bluuebunny/crossref_metadata_2025 huggingface dataset:
URBANISATION AND 3D SPATIAL MODELLING- A GEOMETRIC APPROACH
Authors: Duncan E. E. , Abdul Rahman A.
Published: September 2013

Abstract. Urbanisation creates immense competition for space, this may be attributed to an increase in population owing to domestic and external tourism. Most cities are constantly exploring all avenues in maximising its limited space. Hence, urban or city authorities need to plan, expand and use such three dimensional (3D) space above, on and below the city space. Thus, difficulties in property ownership and the geometric representation of the 3D city space is a major challenge. This research, investigates the concept of representing a geometric topological 3D spatial model capable of representing 3D volume parcels for man-made constructions above and below the 3D surface volume parcel. A review of spatial data models suggests that the 3D TIN (TEN) model is significant and can be used as a unified model. The concepts, logical and physical models of 3D TIN for 3D volumes using tetrahedrons as the base geometry is presented and implemented to show man-made constructions above and below the surface parcel within a user friendly graphical interface. Concepts for 3D topology and 3D analysis are discussed. Simulations of this model for 3D cadastre are implemented. This model can be adopted by most countries to enhance and streamline geometric 3D property ownership for urban centres. 3D TIN concept for spatial modelling can be adopted for the LA_Spatial part of the Land Administration Domain Model (LADM) (ISO/TC211, 2012), this satisfies the concept of 3D volumes.
DESIGN OF AN INTELLIGENT INDIVIDUAL EVACUATION MODEL FOR HIGH RISE BUILDING FIRES BASED ON NEURAL NETWORK WITHIN THE SCOPE OF 3D GIS
Authors: Atila U. , Karas I. R. , Turan M. K. , Rahman A. A.
Published: September 2013

Abstract. One of the most dangerous disaster threatening the high rise and complex buildings of today's world including thousands of occupants inside is fire with no doubt. When we consider high population and the complexity of such buildings it is clear to see that performing a rapid and safe evacuation seems hard and human being does not have good memories in case of such disasters like world trade center 9/11. Therefore, it is very important to design knowledge based realtime interactive evacuation methods instead of classical strategies which lack of flexibility. This paper presents a 3D-GIS implementation which simulates the behaviour of an intelligent indoor pedestrian navigation model proposed for a self -evacuation of a person in case of fire. The model is based on Multilayer Perceptron (MLP) which is one of the most preferred artificial neural network architecture in classification and prediction problems. A sample fire scenario following through predefined instructions has been performed on 3D model of the Corporation Complex in Putrajaya (Malaysia) and the intelligent evacuation process has been realized within a proposed 3D-GIS based simulation.
3D VISUALISATION OF UNDERGROUND PIPELINES: BEST STRATEGY FOR 3D SCENE CREATION
Authors: Guerrero J. , Zlatanova S. , Meijers M.
Published: September 2013

Abstract. Underground pipelines pose numerous challenges to 3D visualization. Pipes and cables are conceptually simple and narrow objects with clearly defined shapes, spanned over large geographical areas and made of multiple segments. Pipes are usually maintained as linear objects in the databases. However, the visualization of lines in 3D is difficult to perceive as such lines lack the volumetric appearance, which introduces depth perception and allows understanding the disposition and relationships between the objects on the screen. Therefore the lines should be replaced by volumetric shapes, such as parametric shapes (cylinders) or triangular meshes. The reconstruction of the 3D shape of the pipes has to be done on the fly and therefore it is important to select a 3D representation which will not degrade the performance. If a reconstruction method provides a good performance, the visualization of pipes and cables is guaranteed to provide a smooth experience to the final user, enabling richer scenes but also establishing the visualization requirements in terms of hardware and software to display underground utilities. This paper presents our investigations on a strategy for creating a 3D pipes for 3D visualisation. It is assumed that the pipelines are stored in a database and portions of them are retrieved for 3D reconstruction and 3D visualization. Generally, the reconstruction of underground utilities can be performed in different ways and should lead to realistic appearance, produce visual continuity between segments, include objects depicting specific connections and even consider buffer volumes displaying the uncertainty and the security distance between objects. The creation of such visually pleasing reconstructions may require very detailed shapes, which will increase the complexity of the scene and degrade the performance. This research has identified four criteria to measure the complexity of the scene and conclude on a 3D reconstruction strategy: number of scene graph nodes, number of triangles and vertices on the screen, needed transformations and appearance options. On the basis of these criteria a testing framework is developed. Ten different strategies for 3D reconstruction are defined and tested for X3D, X3DOM and WebGL. The paper analyses the results of the tests and concludes on the best strategy.
A WEB SERVICE APPROACH FOR LINKING SENSORS AND CELLULAR SPACES
Authors: Isikdag U.
Published: September 2013

