bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparisons between Field and Laboratory Suction Measurements of Expansive Clays
Authors: Manosuthkij Thammanoon , Puppala Anand J. , Nazarian Soheil , Saride Sireesh , Hoyos Laureano
Published: October 2008

Field suction measurements are especially important for pavements constructed on unsaturated expansive soils. Because these subgrade soils can experience high suction during dry seasons, field sensors that can measure high soil suctions are necessary. In this research, thermal conductivity-based soil suction sensors were evaluated for matric suction measurements at several sites. Laboratory suction measurements with the filter paper method were compared with the field suction measurements with the sensors. Soil water characteristic curves derived from the laboratory and field measurements agreed closely. Volume change measurements using swell and shrinkage tests were conducted separately on the subgrade soils retrieved from the instrumented test sites. The laboratory and field suction data need an adjustment or shift of the time factor to obtain comparable values at high suctions. The influence of total suction on the volumetric swell and shrinkage characteristics of the field subsoils were also addressed.
Computerized Cone Penetration Test for Soil Classification
Authors: Abu-Farsakh Murad Y. , Zhang Zhongjie , Tumay Mehmet , Morvant Mark
Published: October 2008

Computerized MS-Windows Visual Basic software of a cone penetration test (CPT) for soil classification was developed as part of an extensive effort to facilitate the implementation of CPT technology in many geotechnical engineering applications. Five CPT soil engineering classification systems were implemented as a handy, user-friendly, software tool for geotechnical engineers. In the probabilistic region estimation and fuzzy classification methods, a conformal transformation is first applied to determine the profile of soil classification index (U) with depth from cone tip resistance (qc) and friction ratio (Rf). A statistical correlation was established in the probabilistic region estimation method between the U index and the compositional soil type given by the Unified Soil Classification System. Conversely, the CPT fuzzy classification emphasizes the certainty of soil behavior. The Schmertmann and Douglas and Olsen methods provide soil classification charts based on cone tip resistance and friction ratio. However, Robertson et al. proposed a three-dimensional classification system that is presented in two charts: one chart uses corrected tip resistance (qt) and friction ratio (Rf); the other chart uses qt and pore pressure parameter (Bq) as input data. Five sites in Louisiana were selected for this study. For each site, CPT tests and the corresponding soil boring results were correlated. The soil classification results obtained using the five different CPT soil classification methods were compared.
Correlations between PENCEL Pressuremeter, Cone Penetrometer, and Dilatometer Parameters
Authors: Cosentino Paul J. , Kalajian Edward , Messaoud Farid , Sundaram Sunil , Misilo Thaddeus J. , Horhota David J.
Published: October 2008

PENCEL pressuremeter (PPMT), cone penetrometer (CPT), and dilatometer (DMT) tests were performed at three Florida sites. Two were sands and the third was clay. The PENCEL was pushed to the test depth using CPT equipment. During PPMT testing, both a smooth cone tip and a cone tip with a friction reducer were evaluated. Standardized testing procedures were followed for all tests. Initial or lift-off pressures (po), elastic moduli (E), and limit pressures (pL) were determined from the PPMT, whereas po and E values were determined from the DMT. CPT testing produced friction and tip resistances. Manual plus digital pressures and volumes were recorded during pressuremeter testing. Correlations were developed within the engineering parameters obtained from the PENCEL and between the PENCEL, cone, and dilatometer engineering parameters. All correlations matched published values. The PENCEL produced excellent correlations between the initial E and pL as well as the initial E and the reload E. Correlations based on digital elastic and reload moduli, from software called APMT, were higher than those based on the other recorded data. From the comparisons, promising correlations were developed between PPMT initial E values and CPT tip resistances. Promising correlations were also developed between PPMT pL and CPT tip resistances. Consistent ratios existed between PPMT and DMT po values as well as PPMT and DMT initial E values. Smooth and friction reducer cone tips evaluation indicated that soil disturbance, associated with the friction reducer, decreases the engineering parameters, and the friction reducer is not recommended.
Correlation between Resilient Modulus and Plastic Deformation for Cohesive Subgrade Soil under Repeated Loading
Authors: Yang Shu-Rong , Huang Wei-Hsing , Liao Chi-Chou
Published: October 2008

Pavement performance is related to resilient modulus and plastic deformation of pavement materials, which in turn are affected by environmental conditions and traffic loading. A series of triaxial tests was conducted on a residual lateritic soil for 10,000 load repetitions, with some specimens subjected to 100,000 load repetitions, to characterize the behavior of cohesive subgrades under repeated loading, including resilient modulus and plastic deformation. The shakedown concept was used to describe the accumulated plastic deformation and the strain-hardening and softening behavior. Experimental results show that the resilient modulus of cohesive subgrades exhibits strain-hardening behavior under low stress levels. In the meantime, the rate of plastic strain accumulation becomes diminutive. Soil under this condition is in a stable state. Conversely, under high stress levels, cohesive soil tends to soften after a specific number of load applications and accumulates excessive plastic strain and leads to an unstable state. To predict the plastic strain of subgrade soil under repetitive loading, regression models incorporating the strain-hardening behavior for a cohesive soil were used.
Electromagnetic Nanoscale Metrology Based on Entropy Production and Fluctuations
Authors: Baker-Jarvis James
Published: October 2008

