bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of amyloid fibril-forming segments based on a support vector machine
Authors: Tian Jian , Wu Ningfeng , Guo Jun , Fan Yunliu 
Published: January 2009

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

SummaryIndividuals 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

BackgroundDepression is associated with neural abnormalities in emotional processing.AimsThis study explored whether these abnormalities underlie risk for depression.MethodWe 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).ResultsThe 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.ConclusionsRisk for depression is associated with enhanced neural responses to fearful facial expressions similar to those observed in acute depression.
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

SUMMARY
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.
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

AbstractAlthough 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

AbstractBackground: 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

AbstractBackground: 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 &lt; 0.01). CNAs had a significantly lower proportion of L1 and L2 long interspersed nuclear element sequences (P &lt; 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

AbstractBackground: 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&gt;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&gt;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

AbstractBackground: 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

Abstract
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

Abstract
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.