bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutral network sizes of biological RNA molecules can be computed and are not atypically small
Authors: Jörg Thomas , Martin Olivier C , Wagner Andreas
Published: October 2008

Background

Neutral networks or sets consist of all genotypes with a given phenotype. The size and structure of these sets has a strong influence on a biological system's robustness to mutations, and on its evolvability, the ability to produce phenotypic variation; in the few studied cases of molecular phenotypes, the larger this set, the greater both robustness and evolvability of phenotypes. Unfortunately, any one neutral set contains generally only a tiny fraction of genotype space. Thus, current methods cannot measure neutral set sizes accurately, except in the smallest genotype spaces.

Results

Here we introduce a generalized Monte Carlo approach that can measure neutral set sizes in larger spaces. We apply our method to the genotype-to-phenotype mapping of RNA molecules, and show that it can reliably measure neutral set sizes for molecules up to 100 bases. We also study neutral set sizes of RNA structures in a publicly available database of functional, noncoding RNAs up to a length of 50 bases. We find that these neutral sets are larger than the neutral sets in 99.99% of random phenotypes. Software to estimate neutral network sizes is available at http://www.bioc.uzh.ch/wagner/publications-software.html.

Conclusion

The biological RNA structures we examined are more abundant than random structures. This indicates that their robustness and their ability to produce new phenotypic variants may also be high.
Social and cultural aspects of 'malaria' and its control in central Côte d'Ivoire
Authors: Essé Clémence , Utzinger Jürg , Tschannen Andres B , Raso Giovanna , Pfeiffer Constanze , Granado Stefanie , Koudou Benjamin G , N'Goran Eliézer K , Cissé Guéladio , Girardin Olivier , Tanner Marcel , Obrist Brigit
Published: October 2008

Background

A sound local understanding of preventive measures and health-seeking behaviour is important for the effective control of malaria. The purpose of this study was to assess the knowledge, attitudes, practices and beliefs of 'malaria' and its control in two rural communities of central Côte d'Ivoire, and to examine associations between 'malaria' and the households' socioeconomic status.

Methods

A cross-sectional household survey was carried out, using a combination of qualitative and quantitative methods. People's socioeconomic status was estimated, employing a household asset-based approach.

Results

Malaria was identified as djèkouadjo, the local folk name of the disease. Although people were aware of malaria-related symptoms and their association with mosquitoes, folk perceptions were common. In terms of treatment, a wide array of modern and traditional remedies was employed, often in combination. Individuals with a sound knowledge of the causes and symptoms of malaria continued to use traditional treatments and only a few people sleep under bed nets, whereas folk beliefs did not necessarily translate into refusal of modern treatments. Perceived causes of malaria were linked to the household's socioeconomic status with wealthier individuals reporting mosquitoes more frequently than poorer households. Bed nets were more frequently used in wealthier social strata, whereas other protective measures – perceived to be cheaper – were more prominent among the poorest.

Conclusion

Equitable access to resources at household, community and health system levels are essential in order to enable community members to prevent and treat malaria. There is a need for community-based approaches that match health care services with poor people's needs and resources.
Eating habits and obesity among Lebanese university students
Authors: Yahia Najat , Achkar Alice , Abdallah Abbass , Rizk Sandra
Published: October 2008

Background

In the past year Lebanon has been experiencing a nutritional transition in food choices from the typical Mediterranean diet to the fast food pattern. As a consequence, the dietary habits of young adults have been affected; thus, overweight and obesity are increasingly being observed among the young. The purpose of this study is to assess the prevalence of overweight and obesity on a sample of students from the Lebanese American University (in Beirut) and to examine their eating habits.

Methods

A cross-sectional survey of 220 students (43.6% male and 56.4% female), aged 20 ± 1.9 years, were chosen randomly from the Lebanese American University (LAU) campus during the fall 2006 semester. Students were asked to fill out a self-reported questionnaire that included questions on their eating, drinking and smoking habits. Also, their weight, height, percentage body fat and body mass index were measured. Body mass index (BMI) was used to assess students' weight status. Statistical analyses were performed using the Statistical Package for Social Sciences software (version 13.0) to determine overweight and obesity among students and to categorize eating habits.

Results

This study showed that the majority of the students (64.7%) were of normal weight (49% male students compared to 76.8% female students). The prevalence of overweight and obesity was more common among male students compared to females (37.5% and 12.5% vs. 13.6% and 3.2%, respectively). In contrast, 6.4% female students were underweight as compared to 1% males. Eating habits of the students showed that the majority (61.4%) reported taking meals regularly. Female students showed healthier eating habits compared to male students in terms of daily breakfast intake and meal frequency. 53.3% of female students reported eating breakfast daily or three to four times per week compared to 52.1% of male students. There was a significant gender difference in the frequency of meal intake (P = 0.001). Intake of colored vegetables and fruits was common among students. A total of 30.5% reported daily intake of colored vegetables with no gender differences (31.5% females vs. 29.2% males). Alcohol intake and smoking were not common among students.

