bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rapid, Rigsite-Deployable, Electrochemical Test for Evaluating the Membrane Potential of Shales
Authors: Al-Bazali Talal , Zhang Jianguo , Chenevert Martin E. , Sharma Mukul M. 
Published: October 2007

Summary
The membrane efficiency of shales is usually measured in the laboratory using pressure-transmission techniques that can be very time consuming and require shale core samples that may not be available. These tests also require special high-pressure equipment and cannot be conducted at the rigsite.
This paper presents a quick and relatively easy method for obtaining the membrane efficiency of shale cuttings (or cores) through electrochemical-potential measurements. The electrochemical test measures the voltage drop across shales that are in contact with fluids of different salinities. The measured voltage drop is used to calculate the shale's ion selectivity, which reflects the shale's ability to restrict ion flow (membrane potential). Data are presented to show the influence of ion type and ion concentration, shale permeability, and cation exchange capacity (CEC) on the ion selectivity. It was found that the shale membrane efficiency is well correlated with the membrane potential. The membrane potential is shown to be proportional to the ratio of the CEC and to the permeability of shales. A higher CEC/k ratio correlates very well with higher ion selectivity. The rigsite-measured ion selectivity can be correlated with the spontaneous-potential (SP) curves in the well.
The rapid determination of shale membrane efficiency using shale drill cuttings allows chemical interactions between shales and water-based fluids to be taken into account in wellborestability calculations without the need for shale core samples.
The Australasian Radiation Protection Society's Position Statement on Risks from Low Levels of Ionizing Radiation
Authors: Higson Donald 
Published: October 2007

Controversy continues on whether or not ionizing radiation is harmful at low doses, with unresolved scientific uncertainty about effects below a few tens of millisieverts. To settle what regulatory controls should apply in this dose region, an assumption has to be made relating dose to the possibility of harm or benefit. The position of the Australasian Radiation Protection Society on this matter is set out in a statement adopted by the Society in 2005. Its salient features are: There is insufficient evidence to establish a dose-effect relationship for doses that are less than a few tens of millisieverts in a year. A linear extrapolation from higher dose levels should be assumed only for the purpose of applying regulatory controls. Estimates of collective dose arising from individual doses that are less than some tens of millisieverts in a year should not be used to predict numbers of fatal cancers. The risk to an individual of doses significantly less than 100 microsieverts in a year is so small, if it exists at all, that regulatory requirements to control exposure at this level are not warranted.
Vascular inflammatory markers in early-onset obese and type 2 diabetes subjects before and after three months' aerobic exercise training
Authors: Hatunic Mensud , Finucane Francis , Burns Nicole , Gasparro Declan , Nolan John J 
Published: October 2007

Early-onset type 2 diabetes (T2DM) may lead to very early vascular complications. Cardiovascular mortality is two to five times higher in adults with diabetes than in people without diabetes. The cardiovascular risk of young people with T2DM is unknown. T2DM in young people is associated with marked visceral obesity, insulin resistance and microalbuminuria. We recently showed that these subjects did not improve in either fitness (maximum volume of oxygen consumption, VO2max) or glucose disposal after exercise training. Seven subjects with early-onset T2DM (aged 26.1±0.9 years, body mass index [BMI] 35.6±1.2 kg/m2) and 14 age-matched obese subjects with normal glucose tolerance (aged 25. 6±0.9 years, BMI 34. 3±1.4 kg/m2) underwent aerobic training for 12 weeks. Serum vascular inflammatory markers (high-sensitivity C-reactive protein [hsCRP], soluble intercellular adhesion molecule [sICAM-1], soluble vascular cell adhesion molecule [sVCAM-1], E-Selectin and P-Selectin) were measured before and after the training programme. At baseline, plasma concentrations of vascular inflammatory markers were significantly elevated in both groups. They did not improve after exercise.
Beneficial effects of spironolactone on glomerular injury in streptozotocin-induced diabetic rats
Authors: Jun Yuan  , Ruhan Jia  , Yan Bao  
Published: October 2007

