bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative disease classification based on cross-platform microarray data
Authors: Liu Chun-Chi , Hu Jianjun , Kalakrishnan Mrinal , Huang Haiyan , Zhou Xianghong Jasmine
Published: January 2009

Background

Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification.

Results

In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank ratios across datasets. In addition, we systematically map textual annotations of datasets to concepts in Unified Medical Language System (UMLS), permitting quantitative analysis of the phenotype "distance" between datasets and automated construction of disease classes. We design a new classification approach named ManiSVM, which integrates Manifold data transformation with SVM learning to exploit the data properties. Using the leave one dataset out cross validation, ManiSVM achieved the overall accuracy of 70.7% (68.6% precision and 76.9% recall) with many disease classes achieving the accuracy higher than 80%.

Conclusion

Our results not only demonstrated the feasibility of the integrated disease classification approach, but also showed that the classification accuracy increases with the number of homogenous training datasets. Thus, the power of the integrative approach will increase with the continuous accumulation of microarray data in public repositories. Our study shows that automated disease diagnosis can be an important and promising application of the enormous amount of costly to generate, yet freely available, public microarray data.
Prediction of amyloid fibril-forming segments based on a support vector machine
Authors: Tian Jian , Wu Ningfeng , Guo Jun , Fan Yunliu
Published: January 2009

Background

Amyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these short peptides is critical for understanding diseases and finding potential therapeutic targets.

Results

We propose a method, named Pafig (P rediction of a myloid fi bril-forming seg ments) based on support vector machines, to identify the hexpeptides associated with amyloid fibrillar aggregates. The features of Pafig were obtained by a two-round selection from AAindex. Using a 10-fold cross validation test on Hexpepset dataset, Pafig performed well with regards to overall accuracy of 81% and Matthews correlation coefficient of 0.63. Pafig was used to predict the potential fibril-forming hexpeptides in all of the 64,000,000 hexpeptides. As a result, approximately 5.08% of hexpeptides showed a high aggregation propensity. In the predicted fibril-forming hexpeptides, the amino acids – alanine, phenylalanine, isoleucine, leucine and valine occurred at the higher frequencies and the amino acids – aspartic acid, glutamic acid, histidine, lysine, arginine and praline, appeared with lower frequencies.

Conclusion

The performance of Pafig indicates that it is a powerful tool for identifying the hexpeptides associated with fibrillar aggregates and will be useful for large-scale analysis of proteomic data.
Human gene expression sensitivity according to large scale meta-analysis
Authors: Hao Pei , Zheng Siyuan , Ping Jie , Tu Kang , Gieger Christian , Wang-Sattler Rui , Zhong Yang , Li Yixue
Published: January 2009

Background

Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc. J.H. Ohn et al. first studied this gene property with yeast transcriptional profiling data.

Results

Here we propose a calculation framework for gene expression sensitivity analysis. We also compared the functions, centralities and transcriptional regulations of the sensitive and robust genes. We found that the robust genes tended to be involved in essential cellular processes. Oppositely, the sensitive genes perform their functions diversely. Moreover while genes from both groups show similar geometric centrality by coupling them onto integrated protein networks, the robust genes have higher vertex degree and betweenness than that of the sensitive genes. An interesting fact was also found that, not alike the sensitive genes, the robust genes shared less transcription factors as their regulators.

Conclusion

Our study reveals different propensities of gene expression to external perturbations, demonstrates different roles of sensitive genes and robust genes in the cell and proposes the necessity of combining the gene expression sensitivity in the microarray analysis.
Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites
Authors: Burrow Allison A , Williams Laura E , Pierce Levi CT , Wang Yuh-Hwa
Published: January 2009

Background

Gene rearrangements such as chromosomal translocations have been shown to contribute to cancer development. Human chromosomal fragile sites are regions of the genome especially prone to breakage, and have been implicated in various chromosome abnormalities found in cancer. However, there has been no comprehensive and quantitative examination of the location of fragile sites in relation to all chromosomal aberrations.

Results

Using up-to-date databases containing all cancer-specific recurrent translocations, we have examined 444 unique pairs of genes involved in these translocations to determine the correlation of translocation breakpoints and fragile sites in the gene pairs. We found that over half (52%) of translocation breakpoints in at least one gene of these gene pairs are mapped to fragile sites. Among these, we examined the DNA sequences within and flanking three randomly selected pairs of translocation-prone genes, and found that they exhibit characteristic features of fragile DNA, with frequent AT-rich flexibility islands and the potential of forming highly stable secondary structures.

