bluuebunny/crossref_metadata_2025 huggingface dataset:
Chest physiotherapy during immediate postoperative period among patients undergoing upper abdominal surgery: randomized clinical trial
Authors: Manzano Roberta Munhoz , Carvalho Celso Ricardo Fernandes de , Saraiva-Romanholo Beatriz Mangueira , Vieira Joaquim Edson
Published: December 2008

CONTEXT AND OBJECTIVE: Abdominal surgical procedures increase pulmonary complication risks. The aim of this study was to evaluate the effectiveness of chest physiotherapy during the immediate postoperative period among patients undergoing elective upper abdominal surgery. DESIGN AND SETTING: This randomized clinical trial was performed in the post-anesthesia care unit of a public university hospital. METHODS: Thirty-one adults were randomly assigned to control (n = 16) and chest physiotherapy (n = 15) groups. Spirometry, pulse oximetry and anamneses were performed preoperatively and on the second postoperative day. A visual pain scale was applied on the second postoperative day, before and after chest physiotherapy. The chest physiotherapy group received treatment at the post-anesthesia care unit, while the controls did not. Surgery duration, length of hospital stay and postoperative pulmonary complications were gathered from patients' medical records. RESULTS: The control and chest physiotherapy groups presented decreased spirometry values after surgery but without any difference between them (forced vital capacity from 83.5 ± 17.1% to 62.7 ± 16.9% and from 95.7 ± 18.9% to 79.0 ± 26.9%, respectively). In contrast, the chest physiotherapy group presented improved oxygen-hemoglobin saturation after chest physiotherapy during the immediate postoperative period (p < 0.03) that did not last until the second postoperative day. The medical record data were similar between groups. CONCLUSIONS: Chest physiotherapy during the immediate postoperative period following upper abdominal surgery was effective for improving oxygen-hemoglobin saturation without increased abdominal pain. Breathing exercises could be adopted at post-anesthesia care units with benefits for patients.
Richness, abundance, and mass in snake assemblages from two Atlantic Rainforest sites (Ilha do Cardoso, São Paulo) with differences in environmental productivity
Authors: Rocha Carlos Frederico Duarte , Bergallo Helena Godoy , Vera y Conde Carla Fabiane , Bittencourt Emerson Brum , Santos Hilda de Carvalho
Published: December 2008

We analyzed richness, composition and mass of snakes in two sites in the Atlantic forest of Ilha do Cardoso (25º 03' S and 47º 53' W), an island (22,500 ha), Cananéia municipality, São Paulo State, Brazil. A monthly index of arthropod availability (in mm³) was estimated in each site through capture rates in pit-fall traps. Fallen fruits were collected along trails in the study sites (mass of fruit gave an index of fruit availability) and small mammals were sampled in grids with 120 traps which covered the lowland (5.2 ha) and in the slope forests (3.6ha). The abundance and mass of small mammals were standardized for the size of each sampled area (in g.ha-1). To sample snakes we established 20 pit-fall traps in each area and performed monthly transects in four consecutive days (totaling 1000 m long) along trails in the study sites. Snakes found were measured, weighted marked and released. Abundance and total mass of snakes were standardized by the size of each area. The areas differed consistently in in the productivity of arthropods, fruits and small mammals, and also in richness, composition and total mass of snakes. We found 36 individuals (total mass = 9884 g) of 12 snake species belonging to three Families (Colubridae, Elapidae and Viperidae) in the lowland forest, whereas in the slope forest we sampled only 9 individuals of 2 species (total mass = 1820 g). Our results suggest that the area of lowland forest, showing higher productivity of arthropods, fruits and small mammals, maintains a snake community with a higher richness, diversity and biomass than its slope forest counterpart.
Prevalência de aspergilose broncopulmonar alérgica em pacientes com fibrose cística na Bahia, Brasil
Authors: Carneiro Ana Cláudia Costa , Lemos Antônio Carlos Moreira , Arruda Sérgio Marcos , Santana Maria Angélica Pinheiro Santos
Published: December 2008

OBJETIVO: Determinar a prevalência de aspergilose broncopulmonar alérgica (ABPA) em pacientes com fibrose cística acompanhados em um centro de referência da Bahia. MÉTODOS: Estudo transversal, com coleta prospectiva de dados, realizado no Centro de Referência de Fibrose Cística da Bahia do Hospital Especializado Octavio Mangabeira. Foram incluídos no estudo 74 pacientes que tinham diagnóstico de fibrose cística, com idade acima de 6 anos e tratados entre 9 de dezembro de 2003 e 7 de março de 2005. Foram analisadas as seguintes variáveis: gênero, idade, capacidade vital forçada, volume expiratório forçado no primeiro segundo, resposta a prova farmacodinâmica, achados em radiografia torácica e de seios de face, presença de sibilância, culturas para Aspergillus spp., imunoglobulina E (IgE) total, IgE específica para Aspergillus fumigatus e teste cutâneo de leitura imediata para aspergilina. RESULTADOS: Dos 74 pacientes, 2 foram diagnosticados com ABPA. Níveis de IgE total > 1.000 UI/mL foram observados em 17 pacientes (23%), teste cutâneo de leitura imediata para A. fumigatus positivos em 19 (25,7%) e sibilância em 60 (81,1%). CONCLUSÕES: A taxa de prevalência de ABPA foi de 2,7%. As altas taxas de IgE total, de teste cutâneo imediato para A. fumigatus positivos e de sibilância sugerem que estes pacientes devam ser acompanhados cuidadosamente por haver a possibilidade do desenvolvimento de ABPA.
Nocardiose pulmonar em portador de doença pulmonar obstrutiva crônica e bronquiectasias
Authors: Aidê Miguel Abidon , Lourenço Silvia Soares , Marchiori Edson , Zanetti Gláucia , Mondino Pedro Juan José
Published: December 2008