The goal in this paper is to show how many high-frequency electromagnetic metrology areas can be understood and formulated in terms of entropy evolution, production, and fluctuations. This may be important in nanotechnology where an understanding of fluctuations of thermal and electromagnetic energy and the effects of nonequilibrium are particularly important. The approach used here is based on a new derivation of an entropy evolution equation using an exact Liouville-based statistical-mechanical theory rooted in the Robertson-Zwanzig-Mori formulations. The analysis begins by developing an exact equation for entropy rate in terms of time correlations of the microscopic entropy rate. This equation is an exact fluctuation-dissipation relationship. We then define the entropy and its production for electromagnetic driving, both in the time and frequency domains, and apply this to study dielectric and magnetic material measurements, magnetic relaxation, cavity resonance, noise, measuring Boltzmann’s constant, and power measurements.
BEGINNING A NEW STAGE OF DEVELOPMENT
Authors: Zavadskas Edmundas Kazimieras
Published: October 2008

„Beginning a new stage of development" Ukio Technologinis ir Ekonominis Vystymas, 14(3), p. 241-243
ON THE “MODELLING OF BUSINESS, INDUSTRIAL AND TRANSPORT SYSTEMS” INTERNATIONAL CONFERENCE
Authors: Kopytov Eugene , Pranevičius Henrikas , Yatskiv Irina
Published: October 2008

„On the “Modelling of business, industrial and transport systems” international conference" Ukio Technologinis ir Ekonominis Vystymas, 14(3), p. 244-246
FORECASTING THE LABOUR FORCE DEMAND AND SUPPLY IN LATVIA / LATVIJOS DARBO JĖGOS PAKLAUSOS IR PASIŪLOS MODELIAVIMAS
Authors: Dubra Elena , Gulbe Māra
Published: October 2008

The purpose of this paper is to analyse the problems of Latvian labour market and its possible development. An econometric model for labour force demand and supply forecasting is elaborated and it comprises 120 professions, 37 aggregated groups of professions and covers time period 2007–2030. The results of the quantitative and qualitative Employers’ Survey are analysed and taken into account. The novelty of this research study lies in the complex approach to the labour force demand and supply analyses and to the forecasts to the Latvian economy in general and for its 15 separate sectors.

Santrauka

Šio straipsnio tikslas – išanalizuoti Latvijos darbo rinkos problemas ir galimus pokyčius. Sudarytas
darbo jėgos paklausos ir pasiūlos prognozavimo ekonometrinis modelis, kuris susideda iš 120 profesijų ir 37 jų grupių. Modelis apima laiko periodą nuo 2007 iki 2030 metų. Atliktas kiekybinis ir kokybinis darbdavių tyrimas, o jo rezultatai naudojami skaičiuojant. Šio tyrimo naujumas yra tas, kad darbo jėgos paklausa ir pasiūla nagrinėjama kompleksiškai, skaičiavimai teikia prognozes Latvijos ekonomikai bendrai ir atskiriems 15 sektorių.
WAYS OF TRANSFORMING AIMS INTO RESULTS AT SUCCESSFUL COMPANIES / TIKSLŲ VERTINIMO REZULTATAIS BŪDAI SĖKMINGAI VEIKIANČIOSE ĮMONĖSE
Authors: Kopitov Rostislav , Faingloz Lev
Published: October 2008

The combination of coupled managerial approaches directed to designing a full‐functional system of improving the business functioning is examined in this research. This improvement could be achieved on the basis of the business processes uninterrupted monitoring. Such system is oriented to the establishment of the integral analytical business platform for providing the coordinated objectives setting, timely revealing and neutralising the unforeseen events, decision‐making at different levels of an organization.

Santrauka

Šiame straipsnyje nagrinėjami vadybos metodų deriniai, siekiant sukurti daugiafunkcę sistemą, gerinančią verslo funkcionavimą. Sukurtoji sistema užtikrintų vadinamosios integruotos analitinės verslo platformos funkcionavimą, kuri vykdytų nenutrūkstamą verslo monitoringą. Sistema padėtų nustatyti tikslus, išaiškinti ir neutralizuoti neprognozuojamus įvykius, priimti sprendimus įvairiais organizacijos lygmenimis.
PLA‐BASED FORMALIZATION OF BUSINESS RULES AND THEIR ANALYSIS BY MEANS OF KNOWLEDGE‐BASED TECHNIQUES / PLA METODU GRĮSTAS VERSLO TAISYKLIŲ FORMALIZAVIMAS IR ANALIZĖ TAIKANT ŽINIOMIS GRĮSTAS METODIKAS
Authors: Pranevičius Henrikas , Budnikas Germanas
Published: October 2008

