bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel representation of RNA secondary structure based on element-contact graphs
Authors: Shu Wenjie , Bo Xiaochen , Zheng Zhiqiang , Wang Shengqi 
Published: April 2008

Abstract

Background
Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent years, as such indices can be used to compare, identify and classify RNAs. Although the topological indices presented before characterize the main topological features of RNA secondary structures, information on RNA structural details is ignored to some degree. Therefore, it is necessity to identify topological features with low degeneracy based on complete and fine-grained RNA graphical representations.

Results
In this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertex-weighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded completely in the ECGs. The relationship among the three typical topological index families defined by their ECGs and RNA secondary structures was investigated from a dataset of 6,305 ncRNAs. The applicability of topological indices is illustrated by three application case studies. Based on the applied small dataset, we find that the topological indices can distinguish true pre-miRNAs from pseudo pre-miRNAs with about 96% accuracy, and can cluster known types of ncRNAs with about 98% accuracy, respectively.

Conclusion
The results indicate that the topological indices can characterize the details of RNA structures and may have a potential role in identifying and classifying ncRNAs. Moreover, these indices may lead to a new approach for discovering novel ncRNAs. However, further research is needed to fully resolve the challenging problem of predicting and classifying noncoding RNAs.
Exploiting and integrating rich features for biological literature classification
Authors: Wang Hongning , Huang Minlie , Ding Shilin , Zhu Xiaoyan 
Published: April 2008

Abstract

Background
Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are described by a large number of features; domain dependent features would significantly improve the classification performance. How to effectively select and integrate different types of features to improve the biological literature classification performance is the major issue studied in this paper.

Results
To efficiently classify the biological literatures, we propose a novel feature value schema TF*ML, features covering from lower level domain independent “string feature” to higher level domain dependent “semantic template feature”, and proper integrations among the features. Compared to our previous approaches, the performance is improved in terms of AUC and F-Score by 11.5% and 8.8% respectively, and outperforms the best performance achieved in BioCreAtIvE 2006.

Conclusions
Different types of features possess different discriminative capabilities in literature classification; proper integration of domain independent and dependent features would significantly improve the performance and overcome the over-fitting on data distribution.
Autosomal mutations affecting Y chromosome loops in Drosophila melanogaster
Authors: Ceprani Francesca , Raffa Grazia D , Petrucci Romano , Piergentili Roberto 
Published: April 2008

Abstract

Background
The Y chromosome of Drosophila melanogaster harbors several genes required for male fertility. The genes for these fertility factors are very large in size and contain conspicuous amounts of repetitive DNA and transposons. Three of these loci (ks-1, kl-3 and kl-5) have the ability to develop giant lampbrush-like loops in primary spermatocytes, a cytological manifestation of their active state in these cells. Y-loops bind a number of non-Y encoded proteins, but the mechanisms regulating their development and their specific functions are still to be elucidated.

Results
Here we report the results of a screen of 726 male sterile lines to identify novel autosomal genes controlling Y-loop function. We analyzed mutant testis preparations both in vivo and by immunofluorescence using antibodies directed against Y-loop-associated proteins. This screen enabled us to isolate 17 mutations at 15 loci whose wild-type function is required for proper Y-loop morphogenesis. Six of these loci are likely to specifically control loop development, while the others display pleiotropic effects on both loops and meiotic processes such as spermiogenesis, sperm development and maturation. We also determined the map position of the mutations affecting exclusively Y-loop morphology.

Conclusion
Our cytological screening permitted us to identify novel genetic functions required for male spermatogenesis, some of which show pleiotropic effects. Analysis of these mutations also shows that loop development can be uncoupled from meiosis progression. These data represent a useful framework for the characterization of Y-loop development at a molecular level and for the study of the genetic control of heterochromatin.
Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis
Authors: Stupar Robert M , Gardiner Jack M , Oldre Aaron G , Haun William J , Chandler Vicki L , Springer Nathan M 
Published: April 2008

