bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract
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

AbstractWe 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.
Petri Dish Incubation of Eyed Eggs from Rainbow Trout and Splake
Authors: Barnes Michael E , Durben Dan J 
Published: October 2008

Abstract
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

Abstract
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

Abstract
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 &lt; 0.05) increased walleye survival in comparison with controls. In the channel catfish trial, survival at 10 d posttreatment was significantly (P &lt; 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

Abstract
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).
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.
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

Abstract
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

Abstract
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

Abstract
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.
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.
Correlation of Pain Scores, Analgesic Use, and Beck Anxiety Inventory Scores During Hospitalization in Lower Extremity Amputees
Authors: Trame Cathy D , Greene Erin , Moddeman Gail , Booth Branyan A , Konstantakos Emmanuel K , Parada Stephen , Siebuhr Karl , Laughlin Richard T 
Published: October 2008

Post amputation pain can be debilitating for patients and families. Chronic pain is a common phenomenon after lower extremity amputation, occurring in up to 80% of this population. The purpose of this pilot study was to correlate post amputation pain scores to opioid analgesic consumption and Beck Anxiety Inventory (BAI) scores. Twenty-three patients with lower extremity amputation at an 827-bed acute care inner-city hospital were surveyed pre-operatively and post-operatively to determine if there was a significant correlation between anxiety and pain. A numeric scale was utilized by patients to rate their pain level, while the BAI was utilized to measure their anxiety levels.A significant correlation was found between the pre-operative BAI levels and the BAI levels identified at time of discharge. Patients were found to have a higher than normal level of anxiety pre-operatively. No significant correlations were found between anxiety and pain.