Relatamos o caso de um paciente com doença pulmonar obstrutiva crônica e bronquiectasias, em uso crônico de corticosteróides, que desenvolveu nocardiose pulmonar, sob a forma de múltiplos nódulos pulmonares escavados. Os sintomas principais foram a tosse produtiva com escarro purulento, febre e dispnéia A radiografia simples e a tomografia computadorizada do tórax mostravam nódulos em ambos os pulmões, alguns escavados. O exame direto de escarro e a cultura mostraram a presença de Nocardia spp. A paciente foi tratada com imipenem e cilastatina, com excelente resposta clínica.
Identification of a Small Subpopulation of Candidate Leukemia-Initiating Cells in the Side Population of Patients with Acute Myeloid Leukemia
Authors: Moshaver Bijan , van Rhenen Anna , Kelder Angèle , van der Pol Marjolein , Terwijn Monique , Bachas Costa , Westra August H. , Ossenkoppele Gert J. , Zweegman Sonja , Schuurhuis Gerrit Jan
Published: December 2008

In acute myeloid leukemia (AML), apart from the CD34+CD38− compartment, the side population (SP) compartment contains leukemic stem cells (LSCs). We have previously shown that CD34+CD38− LSCs can be identified using stem cell-associated cell surface markers, including C-type lectin-like molecule-1 (CLL-1), and lineage markers, such as CD7, CD19, and CD56. A similar study was performed for AML SP to further characterize the SP cells with the aim of narrowing down the putatively very low stem cell fraction. Fluorescence-activated cell sorting (FACS) analysis of 48 bone marrow and peripheral blood samples at diagnosis showed SP cells in 41 of 48 cases that were partly or completely positive for the markers, including CD123. SP cells in normal bone marrow (NBM) were completely negative for markers, except CD123. Further analysis revealed that the SP fraction contains different subpopulations: (a) three small lymphoid subpopulations (with T-, B-, or natural killer-cell markers); (b) a differentiated myeloid population with high forward scatter (FSChigh) and high sideward scatter (SSChigh), high CD38 expression, and usually with aberrant marker expression; (c) a more primitive FSClow/SSClow, CD38low, marker-negative myeloid fraction; and (d) a more primitive FSClow/SSClow, CD38low, marker-positive myeloid fraction. NBM contained the first three populations, although the aberrant markers were absent in the second population. Suspension culture assay showed that FSClow/SSClow SP cells were highly enriched for primitive cells. Fluorescence in situ hybridization (FISH) analyses showed that cytogenetically abnormal colonies originated from sorted marker positive cells, whereas the cytogenetically normal colonies originated from sorted marker-negative cells. In conclusion, AML SP cells could be discriminated from normal SP cells at diagnosis on the basis of expression of CLL-1 and lineage markers. This reveals the presence of a low-frequency (median, 0.0016%) SP subfraction as a likely candidate to be enriched for leukemia stem cells.

Disclosure of potential conflicts of interest is found at the end of this article.
Undrained shear strength of soils under flow deformation
Authors: Tsukamoto Y. , Ishihara K. , Kamata T.
Published: December 2008

The initial stress and density condition leading to flow deformation and the resultant undrained strength of clean and silty sands are examined based on the un-drained triaxial tests. The effective major stress at consolidation σ′1c is found to serve as a primary parameter in defining a series of characteristic state lines and undrained strength ratios. The largest possible undrained strength ratio Sus/σ′1c under flow deformation was found not to differ largely among soils, though the range of such initial density conditions differs. The estimation of undrained strength would therefore be practically useful in determining the occurrence of flow deformation.
Modeling Cd2 +  sorption onto ferrihydrite in the presence of phthalic acid
Authors: Song Y. , Singhal N. , Swedlund P. , Swift S.
Published: December 2008

Cadmium sorption by ferrihydrite in the presence of phthalic acid was examined over a range of pH (4.0 ∼ 8.5) conditions and sorbate/sorbent ratios. The presence of phthalic acid enhanced Cd2 +  sorption by forming ternary complexes on ferrihydrite surface, especially at low pH, but for high pH and high total organic ligand/Fe(mmol/mol) ratios, it decreased Cd2 +  sorption onto ferrihydrite by forming soluble complexes with the phthalate in solution. In binary systems, Cd2 +  and phthalic acid sorption by ferrihydrite was well reproduced using the diffuse layer model with sorption constants derived from the experimental data. Prediction using the optimised binary sorption constants for Cd2 +  sorption onto ferrihydrite in the presence of phthalic was poor and achieving a good fit required the inclusion of two additional ternary complexes.
Transport and biotransformation of organic carbon and nitrate compounds in unsaturated soil conditions
Authors: Bunsri Thidarat , Sivakumar Muttucumaru , Hagare Dharmappa
Published: December 2008