Abstract. More and more devices are starting to be connected to the Internet. In the future the Internet will not only be a communication medium for people, it will in fact be a communication environment for devices. The connected devices which are also referred as Things will have an ability to interact with other devices over the Internet, i.) provide information in interoperable form and ii.) consume /utilize such information with the help of sensors embedded in them. This overall concept is known as Internet-of- Things (IoT). This requires new approaches to be investigated for system architectures to establish relations between spaces and sensors. The research presented in this paper elaborates on an architecture developed with this aim, i.e. linking spaces and sensors using a RESTful approach. The objective is making spaces aware of (sensor-embedded) devices, and making devices aware of spaces in a loosely coupled way (i.e. a state/usage/function change in the spaces would not have effect on sensors, similarly a location/state/usage/function change in sensors would not have any effect on spaces). The proposed architecture also enables the automatic assignment of sensors to spaces depending on space geometry and sensor location.
CITY-WIDE TOTAL ENERGY DEMAND ESTIMATION OF BUILDINGS USING SEMANTIC 3D CITY MODELS AND STATISTICAL DATA
Authors: Kaden R. , Kolbe T. H.
Published: September 2013

Abstract. The present climate and environmental policy efforts require comprehensive planning regarding the modification of the energy supply and infrastructures in cities. The strategic planning of the different measures requires a holistic approach and the combination of extensive and complex information. Within this paper, current developments in the context of the project Energy Atlas Berlin are presented. The Energy Atlas Berlin is based on the semantic information model of CityGML and provides an integrative data backbone for the common spatio-semantic representation of the city structure including energy related information of different themes. The virtual 3D city model of Berlin (mainly LOD2 building models) is used as data basis and has been enriched by information of different stakeholders and disciplines. In order to ensure the energy supply, the knowledge about the energy demands of buildings during the planning and optimization of measures is of great strategic importance. Therefore, this paper focuses on the city-wide estimation of the energy demands of buildings including heating, electricity and warm water energy in the city of Berlin using available official geobase and statistical data integrated within the Energy Atlas Berlin. It is explained in detail how the spatial and semantic properties of the 3D building models are being used to estimate these energy demands on an individual building level for the entire city.
SCALABLE MULTI-PLATFORM DISTRIBUTION OF SPATIAL 3D CONTENTS
Authors: Klimke J. , Hagedorn B. , Döllner J.
Published: September 2013

Abstract. Virtual 3D city models provide powerful user interfaces for communication of 2D and 3D geoinformation. Providing high quality visualization of massive 3D geoinformation in a scalable, fast, and cost efficient manner is still a challenging task. Especially for mobile and web-based system environments, software and hardware configurations of target systems differ significantly. This makes it hard to provide fast, visually appealing renderings of 3D data throughout a variety of platforms and devices. Current mobile or web-based solutions for 3D visualization usually require raw 3D scene data such as triangle meshes together with textures delivered from server to client, what makes them strongly limited in terms of size and complexity of the models they can handle. In this paper, we introduce a new approach for provisioning of massive, virtual 3D city models on different platforms namely web browsers, smartphones or tablets, by means of an interactive map assembled from artificial oblique image tiles. The key concept is to synthesize such images of a virtual 3D city model by a 3D rendering service in a preprocessing step. This service encapsulates model handling and 3D rendering techniques for high quality visualization of massive 3D models. By generating image tiles using this service, the 3D rendering process is shifted from the client side, which provides major advantages: (a) The complexity of the 3D city model data is decoupled from data transfer complexity (b) the implementation of client applications is simplified significantly as 3D rendering is encapsulated on server side (c) 3D city models can be easily deployed for and used by a large number of concurrent users, leading to a high degree of scalability of the overall approach. All core 3D rendering techniques are performed on a dedicated 3D rendering server, and thin-client applications can be compactly implemented for various devices and platforms.
3D DATA ACQUISITION FOR INDOOR ASSETS USING TERRESTRIAL LASER SCANNING
Authors: Lee S. Y. , Majid Z. , Setan H.
Published: September 2013