The paper presents an approach that applies the knowledge engineering techniques for representing and analysing business rules. These rules are represented by production rules using concepts of a state‐based piece‐linear aggregate (PLA) model. A knowledge base of the business rules is analysed by checking its consistency (static properties) and dynamic constraints (dynamic properties). The analysis is performed by applying methods for decision table verification and reachable state validation as well as supporting tools. The proposed approach is illustrated by an example of Userv insurance company services. Santrauka Straipsnyje pateikiamas būdas, kurio remiantis taikomos žiniomis grįstos metodikos verslo taisyklėms pavaizduoti ir analizuoti. Verslo taisyklės iliustruojamos produkcinėmis taisyklėmis, naudojant būsenomis grįsto atkarpomis tiesinių agregatų (PLA) modelio konceptus. Verslo taisyklių žinių bazė analizuojama tikrinant jos suderinamumą (statines savybes) ir dinaminius suvaržymus (dinamines savybes). Analizė atliekama taikant sprendimo lentelių verifikavimo ir pasiekiamų būsenų validavimo metodus bei šiuos metodus realizuojančias programines priemones. Siūlomas būdas iliustruojams Userv draudimo kompanijos paslaugų pavyzdžiu.
A STRATEGIC MANAGEMENT MODEL FOR ECONOMIC DEVELOPMENT / ŪKIO PLĖTOTĖS STRATEGINIO VALDYMO MODELIS
Authors: Diskienė Danuta , Galinienė Birutė , Marčinskas Albinas
Published: October 2008

In this article the authors aim to justify the structure of the strategic management model for rational economic development by evaluating the new challenges facing the national economy development. The use of the SWOT strategic planning tool is critically evaluated, and the benefits of a balanced economic expert analysis structure are substantiated. Based on the findings in this article, it is recommended that government action programmes be based on the national economic development strategy formed by independent experts and given approval by the Lithuanian Seimas (Parliament).

Santrauka

Straipsnyje, įvertinant naujus iššūkius nacionalinio ūkio plėtrai, siekiama pagrįsti racionalaus ūkio
vystymo strateginio valdymo organizacinio modelio struktūrą. Kritiškai įvertinamas strateginės analizės instrumento SWOT naudojimas, pagrindžiama subalansuotos ūkio ekspertizės struktūra. Siūloma vyriausybių veiklos programose remtis nacionaline ūkio plėtros strategija, kurią formuoja nepriklausomi specialistai, įstatymais įtvirtina Lietuvos Respublikos Seimas.
MATHEMATICAL MODELLING OF FORECASTING THE RESULTS OF KNOWLEDGE TESTING / ŽINIŲ TIKRINIMO REZULTATŲ PROGNOZĖS MATEMATINIS MODELIAVIMAS
Authors: Krylovas Aleksandras , Kosareva Natalja
Published: October 2008

In this paper a mathematical model for obtaining probability distribution of the knowledge testing results is proposed. Differences and similarities of this model and Item Response Theory (IRT) logistic model are discussed. Probability distributions of 10 items test results for low, middle and high ability populations selecting characteristic functions of the various difficulty items combinations are obtained. Entropy function values for these items combinations are counted. These results enable to formulate recomendations for test items selection for various testing groups according to their attainment level. Method of selection of a suitable item characteristic function based on the Kolmogorov compatibility test, is proposed. This method is illustrated by applying it to a discreet mathematics test item. Santrauka Straipsnyje pasiūlytas matematinis modelis žinių tikrinimo rezultatų tikimybiniam skirstiniui gauti. Aptarti šio modelio ir užduočių sprendimo teorijos (IRT) logistinio modelio skirtumai ir panašumai. Išnagrinėti 10 klausimų testo rezultatų tikimybiniai skirstiniai silpnai, vidutinei ir stipriai testuojamųjų populiacijoms parenkant įvairias testo klausimų sunkumo funkcijų kombinacijas. Apskaičiuotos entropijos funkcijos reikšmės. Gauti rezultatai leidžia formuluoti rekomendacijas testo klausimams parinkti skirtingoms testuojamųjų grupėms pagal jų žinių lygį. Pasiūlytas tinkamiausios klausimo charakteristinės funkcijos parinkimo būdas, grindžiamas Kolmogorovo kriterijumi. Ši procedūra iliustruojama taikant ją konkrečiam diskrečiosios matematikos testo klausimui.
REASONED DECISIONS IN CONSTRUCTION CONTRACTS EVALUATION / RACIONALUŪS SPRENDIMAI VERTINANT STATYBOS RANGOS SUTARTIS
Authors: Mitkus Sigitas , Trinkūnienė Eva
Published: October 2008

Preparation of an agreement has a great influence on economic success of both parties and on their behaviour in order to increase their profits and to protect themselves against a possible loss. It is important to use technological innovations in construction contracting. Even when the contractor is selected and the price and work terms are negotiated, it is possible to choose several variants of agreements. The aim of this article is to develop a hierarchical model of criteria of a construction contract agreement based on their functions. Construction contract agreements can be concluded, evaluated and compared on the basis of this model. The model forms the basis of decision support system for analysis of construction contracts. Decision support system created on the basis of the presented model can be very useful and helpful in construction contract agreement and can be widely implemented in different construction sectors. Santrauka Tinkamas statybos rangos sutarčių parengimas turi didelę įtaką abiejų šalių sutarties įvykdymo ekonominei sėkmei. Netgi tais atvejais, kai statybos rangovas yra jau parinktas, sutarta dėl statybos kainos ir kitų esminių sutarties sąlygų, galimi daugiau negu vienas statybos rangos sutarčių variantai. Siekiant parinkti racionalų sutarties variantą reikia sudaryti statybos rangos sutarties modelį ir paruošti sutarties vertinimo sprendimo paramos sistemą. Autoriai siūlo statybos rangos sutartis vertinti naudojant hierarchinį statybos rangos sutarties modelį. Straipsnyje aprašyta autorių siūloma internetinė statybos rangos sutarčių vertinimo sistema, pagrįsta pasiūlytu statybos rangos sutarties modeliu.
INVESTMENT DECISIONS MODELLING ALONG SUSTAINABLE DEVELOPMENT CONCEPT ON FINANCIAL MARKETS / INVESTICINIŲ SPRENDIMŲ MODELIAVIMAS VARTOJANT TVARIOSIOS PLĖTROS SĄVOKĄ FINANSŲ RINKOSE
Authors: Rutkauskas Aleksandras Vytautas , Miečinskienė Algita , Stasytytė Viktorija
Published: October 2008