AbstractBackgroundHeterosis is the superior performance of F1hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.ResultsWe observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.ConclusionWe have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.
ERCC1 and BRCA1 mRNA expression levels in metastatic malignant effusions is associated with chemosensitivity to cisplatin and/or docetaxel
Authors: Wang Lifeng , Wei Jia , Qian Xiaoping , Yin Haitao , Zhao Yang , Yu Lixia , Wang Tingting , Liu Baorui 
Published: April 2008

Abstract

Background
One of the major challenges in currently chemotherapeutic theme is lacking effective biomarkers for drug response and sensitivity. Our current study focus on two promising biomarkers, ERCC1 (excision repair cross-complementing group 1) and BRCA1 (breast cancer susceptibility gene 1). To investigate their potential role in serving as biomarkers for drug sensitivity in cancer patients with metastases, we statistically measure the mRNA expression level of ERCC1 and BRCA1 in tumor cells isolated from malignant effusions and correlate them with cisplatin and/or docetaxel chemosensitivity.

Methods
Real-time quantitative PCR is used to analysis related genes expression in forty-six malignant effusions prospectively collected from non-small cell lung cancer (NSCLC), gastric and gynecology cancer patients. Viable tumor cells obtained from malignant effusions are tested for their sensitivity to cisplatin and docetaxel using ATP-TCA assay.

Results
ERCC1 expression level is negatively correlated with the sensitivity to cisplatin in NSCLC patients (P = 0.001). In NSCLC and gastric group, BRCA1 expression level is negatively correlated with the sensitivity to cisplatin (NSCLC: P = 0.014; gastric: P = 0.002) while positively correlated with sensitivity to docetaxel (NSCLC: P = 0.008; gastric: P = 0.032). A significant interaction is found between ERCC1 and BRCA1 mRNA expressions on sensitivity to cisplatin (P = 0.010, n = 45).

Conclusion
Our results demonstrate that ERCC1 and BRCA1 mRNA expression levels are correlated with in vitro chemosensitivity to cisplatin and/or docetaxel in malignant effusions of NSCLC and gastric cancer patients. And combination of ERCC1 and BRCA1 may have a better role on predicting the sensitivity to cisplatin than the single one is considered.
A cohort study of infant feeding practices in city, suburban and rural areas in Zhejiang Province, PR China
Authors: Qiu Liqian , Zhao Yun , Binns Colin W , Lee Andy H , Xie Xing 
Published: April 2008

Abstract

Background
Breastfeeding is the basis for appropriate nutrition for infants and is strongly supported by the Ministry of Health in China. However, there are differences in infant feeding practices in different areas of the country. The aim of this study was to compare the infant feeding practices and the prevalence of determinants of initiation and continuing to breastfeed until six months of age in city, suburb and rural areas in Zhejiang Province, PRC.

Methods
A longitudinal cohort study of infant feeding practices was undertaken in city, suburban and rural areas in 2004/2005. Mothers were recruited and interviewed before discharge from hospitals. A total of 1520 mothers were recruited into the study. Follow-up interviews were administered at 1, 3 and 6 months after birth to obtain details of infant feeding practices.

Results
'Any breastfeeding' rates were high before discharge at all three locations, 96.5% in city, 96.8% in suburb and 97.4% in the rural area. The 'exclusive breastfeeding' rates in the city, suburban and rural areas before discharge were 38.0%, 63.4% and 61.0% respectively. By sixth months the 'any breastfeeding' rates had declined to 62.8%, 76.9% and 83.6% and the 'exclusive breastfeeding' rates had fallen to 0.2%, 0.5% and 7.2% in city, suburb and rural areas respectively. There were differences in feeding practices between the three locations, including the use of prelacteal feeds and the introduction of supplementary feeds.