The lack of drinking water was one of the hot environmental issues that focused on the contaminants released from the failure of sanitary systems. Organic carbon and nitrate compounds were concerned since they represented a potential risk to human health and environment. Mathematical modelling was an effective tool for understanding and estimating the fate and transport of contaminants. An organic carbon and nitrate compounds transport model was developed using the mass balance concept. Richards and multiplicative Monod equations supported the estimating of advection-dispersion transport and biodegradation processes, respectively. The numerical solutions were obtained using the MATLAB programme. The model capability was evaluated using pilot scale experimental data. The depth-averaged time series of pressure head and contaminants concentration profiles were measured several times a week during 91 days. Simulations were found to provide reasonable agreement with the observed data. The aerobic biodegradation zone was observed within 15 cm depth of soil column. Even though the column was operated for 91 days, soil microbes were enough to retard these contaminants. This confirmed that the developed model could be applied to simulate the transport of the contaminants under real time boundary conditions.
Eutrophication of agricultural streams: defining nutrient concentrations to protect ecological condition
Authors: Chambers Patricia A. , Vis C. , Brua R. B. , Guy M. , Culp J. M. , Benoy G. A.
Published: December 2008

Inputs of nutrients (phosphorus, P, and nitrogen, N) to coastal and fresh waters can accelerate eutrophication, resulting in excessive aquatic plant growth, depletion of oxygen, and deleterious changes in abundance and diversity of organisms. Using long-term (∼1995–2005) monitoring data from agriculturally-dominated watersheds in southern Ontario and Quebec, Canada, we developed and tested several approaches for setting targets for N and P. Our research showed that it is possible to set scientifically-credible targets for total P and total N to protect ecological condition of streams in agricultural landscapes, and define achievable targets attainable following adoption of beneficial management practices.
Assessing necessary nutrient reduction for measurement planning in groundwater bodies
Authors: Kunkel Ralf , Eisele Michael , Wendland Frank
Published: December 2008

For the Federal State of Lower Saxony, Germany, nitrogen management options are developed and implemented in three pilot areas using new participation approaches and technologies suitable for programs of measures to reduce diffuse pollution from agriculture. As a target value for water protection measures a nitrate concentration in percolation water of 50 mg/l as an average for a larger area defined by the groundwater bodies and their hydrogeological subdivisions has been defined. An integrative emission model is used to simulate the interactions between agricultural practice, nitrogen surpluses and the nitrogen flow through the soil and aquifer to the outflow into surface waters. The actual nitrate concentrations in percolation water are calculated for the entire Federal State of Lower Saxony considering site-characteristics, N-surpluses, water balance and denitrification in the soil. The tolerable N-surpluses needed to meet the environmental target are quantified as averages for each of the hydrogeological subdivisions by “backward” calculation using this model system. The required reduction of N-surpluses was estimated by comparing the tolerable N-surpluses with the actual state of nitrogen emission. For the evaluation of the amount and efficiency of water protection measures, the required reduction of N-surpluses to accomplish the environmental target is quantified, using the current status as a reference.
Estimation of pollutant loads considering dam operation in Han River Basin by BASINS/Hydrological Simulation Program-FORTRAN
Authors: Jung Kwang-Wook , Yoon Choon-G , Jang Jae-Ho , Kong Dong-Soo
Published: December 2008

Effective watershed management often demands qualitative and quantitative predictions of the effect of future management activities as arguments for policy makers and administration. The BASINS geographic information system was developed to compute total maximum daily loads, which are helpful to establish hydrological process and water quality modeling system. In this paper the BASINS toolkit HSPF model is applied in 20,271 km2 large watershed of the Han River Basin is used for applicability of HSPF and BMPs scenarios. For proper evaluation of watershed and stream water quality, comprehensive estimation methods are necessary to assess large amounts of point source and nonpoint-source (NPS) pollution based on the total watershed area. In this study, The Hydrological Simulation Program–FORTRAN (HSPF) was estimated to simulate watershed pollutant loads containing dam operation and applied BMPs scenarios for control NPS pollution. The 8-day monitoring data (about three years) were used in the calibration and verification processes. Model performance was in the range of “very good” and “good” based on percent difference. The water-quality simulation results were encouraging for this large sizable watershed with dam operation practice and mixed land uses; HSPF proved adequate, and its application is recommended to simulate watershed processes and BMPs evaluation.
Settling velocity of particulate pollutants from combined sewer wet weather discharges
Authors: Gromaire M. C. , Kafi-Benyahia M. , Gasperi J. , Saad M. , Moilleron R. , Chebbo G.
Published: December 2008

Settling velocities of TSS and of particulate pollutants (COP, PDCO, PTKN, PCu, PPb, PZn, PPAH) measured on a wide range of wet weather flow (WWF) samples collected at different levels of the Parisian combined sewer system are reported. The recorded V30 (0.01 to 0.1 mm.s-1) and V50 (0.09 to 0.6 mm.s−1) values exceed by a factor 10 those of dry weather sewage and also exceed the values measured for pavement runoff. These values lie however often below the 0.28 mm.s−1 reference value considered in France for the design of WWF settling facilities. A decrease in settleability is observed between a small upstream catchment and larger scaled downstream catchments. The settling behaviour of particulate pollutants varies depending on the considered parameter and can differ significantly from the TSS behaviour, due to a non homogeneous distribution of micropolluants over the different classes of particles. PZn and PTKN appear far less settleable than TSS, whereas PPAH show higher settleability.
Physiological heterogeneity of suspended microbial aggregates
Authors: Ivanov Volodymyr , Nejad Saeid Rezaei , Yi Shan , Wang Xiao Hui
Published: December 2008