Introduction. To investigate the beneficial effects of spironolactone (SPL) on glomerular injury in streptozotocin (STZ)-induced diabetic rats and the possible mechanism. Methods and results. STZ-induced diabetic rats were divided into control group, STZ group, and SPL group. Glomerular morphology was observed by light microscopy after the rats were sacrificed after 30 days treatment.The mRNA expressions of transforming growth factor-beta 1 (TGF-β1) and type-1 plasminogen activator inhibitor (PAI-1) in renal cortex were measured by transcription-polymyerase chain reaction (RT-PCR).The protein expressions of PAI-1, fibronectin (FN) and TGF-β1 were detected by western blotting and immunohistochemistry respectively. In addition, levels of malondialdehyde (MDA) and the activity of antioxidants including superoxide diamutase (SOD), glutathione peroxidase (GSH-P X) in the cortex of kidney were measured. Results. In untreated diabetic rats, the glomerular volume, the expression of FN and the urinary albumin excretion increased. The mRNA and protein expression of PAI-1 and TGF-β 1 significantly increased in the STZ group. Treatment with SPL partially reversed these changes. Meanwhile, elevated MDA levels as well as decreased SOD and GSH-PX activities in the cortex of kidney were significantly ameliorated in the treated group. Conclusion. SPL ameliorates the glomerular injury in STZ-induced early diabetic renal injury, which is closely related with the reduction of PAI-1 and TGF-β1 expression and the attenuation of oxidative stress.
Interactions of angiotensin IV and oxytocin on behaviour in mice
Authors: Gard Paul R , Daw Pauline , Sayyad Mashhour Zhila , Tran Paula 
Published: October 2007

Introduction. Angiotensin (Ang) IV enhances learning and memory in rats but there are strain differences in its effects in mice. Oxytocin (OT) also influences learning and memory in rats and mice and, in the light of the proposed effects of Ang IV on oxytocinase, the hypothesis that the effects of Ang IV on cognition in mice involve OT was tested.Materials and methods. The effects of Ang IV and OT, alone and combined, were determined in rat isolated uterine smooth muscle and in object recognition and forced swim tests in BKW mice.Results. Ang potentiated the contractile effects of OT in the uterus. Neither peptide had any effect on object recognition nor locomotor activity. Ang IV had no effect in the forced swim test but abolished the effects of OT.Conclusions. Ang IV influences the actions of OT in vitro and in vivo, possibly by inhibition of oxytocinase, but the lack of effect of Ang IV on object recognition in BKW mice is unlikely to be a consequence of a deficiency endogenous OT. Unlike OT, Ang IV alone has no effect on learned helplessness in the forced swim test, an effect often used to predict potential antidepressant efficacy in humans.
Angiotensin type 1 receptor blockade prevents endocardial dysfunction of rapidly paced atria in rats
Authors: Yamashita Takeshi , Sekiguchi Akiko , Kato Takeshi , Tsuneda Takayuki , Iwasaki Yu-ki , Sagara Kouichi , Iinuma Hiroyuki , Sawada Hitoshi , Aizawa Tadanori 
Published: October 2007

Introduction. Atrial fibrillation (AF) per se causes atrial endocardial dysfunction leading to local coagulation imbalance on the internal surface of the atrium, which contributes to thrombus formation in the fibrillating left atrium. Materials and methods. To test a hypothesis that blockade of angiotensin II type 1 receptor (AT1-receptor) prevents the endocardial dysfunction by AF, we examined the effects of olmesartan on the expression of tissue factor pathway inhibitor (TFPI), thrombomodulin (TM), endothelial nitric oxide synthase (eNOS) and plasminogen activator inhibitor-1 (PAI-1) in the endocardium of the rapidly paced rat atria. Results. Rapid pacing induced a significant decrease in TFPI,TM and eNOS and an increase in PAI-1 protein in the left atrium. Pre-administration of low-dose olmesartan significantly prevented the down-regulation of TFPI,TM and eNOS and also attenuated the up-regulation of PAI-1. Immunohistochemistry identified these changes predominantly in the atrial endocardium. While the drug was without any effect on mRNA levels of TFPI,TM and eNOS, there was a significant decrease in its PAI-1 mRNA expression. Conclusions. AT1-receptor blocker could partially prevent the atrial endocardial dysfunction by rapid atrial pacing, which would provide one theoretical basis for beneficial effects for stroke prevention in AF.
Rodent Models of Depression: Forced Swim and Tail Suspension Behavioral Despair Tests in Rats and Mice
Authors: Castagné Vincent , Moser Paul , Roux Sylvain , Porsolt Roger D. 
Published: October 2007