Conclusion
Mothers who lived in the city were least likely to be 'exclusive breastfeeding' at discharge. At six months the city infants also had lower rates of 'any breastfeeding' and 'exclusive breastfeeding'.
Fiscal Bargains, Political Institutions, and Economic Performance
Authors: Summerhill William R. 
Published: April 2008

Abstract
In “Bargaining for Absolutism,” Alejandra Irigoin and Regina Grafe argue three points of considerable interest to historians: political absolutism in Castile did not extend to fiscal matters; fiscal relations within Spain and its empire were characterized by bargaining, not directives from the crown; and the differences between Spanish and British imperial fiscal systems have been overstated. Their first and second points are a welcome corrective to oversimplified treatments of early modern Spanish fiscal politics, and echo findings on absolutism in France. In practice, absolutist sovereigns were not autocrats. They needed money to wage war and defend against predatory rivals, and had to exchange rent-generating privileges and monopolies in order to levy taxes and borrow. Irigoin and Grafe understate, however, the differences between fiscal relations in the British and Spanish empires. The institutions governing economic policy making at home were quite distinct in the two cases. After 1688 Britain relied heavily on Parliament for the formulation and approval of economic policies. The formal mechanisms by which the economic interests of different groups were articulated and brokered between Parliament and the government led to more efficient outcomes. In Spain, where the crown could selectively assign and abrogate property rights in a manner unchecked by formal political institutions, fiscal weakness and economic stagnation resulted. This institutional gap was reflected as well in the implementation of economic policy in their respective colonies. In this difference one can trace one important source of differing economic trajectories in the late colonial and early national periods.
Rapid and Sensitive Detection of BRCA1/2 Mutations in a Diagnostic Setting: Comparison of Two High-Resolution Melting Platforms
Authors: De Leeneer Kim , Coene Ilse , Poppe Bruce , De Paepe Anne , Claes Kathleen 
Published: April 2008

Abstract
Background: High-resolution melting is an emerging technique for detection of nucleic acid sequence variations. Developments in instrumentation and saturating intercalating dyes have made accurate high-resolution melting analysis possible and created opportunities to use this technology in diagnostic settings. We evaluated 2 high-resolution melting instruments for screening BRCA1 and BRCA2 mutations.
Methods: To cover the complete coding region and splice sites, we designed 112 PCR amplicons (136–435 bp), amplifiable with a single PCR program. LCGreen® Plus was used as the intercalating dye. High-resolution melting analysis was performed on the 96-well Lightscanner™ (Idaho Technology Inc.) and the 96-well LightCycler® 480 (Roche) instruments. We evaluated sensitivity by analyzing 212 positive controls scattered over almost all amplicons and specificity by blind screening of 22 patients for BRCA1 and BRCA2. In total, we scanned 3521 fragments.
Results: All 212 known heterozygous sequence variants were detected on the Lightscanner by analysis on normal sensitivity setting. On the LightCycler 480, the standard instrument sensitivity setting of 0.3 had to be increased to 0.7 to detect all variants, decreasing the specificity to 95.9% (vs 98.7% for the Lightscanner).
Conclusions: Previously, we screened BRCA1/2 by direct sequencing of the large exon 11 and denaturing gel gradient electrophoresis (DGGE) for all other coding exons. Since the introduction of high-resolution melting, our turnaround time has been one third of that with direct sequencing and DGGE, as post-PCR handling is no longer required and the software allows fast analyses. High-resolution melting is a rapid, cost-efficient, sensitive method simple enough to be readily implemented in a diagnostic laboratory.
Stochastische Hill-Climbing-Algorithmen zur Produktionssteuerung von Grobblechwalzstraßen (Production Scheduling of Heavy Plate Rolling Mills by Stochastic Hill-Climbing-Algorithms)
Authors: Busch Heike 
Published: April 2008

Die Bestimmung der optimalen Bearbeitungsreihenfolge auf einer Grobblechwalzstraße stellt ein komplexes kombinatorisches Optimierungsproblem mit mehreren unterschiedlichen Zielsetzungen und zahlreichen technischen und logistischen Restriktionen dar. Stochastische Hill-Climbing-Algorithmen sind lokale Optimierungsverfahren, die zufällige mit strategischen Elementen kombinieren. Mit ihrer Hilfe ist es möglich, den Fertigungsprozess an der Grobblechwalzstraße zu optimieren und eine maximale Flexibilität im Produktmix zu erhalten. Gleichzeitig wird die Prozess-Sicherheit erhöht, Engpässe werden vermieden und Kosten gesenkt.
The optimization of the manufacturing sequence on a heavy plate rolling mill yields in a complex combinatorial optimization problem, including several different objectives and a large set of technical and logistic constraints. Stochastic Hill-Climbing-Algorithms are methods of local optimization, combining random and strategy. By means of these algorithms it is possible to improve the manufacturing process of heavy plate rolling mills with main focus on providing maximum flexibility in the product mix. In addition the reliability of the process is enhanced, bottlenecks are avoided and total costs can be reduced.
Produktionssteuerung auf der Grundlage von Echtzeitautomaten (Production Scheduling Using Timed Automata)
Authors: Panek Sebastian , Stursberg Olaf , Engell Sebastian 
Published: April 2008