Abstract. The newly development of technology clearly shows an improvement of three-dimension (3D) data acquisition techniques. The requirements of 3D information and features have been obviously increased during past few years in many related fields. Generally, 3D visualization can provide more understanding and better analysis for making decision. The need of 3D GIS also pushed by the highly demand of 3D in geospatial related applications as well as the existing fast and accurate 3D data collection techniques. This paper focuses on the 3D data acquisition by using terrestrial laser scanning. In this study, Leica C10 terrestrial laser scanner was used to collect 3D data of the assets inside a computer laboratory. The laser scanner device is able to capture 3D point cloud data with high speed and high accuracy. A series of point clouds was produced from the laser scanner. However, more attention must be paid during the point clouds data processing, 3D modelling, and analysis of the laser scanned data. Hence, this paper will discuss about the data processing from 3D point clouds to 3D models. The processing of point cloud data divided into pre-processing (data registration and noise filter) and post-processing (3D modelling). During the process, Leica Cyclone 7.3 was used to process the point clouds and SketchUp was used to construct the 3D asset models. Afterward, the 3D asset models were exported to multipatch geometry format, which is a 3D GIS-ready format for displaying and storing 3D model in GIS environment. The final result of this study is a set of 3D asset models display in GIS-ready format since GIS can provides the best visual interpretation, planning and decision making process. This paper shows the 3D GIS data could be produced by laser scanning technology after further processing of point cloud data.
3D VISIBILITY ANALYSIS IN URBAN ENVIRONMENT – COGNITION RESEARCH BASED ON VGE
Authors: Lin T. P. , Lin H. , Hu M. Y.
Published: September 2013

Abstract. The author in this research attempts to illustrate a measurable relationship between the physical environment and human’s visual perception, including the distance, visual angle impact and visual field (a 3D isovist conception) against human's cognition way, by using a 3D visibility analysis method based on the platform of Virtual Geographic Environment (VGE). The whole project carries out in the CUHK campus (the Chinese University of Hong Kong), by adopting a virtual 3D model of the whole campus and survey in real world. A possible model for the simulation of human cognition in urban spaces is expected to be the output of this research, such as what the human perceive from the environment, how their feelings and behaviours are and how they affect the surrounding world. Kevin Lynch raised 5 elements of urban design in 1960s, which are "vitality, sense, fit, access and control". As the development of urban design, several problems around the human's cognitive and behaviour have come out. Due to the restriction of sensing knowledge in urban spaces, the research among the "sense" and the "fit" of urban design were not quite concerned in recent decades. The geo-spatial cognition field comes into being in 1997 and developed in recent 15 years, which made great effort in way-finding and urban behaviour simulation based on the platform of GIS (geographic information system) or VGE. The platform of VGE is recognized as a proper tool for the analysis of human's perception in urban places, because of its efficient 3D spatial data management and excellent 3D visualization for output result. This article will generally describe the visibility analysis method based on the 3D VGE platform. According to the uncertainty and variety of human perception existed in this research, the author attempts to arrange a survey of observer investigation and validation for the analysis results. Four figures related with space and human’s perception will be mainly concerned in this proposal: openness, permeability, environmental pressure and visibility, and these will also be used as the identification for different type of spaces. Generally, the author is aiming at contributing a possible way to understand the reason of human’s cognition in geo-spatial area, and provides efficient mathematical model between spatial information and visual perception to the related research field.
Towards Precise Metadata-set for Discovering 3D Geospatial Models in Geo-portals
Authors: Zamyadi A. , Pouliot J. , Bédard Y.
Published: September 2013

Abstract. Accessing 3D geospatial models, eventually at no cost and for unrestricted use, is certainly an important issue as they become popular among participatory communities, consultants, and officials. Various geo-portals, mainly established for 2D resources, have tried to provide access to existing 3D resources such as digital elevation model, LIDAR or classic topographic data. Describing the content of data, metadata is a key component of data discovery in geo-portals. An inventory of seven online geo-portals and commercial catalogues shows that the metadata referring to 3D information is very different from one geo-portal to another as well as for similar 3D resources in the same geo-portal. The inventory considered 971 data resources affiliated with elevation. 51% of them were from three geo-portals running at Canadian federal and municipal levels whose metadata resources did not consider 3D model by any definition. Regarding the remaining 49% which refer to 3D models, different definition of terms and metadata were found, resulting in confusion and misinterpretation. The overall assessment of these geo-portals clearly shows that the provided metadata do not integrate specific and common information about 3D geospatial models. Accordingly, the main objective of this research is to improve 3D geospatial model discovery in geo-portals by adding a specific metadata-set. Based on the knowledge and current practices on 3D modeling, and 3D data acquisition and management, a set of metadata is proposed to increase its suitability for 3D geospatial models. This metadata-set enables the definition of genuine classes, fields, and code-lists for a 3D metadata profile. The main structure of the proposal contains 21 metadata classes. These classes are classified in three packages as General and Complementary on contextual and structural information, and Availability on the transition from storage to delivery format. The proposed metadata set is compared with Canadian Geospatial Data Infrastructure (CGDI) metadata which is an implementation of North American Profile of ISO-19115. The comparison analyzes the two metadata against three simulated scenarios about discovering needed 3D geo-spatial datasets. Considering specific metadata about 3D geospatial models, the proposed metadata-set has six additional classes on geometric dimension, level of detail, geometric modeling, topology, and appearance information. In addition classes on data acquisition, preparation, and modeling, and physical availability have been specialized for 3D geospatial models.
TOWARDS A 3D SPATIAL URBAN ENERGY MODELLING APPROACH
Authors: Bahu J.-M. , Koch A. , Kremers E. , Murshed S. M.
Published: September 2013