Suspended microbial aggregates, which are always in dynamic equilibrium with suspended cells and cells attached to surface, are very common structures in natural and engineering environmental systems. To study and design physiologically diverse suspended microbial aggregates the physiological classification of chemotrophic prokaryotes in 12 groups formed by four evolutionary periods (fermenting, anaerobic respiring, microaerophilic and facultative aerobic, aerobic prokaryotes) and three parallel lines (Gram-negative, Gram-positive Eubacteria, and Archaea) could be used. This type of physiological heterogeneity has been studied in microbial granules using fluorescence in situ hybridization, identification of 16S rRNA genes, and conferring the physiological properties from the description of the species. In spherical granules with diameter of 2.4 mm cells of aerobes were spread to the depth 0.55 mm below surface (85% of granule volume), facultative anaerobes dominated between the depths 0.55 mm and 0.85 mm (13% of granule volume), and anaerobes were concentrated at the depths from 0.85 to 1.0 mm (2% of granule volume). Percentages of aerobic, facultative anaerobic, and anaerobic species in granules, identified by 16S rRNA gene sequencing, were 69%, 9%, and 2% of total number of bacterial clones, respectively. Another type of physiological heterogeneity on the cellular level was due to the changes of cell physiological status during cell cycle. This type of heterogeneity has been studied in the populations of Escherichia coli, Bacillus megaterium, Saccharomyces cerevisiae, and Candida tropicalis. A significant proportion of cells from the exponential phase were killed after 10 min treatment with 1% solution of allyl alcohol, which specifically kills cells with high activity of alcohol dehydrogenase (ADH). However, there was no such effect in starved cell population. Percentage of cells with high activity ADH in microbial population can be used to monitor its physiological status. Physiological diversity of ecosystem may be due to mechanical mixing of cells from the different inflows. An example of such system is an ecosystem of aeration tank in municipal wastewater treatment plant. This ecosystem contains a mechanical mixture of dead anaerobic and live aerobic bacteria as well as attached and suspended cell aggregates supplied from anaerobic digester, raw sewage, and settling tank.
Mapping areas at risk of diffuse phosphorus losses to water: a pilot study of Lake Haderslev Dam, Denmark
Authors: Andersen Hans Estrup , Heckrath Goswin , Thodsen Hans
Published: December 2008

Haderslev Dam is a 272 ha lake in southern Denmark with a high recreational value. For decades the lake has been severely eutrophicated due to excessive phosphorus loading. Major point sources were cut off in the early 1990s and an upstream wetland was recreated. However, the ecological quality remains unsatisfactory. In this study we estimate the importance of agriculture on diffuse phosphorus (P) input to the lake by modelling combined with independent estimates for contributions from scattered dwellings not connected to a sewer and from background losses. We apply a newly developed Danish P index to the lake catchment for mapping of risk areas for diffuse phosphorus losses. For risk areas we suggest mitigation measures and estimate the effect of the mitigation measures on the total P loading of the lake as well as the associated costs.
Modelling 132 kV Substation for Surge Arrester Studies
Authors: Ab Kadir Mohd Zainal Abidin , Mohamed Ariff Hatta , Azmi Aida Maria
Published: December 2008

Insulation coordination models are an essential part of power system studies and are used to determine the performance of a transmission line or substation. This paper generalizes the guidelines and parameters to be used in modelling the substation and in performing the analysis on the prediction of the transformer damage. Modelling parameters and the substation layout design are based and adapted from 132/11 kV Simpang Renggam  Ayer Hitam substation in Johor Baharu, Malaysia, courtesy of the Tenaga Nasional Berhad (TNB). The model is based on the single phase line model, as was suggested by the IEEE, to be adequate to represent the substation in transient analysis simulation. Extensive analyses on the placement of the surge arresters at the substation and a prediction of the transformer damage are also presented. The results obtained from this analysis are then compared with the suggested Basic Lightning Insulation Level (BIL) by the TNB, according to the standards, for assessing the percentage of transformer damage and optimizing the substation performance in terms of its reliability and cost effectiveness.
A Model Curriculum for Education in Fraud and Forensic Accounting
Authors: Kranacher Mary-Jo , Morris Bonnie W. , Pearson Timothy A. , Riley Richard A.
Published: December 2008

ABSTRACT: The following paper describes the promise and reality of creating fraud and forensic accounting courses and curriculum. The project was supported by the National Institute of Justice (NIJ), the research, development, and evaluation agency of the U.S. Department of Justice. The Model Curriculum guidelines were developed in three main phases: (1) constituting a planning panel to guide the project and selecting the members of a technical working group of subject matter experts, (2) developing the curriculum guidelines, and (3) field-testing those guidelines. This paper provides background and motivation for the project, an overview of the project processes, and the educational guidelines (outcomes) that were developed by experts in the field.
Serum Monocyte Chemoattractant Protein-1 Concentrations Associate With Diabetes Status but Not Arterial Stiffness in Children With Type 1 Diabetes
Authors: Zineh Issam , Beitelshees Amber L. , Silverstein Janet H. , Haller Michael J.
Published: December 2008

OBJECTIVE

The relationship between circulating markers of inflammation and arterial stiffness in children with type 1 diabetes is not well studied. We tested whether inflammatory monocyte chemoattractant protein (MCP)-1 concentrations correlate with arterial stiffness or type 1 diabetes status.