The goal of the paper is development of the conception of sustainable return investment decisions strategy in capital and money markets and modeling of investment decisions along sustainable development concept in capital and money markets. The research was performed with an experiment in FOREX and in some matured and emerging capital markets. The adequate for investments decisions reliability assessment portfolio will be presented and analysed as main instrument for developing sustainable return investment decisions strategy. The cases of practical implementation of adequate portfolio will be widely described. Further, the pragmatical problems how to use the strategy as innovative and effective financial instrument for investors and stock treasury will be discussed. Practical calculation was made on the very last data of different markets. Santrauka The goal of the paper is development of the conception of sustainable return investment decisions strategy in capital and money markets and modeling of investment decisions along sustainable development concept in capital and money markets. The research was performed with an experiment in FOREX and in some matured and emerging capital markets. The adequate for investments decisions reliability assessment portfolio will be presented and analysed as main instrument for developing sustainable return investment decisions strategy. The cases of practical implementation of adequate portfolio will be widely described. Further, the pragmatical problems how to use the strategy as innovative and effective financial instrument for investors and stock treasury will be discussed. Practical calculation was made on the very last data of different markets.
BOOK REVIEW
Authors: Lenz Barbara
Published: October 2008

"Book ‘Pletros krypčiu vertinimo ir valdymo informaciniai modeliai: monografija’ review." Ukio Technologinis ir Ekonominis Vystymas, 14(3), pp. 444-447
Multispectral processing of high‐resolution radiometric data for soil mapping
Authors: Beckett Kirsty
Published: October 2008

Soil radioactivity is dominantly a product of the local geology and mineralization, physical and chemical weathering processes within the profile, and soil organic content. Recent studies have shown that local soil patterns can be confidently mapped at scales of 1:10 000 using new high spatial resolution airborne and ground radiometric data acquired with standard 256‐channel gamma‐ray spectrometry systems and sodium‐iodide (NaI) crystal packs. In this study, a new multispectral processing methodology was developed to assess the 256‐channel spectral soil response. The study identified seven distinct gamma‐ray energy peaks, all products of the potassium‐40, uranium‐238 or thorium‐232 decay series, whose spatial and spectral relationships could be used to interpret soil properties and/or soil conditions.

In the case studies presented, interpretation of complementary thorium and uranium channels (isolated using the new multispectral processing methodology) reveal additional spatial patterns and spectral information that were unattainable using standard processing methods. In one example, soil conditions attributed to a local, developing clay‐soil unit were resolved by the increased 228Ac (actinium) to 208Tl (thorium) channel response. In a separate example, a change in ratio between 214Bi (uranium) energies 1120 keV and 1764 keV, produced during the same decay emission, was used to differentiate soil conditions in the top 40 cm of an expansive sandy loam on clay duplex soil unit. A decrease in the 1120 keV to 1764 keV ratio was interpreted as an increase in soil density as the lower gamma‐ray energy emissions are preferentially attenuated with increased density. Relative increases in the 1120 keV and 1764 keV channel responses were interpreted as an increase in uranium concentration in the soil profile. With the clay as the dominant uranium contributor, integrated interpretation of the 214Bi channels suggested that in these areas there was an increase in clay percentage within the surface sandy loam, which may result in local increased water‐logging susceptibility.

This paper also theorizes that interpretation of the spatial displacement of thorium‐232 decay series 228Ac and 208Tl peaks, produced from decay events approximately 2 years (half‐life) apart, can be used to identify decay series disequilibrium conditions resulting from local soil–water processes or other recent soil activity. This information contributes to an understanding of the soil processes active in the area. In addition, identification of disequilibrium decay conditions may highlight locations where standard radiometric (radioelement) processing, which relies on equilibrium conditions, may be erroneous.
The
Nrf
H
Cytochrome

c

Quinol Dehydrogenase
Authors: Thackray Sarah J , Bruckmann Chiara , Mowat Christopher G , Forouhar Farhad , Chapman Stephen K , Tong Liang
Published: October 2008

Indoleamine 2,3‐dioxygenase (IDO) and tryptophan 2,3‐dioxygenase (TDO) are heme‐containing enzymes from a small family of homologous enzymes. Despite both catalyzing the dioxygenation of
L
‐tryptophan, the first step in the kynurenine pathway, the sequence similarity between TDO and IDO is low. Alignment of sequences across this family of enzymes is only possible on the basis of their structures. Human IDO shows activity toward a wider range of substrates than TDO, and is found throughout the body, while TDO is limited to the liver and epidermis in mammals. To date, no functional prokaryotic IDO has been identified, while TDO is found in many bacteria. TDO and IDO have been implicated in a number of human physiological conditions, including suppression of T‐cell proliferation and the immune escape of cancers, making them attractive targets for drug discovery.
Nickel Regulatory Transcription Factor,
Nik
R
Authors: Phillips Christine M , Drennan Catherine L
Published: October 2008