Conclusion

In spite of the overall low prevalence of overweight and obesity in the studied sample, results indicate that university students would possibly benefit from a nutrition and health promotion program to reduce the tendency of overweight and obesity, especially among male students, and to improve students' eating habits.
Non coding extremities of the seven influenza virus type C vRNA segments: effect on transcription and replication by the type C and type A polymerase complexes
Authors: Crescenzo-Chaigne Bernadette , Barbezange Cyril , van der Werf Sylvie
Published: October 2008

Background

The transcription/replication of the influenza viruses implicate the terminal nucleotide sequences of viral RNA, which comprise sequences at the extremities conserved among the genomic segments as well as variable 3' and 5' non-coding (NC) regions. The plasmid-based system for the in vivo reconstitution of functional ribonucleoproteins, upon expression of viral-like RNAs together with the nucleoprotein and polymerase proteins has been widely used to analyze transcription/replication of influenza viruses. It was thus shown that the type A polymerase could transcribe and replicate type A, B, or C vRNA templates whereas neither type B nor type C polymerases were able to transcribe and replicate type A templates efficiently. Here we studied the importance of the NC regions from the seven segments of type C influenza virus for efficient transcription/replication by the type A and C polymerases.

Results

The NC sequences of the seven genomic segments of the type C influenza virus C/Johannesburg/1/66 strain were found to be more variable in length than those of the type A and B viruses. The levels of transcription/replication of viral-like vRNAs harboring the NC sequences of the respective type C virus segments flanking the CAT reporter gene were comparable in the presence of either type C or type A polymerase complexes except for the NS and PB2-like vRNAs. For the NS-like vRNA, the transcription/replication level was higher after introduction of a U residue at position 6 in the 5' NC region as for all other segments. For the PB2-like vRNA the CAT expression level was particularly reduced with the type C polymerase. Analysis of mutants of the 5' NC sequence in the PB2-like vRNA, the shortest 5' NC sequence among the seven segments, showed that additional sequences within the PB2 ORF were essential for the efficiency of transcription but not replication by the type C polymerase complex.

Conclusion

In the context of a PB2-like reporter vRNA template, the sequence upstream the polyU stretch plays a role in the transcription/replication process by the type C polymerase complex.
Pituitary-adrenal function in patients with acute subarachnoid haemorrhage: a prospective cohort study
Authors: Bendel Stepani , Koivisto Timo , Ruokonen Esko , Rinne Jaakko , Romppanen Jarkko , Vauhkonen Ilkka , Kiviniemi Vesa , Uusaro Ari
Published: October 2008

Introduction

Subarachnoid haemorrhage (SAH) may damage the hypothalamo-pituitary-adrenal gland (HPA) axis and disturb cortisol metabolism. There are no available data that relates to the response of the HPA axis in the acute phase of SAH. We aimed to characterise the behavior of serum adrenocorticotropic hormone (ACTH), total cortisol, stimulated total cortisol and free cortisol concentrations in acute aneurysmal SAH.

Methods

A prospective cohort study was conducted of patients with acute aneurysmal SAH (n = 30) admitted to a tertiary university hospital. Patients admitted for elective aneurysmal surgery (n = 16) served as the control group. An ACTH stimulation test was performed twice during the first week and at three months. The main outcome measure was description of the ACTH-cortisol response by calculating serum free cortisol and measuring total cortisol and ACTH concentrations. A mixed models method was used for testing between the groups, allowing heterogeneity between the groups.

Results

Patients with SAH had higher initial serum total cortisol (mean +/- SD; 793 +/- 312 nmol/L) and free cortisol concentrations (83 +/- 55 nmol/L) than control patients (535 +/- 193 nmol/L, p = 0.001 and 33 +/- 18 nmol/L, p < 0.001, respectively). Thereafter, there were no differences in this respect. Serum free and total cortisol concentrations correlated but were unaffected by the severity of SAH. ACTH concentrations were comparable between SAH and control groups. Patients with Hunt-Hess grades IV to V had higher ACTH concentrations at day one (10.7 +/- 7.1 pmol/l/L) and day five (8.2 +/- 7.7 pmol/L) than patients with grade I-III (day one: 3.8 +/- 2.0 pmol/L, p = 0.002; day five: 4.7 +/- 1.8 pmol/L, p = 0.04).

Conclusions

Calculation of serum free cortisol concentration was not helpful in identifying patients with potential hypocortisolism. SAH severity did not affect cortisol concentrations, possibly indicating relative pituitary-adrenal insufficiency in patients with more severe bleeding.

Trial registration

ClinicalTrials.gov Identifier NCT00614887.
Boolean implication networks derived from large scale, whole genome microarray datasets
Authors: Sahoo Debashis , Dill David L , Gentles Andrew J , Tibshirani Robert , Plevritis Sylvia K
Published: October 2008

We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other methods. These relationships capture gender differences, tissue differences, development, and differentiation. New relationships are discovered that are preserved across all three species.
Cell Differentiation in Multispectral Image Cytology
Authors: Thigpen James , Shah Shishir , Merchant Fatima
Published: October 2008

This paper presents a multispectral microscopy system for quantitative cytology. The automated system aims to classify microscopic samples for the purpose of disease diagnosis. While conventional practices rely on the analysis of grey scale or RGB color images, presented system uses thirty one spectral bands for analysis. Algorithms designed to enable image acquisition, image segmentation, feature extraction, and classification are presented. Results are presented for the problem of discriminating among four cell types. In addition, classification performance is compared to the case where multispectral information is not taken into consideration. Results show that the developed system and the use of multispectral information along with morphometric information extracted from spectral images can significantly improve the classification performance and aid in the process of disease diagnosis.
A Fast Navier Stokes Flow Simulation Tool Forimage Based CFD
Authors: Hadri Bilel , Garbey Marc
Published: October 2008