Abstract. Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies conceptually and practically integrate urban spatial and energy planning approaches. The combined modelling approach that will be developed based on the described sectorial models holds the potential to represent hybrid energy systems coupling distributed generation of electricity with thermal conversion systems.
CALCULATION AND UPDATE OF A 3D BUILDING MODEL OF BAVARIA USING LIDAR, IMAGE MATCHING AND CATASTRE INFORMATION
Authors: Aringer K. , Roschlaub R.
Published: September 2013

Abstract. The Bavarian State Office for Surveying and Geoinformation has launched a statewide 3D Building Model with standardized roof shapes without textures for all 8.1 million buildings in Bavaria. For acquisition of the 3D Building Model LiDAR-data are used as data basis as well as the building ground plans of the official cadastral map and a list of standardized roof shapes. The data management of the 3D Building Model is carried out by a central database with the usage of a nationwide standardized data model and the data exchange interface CityGML. On the one hand the update of the 3D Building Model for new buildings is done by terrestrial building measurements within the maintenance process of the cadastre. On the other hand the roofs of buildings which were built after the LiDAR flight and which were not measured terrestrially yet, are captured by means of picture-based digital surface-models derived from image-matching of oriented aerial photographs (DSM from image matching).
GIS and remote sensing techniques for the assessment of land use changes impact on flood hydrology: the case study of Yialias Basin in Cyprus
Authors: Alexakis D. D. , Gryllakis M. G. , Koutroulis A. G. , Agapiou A. , Themistocleous K. , Tsanis I. K. , Michaelides S. , Pashiardis S. , Demetriou C. , Aristeidou K. , Retalis A. , Tymvios F. , Hadjimitsis D. G.
Published: September 2013

Abstract. Flooding is one of the most common natural disasters worldwide, leading to economic losses and loss of human lives. This paper highlights the hydrological effects of multi-temporal land use changes in flood hazard within the Yialias catchment area, located in central Cyprus. Calibrated hydrological and hydraulic models were used to describe the hydrological processes and internal basin dynamics of the three major sub-basins, in order to study the diachronic effects of land use changes. For the implementation of the hydrological model, land use, soil and hydrometeorological data were incorporated. The climatic and stream flow data were derived from rain and flow gauge stations located in the wider area of the watershed basin. In addition, the land use and soil data were extracted after the application of object oriented nearest neighbor algorithms of ASTER satellite images. Subsequently, the CA-Markov chain analysis was implemented to predict the 2020 Land use/Land cover (LULC) map and incorporate it to the hydrological impact assessment. The results denoted the increase of runoff in the catchment area due to the recorded extensive urban sprawl phenomenon of the last decade.
3-D reflection seismic imaging of the Hontomín structure in the Basque-Cantabrian Basin (Spain)
Authors: Alcalde J. , Martí D. , Juhlin C. , Malehmir A. , Sopher D. , Saura E. , Marzán I. , Ayarza P. , Calahorrano A. , Pérez-Estaún A. , Carbonell R.
Published: September 2013

Abstract. The Basque-Cantabrian Basin of the Northern Iberia peninsula constitutes a unique example of a major deformation system, featuring a dome structure developed by extensional tectonics followed by compressional reactivation. The occurrence of natural resources in the area and the possibility of establishing a geological storage site for carbon dioxide motivated the acquisition of a 3-D seismic reflection survey in 2010, centered on the Jurassic Hontomín dome. The objectives of this survey were to obtain a geological model of the overall structure and to establish a baseline model for a possible geological CO2 storage site. The 36 km2 survey included approximately 5000 mixed (Vibroseis and explosives) source points recorded with a 25 m inline source and receiver spacing. The target reservoir is a saline aquifer, at approximately 1450 m depth, encased and sealed by carbonate formations. Acquisition and processing parameters were influenced by the rough topography and relatively complex geology. A strong near surface velocity inversion is evident in the data, affecting the quality of the data. The resulting 3-D image provides constraints on the key features of the geologic model. The Hontomín structure is interpreted to consist of an approximately 107 m2 large elongated dome with two major W–E and NW–SE striking faults bounding it.
Exploring gender differences in Malaysian urban adolescent Internet usage
Authors: Soh Patrick C-H , Teh Boon Heng , Hong Yong Hoe , Ong Tze San , Charlton John P.
Published: September 2013

