bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified computational model for revealing and predicting subtle subtypes of cancers
Authors: Ren Xianwen , Wang Yong , Wang Jiguang , Zhang Xiang-Sun 
Published: May 2012

Abstract

Background
Gene expression profiling technologies have gradually become a community standard tool for clinical applications. For example, gene expression data has been analyzed to reveal novel disease subtypes (class discovery) and assign particular samples to well-defined classes (class prediction). In the past decade, many effective methods have been proposed for individual applications. However, there is still a pressing need for a unified framework that can reveal the complicated relationships between samples.

Results
We propose a novel convex optimization model to perform class discovery and class prediction in a unified framework. An efficient algorithm is designed and software named OTCC (Optimization Tool for Clustering and Classification) is developed. Comparison in a simulated dataset shows that our method outperforms the existing methods. We then applied OTCC to acute leukemia and breast cancer datasets. The results demonstrate that our method not only can reveal the subtle structures underlying those cancer gene expression data but also can accurately predict the class labels of unknown cancer samples. Therefore, our method holds the promise to identify novel cancer subtypes and improve diagnosis.

Conclusions
We propose a unified computational framework for class discovery and class prediction to facilitate the discovery and prediction of subtle subtypes of cancers. Our method can be generally applied to multiple types of measurements, e.g., gene expression profiling, proteomic measuring, and recent next-generation sequencing, since it only requires the similarities among samples as input.
LKB1 tumor suppressor protein regulates actin filament assembly through Rho and its exchange factor Dbl independently of kinase activity
Authors: Xu Xiaojian , Omelchenko Tatiana , Hall Alan 
Published: May 2012

Abstract

Background
Germline mutations in LKB1 result in Peutz-Jeghers Syndrome characterized by intestinal hamartomas and increased incidence of epithelial cancers. LKB1 encodes a serine/threonine kinase that plays an important role in regulating energy metabolism through the AMPK/mTOR signaling pathway. In addition, LKB1 is homologous to PAR-4, a polarity protein first described in C. elegans, while activation of LKB1 in mammalian epithelial cells induces the polarized assembly of actin filaments.

Results
To explore the mechanism by which LKB1 interacts with the actin cytoskeleton, we introduced LKB1 into HeLa cells that lack endogenous LKB1. This results in activation of the small GTPase Rho and the assembly of linear actin filaments associated with focal adhesions. These effects on the actin cytoskeleton are attenuated by siRNA-mediated depletion of the guanine nucleotide exchange factor Dbl. Co-expression of the LKB1 with the adaptor protein STRAD induces actin filament puncta associated with phospho-ezrin.

Conclusions
This study reveals that LKB1 regulates the actin cytoskeleton through a Dbl/Rho pathway.
Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map
Authors: McGraw Lisa A , Davis Jamie K , Lowman Josh J , ten Hallers Boudewijn FH , Koriabine Maxim , Young Larry J , de Jong Pieter J , Rudd M Katharine , Thomas James W 
Published: May 2012

AbstractBackgroundThe prairie vole (Microtus ochrogaster) is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC) library from a single male prairie vole and a prairie vole-mouse (Mus musculus) comparative cytogenetic map.ResultsWe constructed a prairie vole BAC library (CHORI-232) consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH) mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements.ConclusionsThe construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this species. The BAC library will support future genomic, genetic and molecular characterization of this genome and species, and the isolation of clones of high interest to the vole research community will allow for immediate characterization of the regulatory and coding sequences of genes known to play important roles in social behaviors. In addition, these resources provide an excellent platform for future higher resolution cytogenetic mapping and full genome sequencing.
Phylogenetic analysis and molecular characteristics of seven variant Chinese field isolates of PRRSV
Authors: Wang Chengmin , Wu Bin , Amer Said , Luo Jing , Zhang Hongmei , Guo Yunhai , Dong Guoying , Zhao Baohua , He Hongxuan 
Published: May 2012