The objective of this paper is to present a fast parallel incompressible Navier Stokes (NS) simulator that has enough versatility to apply to various endovascular situations with ease in medical image integration. Our long term goal is to bring NS simulation to surgeons as an additional routine image modality that can complement existing medical imaging channels. Given a medical image describing the geometry of an artery, we are able to simulate the blood flow through an artery close to clinical conditions. To achieve this goal, our interface relies on the combination of the L2 penalty method to deal with complex geometry for solving the NS equations. We present here a high performance portable domain decomposition solver based on a tuning of the fastest linear solver depending on the subdomain and the processor architecture. This paper provides a detailed proof of concept in the two dimensional case. The three dimensional results will be reported in a companion paper.
Crystal structure of an RNA aptamer bound to thrombin
Authors: Long Stephen B. , Long Meredith B. , White Rebekah R. , Sullenger Bruce A.
Published: October 2008

Aptamers, an emerging class of therapeutics, are DNA or RNA molecules that are selected to bind molecular targets that range from small organic compounds to large proteins. All of the determined structures of aptamers in complex with small molecule targets show that aptamers cage such ligands. In structures of aptamers in complex with proteins that naturally bind nucleic acid, the aptamers occupy the nucleic acid binding site and often mimic the natural interactions. Here we present a crystal structure of an RNA aptamer bound to human thrombin, a protein that does not naturally bind nucleic acid, at 1.9 Å resolution. The aptamer, which adheres to thrombin at the binding site for heparin, presents an extended molecular surface that is complementary to the protein. Protein recognition involves the stacking of single-stranded adenine bases at the core of the tertiary fold with arginine side chains. These results exemplify how RNA aptamers can fold into intricate conformations that allow them to interact closely with extended surfaces on non-RNA binding proteins.
Petri Dish Incubation of Eyed Eggs from Rainbow Trout and Splake
Authors: Barnes Michael E , Durben Dan J
Published: October 2008

Four experiments were conducted from 2004 to 2006 to evaluate different protocols for incubating eyed eggs of salmonids in petri dishes. In the first two experiments, which used eyed eggs from Erwin strain rainbow trout Oncorhynchus mykiss or splake (lake trout Salvelinus namaycush ×brook trout S. fontinalis), dishes were loaded at either 10 or 20 eggs/dish and incubated at 10°C. Water changes occurred every 3 or 7 d until complete hatch; for each species, one group of dishes received no water change. Survival to hatch was not affected by the number of eggs per dish or the frequency of water changes in either species. However, in experiments 1 and 2, hatch was significantly earlier in the dishes containing 20 eggs than in dishes containing 10 eggs. In the last two experiments, 15 eyed eggs from Shasta or McConaughy strain rainbow trout were incubated at either 10°C or 12°C; the water was changed every 3 d or not at all. Shasta strain eggs exhibited no significant difference in survival or time to hatch between any of the treatments. For McConaughy strain eyed eggs, survival to hatch was significantly greater at 10°C than at 12°C, but water change treatment did not affect survival. No significant differences in time (d) to complete hatch were observed between temperature treatments or between water change regimes. To successfully mimic vertical-flow incubation of eyed salmonid eggs in petri dishes, we recommend a density of no more than 15 eggs/dish; no water change is needed at a temperature of 10°C. Daily removal of dead eggs and hatched fry is also required.
Cortisol Response to a Crowding Stress: Heritability and Association with Disease Resistance to Yersinia ruckeri in Rainbow Trout
Authors: Weber Gregory M , Vallejo Roger L , Lankford Scott E , Silverstein Jeffrey T , Welch Timothy J
Published: October 2008

The U.S. Department of Agriculture's National Center for Cool and Cold Water Aquaculture is conducting a breeding program for rainbow trout Oncorhynchus mykiss to develop improved germplasm for the U.S. aquaculture industry. Current selection efforts are focused on growth and disease resistance, but stress response is also a concern. Using plasma cortisol concentrations after a 3-h crowding stress as a measure of stress responsiveness, we have previously shown family variation in cortisol responsiveness and a positive phenotypic correlation between poststressor cortisol level and growth performance within our broodstock. Selection for improved growth performance may therefore increase cortisol responsiveness to stress. In the present studies, narrow-sense heritability (h  2) for cortisol responsiveness was estimated to be moderately high by means of midparent–offspring regression and nested family design analyses (h  2 ≥ 0.40 and 0.56, respectively). In addition, fish from the same families were used to determine associations between cortisol responsiveness to crowding and resistance to Yersinia ruckeri, the pathogenic agent of enteric redmouth disease, in an immersion challenge. Phenotypic and breeding values for cortisol responsiveness were not correlated with survivability with respect to Y. ruckeri whether or not the fish experienced repeated daily exposure to a crowding stress before the disease challenge. Furthermore, phenotypic and breeding values for poststressor plasma glucose and chloride levels and lysozyme activity did not correlate with disease survivability in stressed and unstressed fish. Finally, there was no correlation between the survival values of families when they were stressed before the disease challenge and when they were not, suggesting that there is variability among families in the effect of stress on resistance to Y. ruckeri.
Efficacy of Oxytetracycline Hydrochloride Bath Immersion to Control External Columnaris Disease on Walleye and Channel Catfish Fingerlings
Authors: Rach Jeff J , Johnson Alan , Rudacille James B , Schleis Susan M
Published: October 2008