The variety of roles that transition metals fulfill within the cell is staggering, but the concentrations of these metals must be tightly regulated to maintain minimal requisite levels and simultaneously prevent metal‐induced oxidative stress or inappropriate metal‐binding events. A variety of bacteria control the concentration of the transition metal nickel using the transcriptional repressor NikR. To suppress the import of nickel, the NikR protein binds nickel ions, inducing NikR's affinity for a promoter region upstream of a gene encoding a nickel‐specific importer. This binding event blocks RNA polymerase from attaching to the DNA, preventing the expression of further nickel‐specific importers. A variety of biochemical, structural, and spectroscopic studies on NikR have provided interesting insight into the overall function and structure of this regulatory protein.
The
Mgt
E
Mg
2+
Transporter
Authors: Maguire Michael E
Published: October 2008

The MgtE class of Mg
2+
ion transporter is widespread in the bacteria, with over 50% of current genomic sequences and most marine metagenome sequences exhibiting a homolog. MgtE is the primary provider of cytosolic Mg
2+
in those organisms that carry it. MgtE homologs are widespread in the metazoa and fungi (SLC41 family) but apparently absent in the plants. In bacteria, MgtE functions as a Mg
2+
influx system, while in eukaryotes specific MgtE proteins may function as either influx or efflux systems. Despite their ubiquity, virtually nothing is known about the physiological role of MgtE. Bacterial MgtE proteins are homodimers, with the entire soluble domain at the N terminus and the entire membrane domain at the C terminus. A recent crystal structure of

Thermus thermophilus

MgtE putatively in the closed form shows that the membrane domain consists of 5 transmembrane helices, each at a substantial angle to the plane of the membrane, giving 10 transmembrane helices in the dimer. The pore is formed primarily by transmembrane segments 2 and 5. Each membrane domain is connected to the soluble domain by a single α‐helix orthogonal to the membrane. Attached to this ‘connecting helix’ is a soluble domain containing a superhelical bundle of 10 α‐helices (‘N domain’) followed by duplicated tandem cystathionine β‐synthase‐like motifs, which end in the ‘connecting helix.’ The N domain has structural homology to the FliG protein of the flagellar motor. It is not clear how Mg
2+
is recognized and selected. The crystal structure also contains several sites for bound Mg
2+
ions, one within the pore. Two Mg
2+
sites per monomer connect the ‘connecting helice’ and CBS domain to the membrane domain, while two additional sites per monomer connect the CBS‐ and N domains. The structure of the soluble domain with and without Mg
2+
has also been solved. The absence of Mg
2+
does not alter the structure of the N domain significantly, but the structure of the tandem cystathionine β‐synthase domains within each monomer does change to some extent. The largest change due to the absence of Mg
2+
is that the entire cystathionine β‐synthase domain rotates and slightly twists 120° from the N domain. It is not clear if this rotation is part of the mechanism by which the pore opens and closes. Presumably, the bound Mg
2+
ions in the soluble domain play a role in sensing Mg
2+
, and their dissociation could allow domain movement and lead to opening of the pore.
Hydropedology and Surface/Subsurface Runoff Processes
Authors: Lin Henry , Brooks Erin , McDaniel Paul , Boll Jan
Published: October 2008

The role of soils has long been recognized as critical to rainfall–runoff processes in watersheds. Hydropedology is an emerging interdisciplinary field that integrates pedology, hydrology, geomorphology, and other related bio‐ and geosciences to study interactive pedologic and hydrologic processes and the landscape–soil–hydrology relationships across space and time. This article presents an overview of hydropedology's contributions to the understanding and modeling of surface/subsurface runoff processes, especially the diagnosis of soil features that can help answer “why‐type” questions in watershed hydrology and the ubiquitous nature of preferential flow and its networks. We highlight two bottlenecks for advancing watershed hydrology and hydropedology: a conceptual bottleneck of modeling subsurface preferential flow networks and a technological bottleneck of nondestructively mapping or imaging subsurface architecture. Quantification of “soil architecture” at various scales and the identification of “hydropedologic functional units” in different landscapes offer promising potentials to advance hydrologic modeling. We present the information of linking surface/subsurface runoff processes to pedologic understanding at three scales of microscopic (macropores and aggregates), mesoscopic (horizons and pedons), and macroscopic (hillslopes and catchments) levels. Various examples from the literature are synthesized to illustrate the key points. Further research needs are suggested in the end.
Purification of Intact Chloroplasts from Arabidopsis and Spinach Leaves by Isopycnic Centrifugation
Authors: Seigneurin‐Berny Daphné , Salvi Daniel , Joyard Jacques , Rolland Norbert
Published: October 2008