Conclusion

Our study is the first to examine gene pairs involved in all recurrent chromosomal translocations observed in tumor cells, and to correlate the location of more than half of breakpoints to positions of known fragile sites. These results provide strong evidence to support a causative role for fragile sites in the generation of cancer-specific chromosomal rearrangements.
A four year longitudinal sero-epidemiological study of bovine herpesvirus type-1 (BHV-1) in adult cattle in 107 unvaccinated herds in south west England
Authors: Woodbine Kerry A , Medley Graham F , Moore Stephen J , Ramirez-Villaescusa Ana M , Mason Sam , Green Laura E
Published: January 2009

Background

Bovine herpesvirus type-1 (BHV-1) is an important pathogen of cattle that presents with a variety of clinical signs, including the upper respiratory tract infection infectious bovine rhinotracheitis (IBR). A seroepidemiological study of BHV-1 antibodies was conducted in England from 2002 – 2004: 29,782 blood samples were taken from 15,736 cattle from 114 herds which were visited on up to three occasions. Antibody concentration was measured using a commercial ELISA. Farm management information was collected using an interview questionnaire, and herd size and cattle movements were obtained from the cattle tuberculosis testing database and the British Cattle Movement Service. Hierarchical statistical models were used to investigate associations between cattle and herd variables and the continuous outcome percentage positive (PP) values from the ELISA test in unvaccinated herds.

Results

There were 7 vaccinated herds, all with at least one seropositive bovine. In unvaccinated herds 83.2% had at least one BHV-1 seropositive bovine, and the mean cattle and herd BHV-1 seroprevalence were 42.5% and 43.1% respectively. There were positive associations between PP value, age, herd size, presence of dairy cattle. Adult cattle in herds with grower cattle had lower PP values than those in herds without grower cattle. Purchased cattle had significantly lower PP values than homebred cattle, whereas cattle in herds that were totally restocked after the foot-and-mouth epidemic in 2001 had significantly higher PP values than those in continuously stocked herds. Samples taken in spring and summer had significantly lower PP values than those taken in winter, whereas those taken in autumn had significantly higher PP values than those taken in winter. The risks estimated from a logistic regression model with a binary outcome (seropositive yes/no) were similar.

Conclusion

The prevalence of BHV-1 seropositivity in cattle and herds has increased since the 1970s. Although the study population prevalence of BHV-1 was temporally stable during study period, the associations between serological status and cattle age, herd size, herd type, presence of young stock and restocked versus continuously stocked herds indicate that there is heterogeneity between herds and so potential for further spread of BHV-1 within and between herds.
Minimal acupuncture is not a valid placebo control in randomised controlled trials of acupuncture: a physiologist's perspective
Authors: Lund Iréne , Näslund Jan , Lundeberg Thomas
Published: January 2009

Placebo-control of acupuncture is used to evaluate and distinguish between the specific effects and the non-specific ones. During 'true' acupuncture treatment in general, the needles are inserted into acupoints and stimulated until deqi is evoked. In contrast, during placebo acupuncture, the needles are inserted into non-acupoints and/or superficially (so-called minimal acupuncture). A sham acupuncture needle with a blunt tip may be used in placebo acupuncture. Both minimal acupuncture and the placebo acupuncture with the sham acupuncture needle touching the skin would evoke activity in cutaneous afferent nerves. This afferent nerve activity has pronounced effects on the functional connectivity in the brain resulting in a 'limbic touch response'. Clinical studies showed that both acupuncture and minimal acupuncture procedures induced significant alleviation of migraine and that both procedures were equally effective. In other conditions such as low back pain and knee osteoarthritis, acupuncture was found to be more potent than minimal acupuncture and conventional non-acupuncture treatment. It is probable that the responses to 'true' acupuncture and minimal acupuncture are dependent on the aetiology of the pain. Furthermore, patients and healthy individuals may have different responses. In this paper, we argue that minimal acupuncture is not valid as an inert placebo-control despite its conceptual brilliance.
Duration of untreated prodromal symptoms and 12-month functional outcome of individuals at risk of psychosis
Authors: Fusar-Poli P. , Meneghelli A. , Valmaggia L. , Allen P. , Galvan F. , McGuire P. , Cocchi A.
Published: January 2009

Individuals seeking help from prodromal services may have been experiencing attenuated psychotic features and psychosocial impairments for a long period prior to referral. The effect of an extended duration of these untreated ‘at risk’ symptoms on patients' long-term functional outcome was assessed in a 12-month longitudinal observational study (n=49). A longer duration of untreated ‘at risk’ symptoms was correlated with a reduced improvement in Global Assessment of Functioning scores after 12 months (β=0.375, P=0.008). This effect was independent of age and gender and may have implications for the improvement of treatment strategies in pre-psychotic phases.
Risk for depression and neural responses to fearful facial expressions of emotion
Authors: Chan Stella W. Y. , Norbury Ray , Goodwin Guy M. , Harmer Catherine J.
Published: January 2009

Background

Depression is associated with neural abnormalities in emotional processing.

Aims

This study explored whether these abnormalities underlie risk for depression.

Method

We compared the neural responses of volunteers who were at high and low-risk for the development of depression (by virtue of high and low neuroticism scores; high-N group and low-N group respectively) during the presentation of fearful and happy faces using functional magnetic resonance imaging (fMRI).