RESEARCH DESIGN AND METHODS

MCP-1 concentrations and radial tonometry data were available for 98 children with type 1 diabetes and 55 healthy control subjects. Arterial stiffness was calculated as augmentation index corrected for a heart rate of 75 (AI75). Correlation between MCP-1 and AI75 and differences in MCP-1 concentrations between case and control subjects were tested.

RESULTS

MCP-1 was significantly higher in children with type 1 diabetes than in control subjects (P < 0.001). However, there were no correlations between MCP-1 and AI75 in the overall sample or upon stratification by type 1 diabetes status (range P = 0.28–0.66).

CONCLUSIONS

Circulating MCP-1 was not associated with arterial stiffness but was significantly elevated in children with type 1 diabetes, indicating a proinflammatory state in children as young as 10 years. The clinical significance of MCP-1 elevation in type 1 diabetes needs further investigation.
Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels
Authors: Trepalin Sergei V. , Yarkov Alexander V.
Published: December 2008

A new algorithm for divisive hierarchical clustering of chemical compounds based on 2D structural fragments is suggested. The algorithm is deterministic, and given a random ordering of the input, will always give the same clustering and can process a database up to 2 million records on a standard PC. The algorithm was used for classification of 1,183 antibiotics mixed with 999,994 random chemical structures. Similarity threshold, at which best separation of active and non active compounds took place, was estimated as 0.6. 85.7% of the antibiotics were successfully classified at this threshold with 0.4% of inaccurate compounds. A .sdf file was created with the probe molecules for clustering of external databases.
Antibacterial Properties of 3 H-Spiro[1-benzofuran-2,1’-cyclohexane] Derivatives from Heliotropium filifolium
Authors: Urzúa Alejandro , Echeverría Javier , Rezende Marcos C. , Wilkens Marcela
Published: December 2008

A re-examination of cuticular components of Heliotropium filifolium allowed the isolation of four new compounds: 3’-hydroxy-2’,2’,6’-trimethyl-3H-spiro[1-benzo-furan-2,1’-cyclohexane]-5-carboxylic acid(2), methyl 3’-acetyloxy-2’,2’,6’-trimethyl-3H-spiro[1-benzofuran-2,1’-cyclohexane]-5-carboxylate (3), methyl 3’-isopentanoyloxy-2’,2’,6’-trimethyl-3H-spiro[1-benzofuran-2,1’-cyclohexane]-5-carboxylate (4) and methyl 3’-benzoyloxy-2’,2’,6’-trimethyl-3H-spiro[1-benzofuran-2,1’-cyclohexane]-5-carboxylate (5).Compounds 2-5 were identified by their spectroscopic analogies with filifolinol (1), and their structures confirmed by chemical correlation with 1. The antimicrobial properties of the compounds were tested against Gram positive and Gram negative bacteria. Some of them proved to be active against Gram positive, but inactive against Gram negative bacteria. In searching for structure-activity relationships from the obtained MIC values, lipophilicity was shown to be an important variable.
Dodecatungstophosphoric Acid (H3PW12O40), Samarium and Ruthenium (ІІІ) Chloride Catalyzed Synthesis of Unsaturated 2-Phenyl-5(4H)-oxazolone Derivatives under Solvent-free Conditions
Authors: Tikdari Ahmad Momeni , Fozooni Samieh , Hamidian Hooshang
Published: December 2008

We found that dodecatungstophosphoric acid (H3PW12O40), samarium and ruthenium(III) chloride act as efficient catalysts for synthesis of unsaturated 2-phenyl-5(4H)oxazolone derivatives under solvent-free conditions. The key features of the reported protocols are short reaction times, high yields of products, ambient conditions and simple workup.
Radioligand Binding Characterization of Neuronal Nicotinic Acetylcholine Receptors
Authors: Anderson David J.
Published: December 2008

Described in this unit are radioligand binding protocols for three neuronal nicotinic acetylcholine receptor (nAChR) subtypes. Detailed descriptions of binding protocols are presented for the two predominant CNS subtypes of nAChRs, α4β2 and α7, as well as the ganglionic α3β4 nAChR. [3H]Cytisine is utilized for α4β2 nAChRs, while [3H]methyllycaconitine is utilized for α7 nAChRs, both in rat brain. α3β4 nAChRs in IMR‐32 cells are labeled with [3H]epibatidine. Reference data are presented, as well as commentary on the current state of neuronal nicotinic receptor research.Curr. Protoc. Pharmacol. 43:1.8.1‐1.8.15. © 2008 by John Wiley & Sons, Inc.
Models of Anxiety: Ultrasonic Vocalizations of Isolated Rat Pups
Authors: Groenink Lucianne , Verdouw P. Monika , van Oorschot Ruud , Olivier Berend
Published: December 2008