The efficacy of oxytetracycline hydrochloride (OTC-HCl) in controlling external columnaris disease caused by Flavobacterium columnare on fingerling walleyes Sander vitreus and channel catfish Ictalurus punctatus was evaluated in two on-site hatchery trials. Microscopic examination of skin scrapings before treatment confirmed the presence of bacteria with characteristics indicative of F. columnare. In separate trials, walleyes (4.4 g) and channel catfish (1.5 g) were exposed to 60-min static bath treatments of OTC-HCl at 0, 10, and 20 mg/L (walleyes) or 0, 10, 20, and 40 mg/L (channel catfish) on three consecutive days. Each treatment regimen was tested in triplicate, and each replicate contained either 30 walleyes or 55 channel catfish. Posttreatment presumptive disease diagnosis indicated that F. columnare was the disease agent causing the mortality in both species of fish. Walleye survival at 10 d posttreatment was greater in the 10- and 20-mg/L treatment groups than in the control group; however, only the 10-mg/L treatment significantly (P < 0.05) increased walleye survival in comparison with controls. In the channel catfish trial, survival at 10 d posttreatment was significantly (P < 0.05) greater for all OTC-HCl treatment groups relative to controls. Results from these trials indicated that OTC-HCl treatments effectively reduced mortality in walleyes (10 mg/L only) and channel catfish infected with F. columnare.
Induced Spawning, Artificial Fertilization, and Egg Incubation Techniques for Green Sturgeon
Authors: Van Eenennaam Joel P , Linares-Casenave Javier , Muguet Jean-Benoit , Doroshov Serge I
Published: October 2008

Establishment of hatchery breeding techniques for the threatened green sturgeon Acipenser medirostris is important for research and conservation hatcheries. Injections of either gonadotropin-releasing hormone analog (GnRHa) or GnRHa plus domperidone were used to induce ovulation in 13 female Klamath River green sturgeon and to induce spermiation in 19 males. Ovulated eggs were either rinsed in water or not rinsed before fertilization, and the eggs were fertilized with different milt dilutions and for different lengths of time. After fertilization, eggs either were allowed to adhere to the bottom of glass dishes or were silted for 1 h and then incubated in McDonald or upwelling jars. All broodfish ovulated or spermiated in all hormonal treatments, and the best treatment was GnRHa injected alone in a single dose of 10 μg/kg for males or in a 1-μg/kg priming dose and a 19-μg/kg resolving dose for females. Females were held at 12–13°C, and ovulation was observed 14 ± 3 h (mean ± SD) after the second injection. Domperidone was not required for successful ovulation and appeared to reduce the adhesion of ovulated eggs. From 49,000 to 115,000 eggs were collected from each female, and from 30 to 300 mL of milt were collected from each male. Sperm cell concentrations in milt ranged from 2.9 × 108 to 5.4 × 109 sperm/mL, and the sperm exhibited 90–100% motility for up to 5 min. In all experiments, egg rinsing improved fertilization success by 5–12%. Embryo survival to neurulation in the McDonald jars was lower (5–32%) than that in the upwelling incubators (60–82%). Green sturgeon eggs were sensitive to the high-impact rolling action at the bottom of the McDonald jars, probably due to the large egg diameter (mean ± SD = 4.33 ± 0.14 mm) and thinner chorion (42 ± 4 μm) relative to eggs of white sturgeon A. transmontanus (diameter = 3.79 ± 0.03 mm; chorion thickness = 115 ± 6 μm).
Testes orais individuais e em pares: um estudo das diferenças de desempenho
Authors: Marochi Thaís Barbosa
Published: October 2008

O objetivo desta pesquisa foi verificar se há diferença no desempenho caso os candidatos façam o teste oral sozinhos ou em pares. Duas versões do First Certificate in English foram aplicadas para dez alunos em duas situações diferentes (examinadorcandidato e candidato-candidato-examinador). Todos os testes foram gravados, transcritos e analisados estatisticamente. Após o segundo teste, os participantes responderam a um questionário para informar suas opiniões sobre os testes. Apesar de haver uma tendência em falar mais, usar uma maior diversidade de vocabulário e uma maior complexidade gramatical quando em pares, oito dos dez candidatos manifestaram uma preferência pela realização do teste individual.
Visitando a interação na prosa literária
Authors: Cunha Dóris de Arruda C. da
Published: October 2008