Results

The high-N group demonstrated linear increases in response in the right fusiform gyrus and left middle temporal gyrus to expressions of increasing fear, whereas the low-N group demonstrated the opposite effect. The high-N group also displayed greater responses in the right amygdala, cerebellum, left middle frontal and bilateral parietal gyri to medium levels of fearful v. happy expressions.

Conclusions

Risk for depression is associated with enhanced neural responses to fearful facial expressions similar to those observed in acute depression.
Leptin Indirectly Regulates Gonadotropin-Releasing Hormone Neuronal Function
Authors: Quennell Janette H. , Mulligan Alicia C. , Tups Alexander , Liu Xinhuai , Phipps Sarah J. , Kemp Christopher J. , Herbison Allan E. , Grattan David R. , Anderson Greg M.
Published: January 2009

The adipose-derived hormone leptin communicates information about metabolic status to the hypothalamic GnRH neuronal system. It is unclear whether leptin can act directly on GnRH neurons. To examine this, we used three approaches. First, the presence of leptin-induced signal transducer and activator of transcription-3 activation was examined in GnRH neurons in male and female rats. Intracerebroventricular treatment with 4 μg leptin-induced robust signal transducer and activator of transcription-3 expression within the anteroventral periventricular nucleus but not in GnRH neurons. Second, fertility was assessed in male and female CRE-loxP transgenic mice with conditional leptin receptor (Lepr) deletion from either all forebrain neurons or GnRH neurons only. Forebrain neuron LEPR deletion prevented the onset of puberty resulting in infertility in males and females and blocked estradiol-induced LH surge. However, mice with GnRH neuron-selective Lepr deletion exhibited normal fertility apart from a slight puberty delay in males. Lastly, the highly sensitive technique of single-cell nested PCR was used to test for Lepr transcript presence in individual GnRH neurons, identified in situ using GnRH-green fluorescent protein transgenics. Whereas 75% of positive control (proopiomelanocortin) neurons contained Lepr mRNA, no (none of 18) GnRH neurons were Lepr mRNA positive. Collectively, these results show that leptin does not act directly on GnRH neurons in rats and mice. Leptin appears to regulate GnRH function via forebrain neurons that are afferent to GnRH because forebrain neuronal LEPR deletion caused infertility. The location and phenotype of these leptin-responsive neurons remains to be elucidated.
Evidence for cranial endothermy in the opah (Lampris guttatus)
Authors: Runcie Rosa M. , Dewar Heidi , Hawn Donald R. , Frank Lawrence R. , Dickson Kathryn A.
Published: January 2009

Cranial endothermy evolved independently in lamnid sharks, billfishes and tunas, and is thought to minimize the effects of ambient temperature change on both vision and neural function during deep dives. The opah, Lampris guttatus, is a large epipelagic–mesopelagic predator that makes repeated dives into cool waters to forage. To determine if L. guttatus exhibits cranial endothermy, we measured cranial temperatures in live, decked fish and identified potential sources of heat and mechanisms to conserve heat. In 40 opah (95.1±7.6 cm fork length), the temperature of the tissue behind the eye was elevated by a mean (±s.e.m.) of 2.1±0.3°C and a maximum of 6.3°C above myotomal muscle temperature (Tm), used as a proxy for ambient temperature. Cranial temperature varied significantly with Tm and temperature elevation was greater at lower Tm. The proximal region of the paired lateral rectus extraocular muscle appears to be the primary source of heat. This muscle is the largest extraocular muscle, is adjacent to the optic nerve and brain and is separated from the brain only by a thin layer of bone. The proximal lateral rectus muscle is darker red in color and has a higher citrate synthase activity, indicating a higher capacity for aerobic heat production, than all other extraocular muscles. Furthermore,this muscle has a layer of fat insulating it from the gill cavity and is perfused by a network of arteries and veins that forms a putative counter-current heat exchanger. Taken together, these results support the hypothesis that the opah can maintain elevated cranial temperatures.
The representational status of pretence: Evidence from typical development and autism
Authors: Jarrold Christopher , Mansergh Ruth , Whiting Claire
Published: January 2009

The question of whether understanding pretend play requires meta‐representational skill was examined among typically developing children and individuals with autism. Participants were presented with closely equated true and false pretence trials in which they had to judge a protagonist's pretend reading of a situation, which either matched or differed from their own. Results showed that individuals' theory of mind abilities determined their performance on false, but not true, pretence trials. These findings imply that meta‐representation is involved when an individual has to make sense of a pretend state of mind that differs from their own, but, crucially, they also show that pretend play can often be understood without meta‐representational competence.
Referential Communication Skills of Children With Williams Syndrome: Understanding When Messages Are Not Adequate
Authors: John Angela E. , Rowe Melissa L. , Mervis Carolyn B.
Published: January 2009