Described in this unit is the ultrasonic distress vocalization test in rat pups. This test is a reliable method for detecting anxiolytic properties of test compounds. In this test, ultrasonic vocalizations (30 to 50 kHz) are elicited by separating rat pups of 9 to 11 days of age from their mother and littermates for a brief period of time. The test can be performed under two different stress conditions. Pups are placed in isolation in either a warm (37°C) or cold (18°C) environment for 5 min. The total number and duration of ultrasonic calls emitted by the pups during this period is used as an index of anxiety. Established anxiolytic compounds, including benzodiazepines, serotonin1A receptor agonists, and selective serotonin reuptake inhibitors (SSRIs), consistently reduce the number and cumulative duration of these ultrasonic distress vocalizations. Curr. Protoc. Pharmacol. 43:5.18.1‐5.18.14. © 2008 by John Wiley & Sons, Inc.
A Model of Cystitis Pain in the Mouse
Authors: Leventhal Liza , Strassle Brian
Published: December 2008

Interstitial cystitis (IC) is a chronic pelvic‐perineal pain syndrome of unknown etiology that mainly targets the lower urinary tract. It is characterized by urinary frequency and urgency, inflammation, stiffening of the bladder wall, and visceral pain. Pain is the most prominent feature of IC and current treatments provide limited relief. To facilitate the identification of novel therapeutic options for IC, efforts are being made to identify more predictive rodent models. A well‐characterized rat model is based on administration of cyclophosphamide (CP). The protocol described in this unit replicates this model in mice, demonstrating that CP increases both spontaneous and evoked pain behaviors in this species. This mouse model can be used for understanding disease etiology as well as for the pharmacological evaluation of novel therapeutics for the treatment of IC pain. Curr. Protoc. Pharmacol. 43:5.52.1‐5.52.11. © 2008 by John Wiley & Sons, Inc.
Murine Retroviral Bone Marrow Transplantation Models for the Study of Human Myeloproliferative Disorders
Authors: Gavrilescu L. Cristina , Van Etten Richard A.
Published: December 2008

Human myeloproliferative diseases are common hematologic disorders characterized by clonal overproduction of maturing myeloid or erythroid cells, often caused by expression of a mutant, dysregulated tyrosine kinase (TK). These diseases can be accurately modeled in laboratory mice by the retroviral transfer of a mutant TK gene into murine hematopoietic stem and progenitor cells, followed by transplantation of these cells into irradiated recipient mice. This yields a model system for analyzing the molecular pathophysiology of these conditions and provides a platform for testing therapies, particularly molecularly targeted new chemical entities (NCEs). The Basic Protocol in this unit describes the preparation of mouse bone marrow cells to express the relevant human oncogene before transplanting them into irradiated recipient mice. An alternate protocol describes a similar technique that allows specific induction of lymphoproliferative disease by some TKs. Support protocols for generating and titering retroviral stocks are also included. Curr. Protoc. Pharmacol. 43:14.10.1‐14.10.28. © 2008 by John Wiley & Sons, Inc.
Synthesis of Alkyne‐ and Azide‐Modified Oligonucleotides and Their Cyclization by the CuAAC (Click) Reaction
Authors: El‐Sagheer Afaf H. , Brown Tom
Published: December 2008

The Cu(I)‐catalyzed alkyne‐azide cycloaddition (CuAAC) reaction has been used to synthesize cyclic mini‐DNA duplexes. The reaction is carried out on 5′‐alkyne‐3′‐azide‐labeled hairpin loop oligonucleotides and proceeds in high yield under mild conditions in as little as 5 min. The resultant duplexes have very high thermal stability and their CD spectra are characteristic of normal B‐DNA. Curr. Protoc. Nucleic Acid Chem. 35:4.33.1‐4.33.21. © 2008 by John Wiley & Sons, Inc.
Photoactivated Localization Microscopy (PALM) of Adhesion Complexes
Authors: Shroff Hari , White Helen , Betzig Eric
Published: December 2008

Key to understanding a protein's biological function is the accurate determination of its spatial distribution inside a cell. Although fluorescent protein markers allow the targeting of specific proteins with molecular precision, much of this information is lost when the resultant fusion proteins are imaged with conventional, diffraction‐limited optics. In response, several imaging modalities that are capable of resolution below the diffraction limit (∼200 nm) have emerged. Here, both single‐ and dual‐color superresolution imaging of biological structures using photoactivated localization microscopy (PALM) are described. The examples discussed focus on adhesion complexes: dense, protein‐filled assemblies that form at the interface between cells and their substrata. A particular emphasis is placed on the instrumentation and photoactivatable fluorescent protein (PA‐FP) tags necessary to achieve PALM images at ∼20 nm resolution in 5 to 30 min in fixed cells. Curr. Protoc. Cell Biol. 41:4.21.1‐4.21.27. © 2008 by John Wiley & Sons, Inc.
Embryonic Organ Culture
Authors: Sakai Takayoshi , Onodera Tomohiro
Published: December 2008

This unit provides detailed protocols for dissecting embryonic organs and performing organ culture to study questions in developmental biology. Procedures are described here for dissecting organs such as kidney, lung, and salivary gland. The unit also contains commentary including troubleshooting for embryonic organ culture. Curr. Protoc. Cell Biol. 41:19.8.1‐19.8.8. © 2008 by John Wiley & Sons, Inc.
Searching NCBI Databases Using Entrez
Authors: Baxevanis Andreas D.
Published: December 2008