Este artigo tem o objetivo analisar a interação por meio dos discursos no romance, partindo do princípio que não são formas sintáticas de transmissão das falas e dos pensamentos das personagens, mas representações da interação entre sujeitos e suas posições axiológicas. Analisa a relação entre Lingüística e Literatura, partilhando a visão de Maingueneau segundo a qual não se pode continuar a pensar dicotomicamente essa relação, uma vez que as duas ciências da linguagem trazem novas descobertas para o texto literário. Tomando por base a teoria bakhtiniana, faz um estudo dos discursos num fragmento de Capitães da Areia, que revela o embate de visões de mundo, a das elites e a dos excluídos, representados artisticamente nesse romance.
Triagem cognitiva: comparações entre o mini-mental e o teste de trilhas
Authors: Mota Márcia Maria Peruzzi Elia da , Banhato Eliane Ferreira Carvalho , Silva Kelly Cristina Atalaia da , Cupertino Ana Paula Fabrino Bretas
Published: October 2008

Este estudo investigou o desempenho de idosos no teste de triagem cognitiva Mini-Mental. Comparando a performance de 92 idosos neste teste e no Teste de Trilhas, demonstrou-se que o teste de triagem cognitiva Mini-Mental não é adequado para identificar comprometimento cognitivo precoce. Embora as análises realizadas tenham demonstrado que os idosos com pior desempenho no Teste de Trilhas tiveram performance inferior no teste de triagem cognitiva Mini-Mental, sujeitos que acertaram o primeiro se saíram melhor no segundo. Em um primeiro momento, pode parecer que o teste de triagem cognitiva Mini-Mental discrimina aqueles sujeitos que apresentam declínio; no entanto, a análise das médias de acertos nos testes mostra que tanto o grupo que completou corretamente o Teste de Trilhas quanto o que não completou apresentaram média de acertos superior ao ponto de corte no teste de triagem cognitiva Mini-Mental, mesmo quando se adotou um ponto de corte para sujeitos escolarizados. Cerca de 90% dos idosos que seriam descritos como portadores de algum prejuízo cognitivo na utilização do Teste de Trilhas B como parâmetro não apresentaram declínio quando o instrumento utilizado foi o teste de triagem cognitiva Mini-Mental. Esses resultados sugerem que o teste de triagem cognitiva Mini-Mental detecta o comprometimento quando ele já ocorreu, mas que tem pouco valor para avaliar o declínio, quando aplicado em uma amostra saudável.
Estratégias de enfrentamento de pais de crianças em tratamento de câncer
Authors: Kohlsdorf Marina , Costa Junior Áderson Luiz da
Published: October 2008

Este trabalho efetua uma revisão de literatura na área de psiconcologia pediátrica, destacando estudos e pesquisas relativos ao tema do enfrentamento da doença e do tratamento, publicados entre 1996 e 2007. Os resultados dos estudos evidenciam que um tratamento onco-hematológico pediátrico está associado a diversas mudanças na dinâmica familiar, rotina pessoal e modificação de repertórios de comportamentos, como conseqüências do tratamento médico prolongado, episódios de internação hospitalar, exposição a procedimentos médicos invasivos e a protocolos de quimioterapia antineoplásica, além de vivências de ansiedade, dúvidas, medos e perdas. Constata-se, ainda, a necessidade de investigação, na literatura nacional, do processo de desenvolvimento de diferentes estratégias de enfrentamento adotadas por cuidadores de populações pediátricas submetidas a tratamento onco-hematológico. A literatura internacional aponta que são necessários mais estudos que investiguem o processo das mudanças psicossociais, ajustamento psicológico, adaptação e modificações nas estratégias de enfrentamento, ao longo das diversas etapas do tratamento.
Análise microgenética do funcionamento cognitivo de crianças por meio do jogo Matix
Authors: Cavalcante Christiany Maria Bassetti , Ortega Antonio Carlos
Published: October 2008

Este trabalho teve por objetivo analisar, em um contexto microgenético, o funcionamento cognitivo de crianças por meio do jogo Matix. Participaram desta pesquisa quatro alunos da quarta série do Ensino Fundamental. Na primeira etapa, cada criança jogou três partidas para conhecer e explorar o jogo. Na segunda, os participantes formaram duplas que competiram entre si. Em seguida houve um rodízio entre eles, até que todos tivessem formado duplas e competido. Na terceira etapa, os participantes formaram uma dupla que resolveu situações-problema. Na última, cada participante jogou uma partida para avaliar que nível de compreensão cada um conseguiu alcançar após passar pelo processo de interação social. Os resultados indicaram uma evolução dos níveis de compreensão do sistema lógico contido no jogo Matix em todos os participantes. Constatou-se que o progresso cognitivo parece estar associado às condições cognitivas de cada sujeito e à possibilidade de sua inter-relação com os parceiros.
Histopathological, immunohistochemical and ultraestructural evaluation of inflammatory response in Arius genus fish under experimental inoculation of BCG
Authors: Sado Ricardo Yuji , Matushima Eliana Reiko
Published: October 2008