AbstractBackgroundPorcine reproductive and respiratory syndrome (PRRS) has now been widely recognized as an economically important disease. The objective of this study was to compare the molecular and biological characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) field isolates in China to those of the modified live virus (MLV) PRRS vaccine and its parent strain (ATCC VR2332).ResultsFive genes (GP2, GP3, GP4, GP5 and NSP2) of seven isolates of PRRSV from China, designated LS-4, HM-1, HQ-5, HQ-6, GC-2, GCH-3 and ST-7/2008, were sequenced and analyzed. Phylogenetic analyses based on the nucleotide sequence of the ORF2-5 and NSP2 showed that the seven Chinese isolates belonged to the same genetic subgroup and were related to the North American PRRSV genotype. Comparative analysis with the relevant sequences of another Chinese isolate (BJ-4) and North American (VR2332 and MLV) viruses revealed that these isolates have 80.8-92.9% homology with VR-2332, and 81.3-98.8% identity with MLV and 80.7-92.9% with BJ-4. All Nsp2 nonstructural protein of these seven isolates exhibited variations (a 29 amino acids deletion) in comparison with other North American PRRSV isolates. Therefore, these isolates were novel strain with unique amino acid composition. However, they all share more than 97% identity with other highly pathogenic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and the Nsp2 protein when compared with the previous isolates.ConclusionsThese results might be useful to study the genetic diversity of PRRSV in China and to track the infection sources as well as for vaccines development.
Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa
Authors: Hu Ruibo , Qi Guang , Kong Yingzhen , Kong Dejing , Gao Qian , Zhou Gongke 
Published: May 2012

Abstract

Background
NAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.

Results
In the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.

Conclusion
Based on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.
RNAi-mediated silencing of the HD-Zip gene HD20 in Nicotiana attenuata affects benzyl acetone emission from corollas via ABA levels and the expression of metabolic genes
Authors: Ré Delfina A , Raud Brenda , Chan Raquel L , Baldwin Ian T , Bonaventure Gustavo 
Published: May 2012

Abstract

Background
The N. attenuata HD20 gene belongs to the homeodomain-leucine zipper (HD-Zip) type I family of transcription factors and it has been previously associated with the regulation of ABA accumulation in leaves and the emission of benzyl acetone (BA; 4-phenyl-2-butanone) from night flowers. In this study, N. attenuata plants stably reduced in the expression of HD20 (ir-hd20) were generated to investigate the mechanisms controlling the emission of BA from night flowers.

Results
The expression of HD20 in corollas of ir-hd20 plants was reduced by 85 to 90% compared to wild-type plants (WT) without affecting flower morphology and development. Total BA emitted from flowers of ir-hd20 plants was reduced on average by 60%. This reduction occurred mainly at the late phase of BA emission and it was correlated with 2-fold higher levels of ABA in the corollas of ir-hd20 plants. When a 2-fold decline in ABA corolla levels of these plants was induced by salt stress, BA emissions recovered to WT levels. Supplying ABA to WT flowers either through the cuticle or by pedicle feeding reduced the total BA emissions by 25 to 50%; this reduction occurred primarily at the late phase of emission (similar to the reduction observed in corollas of ir-hd20 plants). Gene expression profiling of corollas collected at 12 pm (six hours before the start of BA emission) revealed that 274 genes changed expression levels significantly in ir-hd20 plants compared to WT. Among these genes, more than 35% were associated with metabolism and the most prominent group was associated with the metabolism of aromatic compounds and phenylpropanoid derivatives.

Conclusions
The results indicated that regulation of ABA levels in corollas is associated with the late phase of BA emission in N. attenuata plants and that HD20 affects this latter process by mediating changes in both ABA levels and metabolic gene expression.
Genetic variants of NOXA and MCL1 modify the risk of HPV16-associated squamous cell carcinoma of the head and neck
Authors: Zhou Ziyuan , Sturgis Erich M , Liu Zhensheng , Wang Li-E , Wei Qingyi , Li Guojun 
Published: May 2012