Die Ermittlung des optimalen Ressourceneinsatzes in der Produktion mit Hilfe klassischer Optimierungsverfahren (gemischt-ganzzahlige Optimierung) basiert auf einer gleichungsorientierten mathematischen Modellierung. Die Entwicklung und Wartung derartiger Modelle ist zeitaufwändig und erfordert viel Wissen und Erfahrung. Eine Alternative bietet die Modellierung mit Hilfe zeitbewerteter Automaten, wobei die einzelnen Aufgaben und Ressourcen grafisch und modular beschrieben werden. Optimale Produktionsabläufe können durch Erreichbarkeitsanalyse mit leistungsfähigen Tools ermittelt werden. Vergleichsstudien zeigen, dass dieser Zugang auch hinsichtlich der Lösungsqualität mit der gemischt-ganzzahligen Programmierung mithalten kann.
The determination of the optimal allocation of ressources in production processes is traditionally based on equation-oriented modeling and mixed-integer programming. Model development and maintenance require the knowledge of experts and are time-consuming. An alternative approach is based on timed automata (TA). The jobs and the resources are modeled by a set of synchronized TA, and the scheduling problem is solved by searching for a cost-minimizing sequence of states from an initial into a terminal state in which all jobs are finished. The appeal of the approach is the intuitive and modular graphical modeling and the efficient solution by appropriate tools; we illustrate this for a number of difficult job-shop instances.
Effect of hypocaloric diet-induced weight loss in obese women on plasma apelin and adipose tissue expression of apelin and APJ.
Authors: Castan-Laurell Isabelle , Vítkova Michaela , Daviaud Danièle , Dray Cédric , Kováčiková Michaela , Kovacova Zuzana , Hejnova Jindriska , Stich Vladimir , Valet Philippe 
Published: April 2008

ObjectiveApelin is a novel adipokine acting on APJ receptor, regulated by insulin and tumor necrosis factor-α (TNF-α) in adipose tissue (AT). Plasma apelin levels are increased in obese hyperinsulinemic subjects. The aim was to investigate whether the hypocaloric diet associated with weight loss modifies the elevated plasma apelin levels and the expression of apelin and APJ receptor in AT in obese women.Design and methodsFasting plasma levels of apelin and TNF-α as well as mRNA levels of apelin and APJ in AT were measured before and after a 12-week hypocaloric weight-reducing diet in 20 obese women (body mass index (BMI) before diet 32.2±6.4 kg/m2). Twelve healthy women with a BMI of 20.7±0.6 kg/m2 served as reference.ResultsPlasma levels of apelin and TNF-α were higher in obese compared with lean controls. The hypocaloric diet resulted in a significant decrease of BMI to 29.8±6.3 kg/m2, plasma insulin (8.16±0.73 to 6.58±0.66 mU/l), apelin (369±25 pg/ml to 257±12 pg/ml), TNF-α levels (0.66±0.04 pg/ml to 0.56±0.04 pg/ml), and AT mRNAs of apelin and APJ. In addition, changes in AT mRNA apelin were related to changes in AT mRNA APJ levels.ConclusionThe hypocaloric diet associated with weight loss reduces the increased plasma and AT expression of apelin in obese women. This reduced apelin expression in AT could contribute to decreased circulating apelin levels.
Early onset of polyglandular failure is associated with HLA-DRB1*03.
Authors: Dittmar Manuela , Ide Maximilian , Wurm Michael , Kahaly George J 
Published: April 2008

