bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational prediction of novel non-coding RNAs in Arabidopsis thaliana
Authors: Song Dandan , Yang Yang , Yu Bin , Zheng Binglian , Deng Zhidong , Lu Bao-Liang , Chen Xuemei , Jiang Tao 
Published: January 2009

Abstract

Background
Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and Arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. This unexpected finding suggests that the currently known repertoire of ncRNAs may only represent a small fraction of ncRNAs of the organisms. Thus, efficient and effective prediction of ncRNAs has become an important task in bioinformatics in recent years. Among the available computational methods, the comparative genomic approach seems to be the most powerful to detect ncRNAs. The recent completion of the sequencing of several major plant genomes has made the approach possible for plants.

Results
We have developed a pipeline to predict novel ncRNAs in the Arabidopsis (Arabidopsis thaliana) genome. It starts by comparing the expressed intergenic regions of Arabidopsis as provided in two whole-genome high-density oligo-probe arrays from the literature with the intergenic nucleotide sequences of all completely sequenced plant genomes including rice (Oryza sativa), poplar (Populus trichocarpa), grape (Vitis vinifera), and papaya (Carica papaya). By using multiple sequence alignment, a popular ncRNA prediction program (RNAz), wet-bench experimental validation, protein-coding potential analysis, and stringent screening against various ncRNA databases, the pipeline resulted in 16 families of novel ncRNAs (with a total of 21 ncRNAs).

Conclusion
In this paper, we undertake a genome-wide search for novel ncRNAs in the genome of Arabidopsis by a comparative genomics approach. The identified novel ncRNAs are evolutionarily conserved between Arabidopsis and other recently sequenced plants, and may conduct interesting novel biological functions.
Prediction of RNA secondary structure with pseudoknots using integer programming
Authors: Poolsap Unyanee , Kato Yuki , Akutsu Tatsuya 
Published: January 2009

Abstract

Background
RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, and plays an important role in some biological processes. Prediction of RNA secondary structure with pseudoknots is still challenging since the problem is NP-hard when arbitrary pseudoknots are taken into consideration.

Results
We introduce a new method of predicting RNA secondary structure with pseudoknots based on integer programming. In our formulation, we aim at minimizing the value of the objective function that reflects free energy of a folding structure of an input RNA sequence. We focus on a practical class of pseudoknots by setting constraints appropriately. Experimental results for a set of real RNA sequences show that our proposed method outperforms several existing methods in sensitivity. Furthermore, for a set of sequences of small length, our approach achieved good performance in both sensitivity and specificity.

Conclusion
Our integer programming-based approach for RNA structure prediction is flexible and extensible.
Sequence-structure relations of pseudoknot RNA
Authors: Huang Fenix WD , Li Linda YM , Reidys Christian M 
Published: January 2009

Abstract

Background
The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by a novel, ab initio prediction algorithm, cross, capable of searching all 3-noncrossing RNA structures. The algorithm outputs the minimum free energy structure.

Results
After giving some background on RNA pseudoknot structures and providing an outline of the folding algorithm being employed, we present in this paper various, statistical results on the mapping from RNA sequences into 3-noncrossing RNA pseudoknot structures. We study properties, like the fraction of pseudoknot structures, the dominant pseudoknot-shapes, neutral walks, neutral neighbors and local connectivity. We then put our results into context of molecular evolution of RNA.

Conclusion
Our results imply that, in analogy to RNA secondary structures, 3-noncrossing pseudoknot RNA represents a molecular phenotype that is well suited for molecular and in particular neutral evolution. We can conclude that extended, percolating neutral networks of pseudoknot RNA exist.
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Authors: Tai Chin-Hsien , Vincent James J , Kim Changhoon , Lee Byungkook 
Published: January 2009

Abstract

Background
Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly function prediction. Many programs use a dynamic programming algorithm to generate the sequence alignment from superimposed structures. However, this procedure requires using a gap penalty and, depending on the value of the penalty used, can introduce spurious gaps and misalignments. Here we present a new algorithm, Seed Extension (SE), for generating the sequence alignment from a pair of superimposed structures. The SE algorithm first finds "seeds", which are the pairs of residues, one from each structure, that meet certain stringent criteria for being structurally equivalent. Three consecutive seeds form a seed segment, which is extended along the diagonal of the alignment matrix in both directions. Distance and the amino acid type similarity between the residues are used to resolve conflicts that arise during extension of more than one diagonal. The manually curated alignments in the Conserved Domain Database were used as the standard to assess the quality of the sequence alignments.