Although children with Williams syndrome have relatively good structural language and concrete vocabulary abilities, they have difficulty with pragmatic aspects of language. To investigate the impact of pragmatic difficulties on listener-role referential communication, we administered a picture placement task designed to measure ability to verbalize message inadequacy to a speaker separated by a barrier. Participants were 57 children with Williams syndrome 6 to 12 years of age. When messages were inadequate, children verbalized that a problem was encountered less than half the time. The likelihood that children would indicate a message was insufficient and that children who verbalized message inadequacy also would effectively communicate the problem varied as a function of type of problem encountered, theory of mind knowledge, receptive vocabulary, and CA.
Optimization of Transrenal DNA Analysis: Detection of Fetal DNA in Maternal Urine
Authors: Shekhtman Eugene M , Anne Kalpana , Melkonyan Hovsep S , Robbins David J , Warsof Steven L , Umansky Samuil R
Published: January 2009

Background: Fragments of DNA from cells dying throughout the body are detectable in urine (transrenal DNA, or Tr-DNA). Our goal was the optimization of Tr-DNA isolation and detection techniques, using as a model the analysis of fetal DNA in maternal urine.

Methods: We isolated urinary DNA using a traditional silica-based method and using a new technique based on adsorption of cell-free nucleic acids on Q-Sepharose resin. The presence of Y chromosome–specific SRY (sex-determining region Y) sequences in urine of pregnant women was detected by conventional and real-time PCR using primers/probe sets designed for 25-, 39-, 65-, and 88-bp PCR targets.

Results: Method of DNA isolation and PCR target size affected fetal Tr-DNA detection. Assay diagnostic sensitivity increases as the PCR target is shortened. Shorter DNA fragments (50–150 bp) could be isolated by Q-resin–based technique, which also facilitated fetal Tr-DNA analysis. Using DNA isolated by Q-resin–based method and an “ultrashort” DNA target, we successfully detected SRY sequences in 78 of 82 urine samples from women pregnant with male fetuses (positive predictive value 87.6%). Eleven of 91 urine samples from women pregnant with female fetuses produced SRY false-positive results (negative predictive value 95.2%).

Conclusions: Single-copy fetal DNA sequences can be successfully detected in the urine of pregnant women when adequate methods for DNA isolation and analysis are applied. Strong precautions against sample contamination with male cells and DNA are necessary to avoid false-positive results.
Profile of the Circulating DNA in Apparently Healthy Individuals
Authors: Beck Julia , Urnovitz Howard B , Riggert Joachim , Clerici Mario , Schütz Ekkehard
Published: January 2009

Background: Circulating nucleic acids (CNAs) have been shown to have diagnostic utility in human diseases. The aim of this study was to sequence and organize CNAs to document typical profiles of circulating DNA in apparently healthy individuals.

Methods: Serum DNA from 51 apparently healthy humans was extracted, amplified, sequenced via pyrosequencing (454 Life Sciences/Roche Diagnostics), and categorized by (a) origin (human vs xenogeneic), (b) functionality (repeats, genes, coding or noncoding), and (c) chromosomal localization. CNA results were compared with genomic DNA controls (n = 4) that were subjected to the identical procedure.

Results: We obtained 4.5 × 105 sequences (7.5 × 107 nucleotides), of which 87% were attributable to known database sequences. Of these sequences, 97% were genomic, and 3% were xenogeneic. CNAs and genomic DNA did not differ with respect to sequences attributable to repeats, genes, RNA, and protein-coding DNA sequences. CNA tended to have a higher proportion of short interspersed nuclear element sequences (P = 0.1), of which Alu sequences were significant (P < 0.01). CNAs had a significantly lower proportion of L1 and L2 long interspersed nuclear element sequences (P < 0.01). In addition, hepatitis B virus (HBV) genotype F sequences were found in an individual accidentally evaluated as a healthy control.

Conclusions: Comparison of CNAs with genomic DNA suggests that nonspecific DNA release is not the sole origin for CNAs. The CNA profiling of healthy individuals we have described, together with the detailed biometric analysis, provides the basis for future studies of patients with specific diseases. Furthermore, the detection of previously unknown HBV infection suggests the capability of this method to uncover occult infections.
Rapid Single-Nucleotide Polymorphism Detection of Cytochrome P450 (CYP2C9) and Vitamin K Epoxide Reductase (VKORC1) Genes for the Warfarin Dose Adjustment by the SMart-Amplification Process Version 2
Authors: Aomori Tohru , Yamamoto Koujirou , Oguchi-Katayama Atsuko , Kawai Yuki , Ishidao Takefumi , Mitani Yasumasa , Kogo Yasushi , Lezhava Alexander , Fujita Yukiyoshi , Obayashi Kyoko , Nakamura Katsunori , Kohnke Hugo , Wadelius Mia , Ekström Lena , Skogastierna Cristine , Rane Anders , Kurabayashi Masahiko , Murakami Masami , Cizdziel Paul E , Hayashizaki Yoshihide , Horiuchi Ryuya
Published: January 2009

Background: Polymorphisms of the CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9) gene (CYP2C9*2, CYP2C9*3) and the VKORC1 (vitamin K epoxide reductase complex, subunit 1) gene (−1639G>A) greatly impact the maintenance dose for the drug warfarin. Prescreening patients for their genotypes before prescribing the drug facilitates a faster individualized determination of the proper maintenance dose, minimizing the risk for adverse reaction and reoccurrence of thromboembolic episodes. With current methodologies, therapy can be delayed by several hours to 1 day if genotyping is to determine the loading dose. A simpler and more rapid genotyping method is required.