Chloroplasts are plant‐specific organelles. They are the site of photosynthesis but also of many other essential metabolic pathways, such as syntheses of amino acids, vitamins, lipids, and pigments. This unit describes the isolation and purification of chloroplasts from Arabidopsis and spinach leaves. Differential centrifugation is first used to obtain a suspension enriched in chloroplasts (crude chloroplasts extract). In a second step, Percoll density gradient centrifugation is used to recover pure and intact chloroplasts. The Basic Protocol describes the purification of chloroplasts from Arabidopsis leaves. This small flowering plant is now widely used as a model organism in plant biology as it offers important advantages for basic research in genetics and molecular biology. The Alternate Protocol describes the purification of chloroplasts from spinach leaves. Spinach, easily available all through the year, remains a model of choice for the large‐scale preparation of pure chloroplasts with a high degree of intactness. Curr. Protoc. Cell Biol. 40:3.30.1‐3.30.14. © 2008 by John Wiley & Sons, Inc.
The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
Authors: Blake Judith A. , Harris Midori A.
Published: October 2008

Scientists wishing to utilize genomic data have quickly come to realize the benefit of standardizing descriptions of experimental procedures and results for computer‐driven information retrieval systems. The focus of the Gene Ontology project is three‐fold. First, the project goal is to compile the Gene Ontologies: structured vocabularies describing domains of molecular biology. Second, the project supports the use of these structured vocabularies in the annotation of gene products. Third, the gene product‐to‐GO annotation sets are provided by participating groups to the public through open access to the GO database and Web resource. This unit describes the current ontologies and what is beyond the scope of the Gene Ontology project. It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research. Curr. Protoc. Bioinform. 23:7.2.1‐7.2.9. © 2008 by John Wiley & Sons, Inc.
Browsing Multidimensional Molecular Networks with the Generic Network Browser (N‐Browse)
Authors: Kao Huey‐Ling , Gunsalus Kristin C.
Published: October 2008

N‐Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. N‐Browse runs as a Java applet in a Web browser, providing highly dynamic and interactive on‐demand access to network data available from a remote server. The N‐Browse interface is easy to use and accommodates multiple types of functional linkages with associated information, allowing the exploration of many layers of functional information simultaneously. Although created for applications in biology, N‐Browse uses a generic database schema that can be adapted to network representations in any knowledge domain. The N‐Browse client‐server package is freely available for distribution, providing a convenient way for data producers and providers to distribute and offer interactive visualization of network‐based data. Curr. Protoc. Bioinform. 23:9.11.1‐9.11.21. © 2008 by John Wiley & Sons, Inc.
Superiority Trial
Authors: Sackett David L.
Published: October 2008

When busy clinicians encounter a new treatment, they ask themselves two questions. First, is itbetterthan (“superior to”) what they are using now? Second, if is not superior, is itas good aswhat they are using now (“noninferior”) and preferable for some other reason (e.g., fewer side effects or more affordable)? In statistical terms, these clinical questions are “one‐sided.” However, traditional statistical concepts call for two‐sided tests of statistical significance and require rejection of the null hypothesis. A solution to both this incompatibility (between one‐sided clinical reasoning and two‐sided statistical testing) and confusion (about the clinical interpretation of statistically nonsignificant results) is now gaining widespread recognition and application. It is encompassed by the concepts of “superiority” and “noninferiority,” and these inextricable concepts are the subjects of this entry.
Intention‐to‐Treat Analysis
Authors: Lachin John M.
Published: October 2008

The intention‐to‐treat principle developed from concerns that analysis of a subset of subjects into randomized a clinical trial may provide a severely biased comparison of the study treatments, and it may not describe the expected outcome in all subjects for whom a treatment might be administered. Theintention‐to‐treat analysisincludes all subjects randomized into the study to provide a pragmatic assessment of the effects of therapy in general use, regardless of other considerations such as drug tolerability or compliance. This approach is contrasted with subset analyses, such as the “efficacy subset” that only includes the subset that tolerated the assigned agent, who were largely compliant and who completed follow‐up.

However, a true intention‐to‐treat analysis requires that all those randomized should complete follow‐up and outcome assessments to the extent possible, even if no longer taking the drug, and that their outcome data should be employed in the analysis. This design is termed anintention‐to‐treat design.

Many statistical methods provide an unbiased comparison of treatment effects when all missing observations are ignorable, assuming that no bias is introduced. However, this assumption is inherently unverifiable. Thus, the only incontrovertibly unbiased study is one in which all randomized patients are evaluated and included in the analysis, assuming that other features of the study are also unbiased. This design is the essence of the intent‐to‐treat philosophy.
Cardiac Arrhythmia Suppression Trial (CAST)
Authors: Moyé Lemuel A.
Published: October 2008

The development of new antiarrhythmic agents seemed to herald a new era in which the treatment of serious ventricular arrhythmias would be reduced. The arrhythmia suppression hypothesis, for example, the suppression of mild ventricular arrhythmias would reduce the subsequent rate of adverse arrhythmic clinical events, was accepted by many, and FDA approval of these agents preceded a formal proof of the theory.
Integrated Database
Authors: Kenny Susan J.
Published: October 2008