This study explored gender differences in urban adolescent Internet access, usage and motives. Data were collected from 914 urban school students in Malaysia. Factor analysis revealed that eroticism, entertainment, social-interaction, shopping and information/ surveillance are the key drivers for adolescence Internet usage. No differences between boys and girls were detected in Internet accessibility and home computer ownership. Boys and girls differed in their intensity of usage, place of access and their motivations to use the Internet. Girls were more motivated by social-interaction, shopping and surveillance/ information, while boys were more motivated by eroticism and had a higher tendency to be addicted to the Internet. However, boys and girls did not exhibit any significant differences in online entertainment motivation.
Assessment of Cellular Reactions to Magnesium as Implant Material in Comparison to Titanium and to Glyconate Using the Mouse Tail Model
Authors: Reifenrath Janin , Badar Muhammad , Dziuba Dina , Müller Peter P. , Heidenblut Torsten , Bondarenko Alexander , Meyer-Lindenberg Andrea
Published: September 2013

Purpose

Nowadays, research in magnesium alloys as a biodegradable implant material has increased. The aim of this study was to examine osteoinductive properties and tissue responses to pure magnesium in comparison to conventional permanent (titanium) and to degradable (glyconate) implant materials.

Methods

Magnesium wires (0.4 mm in diameter, 10 mm length) were implanted into tail veins of mice and examined after 2, 4, 8, 16 and 32 weeks. Titanium and glyconate as controls were assessed after 2, 4, 8 and 24 weeks. μ-computed tompgraphy, histology and SEM examinations were performed.

Results

Magnesium implants showed increasing structural losses over time with fragmentation after an observation period of 32 weeks. Glyconate was fully degraded and titanium remained almost unaffected after 24 weeks. In contrast to some titanium and glyconate implants, first calcium and phosphate precipitations could be observed around magnesium implants after two weeks. However, ossification could not be observed even after 32 weeks, whereas enchondral ossification was found partially in the sourrounding of glyconate and titanium implants after eight weeks. Nevertheless, magnesium implants showed less inflammatory responses and fibrosing properties than the conventional implant materials.

Conclusions

Although the assumed osteoinductive properties could not be detected, magnesium appears to be a promising degradable implant material because of the low sensitizing and inflammatory potential.
Biofilm Medium Leads to Apatite Formation on Bioactive Surfaces
Authors: Kulkova Julia , Abdulmajeed Aous A. , Könönen Eija , Närhi Timo O.
Published: September 2013

Purpose

When investigating apatite formation on biomaterial surfaces, simulated body fluid (SBF) is used as an in vitro solution, however, it does not provide an appropriate environment for the growth of bacterial biofilm. The aim of the present study was to compare the bioactivity in terms of apatite formation on two bioactive glass (BAG) composite surfaces using both SBF and bacterial-biofilm growing medium (BM).

Methods

Polymer composite substrates with different percentages of BAG–particles (50% and 75% by weight) were prepared. Plain resin substrates were used as a negative control. The substrates were immersed in SBF and BM for 3 days. The surface and, subsequently, the cross-sections of the substrates were examined with scanning electron microscopy (SEM) and x-ray energy dispersive spectroscopy (EDS).

Results

All the investigated BAG-composite surfaces showed apatite formation after immersion in SBF and BM liquid media. Conclusions: The use of BM is a promising method for studies involving simultaneous biofilm growth and apatite formation on bioactive surfaces.
Effect of Acrylamide on Liver Proteins Expression in Mice
Authors: Al-Azkawi Ahlam S. , Al-Bahry Saif N. , Mahmoud Ibrahim Y. , Barry Michael J.
Published: September 2013

Carbohydrate rich food cooked at high temperature can lead to the formation of acrylamide. The aim of this investigation is to analyze the proteomics of mice liver in response to acrylamide intoxication since the liver is the major site of acrylamide detoxification and metabolism. The liver protein pattern from sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) treated mice with acrylamide in drinking water for 9 weeks did not show variations from the control. However, analysis by 2-D gel of liver proteins from mice treated with 0.5 µg acrylamide/kg for 9 weeks showed variations in protein expression. At least 10 protein spots were significantly affected (T > 2) by the acrylamide treatment. The affected proteins were identified using MALDI TOF/TOF and mass searches through Mascot. These proteins were up-regulated or down-regulated depending on their physiological function. Probably the proteins are involved in detoxification of acrylamide or cell protection. The data from this study shows that proteomics is a valuable tool for assessing acrylamide toxicity in the affected tissues.
Students drop out of STEM fields due to poor grades
Authors: Balcerak Ernie
Published: September 2013