Methods: We developed a single-nucleotide polymorphism (SNP)-detection assay based on the SMart Amplification Process version 2 (SMAP 2) to analyze CYP2C9*2, CYP2C9*3, and VKORC1 −1639G>A polymorphisms. Blood from consenting participants was used directly in a closed-tube real-time assay without DNA purification to obtain results within 1 h after blood collection.

Results: We analyzed 125 blood samples by both SMAP 2 and PCR-RFLP methods. The results showed perfect concordance.

Conclusions: The results validate the accuracy of the SMAP 2 for determination of SNPs critical to personalized warfarin therapy. SMAP 2 offers speed, simplicity of sample preparation, the convenience of isothermal amplification, and assay-design flexibility, which are significant advantages over conventional genotyping technologies. In this example and other clinical scenarios in which genetic testing is required for immediate and better-informed therapeutic decisions, SMAP 2–based diagnostics have key advantages.
Fatty Acid Synthase: Association with Insulin Resistance, Type 2 Diabetes, and Cancer
Authors: Menendez Javier A , Vazquez-Martin Alejandro , Ortega Francisco Jose , Fernandez-Real Jose Manuel
Published: January 2009

Background: An emerging paradigm supports the notion that deregulation of fatty acid synthase (FASN)-catalyzed de novo FA biogenesis could play a central role in the pathogenesis of metabolic diseases sharing the hallmark of insulin-resistance.

Content: We reviewed pharmacological and genetic alterations of FASN activity that have been shown to significantly influence energy expenditure rates, fat mass, insulin sensitivity, and cancer risk. This new paradigm proposes that insulin-resistant conditions such as obesity, type 2 diabetes, and cancer arise from a common FASN-driven “lipogenic state”. An important question then is whether the development or the progression of insulin-related metabolic disorders can be prevented or reversed by the modulation of FASN status. If we accept the paradigm of FASN dysfunction as a previously unrecognized link between insulin resistance, type 2 diabetes, and cancer, the use of insulin sensitizers in parallel with forthcoming FASN inhibitors should be a valuable therapeutic approach that, in association with lifestyle interventions, would concurrently improve energy-flux status, ameliorate insulin sensitivity, and alleviate the risk of lipogenic carcinomas.

Conclusions: Although the picture is currently incomplete and researchers in the field have plenty of work ahead, the latest clinical and experimental evidence that we discuss illuminates a functional and drug-modifiable link that connects FASN-driven endogenous FA biosynthesis, insulin action, and glucose homeostasis in the natural history of insulin-resistant pathologies.
Evaluation of Shear Wave Velocity Based Soil Liquefaction Resistance Criteria by Centrifuge Tests
Authors: Fu Lei , Liu Gang , Zeng Xiangwu
Published: January 2009

A new technique has been developed for the evaluation of shear wave velocity based soil liquefaction resistance criteria by centrifuge tests. It involves the application of bender elements in centrifuge tests to measure shear wave velocity while investigating the liquefaction features of a saturated model. A total of six models were tested. Shear wave velocity and shear modulus profiles of the models were obtained. Currently used case history based soil liquefaction criteria were examined. The results show that there is an obvious difference in soil liquefaction resistance before and after the application of an earthquake. It is concluded that currently used case history based soil liquefaction resistance criteria developed from the mixed parameters measured before and after earthquakes need to be modified to take into account this difference.
Membrane Penetration Remedy for the Testing of Lightly Cemented Scrap Rubber Tire Chips
Authors: Tsoi Wa-Yeung , Lee Kin-Man
Published: January 2009

Lightly cemented scrap rubber tire chips have been proposed as lightweight geomaterial (LGM) for various geotechnical applications, not only because of its advantageous engineering properties but also because of its capability to cope with the scrap tire disposal problem. In this research, gravel-sized tire chips are bonded together by portland cement to form a highly porous structure that is ductile and stiff for geotechnical works. However, the study on this material under a conventional triaxial system is difficult because of serious membrane penetration. A plastic-plate-reinforced membrane together with patching up of the sample surface voids by a scrap tire powder paste is proposed to cope with the penetration problem. This method has been successfully applied to tests under confining pressures in the order of MPa. Test results have shown that the extra axial resistance and radial confinement due to this method are slight.
Shear Load Tests on Stone Columns With and Without Geosynthetic Encasement
Authors: Murugesan S. , Rajagopal K.
Published: January 2009