ObjectivesPolyglandular failure or autoimmunity (PGA) involves at least two endocrine diseases. Several genes may play a role in its etiology. This study analyzed 1) whether HLA-DRB1, HLA-DQB1, and MHC class I chain-related gene A (MICA) polymorphisms are associated in PGA and 2) whether PGA patients display stronger associations with these immune genes than patients with monoglandular autoimmunity (MGA).DesignAssociation study.MethodsHLA-DRB1, HLA-DQB1, and MICA alleles were analyzed in 73 patients with PGA, 283 with MGA, and 206 healthy controls. The HLA-DRB1 and HLA-DQB1 polymorphisms were determined with PCR-amplified DNA being hybridized with PCR-sequence-specific oligonucleotide probes. MICA microsatellites were typed by PCR amplification and fragment size analysis on a DNA sequencer.ResultsHLA-DRB1*03 was strongly increased in patients with PGA (50.7%) versus both controls (21.8%, Pc<0.0001; RR=2.32, 95% CI=1.62–3.33) and MGA (11.4%, Pc<0.0001). HLA-DRB1*03 was highly prevalent in PGA patients with early versus late disease onset (P<0.05, logistic regression analysis). HLA-DRB1*04 allele carriers were more present in PGA versus controls (53.4% vs 22.4%, Pc<0.0001, RR=2.38, 95% CI=1.68–3.38). Further, HLA-DQB1*02 was increased in PGA versus controls (Pc<0.01), whereas HLA-DQB1*06 was decreased (Pc<0.001). Patients with PGA showed more MIC A5.1 and less MIC A6 allele carriers than controls (NS). Presence of the MIC A5.1 allele was not associated with the HLA-DRB1*03 or HLA-DQB1 alleles.ConclusionsHLA-DRB1*03 is a stronger genetic marker in PGA than in MGA, foremost in those with early disease onset.
Direct Orthotopic Transplantation of Fresh Surgical Specimen Preserves CD133+ Tumor Cells in Clinically Relevant Mouse Models of Medulloblastoma and Glioma
Authors: Shu Qin , Wong Kwong Kwok , Su Jack M. , Adesina Adekunle M. , Yu Li Tian , Tsang Yvonne T. M. , Antalffy Barbara C. , Baxter Patricia , Perlaky Laszlo , Yang Jianhua , Dauser Robert C. , Chintagumpala Murali , Blaney Susan M. , Lau Ching C. , Li Xiao-Nan 
Published: April 2008

AbstractRecent identification of cancer stem cells in medulloblastoma (MB) and high-grade glioma has stimulated an urgent need for animal models that will not only replicate the biology of these tumors, but also preserve their cancer stem cell pool. We hypothesize that direct injection of fresh surgical specimen of MB and high-grade glioma tissues into anatomically equivalent locations in immune-deficient mouse brains will facilitate the formation of clinically accurate xenograft tumors by allowing brain tumor stem cells, together with their non-stem tumor and stromal cells, to grow in a microenvironment that is the closest to human brains. Eight of the 14 MBs (57.1%) and two of the three high-grade gliomas (66.7%) in this study developed transplantable (up to 12 passages) xenografts in mouse cerebellum and cerebrum, respectively. These xenografts are patient specific, replicating the histopathologic, immunophenotypic, invasive/metastatic, and major genetic (analyzed with 10K single nucleotide polymorphism array) abnormalities of the original tumors. The xenograft tumor cells have also been successfully cryopreserved for long-term preservation of tumorigenicity, ensuring a sustained supply of the animal models. More importantly, the CD133+ tumor cells, ranging from 0.2%–10.4%, were preserved in all the xenograft models following repeated orthotopic subtransplantations in vivo. The isolated CD133+ tumor cells formed neurospheres and displayed multi-lineage differentiation capabilities in vitro. In summary, our study demonstrates that direct orthotopic transplantation of fresh primary tumor cells is a powerful approach in developing novel clinical relevant animal models that can reliably preserve CD133+ tumor cell pools even during serial in vivo subtransplantations.Disclosure of potential conflicts of interest is found at the end of this article.