Results
SE gave an average accuracy of 95.9% over 582 pairs of superimposed proteins tested, while CHIMERA, LSQMAN, and DP extracted from SHEBA, which all use a dynamic programming algorithm, yielded 89.9%, 90.2% and 91.0%, respectively. For pairs of proteins with low sequence or structural similarity, SE produced alignments up to 18% more accurate on average than the next best scoring program. Improvement was most pronounced when the two superimposed structures contained equivalent helices or beta-strands that crossed at an angle. When the SE algorithm was implemented in SHEBA to replace the dynamic programming routine, the alignment accuracy improved by 10% on average for structure pairs with RMSD between 2 and 4 Å. SE also used considerably less CPU time than DP.

Conclusion
The Seed Extension algorithm is fast and, without using a gap penalty, produces more accurate sequence alignments from superimposed structures than three other programs tested that use dynamic programming algorithm.
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
Authors: Lin Guan Ning , Cai Zhipeng , Lin Guohui , Chakraborty Sounak , Xu Dong 
Published: January 2009

Abstract

Background
With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite Distance Phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny.

Results
The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Genome Breakpoint Distance (GBD) and Gene Content Distance (GCD). GDD quantifies the dispersion of orthologous genes along the genomic coordinates from one genome to another; GBD measures the shared breakpoints between two genomes; GCD measures the level of shared orthologs between two genomes. The phylogenetic tree is constructed from the composite distance matrix using a neighbor joining method. We tested our method on 9 datasets from 398 completely sequenced prokaryotic genomes. We have achieved above 90% agreement in quartet topologies between the tree created by our method and the tree from the Bergey's taxonomy. In comparison to several other phylogenetic analysis methods, our method showed consistently better performance.

Conclusion
ComPhy is a fast and robust tool for genome-wide inference of evolutionary relationship among genomes. It can be downloaded from http://digbio.missouri.edu/ComPhy.
Mutual information estimation reveals global associations between stimuli and biological processes
Authors: Suzuki Taiji , Sugiyama Masashi , Kanamori Takafumi , Sese Jun 
Published: January 2009

AbstractBackgroundAlthough microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each group with biological functions are often used methods. However, such methods only detect partial changes within cell processes. Herein, we propose a method for discovering global changes within a cell by associating observed conditions of gene expression with gene functions.ResultsTo elucidate the association, we introduce a novel feature selection method calledLeast-Squares Mutual Information (LSMI), which computes mutual information without density estimaion, and therefore LSMI can detect nonlinear associations within a cell. We demonstrate the effectiveness of LSMI through comparison with existing methods. The results of the application to yeast microarray datasets reveal that non-natural stimuli affect various biological processes, whereas others are no significant relation to specific cell processes. Furthermore, we discover that biological processes can be categorized into four types according to the responses of various stimuli: DNA/RNA metabolism, gene expression, protein metabolism, and protein localization.ConclusionWe proposed a novel feature selection method called LSMI, and applied LSMI to mining the association between conditions of yeast and biological processes through microarray datasets. In fact, LSMI allows us to elucidate the global organization of cellular process control.
On optimal comparability editing with applications to molecular diagnostics
Authors: Böcker Sebastian , Briesemeister Sebastian , Klau Gunnar W 
Published: January 2009

Abstract

Background
The COMPARABILITY EDITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgroups. The task is to identify the minimum number of edge insertions or deletions to transform G into a transitive graph, that is, if edges (u, v) and (v, w) are present then edge (u, w) must be present, too.

Results
We present two new approaches for the problem based on fixed-parameter algorithmics and integer linear programming. In contrast to previously used heuristics, our approaches compute provably optimal solutions.

Conclusion
Our computational results demonstrate that our exact algorithms are by far more efficient in practice than a previously used heuristic approach. In addition to the superior running time performance, our algorithms are capable of enumerating all optimal solutions, and naturally solve the weighted version of the problem.
Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: Evidence from population genetic, phylogeographic, and paleoclimatic data
Authors: Walker Matt J , Stockman Amy K , Marek Paul E , Bond Jason E 
Published: January 2009

Abstract

Background
Species that are widespread throughout historically glaciated and currently non-glaciated areas provide excellent opportunities to investigate the role of Pleistocene climatic change on the distribution of North American biodiversity. Many studies indicate that northern animal populations exhibit low levels of genetic diversity over geographically widespread areas whereas southern populations exhibit relatively high levels. Recently, paleoclimatic data have been combined with niche-based distribution modeling to locate possible refugia during the Last Glacial Maximum. Using phylogeographic, population, and paleoclimatic data, we show that the distribution and mitochondrial data for the millipede genus Narceus are consistent with classical examples of Pleistocene refugia and subsequent post-glacial population expansion seen in other organismal groups.