The use of stone columns (otherwise called granular piles) has proved to be an economical and technically viable ground improvement technique for construction on soft clay soils. Though the stone columns are designed to carry vertical compressive loads, soil movements occurring in the field conditions may cause shear deformations in the stone columns. The stone columns, particularly installed in very soft soils, may not be able to resist these shear movements because of the low confinement offered by the surrounding soil. The shear load capacity of such stone columns can be significantly improved by encasing the individual stone columns with suitable geosynthetic. The encasement confines the aggregate and makes the stone column act like a semirigid pile; thus leading to increased shear stiffness of the column. This paper discusses some laboratory model tests performed to investigate the shear load capacity of stone columns with and without geosynthetic encasement. The laboratory tests were performed by inducing lateral soil movements in a stone column treated soft soil. The results have shown qualitative improvement in the shear stiffness of the stone column due to geosynthetic encasement.
Evaluation of Rock Bolt Integrity using Guided Ultrasonic Waves
Authors: Han Shin-In , Lee In-Mo , Lee Yong-Jun , Lee Jong-Sub
Published: January 2009

Rock bolts play a crucial role in reinforcement support systems for tunnels and rock slopes. In this study documented herein, guided ultrasonic waves are used to evaluate the integrity of rock bolts. The dispersion characteristics of the guided waves are identified by numerical simulations. Experimental studies using the transmission of guided waves are carried out with different defect ratios for grouted nonembedded rock bolts, and for rock bolts embedded into a concrete block and rock mass. Analytical solutions are suggested to estimate the equivalent velocity for both the grouted and the embedment portions. Numerical simulations reveal that the optimal frequency range of guided waves is 20∼70 kHz in the first longitudinal mode. Field and laboratory experimental studies and associated analyses show the velocity of guided waves increases as the defect ratio increases. The velocity for the grouted portion in the nonembedded rock bolts is essentially constant. However, the velocity in the embedment portion decreases with increasing embedment length due to the increase in the size of the influence zone. Results suggest that the integrity of rock bolts can be easily evaluated by the transmission method using guided waves.
Modified Ohio’s Curves: A Rapid Estimation of Compaction Curves for Coarse- and Fine-Grained Soils
Authors: Horpibulsuk Suksun , Katkan Wanchai , Naramitkornburee Anek
Published: January 2009

Compaction curves from 16 coarse- and 9 fine-grained soils, which cover all soil types classified by the Unified Soil Classification System are analyzed to develop the Modified Ohio’s curves. For all soils, the relationships between water content and degree of saturation on both the dry and the wet sides of optimum are represented by power functions. Their compaction curves under standard Proctor energy follow the Ohio’s curves. Optimum degree of saturation, ODS, of coarse-grained soils is lower than that of fine-grained soils. However, for a given soil, the ODS is practically the same for different compaction energies, E. Even though compaction characteristics (optimum water content, OWC, and maximum dry unit weight, γd max) are different for different soils, their relationship between normalized OWC/OWCst and E is practically the same, where OWCst is the OWC at standard Proctor energy. Based on this finding, the Modified Ohio’s curves are introduced under compaction energy levels of the half standard, half modified, and modified Proctor energies. The verification of the Modified Ohio’s curve is also illustrated in this paper. These curves are useful in rapid estimation of laboratory compaction curves from a single set data of dry unit weight and water content.
Cavitation Protection Performance of Nitrite-Free Organic Acid Based Coolant for Heavy-Duty Engines
Authors: Mori Yasuaki , Abel Michael L. , Miyake Yuji
Published: January 2009

For decades, most all heavy-duty engine coolants contain nitrites in order to protect against cavitation erosion/corrosion. So much so that many industry specifications require nitrites by name as well as minimum concentration quantities as they have been found to be very effective in minimizing cavitation erosion/corrosion of heavy-duty engine cast iron cylinder liners. However, the use of nitrites has become an issue because it is commonly known that nitrites could produce carcinogens when mixed with amine-type coolants. Legislation in some countries recommend not using it. This paper introduces nitrite-free, organic acid based, long-life coolant technology that gives the desired cavitation protection.
Evaluation of Functional Approaches to Describe the Moisture Diffusivity of Building Materials
Authors: Scheffler Gregor , Grunewald John , Plagge Rudolf
Published: January 2009

With a set of material parameters and a material model called engineering model of hygrothermal material characteristics, both proposed in (Scheffler, 2004), the material functions used for input to hygrothermal building component simulation programs can be adjusted. Using inverse identification of functional parameters by simulation of laboratory experiments, the model is calibrated to reproduce measured water uptake and drying curves. The developed material functions contain an approach to describe the liquid water conductivity of building materials. In addition, moisture storage data approximated by a GAUSSian functional approach, showing sufficient flexibility in the whole moisture range, is available. There with the derivative of the moisture retention curve is known at high precision and the liquid water diffusivity can be derived, too. There exists a wide interest in applicable material functions based on literature data. But literature reviews of hygrothermal material parameters often yield incomplete datasets and experimentally determined curves are lacking or are available at lower accuracy only. Different authors introduced several diffusivity approaches requiring less input parameters for description of liquid water transport in building materials. These models are evaluated by means of diffusivity data derived from the calibrated liquid water conductivity function of the engineering model. A selection of four accurately measured materials is used for this investigation. The investigation is based on controlled laboratory data of high resolution. With the knowledge gained from this study, the uncertainties in interpretation of incomplete datasets frequently encountered in literature reviews shall be reduced.
Field Test for Carboxylate Inhibitor Levels in OAT Coolants
Authors: Pellet Regis J. , Bartley Leonard S. , Fritz Paul O.
Published: January 2009