College students planning to major in science, technology, engineering, and mathematics (STEM) fields often drop out of those fields because of poorer than expected grades, according to a recent study. Conducted by Ralph Stinebrickner of Berea College in Kentucky and Todd Stinebrickner of the University of Western Ontario, the study is a National Bureau of Economic Research working paper published in June 2013.
Lost Science: Protecting Data Through Improved Archiving
Authors: Simmons Karen E.
Published: September 2013

Mike Carr wrote recently of the wonderful planetary geology accomplished by NASA over the past 50 years of space exploration, with images and descriptions from the early Venus, Mars, and lunar missions as well as more recent missions, which evoked good memories (M. H. Carr, Geologic exploration of the planets: The first 50 years, Eos, 94(3), 29–30, doi:10.1029/2013EO030001, 2013). Unfortunately, memories are not science data, and those 50 years have not been as kind to the scientific information collected by these pioneering missions.
Addressing Questions on Life in Terrestrial Geothermal Systems
Authors: Hedlund Brian P. , Li Wen‐Jun , Zhang Chuanlun
Published: September 2013

A binational research team met on the campus of Yunnan University in Kunming, China, to discuss recent progress and future plans to leverage binational support to address major questions on life in terrestrial geothermal systems. The symposium included about 90 faculty, postdocs, and students from China and about 30 faculty, postdocs, students, and high school teachers from the United States. The introductory session reviewed the progress of the Tengchong PIRE project funded by the U.S. National Science Foundation (NSF) Partnerships for International Research and Education (PIRE) program (OISE‐0836450). It also introduced a new collaborative project funded as a Key Project of International Cooperation by the Chinese Ministry of Science and Technology (MOST, 2013DFA31980), which is the first project funded through a memorandum of understanding between NSF and MOST to promote China‐U.S. collaboration.
How tropical humidity self‐organizes into moist and dry regions
Authors: Balcerak Ernie
Published: September 2013

Numerical simulations have shown that the moisture in the tropical troposphere has a tendency to spontaneously aggregate, forming separate wet and dry regions. To learn more about how this self‐organization occurs, Craig and Mack introduced a simple equation for the tropical troposphere moisture budget and conducted numerical simulations that included convective moistening and horizontal mixing. Based on their simulations, the authors propose that a feedback process in the troposphere causes moisture to aggregate, beginning on small scales and then coarsening to larger scales. Wet regions become wetter and dry regions become drier as the self‐organization continues.
2012 Great Plains drought not caused by climate change
Authors: Schultz Colin
Published: September 2013

From May to July 2012, the Great Plains region of the western United States faced a powerful and unpredicted drought. Following 7 months of normal rainfall, the drought was one of the largest deviations from seasonal precipitation rates seen in the region since observations began in 1895. When such extreme events take place today against the backdrop of ongoing global climate change, they raise questions about the relationship between climate change and natural disasters.
Hawaiian Islands formed through extrusive volcanic activity
Authors: Balcerak Ernie
Published: September 2013

Scientists generally believe that the Hawaiian Islands formed primarily through endogenous growth, or intrusion, in which hot magma intrudes into a rock and then solidifies before it reaches the surface. However, a new study suggests that the islands may actually have formed primarily through extrusion, which occurs when a volcano erupts and magma reaches the surface and flows away from the eruption site before cooling and solidifying.
Phase II study of pegylated liposomal doxorubicin, low‐dose dexamethasone, and lenalidomide in patients with newly diagnosed multiple myeloma
Authors: Baz Rachid C. , Shain Kenneth H. , Hussein Mohamad A. , Lee Ji‐Hyun , Sullivan Daniel M. , Oliver Elizabeth Finley , Nardelli Lisa A. , Nodzon Lisa A. , Zhao Xiuhua , Ochoa‐Bayona Jose Leonel , Nishihori Taiga , Dalton William S. , Alsina Melissa
Published: September 2013