AbstractsBackgroundThe cooperation between phorbol 12-myristate 13-acetate induced protein 1 (NOXA) and myeloid cell leukemia 1 (MCL1) is critical in the intrinsic apoptotic pathway. Human papillomavirus 16 (HPV16), by inducing p53 and pRb-E2F degradation, may play an essential role in development of squamous cell carcinoma of the head and neck (SCCHN) through NOXA-MCL1 axis-mediated apoptosis. Therefore, genetic variants ofNOXAandMCL1may modify the SCCHN risk associated with HPV16 seropositivity.MethodsHPV16 serology was obtained by immunoadsorption assay. Four functional SNPs in the promoter ofNOXA(rs9957673, rs4558496) andMCL1(rs9803935, rs3738485) were genotyped for 380 cases and 335 frequency-matched cancer-free controls of non-Hispanic whites.ResultsAssociations between the four polymorphisms and SCCHN risk were not significant, while we observed a significantly joint effect on SCCHN risk between the polymorphisms and HPV16 seropositivity. Notably, this effect modification was particularly pronounced for oropharyngeal cancer in subgroups including never smokers, never drinkers and younger subjects.ConclusionsOur results suggested that polymorphisms ofNOXAandMCL1may modify the risk of HPV16-associated oropharyngeal cancer. The further identification of population subgroups at higher risk provides evidence that HPV-targeting treatment may help benefit SCCHN. However, larger studies are needed to validate our findings.
Association of ATP binding cassette transporter G8 rs4148217 SNP and serum lipid levels in Mulao and Han nationalities
Authors: Li Qing , Wei Xian-Liang , Yin Rui-Xing 
Published: May 2012

AbstractBackgroundThe association of ATP binding cassette transporter G8 gene (ABCG8) rs4148217 single nucleotide polymorphism (SNP) and serum lipid profiles is still controversial in diverse racial/ethnic groups. Mulao nationality is an isolated minority in China. The aim of this study was to evaluate the association ofABCG8rs4148217 SNP and several environmental factors with serum lipid levels in the Guangxi Mulao and Han populations.MethodsA total of 634 subjects of Mulao nationality and 717 participants of Han nationality were randomly selected from our previous samples. Genotyping of theABCG8rs4148217 SNP was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing.ResultsThe genotypic and allelic frequencies ofABCG8rs4148217 SNP were different between the two nationalities (P < 0.01 for each), the frequency of A allele was higher in Mulao than in Han. The A allele carriers in Han had lower high-density lipoprotein cholesterol (HDL-C) and apolipoprotein (Apo) A1 levels than the A allele noncarriers (P < 0.05 for each), whereas the A allele carriers in Mulao had lower ApoA1 levels than the A allele noncarriers (P < 0.05). Subgroup analyses showed that the A allele carriers in Han had lower HDL-C and higher triglyceride (TG) levels in females but not in males than the A allele noncarriers (P < 0.05 for each), and the A allele carriers in Mulao had lower ApoA1 levels in females but not in males than the A allele noncarriers (P < 0.05). The levels of TG and HDL-C in Han, and ApoA1 in Mulao were associated with genotypes in females but not in males (P < 0.05-0.01). Serum lipid parameters were also correlated with several environmental factors (P < 0.05-0.001).ConclusionsTheABCG8rs4148217 SNP is associated with serum TG, HDL-C and ApoA1 levels in our study populations, but this association is different between the Mulao and Han populations. There is a sex (female)-specific association in both ethnic groups.
Localized geometric topologies with bounded node degree for three-dimensional wireless sensor networks
Authors: Li Fan , Chen Zeming , Wang Yu 
Published: May 2012

Abstract
Three-dimensional (3D) wireless sensor networks have attracted a lot of attention due to their great potential usages in both commercial and civilian applications, such as environmental data collection, pollution monitoring, space exploration, disaster prevention, and tactical surveillance. Topology control in 3D sensor networks has been studied recently, and different 3D geometric topologies were proposed to be the underlying network topologies to achieve the sparseness of the communication networks. However, most of these proposed 3D topologies cannot bound the maximum node degree, i.e., some nodes may need to maintain a large number of neighbors in the constructed topologies, which is not energy efficient and may lead to large contention. In this article, we extend several existing 3D geometric topologies to a set of new 3D topologies with bounded node degree. We provide both theoretical analysis and simulation evaluation on their power efficiency and node degree distributions. Our simulation results over random 3D sensor networks confirm nice performances of these proposed 3D topologies.
On a hybrid algorithm for a family of total quasi-ϕ-asymptotically nonexpansive mappings in Banach spaces
Authors: Zuo Ping , Chang Shih-sen , Liu Min 
Published: May 2012

Abstract
The purpose of this article is to introduce the concept of total quasi- ϕ-asymptotically nonexpansive mapping which contains many kinds of mappings as its special cases and we prove a strong convergence theorem by using a hybrid method for finding a common element of the set of solutions for a generalized mixed equilibrium problems, the set of fixed points of a family of total quasi- ϕ-asymptotically nonexpansive mappings in uniformly smooth and strictly convex Banach space with the Kadec-Klee property. The results presented in the article improve and extend some recent results.