Wet chemistry test methods have been developed to determine the level of alkyl carboxylate inhibition remaining in used OAT coolants. The test strategy of these methods depends on the known alkyl carboxylate ability to protect cooling system metals such as aluminum by forming insoluble metal soaps. Various test configurations make this test strategy suitable for the rapid analysis of used coolants in the field. This paper will document the initial test strategies and the development efforts that led to the first field test for alkyl carboxylate-based coolants. Test kit performance with laboratory and field samples is also discussed.
Multi-Axial Failure Models for Fiber-Reinforced Composites
Authors: Yang N. H. , Nayeb-Hashemi H. , Vaziri A.
Published: January 2009

Combined in-phase tension/torsion loading was applied to 8-ply [±45°]4 E-glass/epoxy composite shafts under monotonic and fatigue conditions to determine the effects of multi-axial loading on its failure. A damage criterion for multi-axial monotonic loading was proposed considering the contribution of both normal and shear stresses on the plane of failure. The experimental data showed an excellent agreement with the proposed model for various loading conditions. Several multi-axial fatigue failure models were proposed considering mean and cyclic normal stress and shear stress at the plane of failure, as well as the mean and cyclic normal strain and shear strain at the plane of failure and their capability for predicting the fatigue life of the composite under study was examined. In addition to the fatigue damage model based on the plane of failure, a multi-axial fatigue failure model was proposed considering the mean and cyclic energy in the fatigue experiments. The experimental data showed a reasonably good correlation with some of the proposed damage models.
Hydration Processes in Pastes of Roman and American Natural Cements
Authors: Vyskocilova R. , Schwarz W. , Mucha D. , Hughes D. , Kozłowski R. , Weber J.
Published: January 2009

Hydration of five Roman and American natural cements was analyzed using X-ray diffraction, mercury intrusion porosimetry, and scanning electron microscopy of cement pastes. Two cements were prepared in the laboratory by burning marls from geological sources in Poland (Folwark) and Austria (Lilienfeld). The selection of raw materials and burning conditions were optimized so that the hydraulic nature and appearance of the final burnt materials matched as closely as possible historic Roman cements widely used in the 19th and the beginning of the 20th centuries in Europe to decorate buildings. Three other cements are produced commercially: quick setting Prompt cement from Vicat, France, and Rosendale cements from Edison Coatings Inc., USA. The hydration of the cements studied was shown to comprise two distinct stages. The immediate setting and early strength is due to the formation of calcium aluminum oxide carbonate (or sulfate) hydroxide hydrates. The development of long-term strength is brought about by the formation of calcium silicate hydrates. Similarities and differences between the individual cements are discussed.
How to Detect and Observe Hidden Window Leaks Using Infrared Thermography
Authors: LaTona Raymond W. , Vlagea Octavian
Published: January 2009

Water intrusion through residential window assemblies is one of the leading causes of damage to the interior. The source is frequently the result of failed seals at window frame jamb/sill intersections or incorrectly installed window flashings. To find the source of and pinpoint the cause(s) of this type of leakage can be destructive, time consuming, and results in high investigation and repair costs. Several instruments can be used to detect and trace water intrusion nondestructively; the most popular are conductive or capacitance-type meters. These meters measure the electrical properties of building materials to indicate wet or dry materials. Often, the readings may be falsely interpreted as an indication of elevated moisture levels when metal is present in the region of the readings. Infrared thermography is successfully being used to detect and trace leakage in building envelopes. Its ability to detect and graphically display heat radiated from a target building area enables an operator to quickly detect leakage with very little interpretation. Although this technology is not new, its use for building envelope diagnostics is new; capabilities in this area are still being discovered. We recently conducted an infrared thermography survey to detect water intrusion at interior window sill regions from failed window frame corner assemblies. The investigative team also used a time-lapse survey to visually track the leakage path. We verified the leak with a capacitance-type meter and through visual observation of materials that became wet from the leak. An infrared thermography survey provides another useful method for quickly and efficiently detecting this type of window leakage.
Experimental Study of the Fracture Toughness Transferability to Pressurized Thermal Shock Representative Loading Conditions
Authors: Scibetta M. , Schuurmans J. , Lucon E.
Published: January 2009