Our previous phase I/II trial of pegylated liposomal doxorubicin (PLD), low‐dose dexamethasone, and lenalidomide in patients with relapsed and refractory myeloma showed an overall response rate of 75%, with 29% achieving ≥ VGPR. Here, we investigated this combination (PLD 30 or 40 mg/m2 intravenously, day 1; dexamethasone 40 mg orally, days 1–4; lenalidomide 25 mg orally, days 1–21; administered every 28 days) in a phase II study in patients with newly diagnosed symptomatic multiple myeloma to determine its efficacy and tolerability (ClinicalTrials.gov NCT00617591). At best response, patients could proceed with high‐dose melphalan or with maintenance lenalidomide and dexamethasone. In 57 patients, we found that the overall response rate and rate of very good partial response and better on intent‐to‐treat, our primary endpoints, were 77.2% and 42.1%, respectively, with responses per the International Myeloma Working Group. Median progression‐free survival was 28 months (95% CI 18.1–34.8), with 1‐ and 2‐year overall survival rates of 98.1 and 79.6%. During induction, grade 3/4 toxicities were neutropenia (49.1%), anemia (15.8%), thrombocytopenia (7%), fatigue (14%), febrile neutropenia (8.8%), and venous thromboembolic events (8.8%). During maintenance, grade 3/4 toxicities were mainly hematologic. We found this combination to be active in patients with newly diagnosed myeloma, with results comparable to other lenalidomide‐based induction strategies without proteasome inhibition. In addition, maintenance therapy with lenalidomide was well tolerated. Am. J. Hematol. 89:62–67, 2014. © 2013 Wiley Periodicals, Inc.
Quantum simulations of the early universe
Authors: Opanchuk Bogdan , Polkinghorne Rodney , Fialko Oleksandr , Brand Joachim , Drummond Peter D.
Published: September 2013

A procedure is described whereby a linearly coupled spinor Bose condensate can be used as a physically accessible quantum simulator of the early universe. In particular, an experiment to generate an analog of an unstable vacuum in a relativistic scalar field theory is proposed. This is related to quantum theories of the inflationary phase of the early universe. There is an unstable vacuum sector whose dynamics correspond to the quantum sine‐Gordon equations in one, two or three space dimensions. Numerical simulations of the expected behavior are reported using a truncated Wigner phase‐space method, giving evidence for the dynamical formation of complex spatial clusters. Preliminary results showing the dependence on coupling strength, condensate size and dimensionality are obtained.
Synthesis, structural and spectral properties of Au complexes: luminescence properties and their non‐covalent DNA binding studies
Authors: Huerta‐Aguilar Carlos , Talamantes Gómez Jose M. , Thangarasu Pandiyan , Camacho‐Arroyo Ignacio , González‐Arenas Aliesha , Narayanan Jayanthi , Srivastava Rajendra
Published: September 2013

Gold complexes of 1,3‐ bis‐pyridylimidazolium chloride (L1), 1,3‐bis‐[2,6‐diisopropylphenyl]imidazolium chloride (L2) and 1,3‐bis‐[benzyl]benzimidazolium chloride (L3) were synthesized and characterized by analytical methods. For the complexes, electronic spectral results show that there is a marked difference in the band feature observed in the spectra, ascribed to the greater relativistic effect of gold. In fluorescence studies, the complexes develop emission bands in the visible region (400–600 nm) after excitation at around 350 nm. Au complex–DNA binding was studied, and it was observed that genomic DNA isolated from the U373‐GB cell line was fragmented and in some cases degraded by the Au complexes. Furthermore, the intensity of the DNA band increased when concentration of the metal complex was augmented. This study shows that the DNA cleavage is mediated by the Au complex. Copyright © 2013 John Wiley & Sons, Ltd.
A new method of preparing superabsorbent PVF porous foam through the simultaneous acidification of water glass solution–aspect of environmental protection
Authors: Chang You‐Im , Cheng Wei‐You , Jang Larry
Published: September 2013

To reduce the wastewater pollution problem, silica particles that have resulted from simultaneous sulfuric acidification of water glass solution serve as the pore‐forming agent for preparing superabsorbent PVF/SiO2 foam in this study. This is a departure from the traditional porous PVF/starch foam's manufacture method. The pore structure of PVF/SiO2 foam is very different from that of PVF/starch foam. The effect of the concentration of these pore‐forming agents on the pore structure, mechanical modulus, and water adsorption capacity of PVF/starch and PVF/SiO2 foams are investigated in this study. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 39894.
Lactobacillus acidophilus La5, Bifidobacterium BB12, and Lactobacillus casei DN001 modulate gene expression of subset specific transcription factors and cytokines in peripheral blood mononuclear cells of obese and overweight people
Authors: Zarrati Mitra , Shidfar Farzad , Nourijelyani Keramat , Mofid Vahid , Hossein zadeh‐Attar Mohammad Javad , Bidad Katayoon , Najafi Forouzan , Gheflati Zahra , Chamari Maryam , Salehi Eisa
Published: September 2013