Integrated databases contain information collected from more than one data source. In the process of combining different data sources, individual data elements often need to be transformed or harmonized so that they represent a consistent or standard context. This transformation must be done without the loss of data integrity and interpretation. Combining data from multiple sources yields increased statistical power to identify important relationships between data elements. Without the increased sample size of an integrated database, the relationship between infrequently occurring rare events with some dependent factor, such as treatment regimen, may be difficult to identify. Integrated databases are used by research institutes, pharmaceutical companies, and regulatory agencies during clinical development and during postmarketing surveillance. Integrated databases have been used for many years, but in recent years, the use of integrated databases has expanded beyond the classic application to clinical trial data to include applications to image, genomic, and other digital data. More advances in data warehousing, enterprise software applications, and efforts in standardization of clinical information have influenced the construction and use of integrated databases.
Women's Health Initiative Hormone Therapy Trials
Authors: Bassuk Shari S. , Manson JoAnn E.
Published: October 2008

The Women's Health Initiative (WHI) postmenopausal hormone therapy (HT) trials were designed to determine the balance of benefits and risks of HT taken for chronic disease prevention by initially healthy postmenopausal women (age range, 50—79 years; mean age, 63 years). Women with an intact uterus were randomized to estrogen–progestin or placebo for a mean of 5.6 years; women with hysterectomy were randomized to estrogen alone or placebo for a mean of 7.1 years. Compared with their respective placebo‐group counterparts, women in the estrogen–progestin group were significantly more likely to experience an adverse health event, whereas women in the estrogen‐alone group were as likely to do so. Specifically, estrogen–progestin was associated with increased risks of coronary heart disease (CHD), stroke, venous thromboembolism, and breast cancer, as well as reduced risks of hip fracture and colorectal cancer. Estrogen alone was associated with an increased risk of stroke and a reduced risk of hip fracture; it had no effect on CHD risk. The results do not support the use of HT for chronic disease prevention in postmenopausal women as a whole. However, because few WHI participants were within 5 years of menopause, these trials cannot conclusively determine the risk–benefit balance of HT in recently menopausal women. Accumulating data suggest that the timing of HT initiation in relation to age or menopause onset may critically influence the relationship between such therapy and risk of CHD as well as its overall risk–benefit balance, with younger or recently menopausal women experiencing more favorable effects than older women or women further from menopause.
TNT
Trial
Authors: C. LaRosa John , M. Grundy Scott , D. Waters David
Published: October 2008

In the Treating to New Targets (TNT) study, 10,001 patients with stable CHD and LDL‐C levels <130 mg/dL (3.4 mmol/L) were randomized to double‐blind therapy with either atorvastatin 10 or 80 mg/day and were followed for a median of 4.9 years. The primary endpoint was an occurrence of a first major cardiovascular event, defined as CHD death, nonfatal, non‐procedure‐related myocardial infarction, resuscitated cardiac arrest, and fatal or nonfatal stroke. Mean LDL‐C levels achieved during treatment were 77 mg/dL (2.0 mmol/L) with atorvastatin 80 mg and 101 mg/dL (2.6 mmol/L) with atorvastatin 10 mg. A primary event occurred in 434 patients (8.7%) receiving atorvastatin 80 mg and 548 patients (10.9%) receiving atorvastatin 10 mg, representing a 2.2% absolute reduction in risk and a 22% reduction in risk of major cardiovascular events (HR = 0.78; CI = 0.69, 0.89;
P
 < 0.001) in the high‐dose group. In conclusion, intensive lipid‐lowering therapy with atorvastatin 80 mg in patients with stable CHD provided significant additional clinical benefit beyond therapy with atorvastatin 10 mg.
Dose Escalation Guided by Graded Toxicities
Authors: O'Quigley John , Wages Nolan
Published: October 2008

In most cancer dose‐finding studies, the toxicities are graded typically from 0 (the absence of any side effects) to 4 based on the presence of serious and potentially life‐threatening toxicity. Usually, these grades are subsequently recoded whereby all toxicity grades between 0 and 3 are given the value 0 and are considered to be non‐dose‐limiting toxicities (DLT), and grade 4 (a dose‐limiting toxicity) is coded as 1. We describe here how greater use can be made of this information, which potentially leads to more efficient and effective dose‐finding studies. Our focus is on two‐stage continual reassessment method (CRM) designs. During this design, an initial escalation stage requires no use of a model until the first toxicity is encountered, at which time the second stage, based on a model, kicks in. In this context, two possible ways can be used to make use of information on toxicity grades. We can make use of this information in either one of these two stages in different ways. In the first stage, the ideas are usually straightforward that appeal mostly to common‐sense arguments. Nonetheless, it can be observed that use of graded toxicity information in the first stage alone can make an important contribution to increased efficiency. Use of graded toxicity information in the second stage requires an additional model to demonstrate the rate of toxicities. This method is described as well as the potential improvements in performance, which can be achieved by the use of such models.
Informed Consent Process, Forms, and Assent
Authors: Glantz Leonard H.
Published: October 2008

Informed consent is a foundational principle for the ethical conduct of research with human subjects. It is essential for researchers to understand the purposes of the doctrine to enhance their ability to obtain both ethically and legally valid informed consent.
“Patients” vs. “Subjects”
Authors: Glantz Leonard H.
Published: October 2008