Results
The phylogeographic structure of Narceus reveals a complex evolutionary history with signatures of multiple refugia in southeastern North America followed by two major northern expansions. Evidence for refugial populations were found in the southern Appalachian Mountains and in the coastal plain. The northern expansions appear to have radiated from two separate refugia, one from the Gulf Coastal Plain area and the other from the mid-Atlantic coastal region. Distributional models of Narceus during the Last Glacial Maximum show a dramatic reduction from the current distribution, with suitable ecological zones concentrated along the Gulf and Atlantic coastal plain. We found a strong correlation between these zones of ecological suitability inferred from our paleo-model with levels of genetic diversity derived from phylogenetic and population estimates of genetic structuring.

Conclusion
The signature of climatic change, during and after the Pleistocene, on the distribution of the millipede genus Narceus is evident in the genetic data presented. Niche-based historical distribution modeling strengthens the conclusions drawn from the genetic data and proves useful in identifying probable refugia. Such interdisciplinary biogeographic studies provide a comprehensive approach to understanding these processes that generate and maintain biodiversity as well as the framework necessary to explore questions regarding evolutionary diversification of taxa.
Comparison of the MicroScan, VITEK 2, and Crystal GP with 16S rRNA sequencing and MicroSeq 500 v2.0 analysis for coagulase-negative Staphylococci
Authors: Kim Miyoung , Heo Se Ran , Choi Soon Hee , Kwon Hyelin , Park Jeong Su , Seong Moon-Woo , Lee Do-Hoon , Park Kyoung Un , Song Junghan , Kim Eui-Chong 
Published: January 2009

Abstract

Background
Three phenotypic identification systems (MicroScan, VITEK 2, and Crystal GP) were evaluated for their accuracy to identify coagulase-negative staphylococci (CNS). A total of 120 clinical isolates confirmed to be CNS via 16S rRNA sequencing and analysis with the MicroSeq 500 v2.0 database were assessed.

Results
The MicroScan, VITEK 2, and Crystal GP systems correctly identified 82.5%, 87.5%, and 67.5% of the isolates, respectively. Misidentification was the main problem in MicroScan (10.8%) and Crystal GP (23.3%) systems, whereas the main problem of VITEK 2 was low-level discrimination (7.5%).

Conclusion
None of the 3 phenotypic systems tested could accurately and reliably identify CNS at the species level. Further verifications such as biochemical testing or 16S rRNA sequencing together with analysis using a comparable database might be helpful in this regard.
Intradialytic versus home based exercise training in hemodialysis patients: a randomised controlled trial
Authors: Koh Kirsten P , Fassett Robert G , Sharman James E , Coombes Jeff S , Williams Andrew D 
Published: January 2009

Abstract

Background
Exercise training in hemodialysis patients improves fitness, physical function, quality of life and markers of cardiovascular disease such as arterial stiffness. The majority of trials investigating this area have used supervised exercise training during dialysis (intradialytic), which may not be feasible for some renal units. The aim of this trial is to compare the effects of supervised intradialytic with unsupervised home-based exercise training on physical function and arterial stiffness.

Methods and design
This is a randomised, controlled clinical trial. A total of 72 hemodialysis patients will be randomised to receive either six months of intradialytic exercise training, home-based exercise training or usual care. Intradialytic patients will undergo three training sessions per week on a cycle ergometer and home-based patients will be provided with a walking program to achieve the same weekly physical activity. Primary outcome measures are six-minute walk distance (6 MWD) and aortic pulse wave velocity (PWV). Secondary outcome measures include augmentation index, peripheral and central blood pressures, physical activity and self-reported health. Measures will be made at baseline, three and six months.

Discussion
The results of this study will help determine the efficacy of home-based exercise training in hemodialysis patients. This may assist in developing exercise guidelines specific for these patients.

Trial Registration
ACTRN12608000247370
Postnatal quality of life in women after normal vaginal delivery and caesarean section
Authors: Torkan Behnaz , Parsay Sousan , Lamyian Minoor , Kazemnejad Anoshirvan , Montazeri Ali 
Published: January 2009

Abstract

Background
Caesarean section might increase the incidence of surgical interventions and problems resulting from hospitalization and thus affecting quality of life in women after delivery. This study aimed to compare quality of life in women after normal delivery and caesarean section.

Methods
This was a prospective study. A sample of women with normal delivery and caesarean section from 5 health care centers in Isfahan, Iran were entered into the study. Quality of life was measured using the SF-36 at two points in time (time 1: 6 to 8 weeks after delivery; time 2: 12 to 14 weeks after delivery). Data were analyzed to compare quality of life in the two study groups.