MR (2000) Subject Classification: 47H09; 47H05.
A never ending race for new and improved fluorescent proteins
Authors: Jones Alexander M , Ehrhardt David W , Frommer Wolf B 
Published: May 2012

Abstract
Bioluminescent and fluorescent proteins are now used as tools for research in all organisms. There has been massive progress over the past 15 years in creating a palette of fluorescent proteins with a wide spectrum of specific properties. One of the big challenges is to decide which variant may be best for a certain application. A recent article by Mann et al. in BMC Biotechnology describes a new orange fluorescent protein in plants.
See research article http://www.biomedcentral.com/1472-6750/12/17
Sporadic Hemangioblastoma of the Kidney: a rare renal tumor
Authors: Liu Yang , Qiu Xue-shan , Wang En-Hua 
Published: May 2012

Abstract

Abstract
Hemangioblastoma is a benign and morphologically distinctive tumor that can occur sporadically or in association with von Hippel-Lindau disease in approximately 25% of the cases, and which involves the central nervous system in the majority of the cases. Rare occurrences of hemangioblastoma in peripheral nerves and extraneural tissues have been reported. This report describes one case of sporadic renal hemangioblastoma happened in a 16-year-old Chinese female patient, presenting with hematuria, and low back pain. Histologically, the tumors were circumscribed, and composed of sheets of large polygonal cells traversed by arborizing thin-walled blood vessels. The diagnosis of hemangioblastoma was confirmed by negative immunostaining for cytokeratin, and positive staining for α-inhibin, S100 and neuron-specific enolase (NSE). This benign neoplasm which can be mistaken for various malignancies such as renal cell carcinoma, epithelioid hemangiopericytoma and epithelioid angiomyolipoma, deserves wider recognition for its occurrence as a primary renal tumor.

Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5445834246942699
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster
Authors: Kim Man-Sun , Kim Jeong-Rae , Kim Dongsan , Lander Arthur D , Cho Kwang-Hyun 
Published: May 2012

Abstract

Background
Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a “spatiotemporal network motif,” a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts.

Results
On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns.

Conclusions
Taken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.
Posttraumatic stress symptoms in children diagnosed with type 1 diabetes
Authors: Şişmanlar Şahika G , Demirbaş-Çakir Emine , Karakaya Işık , Çizmecioğlu Filiz , Yavuz Cavit I , Hatun Şükrü , Ağaoğlu Belma 
Published: May 2012

Abstract

Background
Studies consistently found remarkable rates of posttraumatic stress symptoms (PTSS) in children with chronic diseases. But, only one study had searched PTSS in children with diabetes, until now. So, the present study aimed to examine incidence rate and predictors of PTSS in children with type 1 diabetes.

Method
PTSS were evaluated by Child Posttraumatic Stress Reaction Index in fifty four children with diabetes (aged between 8–18 years). This assessment was based on hypoglycaemia as the potential traumatic event. Children were also introduced a brief questionnaire about demographic and disease related information. Some other information was obtained from families, medical stuff and records. Among 54 children, forty two had complete information. Hence, to evaluate possible predictive factors related with PTSS, multiple regression analysis was conducted for 42 children.

Results
18.5% of children were reported PTSS at severe or very severe level, and 51.9% were reported PTSS at moderate level or above. Multiple regression analyses were shown that child PTSS were not significantly related with possible predictive factors other than number of hypoglycaemic attacks for the last month.

Conclusion
The study results support that posttraumatic stress symptoms are not rarely seen in paediatric patients with diabetes, and even if not severe, hypoglycaemic attacks may be perceived as traumatic by the children with diabetes. But, because of some limitations, the results should be carefully interpreted.