Probiotics are believed to have interaction with immune cells through sustained effects on gene expression of different cytokines and transcription factors. The present randomized doubled‐blind controlled clinical trial was performed recruiting 75 individuals with BMI 25–35, who were randomly assigned to the following three groups: Group 1 (n = 25) who consumed regular yogurt as part of a low calorie diet [RLCD], group 2 (n = 25) who received probiotic yogurt with a LCD [PLCD] and group 3 (n = 25) who consumed probiotic yogurt without LCD [PWLCD] for 8 week. Participants in PLCD and PWLCD groups received 200 g/day yogurt containing Lactobacillus acidophilus La5, Bifidobacterium Bb12, and lactobacillus casei DN001 108cfu/gr. The expression of the FOXP3, T‐bet, GATA3, TNF‐α, IFN‐γ, TGF‐β, and ROR‐γt in PBMCs genes were assessed, before and after intervention. In three groups, ROR‐γt expression was reduced (P = 0.007) and FOXP3 was increased (P < 0.001). The expression of TNFα, TGFβ, and GATA3 genes did not change among all groups after intervention. Interestingly, the expression of T‐bet gene, which was significantly decreased in PLCD and PWLCD groups (P < 0.001), whereas gene expression of IFN‐γ decreased in all three groups. Our results suggest that weight loss diet and probiotic yogurt had synergistic effects on T‐cell subset specific gene expression in peripheral blood mononuclear cells among overweight and obese individuals. © 2013 BioFactors, 39(6):633–643, 2013
Redesigning space for interdisciplinary connections: The Puget Sound Science Center
Authors: DeMarais Alyce , Narum Jeanne L. , Wolfson Adele J.
Published: September 2013

Mindful design of learning spaces can provide an avenue for supporting student engagement in STEM subjects. Thoughtful planning and wide participation in the design process were key in shaping new and renovated spaces for the STEM community at the University of Puget Sound. The finished project incorporated Puget Sound's mission and goals as well as attention to pedagogical principles, and led to connections and integration throughout the learning environment, specifically at the biochemistry and molecular life sciences intersections. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(5):319–324, 2013
Teaching structure: Student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course
Authors: Jaswal Sheila S. , O'Hara Patricia B. , Williamson Patrick L. , Springer Amy L.
Published: September 2013

Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one‐semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open‐source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein‐nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(5):351–359, 2013
Essential concepts and underlying theories from physics, chemistry, and mathematics for “biochemistry and molecular biology” majors
Authors: Wright Ann , Provost Joseph , Roecklein‐Canfield Jennifer A. , Bell Ellis
Published: September 2013

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One‐hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: “We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?” Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(5):302–308, 2013
Problem‐solving test: Conditional gene targeting using the Cre/loxP recombination system
Authors: Szeberényi József
Published: September 2013

Terms to be familiar with before you start to solve the test: gene targeting, knock‐out mutation, bacteriophage, complementary base‐pairing, homologous recombination, deletion, transgenic organisms, promoter, polyadenylation element, transgene, DNA replication, RNA polymerase, Shine‐Dalgarno sequence, restriction endonuclease, polymerase chain reaction, primer, transcription, SV40 virus, malignant transformation, spacer region, gene expression, agarose gel electrophoresis, ethidium bromide staining, Southern‐blotting, probe, reporter gene. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(6):445–449, 2013
Affordable hands‐on DNA sequencing and genotyping: An exercise for teaching DNA analysis to undergraduates
Authors: Shah Kushani , Thomas Shelby , Stein Arnold
Published: September 2013

In this report, we describe a 5‐week laboratory exercise for undergraduate biology and biochemistry students in which students learn to sequence DNA and to genotype their DNA for selected single nucleotide polymorphisms (SNPs). Students use miniaturized DNA sequencing gels that require approximately 8 min to run. The students perform G, A, T, C Sanger sequencing reactions. They prepare and run the gels, perform Southern blots (which require only 10 min), and detect sequencing ladders using a colorimetric detection system. Students enlarge their sequencing ladders from digital images of their small nylon membranes, and read the sequence manually. They compare their reads with the actual DNA sequence using BLAST2. After mastering the DNA sequencing system, students prepare their own DNA from a cheek swab, polymerase chain reaction‐amplify a region of their DNA that encompasses a SNP of interest, and perform sequencing to determine their genotype at the SNP position. A family pedigree can also be constructed. The SNP chosen by the instructor was rs17822931, which is in the ABCC11 gene and is the determinant of human earwax type. Genotypes at the rs178229931 site vary in different ethnic populations. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(6):388–395, 2013