AbstractThe development of antidepressants requires simple rodent behavioral tests for initial screening before undertaking more complex preclinical tests and clinical evaluation. Presented in the unit are two widely used screening tests used for antidepressants, the forced swim (also termed behavioral despair) test in the rat and mouse, and the tail suspension test in the mouse. These tests have good predictive validity and allow rapid and economical detection of substances with potential antidepressant‐like activity. The behavioral despair and the tail suspension tests are based on the same principle, measurement of the duration of immobility occurring following exposure of rodents to an inescapable situation. The majority of clinically used antidepressants decrease the duration of immobility. Testing of new substances in the behavioral despair and tail suspension tests allows a simple assessment of their potential antidepressant activity by the measurement of their effect on immobility. Curr. Protoc. Pharmacol. 38:5.8.1‐5.8.11. © 2007 by John Wiley & Sons, Inc.
Application of Radiotherapy and Chemotherapy Protocols to Pre‐Clinical Tumor Models
Authors: Burd Randy , Wachsberger Phyllis 
Published: October 2007

AbstractThis unit (1) provides background into understanding how agents that target specific molecules or receptors (molecular‐targeted agents), in particular, agents affecting the tumor vasculature (perivasculature network in tumors), interact with and modify radiation therapy; (2) details factors affecting interpretation of results in murine tumor model experiments utilizing radiation therapy and drug combinations; and (3) provides specific protocols for the application of radiation therapy, both alone and in combination with chemotherapy and/or molecular‐targeted agents. Curr. Protoc. Pharmacol. 38:14.7.1‐14.7.24. © 2007 by John Wiley & Sons, Inc.
Assays for Determination of Protein Concentration
Authors: Olson Bradley J.S.C. , Markwell John 
Published: October 2007

AbstractBiochemical analysis of proteins relies on accurate quantitation of protein concentration. This appendix describes how to perform commonly used protein assays, e.g., Lowry, Bradford, BCA, and UV spectroscopic protein assays. The primary focus of the appendix is assay selection, emphasizing sample and buffer compatibility. Protein assay standard curves and data processing fundamentals are discussed in detail. This appendix also details high‐throughput adaptations of the commonly used protein assays, and also contains a protocol for BCA assay of total protein in SDS‐PAGE sample buffer that is used for equal loading of SDS‐PAGE gels, which is reliable, inexpensive, and quick. Curr. Protoc. Pharmacol. 38:A.3A.1‐A.3A.29. © 2007 by John Wiley & Sons, Inc.
The Fluorescent Protein Color Palette
Authors: Olenych Scott G. , Claxton Nathan S. , Ottenberg Gregory K. , Davidson Michael W. 
Published: October 2007

AbstractAdvances in fluorescent protein development over the past 10 years have led to fine‐tuning of the Aequorea victoria jellyfish color palette in the emission color range from blue to yellow, while a significant amount of progress has been achieved with reef coral species in the generation of monomeric fluorescent proteins emitting in the orange to far‐red spectral regions. It is not inconceivable that near‐infrared fluorescent proteins loom on the horizon. Expansion of the fluorescent protein family to include optical highlighters and FRET biosensors further arms this ubiquitous class of fluorophores with biological probes capable of photoactivation, photoconversion, and detection of molecular interactions beyond the resolution limits of optical microscopy. The success of these endeavors certainly suggests that almost any biological parameter can be investigated using the appropriate fluorescent protein–based application.
Using PhyloCon to Identify Conserved Regulatory Motifs
Authors: Wang Ting 
Published: October 2007

AbstractUnderstanding gene regulation has been and remains one of the major challenges for the molecular biology community. Gene regulation is mediated by a variety of short DNA sequences called regulatory elements, which include transcription factor binding sites. A first step toward understanding gene regulation is the identification of regulatory elements present in the genome. This challenge has been defined as the “motif finding problem” in the field of computational biology. Over the past 20 years, many algorithms have been developed to tackle the motif finding problem computationally. The PhyloCon algorithm, developed in 2003, is one of the first motif finding algorithms that take advantage of two important data resources, i.e., phylogenetic conservation and gene co‐regulation, to improve the efficiency of motif identification in biological datasets. This unit presents basic protocols to obtain, install, and apply the PhyloCon program and discusses the underlying algorithm and how to interpret the results. Curr. Protoc. Bioinform. 19:2.12.1‐2.12.29. © 2007 by John Wiley & Sons, Inc.
Using Galaxy to Perform Large‐Scale Interactive Data Analyses
Authors: Taylor James , Schenck Ian , Blankenberg Dan , Nekrutenko Anton 
Published: October 2007