The aim of this study was to evaluate the inflammatory response kinetics after experimental inoculation with BCG in the primitive Arius sp. fish. The BCG was applied through the intramuscular injection in the caudal peduncular region, and the samples were collected for the analyses at days 1, 3, 7, 14, 21, and 33 post-injection. Acute phase inflammatory infiltrate was characterized by the predominant mononuclear cells, intersticial edema, and muscular tissue necrosis. As the inflammatory response evolved, a large number of multinuclear giant cells were formed containing the BCG. These giant cells were positive for the S100 protein at the histochemical analysis, which demonstrate the macrofage activity, confirmed by the ultra-structural analysis showing the lack of the cytoplasmic membrane enveloping the many nuclei within the giant cell. These results led to the conclusion that Arius sp. fish injected with the BCG showed a difuse inflammatory response characterized by a large number of mononuclear cells, absence of granuloma formation, and predominant giant cells.
Study of banana (Musa aaa Cavendish cv Nanica) trigger ripening for small scale process
Authors: Larotonda Fábio Donato Soares , Genena Aziza Kamal , Dantela Daniela , Soares Hugo Moreira , Laurindo João Borges , Moreira Regina Fátima Peralta Muniz , Ferreira Sandra Regina Salvador
Published: October 2008

The present work focuse on the impact of O2, CO2 and ethylene concentrations on ripening rate control of bananas as a contribution for the development of domestic equipments that could allow the user to drive the fruit shelf live. It represented the adjustment of metabolic activity rates in order to manage the maturity process. Ripening variables such as ethylene and CO2 concentrations and temperature were adjusted to accelerate or slow down the process, while the maturity degree was monitored through the physical and chemical parameters and sensorial analysis. Therefore, the objective of this work was to evaluate the influence of these parameters to manage the banana ripening. The optimum temperature was at 25 ÂºC of storage. The presence of oxygen, CO2 withdraws and ethylene injection were relevant for the ripening process. The "ready-to-eat" quality was achieved in 6 days in confined system. The use of ethylene as trigger was adequate to accelerate the ripening process with advantages in fruit color.
Two Essential Ingredients: Phonics and Fluency Getting to Know Each Other
Authors: Rasinski Timothy , Rupley William H. , Nichols William Dee
Published: October 2008

Phonics and fluency have been identified as two essential elements in the effective teaching of reading. Although normally considered two distinct elements of the reading curriculum that are separate, through the use of rhyming poetry both phonics and fluency can be taught in a synergistic and authentic manner. In this article, the authors explore how the repeated reading and performing of rhyming poetry can help children learn to read words accurately, automatically, and with appropriate and meaningful expression.

لقد تم تحديد الصوتيات والطلاقة كعنصرين أساسيين لدى تعليم القراءة الفعّال. وبيد أن غالباً ما يُعتبَران عنصرين مختلفين من منهاج القراءة وهما منفصان عن بعضهما البعض فإن كلا الصوتيات والطلاقة يجوز تعليمهما من خلال شعر القافية بصورة تضافرية وأصلية. وفي هذه المقالة يستكشف المؤلفون كيف قراءة شعر القافية وأداءها المتكرران قد يساعد الأطفال في قراءة الكلمات بدقة وبتلقائي وبنبرة مناسبة ومعنوية.

语音拼读与流畅阅读已被确認为高效阅读教学中两个不可或缺的元素。虽然语音拼读与流畅阅读通常被视为两个截然不同的独立阅读教程元素，但透过押韵诗歌阅读教学，這两个教程元素不但可以同时教授，而且還会促使两者协同增效，更具真实性。本文作者探索重复朗读和表演押韵诗歌如何帮助儿童学习准确地、自动地朗读语词，并且配以适当的和有意义的表情。

La phonétique et la fluidité ont été identifiées comme deux éléments essentiels d'un enseignement efficace de la lecture. Quoiqu'elles soient considérées normalement comme des éléments distincts et indépendants du programme de lecture, grâce à l'utilisation de la poésie rimée on peut enseigner en synergie et de façon authentique la phonétique et la fluidité. Dans cet article, l'auteur examine comment la lecture répétée et la pratique de la poésie rimée peuvent aider les enfants à lire les mots de façon exacte, automatique, et avec le sens et l'expression qui conviennent.

Краеугольными камнями для успешного обучения чтению принято считать беглость чтения и умение соотносить звуковую оболочку слова с его написанием. Согласно учебному плану эти навыки обычно развиваются порознь, но их можно эффективно отрабатывать и вместе – благодаря рифмованным стихам, то есть на основе аутентичных текстов. В данной статье авторы исследуют, как перечитывание и декламация стихов наизусть помогают детям внимательно прочитывать слова, довести чтение до автоматизма и затем выразительно их декламировать.

La fonética y la fluidez han sido identificadas como dos elementos esenciales en la enseñanza efectiva de la lectura. Aunque generalmente se consideran dos elementos distintos en el currículo de lectura, es posible enseñar tanto la fonética como la fluidez de una forma sinergética y auténtica usando poesía que rima. En este artículo, los autores exploran cómo la lectura y la presentación repetida de poesía que rima puede ayudar a los niños a aprender a leer palabras precisamente, automáticamente, y con una expresión apropiada que hace sentido.
A study on the effect of zeolites (clinoptilolite) on volcanic tuff blended cement paste and mortars
Authors: Yilmaz B. , Ertün T. , Uçar A. , Öteyaka B. , Önce G.
Published: October 2008