The terms “patient” and “subject” are often used interchangeably when proposing, conducting, or reporting on research. This error is not just a semantic one but also a conceptual one. Proper use of these terms is essential for all parties involved in the research to understand clearly their roles, expectations, and obligations.
Repository
Authors: Winkler Cheryl A , Groover Kathleen H.
Published: October 2008

Repositories for the acquisition, storage/archival, and distribution of biosamples are essential to the success of clinical trials and biomedical research. In the current era of genomics and proteomics, the banking of human biosamples and associated phenotypes for the discovery of genetic factors underpinning rare and common diseases has expanded the role and impact of repositories and biobanks. Today's repositories are banking an unprecedented number of biosamples and data for molecular‐based research. This article provides an overview of repository models, the core function and management of repositories, and issues that pertain to the protection of donor rights and confidentiality.
Generalized Estimating Equations
Authors: Hardin James W. , Hilbe Joseph M.
Published: October 2008

Correlated datasets develop when multiple observations are collected from a sampling unit (e.g., repeated measures of a bank over time, or hormone levels in a breast cancer patient over time), or from clustered data where observations are grouped based on a shared characteristic (e.g., observations on different banks grouped by zip code, or on cancer patients from a specific clinic). The generalized linear model framework for independent data is extended to model correlated data via the introduction of second‐order variance components directly into the independent data model's estimating equation. This generalization of the estimating equation from the independence model is thus referred to as a Generalized Estimating Equation (GEE). This article discusses the foundation of GEEs as well as how user‐specified correlation structures are accommodated in the model‐building process. This article also discusses the relationship and similarity to the underlying generalized linear model framework and we point out alternative approaches to GEEs for modeling correlated data such as fixed‐effects models and random‐effects models.
Disease Trials in Reproductive Diseases
Authors: Johnson Julia V.
Published: October 2008

Historically, studies in reproductive medicine have been of limited quality mainly because of the challenging group of subjects, the limited effective study design, and the lack of standards advised for clinical trials. In addition, reproductive medicine has classically received limited funding for the National Institute of Child Health and Human Development (NICHD) at the National Institutes of Health (NIH). Because of the importance of reproductive health issues, the NIH has developed programs to increase translational and clinical research. In addition, research has encouraged standards for reproductive research to assure high‐quality clinical trials. This article will review the classic limitations of studies in reproductive medicine, the standards that have improved the quality of research, and it will describe NIH funded programs to promote knowledge and optimize patient care.
Imaging Science in Medicine
Authors: Hendee William R.
Published: October 2008

The use of imaging technologies has expanded tremendously in medicine over the past two decades. This expansion reflects the evolution of new imaging tools that reveal human anatomy and physiology in ever‐increasing detail, as well as the development of digital data acquisition and processing techniques that extract information from human tissues in ever‐expanding degrees of subtlety. A further factor that is stimulating growth in imaging is the expansion of knowledge about biological systems at the cellular, molecular, and genetic levels. This factor is transforming medical imaging from a “technology‐push” discipline into one where fundamental biological questions, as well as important clinical issues, are the force driving development of new imaging technologies. This transformation demands enhanced knowledge about the interface between biological properties of tissues and the characteristics of imaging systems. Exploration of the existing state of knowledge about the interface, and what is needed for the immediate future, is the subject of this article.
Biological Assay, Overview
Authors: Sen Pranab K.
Published: October 2008

Biological essay (or “bioassay”), in its classical form, is concerned with the measurement of the concentration of an active ingredient in a test preparation, by estimation of its potency relative to that of a standard preparation. Assays, usually by animal experimentation, form an essential tool of biological standardization. Standard designs and methods of analysis are described here, including stochastic approximation, radioimmunoassays, semiparametric and nonparametric methods, and bioequivalence studies. In a broader sense, Bioassay refers to experiments, with biological units, to detect possible dose–response (or toxicity‐adverse effect) relationships. Underlying toxicodynamics (and/or pharmacodynamics) and toxicokinetics (and/or pharmacokinetics), possibly in conjunction with toxicogenomics (and/or pharmacogenomics) may render such studies statistically quite different from conventional biometric studies. Some relevant approaches are considered here.
Logistic Regression
Authors: Lemeshow Stanley , Hosmer David W.
Published: October 2008

This article deals with the use of logistic regression to model data, where the response variable is binary and there are potentially numerous explanatory or predictor variables. Methods of estimating the coefficients in the model and procedures for hypothesis testing are considered. The correspondence of the coefficients of the logistic regression model to the odds ratio is noted along with methods for computing point estimates and confidence intervals for the odds ratio. Interpretation of coefficients for dichotomous, polytomous, and continuous independent variables is carefully developed. Confounding and effect modification are easily dealt with through the use of this modeling technique. All these concepts are illustrated through the analysis of low birth weight data.
Outliers
Authors: Hawkins Douglas M.
Published: October 2008

Outliers are observations highly discordant from the rest of the data, either in a univariate distribution or in relation to a model with explanatory variables. They may arise through contamination, errors in data gathering, or misspecification of the model. Approaches to detection include “high‐breakdown” methods involving partitions of the data into acceptable and discordant sets; and sequential identification of individual outliers by forward selection or, preferably, backward elimination. Likelihood ratios or multiple comparison methods may be used. Special cases are considered and the topic is illustrated by an example using data on body weight and brain weight of animals and dinosaurs.