AbstractWhile most experimental biologists know where to download genomic data, few have a concrete plan on how to analyze it. This situation can be corrected by: (1) providing unified portals serving genomic data and (2) building Web applications to allow flexible retrieval and on‐the‐fly analyses of the data. Powerful resources, such as the UCSC Genome Browser already address the first issue. The second issue, however, remains open. For example, how to find human protein‐coding exons with the highest density of single nucleotide polymorphisms (SNPs) and extract orthologous sequences from all sequenced mammals? Indeed, one can access all relevant data from the UCSC Genome Browser. But once the data is downloaded how would one deal with millions of SNPs and gigabytes of alignments? Galaxy (http://g2.bx.psu.edu) is designed specifically for that purpose. It amplifies the strengths of existing resources (such as UCSC Genome Browser) by allowing the user to access and, most importantly, analyze data within a single interface in an unprecedented number of ways. Curr. Protoc. Bioinform. 19:10.5.1‐10.5.25. © 2007 by John Wiley & Sons, Inc.
Defined, Feeder‐Independent Medium for Human Embryonic Stem Cell Culture
Authors: Ludwig Tenneille , A. Thomson James 
Published: October 2007

AbstractThe developmental potential of human ES cells makes them an important tool in developmental, pharmacological, and clinical research. For human ES cell technology to be fully exploited, however, culture efficiency must be improved, large‐scale culture enabled, and safety ensured. Traditional human ES cell culture systems have relied on serum products and mouse feeder layers, which limit the scale, present biological variability, and expose the cells to potential contaminants. Defined, feeder‐independent culture systems improve the safety and efficiency of ES cell technology, enabling translational research. The protocols herein are designed with the standard research laboratory in mind. They contain recipes for the formulation of mTeSR (a defined medium for human ES cell culture) and detailed protocols for the culture, transfer, and passage of cells grown in these feeder‐independent conditions. They provide a basis for routine feeder‐independent culture, and a starting point for additional optimization of culture conditions. Curr. Protoc. Stem Cell Biol. 2:1C.2.1‐1C.2.16. © 2007 by John Wiley & Sons, Inc.
Intelligent control using multiple models and neural networks
Authors: Fu Yue , Chai Tianyou , Yue Heng 
Published: October 2007

AbstractMost adaptive control algorithms for nonlinear discrete time systems become invalid when the controlled systems have non‐minimum phase properties and large uncertainties. In this paper, an intelligent control method using multiple models and neural networks (NN) is developed to deal with those problems. The proposed control method includes a set of fixed controllers, a re‐initialized neural network (NN) adaptive controller and a free‐running NN adaptive controller. The bounded‐input‐bounded‐output (BIBO) stability and performance convergence of the system are guaranteed by the free‐running adaptive controller, while the multiple fixed controllers and the re‐initialized adaptive controller are used to improve the transient response. Simulation results are presented to demonstrate the effectiveness of the proposed method. Copyright © 2007 John Wiley & Sons, Ltd.
Utility of consecutive repeat HIT ELISA testing for heparin‐induced thrombocytopenia
Authors: Chan Maren , Malynn Elizabeth , Shaz Beth , Uhl Lynne 
Published: October 2007

AbstractHeparin‐induced thrombocytopenia (HIT) is a serious complication of heparin therapy. Limited data are available regarding repeat HIT antibody testing after an initial negative test. We conducted a retrospective study to determine the utility of repeat testing. Heparin antibodies were detected using the GTI‐PF4 enzyme‐linked immunoabsorbent assay, ELISA (GTI Diagnostics, Waukesha, WI). Patients (n = 137) were assigned to one of three groups based upon the initial negative test optical density (OD) range of low = 0–0.132, medium = 0.133–0.267, and high = 0.268–0.399. A pretest clinical score was retrospectively determined using the “4T's” (Thrombocytopenia, Timing of platelet fall, Thrombosis, and the absence of oTher causes of thrombocytopenia). A subsequent positive ELISA was found in 16% (22/137) of patients who underwent repeat testing. Most of these patients had a low pretest clinical score (62%). Four patients had an interval change in the pretest score between the initial negative and subsequent positive tests. Only these four patients developed HIT with thrombosis (HITT). Eighty percent of patients with a high initial negative test OD value had a positive ELISA on repeat testing; however, the initial negative test OD value could not predict whether a patient developed HITT. In contrast, an increase in the pretest clinical probability between initial and repeat testing better predicted HITT. Consecutive repeat ELISA testing for heparin antibodies may be warranted in patients with an increase in their pretest clinical score after an initial negative test as an adjunct to confirm the diagnosis of HIT. Am. J. Hematol., 2008. © 2007 Wiley‐Liss, Inc.
The chromosome 9q subtelomere deletion syndrome
Authors: Stewart Douglas R. , Kleefstra Tjitske 
Published: October 2007