Results
In all 100 women were interviewed (50 with normal delivery and 50 with caesarean section). Postnatal quality of life in both groups was improved from time1 to time 2. However, comparing the mean scores between the normal and caesarean delivery groups the results showed that in general the normal vaginal delivery group had a better quality of life for almost all subscales in both assessment times. The differences were significant for vitality (mean score 62.9 vs. 54.4 P = 0.03) and mental health (mean score 75.1 vs. 66.7, P = 0.03) at first assessment and for physical functioning (mean score 88.4 vs. 81.5, P = 0.03) at second evaluation. However, comparing the findings within each group the analysis showed that the normal vaginal delivery group improved more on physical health related quality of life while the caesarean section group improved more on mental health related quality of life.

Conclusion
Although the study did not show a clear cut benefit in favor of either methods of delivery that are normal vaginal delivery or caesarean section, the findings suggest that normal vaginal delivery might lead to a better quality of life especially resulting in a superior physical health. Indeed in the absence of medical indications normal vaginal delivery might be better to be considered as the first priority in term pregnancy.
Identification of a potent herbal molecule for the treatment of breast cancer
Authors: Koduru Srinivas , Sowmyalakshmi Srinivasan , Kumar Raj , Gomathinayagam Rohini , Rohr Jürgen , Damodaran Chendil 
Published: January 2009

AbstractBackgroundBreast cancer (BCa)-related mortality still remains the second leading cause of cancer-related deaths worldwide. Patients with BCa have increasingly shown resistance and high toxicity to current chemotherapeutic drugs for which identification of novel targeted therapies are required.MethodsTo determine the effect of PDBD on BCa cells, estrogen-receptor positive (ER+)-MCF-7 and estrogen-receptor negative (ER-)-MDA 231 cells were treated with PDBD and the cell viability, apoptotic, cell cycle, Western blot and Promoter assays were performed.ResultsPDBD inhibits cell viability of ER+and ER-BCa cells by inducing apoptosis without causing significant toxicity in normal breast epithelial cells. While dissecting the mechanism of action of PDBD on BCa, we found that PDBD inhibits Akt signaling and its downstream targets such as NF-κB activation, IAP proteins and Bcl-2 expression. On the other hand, activation of JNK/p38 MAPK-mediated pro-apoptotic signaling was observed in both ER+and ER-BCa cells.ConclusionThese findings suggest that PDBD may have wide therapeutic application in the treatment of BCa.
Using surveillance data to monitor entry into care of newly diagnosed HIV-infected persons: San Francisco, 2006–2007
Authors: Zetola Nicola M , Bernstein Kyle , Ahrens Katherine , Marcus Julia L , Philip Susan , Nieri Giuliano , Jones Diane , Hare C Bradley , Hsu Ling , Scheer Susan , Klausner Jeffrey D 
Published: January 2009

Abstract

Background
Linkage to care after HIV diagnosis is associated with both clinical and public health benefits. However, ensuring and monitoring linkage to care by public health departments has proved to be a difficult task. Here, we report the usefulness of routine monitoring of CD4 T cell counts and plasma HIV viral load as measures of entry into care after HIV diagnosis.

Methods
Since July 1, 2006, the San Francisco Department of Public Health (SFDPH) incorporated monitoring initial primary care visit into standard HIV public health investigation for newly diagnosed HIV-infected patients in select clinics. Entry into care was defined as having at least one visit to a primary HIV care provider after the initial diagnosis of HIV infection. Investigators collected reports from patients, medical providers, laboratories and reviewed medical records to determine the date of the initial health care visit after HIV diagnosis. We identified factors associated with increased likelihood of entering care after HIV diagnosis.

Results
One -hundred and sixty new HIV-infected cases were diagnosed between July 1, 2006 and June 30, 2007. Routine surveillance methods found that 101 of those cases entered HIV medical care and monitoring of CD4 T cell counts and plasma HIV viral load confirmed entry to care of 25 more cases, representing a 25% increase over routine data collection methods. We found that being interviewed by a public health investigator was associated with higher odds of entry into care after HIV diagnosis (OR 18.86 [1.83–194.80], p = .001) compared to cases not interviewed. Also, HIV diagnosis at the San Francisco county hospital versus diagnosis at the county municipal STD clinic was associated with higher odds of entry into care (OR 101.71 [5.29–1952.05], p < .001).

Conclusion
The time from HIV diagnosis to initial CD4 T cell count, CD4 T cell value and HIV viral load testing may be appropriate surveillance measures for evaluating entry into care, as well as performance outcomes for local public health departments' HIV testing programs. Case investigation performed by the public health department or case management by clinic staff was associated with increased and shorter time to entry into HIV medical care.