealed that advection plays a major role in modifying the aerosol properties over the remote island location, the potential sources contributing to the accumulation mode (coarse mode) aerosols over eastern BoB being the East Asia and South China regions (Indian mainland and the oceanic regions).

Evolution of dispersal traits in a biogeographical context: a study using the heterocarpicRumex bucephalophorusas a model

Summary1.Seed dispersal is crucial in determining the spatial patterns of plant populations, and selection pressure for dispersal varies over different scales. However, few empirical studies have assessed differences in dispersal traits in a biogeographical context.2.We studied dispersal traits in 46 populations ofRumex bucephalophorusfrom mainland and island locations, and from different habitats to test predictions of how insularity and habitat characteristics affect both dispersability (dispersal capacity and number of dispersible diaspores) and dispersal‐distance strategy. We also conducted a greenhouse experiment to compare dispersability of plants in nature and a controlled environment.3.Dispersability drastically changed when plants were cultivated in the greenhouse, revealing a high phenotypic plasticity for dispersal and showing that the maternal environment directly influences dispersal. However, dispersal‐distance strategy, estimated by the production of either long diaspores (LD) or short diaspores (SD), seems to be genetically determined. Dispersability was markedly affected by the habitat in which the plants develop, but the patterns found are not consistent with theoretical predictions. We found two contrasting patterns of dispersal on islands: Atlantic island populations showed a trend to seed monomorphism and mid‐dispersal strategy, whilst Mediterranean island populations showed seed heteromorphism and long‐dispersal strategy. These contrasting patterns support theoretical predictions that long‐distance dispersal evolves in heteromorphic plants, whilst in monomorphic plants only local dispersal evolves. Lastly, we have found a clear mid‐dispersal‐distance strategy in coastal sands and Atlantic islands; we suggest that the low environmental variation shared by these two zones selects for shorter distances of dispersal.4.Synthesis. Most models describing the evolution of dispersal strategies assume that forces selecting for decreased dispersability also select for decreased dispersal distances. However, inR. bucephalophorusdispersal distance and dispersability showed contrasting patterns of variation. The fact that these two traits are differently determined could suggest that they can respond in a different manner to selective pressures.

NTM Localization by Correlation of Te and dB/dt

For electron cyclotron current drive-based stabilization of neoclassical tearing modes (NTMs), it is crucial that the current deposition occurs as close to the island as possible; hence, its location needs to be accurately known. An NTM, rotating in the laboratory frame, causes fluctuations of magnetic flux measurable by Mirnov coils (dB/dt). Temperature perturbations in the vicinity of an NTM are caused by displaced flux surfaces and thus have the same frequency as the Mirnov signal but show a constant phase difference, which depends on the mode topology (poloidal and toroidal periodicity), on the toroidal displacement of the Mirnov coil with respect to the temperature measurement, and on the sign of the temperature change between the X-point profile and the O-point profile, which inverts somewhere inside the island. The sign flip of ΔTe is equivalent to a change of the phase difference between Te and magnetic reference by π and therefore can be localized using the presented correlation method. Using the suggested algorithm, we can determine the rational surface that coincides with the radial island location with low latency and good reliability in real time from electron cyclotron emission temperature profiles when correlated with the appropriate magnetic fluctuations on a modern workstation computer.