One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built‐in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed. Curr. Protoc. Bioinform. 24:1.3.1‐1.3.26. © 2008 by John Wiley & Sons, Inc.
Using VMD: An Introductory Tutorial
Authors: Hsin Jen , Arkhipov Anton , Yin Ying , Stone John E. , Schulten Klaus
Published: December 2008

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step‐by‐step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication‐quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text‐based Tcl/Tk interface, and analyzing both sequence and structure data for proteins. Curr. Protoc. Bioinform. 24:5.7.1‐5.7.48. © 2008 by John Wiley & Sons, Inc.
Using AutoDock for Ligand‐Receptor Docking
Authors: Morris Garrett M. , Huey Ruth , Olson Arthur J.
Published: December 2008

This unit describes how to set up and analyze ligand‐protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X‐ray crystal structure of Indinavir bound to HIV‐1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools. Curr. Protoc. Bioinform. 24:8.14.1‐8.14.40. © 2008 by John Wiley & Sons, Inc.
Piezophiles
Authors: Yayanos A Aristides
Published: December 2008

Piezophilic bacteria (piezophiles) are adapted to high pressures and are prominent among the inhabitants of the cold deep ocean below depths of approximately 2000 m. Whereas their maximum growth rate is close to the upper limiting growth temperature, it is also at a pressure close to that of their deep‐sea habitat. In contrast, bacteria in the upper 2000 m of the ocean and in terrestrial habitats have their maximum growth rate at atmospheric pressure. ThePTk‐diagram for a bacterium shows clearly how the temperature and pressure of its habitat influences its growth rate and allows for comparing organisms from habitats of disparate temperatures and pressures. Laboratory studies of higher organisms from the very deep ocean are rare. At the present time, research on piezophiles offers the best opportunity for learning about biochemical and molecular biological adaptations essential for all life in the deep sea and possibly in extraterrestrial settings.
Kranz Anatomy and the C
4
Pathway
Authors: Berry James O , Patel Minesh
Published: December 2008

C
4
photosynthesis incorporates novel leaf anatomy, metabolic specializations and modified gene expression. Plants that utilize this pathway typically possess a distinctive Kranz (or wreath) leaf anatomy, consisting of two photosynthetic cell types. These are the bundle sheath (bs) cells, which surround the vascular centres, and the mesophyll (mp) cells, which surround the bs cells. This structural framework allows for the compartmentalization and functional separation of two sets of carboxylation and decarboxylation reactions. Within C
4
leaves, selective expression of bs and mp cell‐specific genes leads to the selective accumulation of key photosynthetic enzymes which catalyse the different sets of cell‐type‐specific reactions, thereby enabling these plants to assimilate atmospheric carbon dioxide with very high efficiency. For some plants, C
4
photosynthesis has facilitated their adaptation to arid conditions, high temperatures and marginal environments. Understanding the basis of this pathway has applications for improvements in agricultural productivity and alternative fuel development.
Crassulacean Acid Metabolism
Authors: Lüttge Ulrich
Published: December 2008

Crassulacean acid metabolism (CAM) is a carbon dioxide acquisition, carbon dioxide transient storage and carbon dioxide concentrating mechanism of plants based on organic acid synthesis. In this variant of photosynthesis carbon dioxide can be fixed nocturnally in the dark and is used during the day for assimilation in the light. This has arisen polyphyletically many times during evolution. It is an ecophysiological adaptation that allows carbon dioxide acquisition with exceptionally economic use of water. It is regulated in a natural night/day rhythm but can also oscillate freely under the control of circadian biological clocks.

Key concepts

Metabolic mechanisms concentrating carbon dioxide internally in plants are important for photosynthesis at the low external carbon dioxide concentration in the present atmosphere.

Rearranged internal management of available metabolic housekeeping functions can generate new metabolic options of adaptive value.

Generation of isoforms of housekeeping enzymes can facilitate polyphyletic evolution of new metabolic pathways.

Circadian oscillations can be controlled by different biological clocks, which are feedback related to each other and present in many copies.

Flexibility in the expression of metabolic pathway variants facilitates adaptation under variable stress situations.

Stress adaptation in plants is for survival and mostly not for high productivity.
Plant Respiration
Authors: Sweetlove Lee J , Fernie Alisdair R
Published: December 2008

Respiration is a crucial feature of the metabolism of higher plant cells. Because plants synthesize all their organic molecules from inorganic materials and are sedentary, there are several unique features that distinguish plant respiration from animal respiration. In particular, the respiratory pathways not only oxidize carbohydrate to generate adenosine triphosphate (ATP), but they also provide carbon skeletons that act as precursors for the synthesis of organic molecules such as fatty acids and amino acids. In this article the impact of this dual role for the organization and regulation of the respiratory pathways will be described. Unique features of plant respiration will be detailed and a number of recent discoveries about the organization and regulation of plant respiration will be discussed.
Ion Transport at the Plant Plasma Membrane
Authors: Blatt Michael R
Published: December 2008