Fracture toughness testing on standard specimens in the ductile to brittle transition regime is well established and was first standardized by ASTM in 1997. However, its applicability to structural components and its potential conservatism, due to the high constraint condition in standard specimens, remain a subject of concern. In this work a study of the transferability of the fracture toughness measurements from laboratory specimens to structural components is performed. The structural component of interest is the Reactor Pressure Vessel subjected to an accidental loading condition called Pressurized Thermal Shock (PTS). As the actual component cannot be reasonably tested, an original experimental set-up is developed to simulate PTS representative loading conditions. A semi-elliptical crack is introduced by fatigue in a disk shape specimen which is biaxial loaded in the ductile to brittle transition regime. The developed disk specimen is called PTS-D specimen. Master Curve tests on 15 PTS-D specimens are performed and compared to standard size specimens having deep and shallow cracks. The reference temperature obtained on PTS-D is equivalent to the one obtained on half-inch compact tension specimens. To support the experimental results, finite element calculations are performed. It turns out that, in the tested range, constraint in PTS-D specimens is high. However, loss of constraint appears earlier than in standard specimens. It is found that the Beremin approach combined with analytical tool allows rationalizing all test results.
Carrying Capacity Prediction of Steam Turbine Rotors with Operation Damage
Authors: Shlyannikov V. N. , Ilchenko B. V. , Yarullin R. R.
Published: January 2009

This study is concerned with assessing the integrity of cracked steam turbine rotor which operates under creep conditions. Damage accumulation and growth for turbine rotor took place on the inner surface of hole in a shaft. In this case the crack front was nearly half-elliptical shape. The model based on the critical distance concept is presented for expressing crack growth rate in terms of creep damage accumulation in a process zone ahead of the crack tip. An engineering approach to the prediction of residual lifetime of a turbine rotor which is sensitive to the loading history at maintenance is proposed. Full-size stress-strain state analysis of turbine rotor is represented for different stages of lifetime under considering loading conditions. As a result accumulated creep strain in critical zones of turbine rotor depending on time of loading is defined. The creep fracture mechanics parameters that are found numerically are used to characterize the local strain rate and stress fields at any instant around the crack tip in a turbine rotor subjected extensive creep conditions. The meaning of the critical creep ductility appropriate to the stress state at the crack tip is defined as the difference between permissible and accumulated creep strains at different times of loading. Approximate estimations of carrying capacity are presented for the different stress-strain state of a steam turbine rotor at the operation. It is found that the individual mean lifetime of a turbine rotor can be predicted with reasonable accuracy from knowledge of the stress-strain distributives and the material uniaxial creep ductility and creep rupture strength.
Comparison of Parallel and Serial Methods for Determining Clothing Insulation
Authors: Xu Xiaojiang , Endrusick Thomas , Gonzalez Julio , Santee William , Hoyt Reed
Published: January 2009

This paper examines the fundamental differences between the parallel and serial methods for the calculation of clothing insulation using a thermal manikin and demonstrates the differences in the insulation values calculated using these two methods. The parallel method is based on the condition that manikin surface temperatures remain uniform (UST), while the serial method is based on the condition that manikin heat fluxes remain uniform (UHF). Eleven clothing ensembles were evaluated on manikins in UST mode. Three of them were also evaluated on manikins in UHF mode. Insulation values were then calculated using both the serial and parallel methods. Results from UST mode showed that the parallel insulation values ranged from 1.24 to 5.79 clo, while the serial insulation values ranged from 1.43 to 7.98 clo. Differences in the parallel and serial insulations increased as the insulation increased, and the serial insulations were approximately 14–38 % higher than the parallel insulations. Results from UHF mode showed that the parallel insulations were 1.30 clo to 5.89 clo and close to the serial insulations of 1.34 clo to 5.99 clo. In conclusion, the methods of insulation calculation should be determined by the operating mode of the manikin. Only the parallel method should be used when manikins are operated in UST mode and only the serial method should be used when manikins are operated in UHF mode. Insulation values calculated using the incorrect method will be misleading.
Prespawning, Spawning, and Postspawning Behavior of Striped Bass in the Miramichi River
Authors: Douglas Scott G. , Chaput Gerald , Hayward John , Sheasgreen Joseph
Published: January 2009

Acoustic telemetry was used to describe the behavior of individual striped bass Morone saxatilis and their use of the Miramichi River estuary during two consecutive spawning seasons in 2004 and 2005. In both years, prespawning striped bass staged in the lower and middle sections of the Miramichi River estuary downstream from the spawning area. Males and females moved in synchrony from the staging area to the spawning grounds in the Northwest Miramichi River. The dates of arrival at the spawning grounds were similar between sexes in both years, but significantly later (by about a week) in 2005. There were no significant differences in average daily water temperature on the dates of arrival at the spawning grounds for male and female striped bass, but water temperatures on the arrival dates were significantly cooler in 2005. Increases in temperature rather than the absolute temperature was the apparent cue initiating the movements of striped bass onto the spawning grounds. Females occupied the spawning grounds for 12 and 7 d in 2004 and 2005, respectively, significantly less than the approximately 15 d for males in each year. The shorter occupation of the spawning grounds by female striped bass was determined by their significantly earlier departure dates than males. Staging downstream of the spawning area by males and females, rapid ascent by both sexes to the spawning area, and the longer residency of male striped bass on the spawning grounds are important characteristics that must be considered when developing management actions to protect and rebuild the spawning stock of this northern population of striped bass.