AbstractThe chromosome 9q subtelomere deletion syndrome (9qSTDS) is among the first and most common clinically recognizable syndromes to arise from widespread testing by fluorescent in situ hybridization (FISH) of subtelomere deletions. There are about 50 reported cases worldwide. Affected individuals invariably have severe hypotonia with speech and gross motor delay. The facial gestalt is distinct and features absolute or relative micro‐ or brachycephaly, hypertelorism, synophrys, and/or arched eyebrows, mid‐face hypoplasia, a short nose with upturned nares, a protruding tongue with everted lower lip and down‐turned corners of the mouth. Approximately half of affected individuals have congenital heart defects (primarily ASD or VSD). A significant minority have epilepsy and/or behavioral and sleep disturbances. A variety of other major and minor eye, ear, genital, and limb anomalies have been reported. Most patients have sub‐microscopic deletions of the subtelomere region of chromosome 9q34.3 that range from <400 kb to >3 Mb. The 9qSTDS is caused by haplo‐insufficiency of EHMT1, a gene whose protein product (Eu‐HMTase1) is a histone H3 Lys 9 (H3‐K9) methyltransferase. This was established by identification of three patients with features of the syndrome and either mutations or a balanced translocation in EHMT1. H3‐K9 histone methylation is restricted to the euchromatin of mammals and functions to silence individual genes. Deletion size does not correlate with the severity of the 9qSTDS since patients with mutations in EHMT1 are as severely affected as those with submicroscopic deletions. Patients clinically suspected of having the 9qSTDS but with normal subtelomere deletion testing by FISH or MLPA should be considered for detailed 9q MLPA analysis and/or sequencing of EHMT1. EHMT1 is another example in the growing list of genes responsible for brain development that appear to play a role in chromatin remodeling. Published 2007 Wiley‐Liss, Inc.
Cryptic telomere imbalance: A 15‐year update
Authors: Ledbetter David H. , Martin Christa Lese 
Published: October 2007

AbstractIt has been 15 years since we proposed that assays of telomere integrity might reveal cryptic translocations and deletions as a significant cause of mental retardation (MR) in patients with normal G‐banded karyotypes. Development of unique genomic probes adjacent to the subtelomeric repeats of each chromosome arm allowed multiplex FISH analyses that confirmed such cryptic telomeric imbalances in 3–6% of all unexplained MR. Although such “telomere FISH” analysis quickly became standard of care, limitations of this technology platform included a lack of information on the size and gene content of the deleted/duplicated segments and the failure to detect interstitial deletions not involving the most distal unique clone. The development of “molecular ruler” clone sets for every human telomere provided the foundation for accurate determination of size and gene content of each imbalance, as well as the detection of interstitial deletions within these regions. Array comparative genomic hybridization (aCGH) has emerged as a powerful technology to assess single copy changes (monosomy or trisomy) at targeted loci such as telomeres or across the whole genome. This technology now replaces multiplex FISH for the assessment of telomere integrity in unexplained MR and has the advantage of efficiently determining the size and gene content of the imbalance, as well as detecting interstitial deletions near telomeres or anywhere else in the genome covered by the array design. The application of aCGH in several studies of unexplained MR has confirmed that telomere imbalances are overrepresented compared to “average” chromosomal regions, although this is likely due to random chromosome breakage rather than specific molecular mechanisms associated with the genomic architecture of human telomeres. Telomere imbalances are significantly larger than initially envisioned (∼40% are >5 Mb in size), and indicate the analytic sensitivity of the G‐banded karyotype is much lower than previously thought. Finally, experience with smaller benign variants compared to larger pathogenic imbalances at telomeres serves as a model for approaching whole‐genome aCGH in a clinical setting. © 2007 Wiley‐Liss, Inc.