Membrane transport plays a fundamental role in virtually every aspect of homeostasis, signalling, growth and development in plants. At the plasma membrane, the boundary with the outside world, ion and solute fluxes underpin inorganic mineral nutrient uptake, they trigger rapid changes in second messengers such as cytosolic‐free Ca
2+
concentrations, and they power the osmotic gradients that drive cell expansion, to name just a few roles. Our understanding of the transporters – the ion pumps that generate an H
+
electrochemical driving force, H
+
ion‐coupled symport and antiport systems, and ion channels – now, more than ever, builds on developments in molecular genetics, protein chemistry and crystallography to gain insights into the fine structure and mechanics of these remarkable enzymes. Even so, it is the interface with the biophysical detail of ion transport that drives scientific enquiry in the field and will continue to be essential in informing both the most fundamental research as well as efforts to apply the knowledge gained in resolving some of the dilemmas that face society today.
Mitochondrial
DNA
and Diseases
Authors: Boesch Pierre , Lightowlers Robert N , Chrzanowska‐Lightowlers Zofia MA
Published: December 2008

The mitochondrial genome (mtDNA, mitochondrial
deoxyribonucleic acid
) is an essential source of extranuclear DNA in mammalian cells, located in the matrix of the organelle. It is much smaller than chromosomal DNA (only 16 569 bp) but thousands of copies per nucleated cell are found in nucleoprotein complexes termed nucleoids, which may constitute the heritable unit. mtDNA is maternally inherited and encodes 13 polypeptides, all fundamental for coupling cellular respiration to ATP (adenosine triphosphate) production. Consequently, mutated mtDNA can cause profound cellular dysfunction and death. Many pathogenic mtDNA mutations are known: single point mutations and rearrangements underlie clinical disorders known as mitochondrial cytopathies or encephalomyopathies; several nuclear gene mutations are known to cause mtDNA rearrangements; there exists an association between mtDNA deletions and the ageing process. Models explain how deletions may occur, but it is unknown how these deleted molecules predominate in individual cells over time, a process termed clonal expansion.
RNA
Virus Genomes
Authors: Domingo Esteban
Published: December 2008

RNA (ribonucleic acid) viruses are the most abundant group of molecular parasites that infect humans, animals and plants. They are associated with important diseases such as human influenza, newly emerging haemorrhagic fevers or several forms of hepatitis. Virus particles are disparate in size, shape and composition, and enclose an RNA genome that can be either single‐stranded, double‐stranded, nonsegmented or segmented. The structural diversity of viral RNA is reflected in differences in their replication cycles that are completed through complex interactions between viral and host proteins. RNA viruses share error‐prone replication that confers on them the capacity to adapt to a wide range or environments. Despite considerable progress in the understanding of virus structure and expression of their genetic programmes, the success of preventive and control strategies has been limited. Application of Darwinian principles to RNA viruses might result in new approaches for viral disease control.
Evolution of Secondary Plant Metabolism
Authors: Wink Michael
Published: December 2008

The biosynthesis of secondary metabolites (SM), which are important for the fitness of the plants as defence and signal compounds, occurs universally in higher plants and shows very high structural diversity. Their evolution in higher plants rests on variation in the enzymatic manipulation of a relatively small number of primary precursors. Evidence is presented that at least some of the genes encoding key enzymes of biosynthesis probably have reached plants by ancient horizontal gene transfer (HGT), for example from protobacteria or cyanobacteria which later became mitochondria and plastids. Another source of SM can be ectomycorrhizal and endophytic fungi; they can directly provide plants with defence compounds or might have transferred their pathway genes into the genome of their host plants times ago.
Katz, Bernard
Authors: Tansey EM
Published: December 2008

Katz (1911–2003), a German‐born British biophysicist, best known for his elucidation of the mechanisms of neural transmission, work of immense importance in understanding how the nervous system works in health and disease, and in the development of neuroactive drugs.
T
Lymphocytes: Regulatory
Authors: Fehervari Zoltan , Sakaguchi Shimon
Published: December 2008

CD4+ regulatory (Treg) T cells play a central role in the immune system by potently controlling the responses of other immunocytes. Their activity appears to be essential not only for the maintenance of immunological self‐tolerance but potentially also for the control of all physiological immune responses whether against normal self‐proteins, microbes or cancerous cells. A fuller understanding of these cells should allow us to effectively exploit their suppressive functions for clinical benefit.
Microbial Forensics
Authors: Morse Stephen A , Budowle Bruce
Published: December 2008

Microbial forensics is a newly developed discipline with an epidemiological foundation dedicated to the characterization, analysis and interpretation of evidence from the scene of an act of bioterrorism or a biocrime. It is an evolving subdiscipline of forensic sciences, which combines several disciplines including microbiology, molecular biology, genomics, bioinformatics and biochemistry. Microbial forensic investigations are carried out to obtain information regarding the identification or source of the material used in an act of bioterrorism, biocrime, hoax or unintentional release of a microorganism or toxin, with the ultimate goal of identifying those responsible for the crime (i.e. attribution). Attribution could be key to criminal prosecution of the individual or individuals, or for supporting actions that may be taken as a result of national policy decisions.
McKusick, Victor
Authors: Weatherall David
Published: December 2008

Victor McKusick (1921–2008) was one of the leading founders of the discipline of medical genetics during the second half of the twentieth century.