In this study, the effect of clinoptilolite, which is one of the zeolite minerals, on the properties of tuff (volcanic) blended cement was investigated. The physical, chemical, mineralogical and mechanical properties of blended cements containing tuff, clinoptilolite and tuff-clinoptilolite, as well as the electrokinetic interaction of blend-cement particles were examined. Clinoptilolite can be ground easily because of its large number of channels and cavities. It decreases the specific gravity of the blended cement, increases the surface area and affects the diffusion of the water and dissolution of clinker components because of its microporous structure and accelerates the setting time. Tuff and clinoptilolite show different electrokinetic behaviours compared to ordinary Portland Cement.
Axial behaviour of reinforced concrete short columns strengthened with wire rope and T-shaped steel plate units
Authors: Yang K.-H. , Ashour A.F. , Lee E.-T.
Published: October 2008

This paper presents a relatively simple column strengthening procedure using unbonded wire rope and T-shaped steel plate units. Twelve strengthened columns and an unstrengthened control column were tested to failure under concentric axial load to explore the significance and shortcomings of the proposed strengthening technique. The main variables investigated were the volume ratio of wire ropes as well as geometrical size and configuration of T-shaped steel plates. Axial load capacity and ductility ratio of columns tested were compared with predictions obtained from the equation specified in ACI 318-05 and models developed for conventionally tied columns, respectively. The measured axial load capacities of all strengthened columns were higher than predictions obtained from ACI 318-05, indicating that the ratio of the measured and predicted values increased with the increase of volume ratio of wire ropes and flange width of T-shaped steel plates. In addition, at the same lateral reinforcement index, a much higher ductility ratio was exhibited by strengthened columns having a volume ratio of wire ropes above 0·0039 than tied columns. The ductility ratio of strengthened columns tested increased with the increase of flange width, thickness, and web height of T-shaped steel plates. A mathematical model for the prediction of stress–strain characteristics of confined concrete using the proposed strengthening technique is developed, that was in good agreement with test results.
Bleeding and evaporation in concrete slabs with sequential placement
Authors: Kwak H.-G. , Ha S.-J.
Published: October 2008

An analytical method that can predict the occurrence of plastic shrinkage cracking in sequentially placed concrete slabs is proposed on the basis of a numerical model introduced in previous studies by the current authors. The influence on plastic shrinkage cracking of design variables such as the number of placement steps and the time interval between layers is quantitatively analysed through parametric studies using the previously introduced analytical method. In addition, two regression equations that take into account the effect of the sequential placement on plastic shrinkage cracking in concrete slabs are introduced. The first estimates the time at which the surface of the concrete slab begins to dry and the second determines the critical time interval to prevent surface drying in each concrete layer. The timing of the curing and the sequence of concrete placement, which are important factors in the prevention of plastic shrinkage cracking, can be planned effectively using the introduced equations without rigorous analysis.
Subsurface Drilling Waste Injection: Real-time Waste Domain Characterization Using Injection Monitoring and Pressure Interpretation
Authors: Shokanov T. , Still V. , Hernandez E. , Ovalle A. , Fragachan F.
Published: October 2008

Subsurface drilling waste injection has been proven as an environmentally safe and cost-effective alternative for drilling waste disposal in remote and environmentally sensitive areas. This has resulted in the rapid expansion of waste injection operations into major E&P regions throughout the world, and thus, the dramatic increase in total drilling waste volume injected in recent years.

Despite the outstanding milestones that have been achieved and the millions of barrels of drilling waste successfully injected, there are significant subsurface risks involved with any waste injection project, such as breach to surface, intersection with near-by wells or natural faults and well plugging. Limited understanding and characterization of those risks could potentially have a significant environmental impact and jeopardize the pre-defined project execution plan. Therefore, continuous injection monitoring and pressure interpretation coupled with a proactive subsurface assurance process is the key to mitigate those risks and ensure environmentally safe and seamless waste injection operations. Complexity of fracturing systems created during multiple waste injections render it imperative to monitor and characterize the waste domain in real time through corresponding pressure behavior interpretation.

This paper presents the unique and technically challenging injection monitoring and pressure interpretation experience attained in different waste injection projects in the CIS region, where the in-depth interpretation of fracture behavior and waste domain monitoring helped to minimize subsurface risks and to provide an adequate level of subsurface assurance. Continuous monitoring of injection data and parameters by a group of geo-mechanical experts in close collaboration with the operational team helps to identify and minimize the sub-surface risks and generate appropriate recommendations and mitigation procedures to avoid potential injectivity failures. Currently more than one and a half million barrels of drilling waste have been successfully contained through various waste injection projects in the CIS region.
Petrophysical Properties Evaluation of Tight Gas Sand Reservoirs Using NMR and Conventional Openhole Logs
Authors: Hamada G. M. , AbuShanab M. A. , Oraby M. El.
Published: October 2008

Tight reservoir means that reservoir of low porosity and low permeability. Many tight formations are extremely complex, producing from multiple layers with different permeability that is often enhanced by natural fracturing. The complicity of these reservoirs is attributed to a) Low porosity and low permeability reservoir b) The presence of clay minerals like illite, kaolin and micas in pores, c) The heterogeneity of the reservoir in vertical and lateral directions. Evaluation of tight gas sand reservoirs represents difficult problems. Determination of petrophysical properties using only conventional logs very complicated. Using of NMR in individual bases or in combination with conventional openhole logs and SCAL data leads to better determination of petrophysical properties of heterogeneous tight gas sand reservoirs.

Nuclear magnetic resonance (NMR) logs differ from conventional neutron and density porosity logs, NMR signal amplitude provides detailed porosity free from lithology effects and radioactive sources and relaxation times give other petrophysical parameters such as permeability, capillary pressure, the distribution of pore sizes and hydrocarbon identification

This paper concentrates on determination of three petrophysical parameters of tight gas sand reservoirs: 1) Determination of detailed NMR porosity in combination with density porosity, ϕDMR 2) NMR permeability, KBGMR, it is based on the dynamic concept of gas movement and bulk gas volume in the invaded zone and 3) Capillary pressure derived from relaxation time T2 distribution and then it could be used for formation saturation measurements especially in the transition zone.
Prediction of Temperature Distribution in Intelligent Wells
Authors: Muradov K. M. , Davies D. R.
Published: October 2008

Intelligent well system technology enables downhole monitoring and zonal, fluid production control in real time. This allows well control decisions to be implemented that optimize recovery and avoid future problems. Currently, both pressure and temperature are usually monitored downhole; while often only the pressure data is used to provide the key information about the downhole performance. Temperature measurements have the potential to be as informative as pressure measurements in reflecting the reservoir’s and the well’s production performance. However, currently available models are unable to simulate the temperature profile of an intelligent well correctly.

This paper provides a theoretical underpinning for the temperature data interpretation workflow. A novel temperature model for multiphase flow with (possible) phase changes in an intelligent completion will be presented. Reservoir and sandface temperature performance is also analyzed and coupled with the intelligent well temperature model.

Three example cases illustrate the temperature model’s utility. They demonstrate that a small, but significant temperature response can be observed in the complex system of an intelligent well equilibrated with a reservoir zone. The magnitude of the signal used for influx detection is quantified for wells with different inclinations and influx locations. The importance of measurement resolution is also discussed.

This is a building block for a method to detect gas and/or water influxes and obtain phase flow rates at various locations within an intelligent well, is an important step towards a comprehensive well management scheme.
Advective Desorption of Uranium(VI) from Contaminated Hanford Vadose Zone Sediments under Saturated and Unsaturated Conditions
Authors: Wellman D. M. , Zachara J. M. , Liu C. , Qafoku N. P. , Smith S. C. , Forrester S. W.
Published: October 2008

Sedimentary, hydrologic, and geochemical variations in the Hanford subsurface environment, as well as compositional differences in contaminating waste streams, have created vast differences in the migration and mobility of U within the subsurface environment. A series of hydraulically saturated and unsaturated column experiments were performed to (i) assess the effect of water content on the advective desorption and migration of U from contaminated sediments and (ii) evaluate the U concentration that can develop in pore water and/or groundwater as a result of desorption/dissolution reactions. Flow rate and moisture content were varied to evaluate the influence of contact time, pore water velocity, and macropore desaturation on aqueous U concentrations. Sediments were collected from the T‐TX‐TY tank farm complex and the 300 Area Process Ponds located on the Hanford Site, southeastern Washington State. The sediments vary in depth, mineralogy, and in contamination events. Experiments were conducted under mildly alkaline/calcareous conditions representative of conditions commonly encountered at repository sites across the arid western United States and, in particular, the Hanford site. Results illustrate the release of U from these sediments is kinetically controlled, and low water contents encountered within the Hanford vadose zone result in the formation of mobile–immobile water regimes, which isolate a fraction of the reactive sites within the sediments, effectively reducing the concentration of U released into migrating pore waters.
Water Loss Management: A Case Study in Korea
Authors: Mun J. Y. , Kim D. G. , Kang B. J. , Park Y. H. , Ahn H. W.
Published: October 2008

A case of water loss management on a small city whose water supply is approximately 34,000 m3/day is examined. Revenue water ratio was just 55% mostly because of water loss caused by old pipes and difficulties in pipeline management in the beginning 2004.

A block system was introduced first to monitor and maintain the pipelines more conveniently, from small to medium to large blocks. Depending on the pipeline conditions, such as water leakage or quality, 50km of pipeline have been replaced from 2005 to 2006. Use of pressure control valves have also resulted in an increase of revenue water ratio by 10%. Overall, through systematic management and rehabilitation/replacement of pipelines, water leakage has decreased dramatically, and the revenue water ratio has increased from 55% to 70% in just 2 years.
Application of Artificial Neural Network for Reducing of Chlorine Residual Concentration in Water Distribution Network
Authors: Koo Jayong , Inakazu Toyono , Koizumi Akira , Arai Yasuhiro , Kim Kyoungpil , Ahn Jaechan
Published: October 2008

It is difficult to estimate residual chlorine at the dead-end area of the water distribution network because chlorine consumption is influenced by various factors. Therefore, there are many water utilities that control the amounts of chlorine in reservoirs using empirical trial-and-error methods to maintain safe levels of residual chlorine in the distribution system. In this study, an ANN model of residual chlorine concentration is proposed which could be used to reduce in chlorine use in water distribution system. The ANN model with best performance was selected by training and verification. The five scenarios for the reduction in chlorine use were analyzed by setting the input chlorine as low as 0.05~0.25 mg/L compared with the input chlorine observed in the time series. Case 4 is the best to be satisfied with the input condition (0.4 mg/L or more) and output condition (0.34 mg/L or more) at the same time. It is possible to reduce chlorine in use up to 0.2 mg/L in the maximum amount.