bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and Chemical Stability of Iron Sucrose in Parenteral Nutrition
Authors: MacKay Mark , Rusho William , Jackson Daniel , McMillin Gwendolyn , Winther Brian 
Published: December 2009

Introduction:Current literature supports iron dextran as the only iron preparation compatible with parenteral nutrition (PN). Iron sucrose has been used for iron replacement therapy because of its lower rate of adverse events. The purpose of this study is to determine the physical and chemical stability of iron sucrose in PN.Methods:Physical and chemical stability of iron sucrose in nonlipid PN solutions (PN 1 for neonates and PN 2 for patients weighing >20 kg) is tested over time in triplicate. Physical stability is determined by visually inspecting each PN solution for particulate matter and by filtering and analyzing each aliquot quantitatively for crystal precipitates. Chemical stability is confirmed if the iron concentrations by mass spectrometry remain within United States Pharmacopeia (USP) standards.Results:Visual clarity is maintained in all PN solutions at hours 0 through 4. PN solution 1 remains clear for hours 8 through 24, whereas PN solution 2 shows an increase in particulate matter by 8 hours. All PN solutions 2 are considered visually incompatible by hour 24. Physical stability of iron sucrose for PN solutions 1 and 2 from hours 0 to 4 is within the USP guidelines for crystalline particulate matter. At hour 24, only solution 1 remains within USP guidelines. Chemical stability data indicate that iron concentrations are maintained throughout the 24‐hour time period.Conclusion:The physical stability of iron sucrose in PN is time and concentration dependent. Concentrations >0.25 mg/dL showed increasing particulate and should not be added to PN. However, iron sucrose is chemically stable in PN solutions.
SNP array analysis of tyrosine kinase inhibitor-resistant chronic myeloid leukemia identifies heterogeneous secondary genomic alterations
Authors: Nowak Daniel , Ogawa Seishi , Müschen Markus , Kato Motohiro , Kawamata Norihiko , Meixel Antonie , Nowak Verena , Kim Han S. , Kang Sharon , Paquette Ronald , Chang Mi-Sook , Thoennissen Nils H. , Mossner Max , Hofmann Wolf-Karsten , Kohlmann Alexander , Weiss Tamara , Haferlach Torsten , Haferlach Claudia , Koeffler H. Phillip 
Published: December 2009

AbstractTo elucidate whether tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia is associated with characteristic genomic alterations, we analyzed DNA samples from 45 TKI-resistant chronic myeloid leukemia patients with 250K single nucleotide polymorphism arrays. From 20 patients, matched serial samples of pretreatment and TKI resistance time points were available. Eleven of the 45 TKI-resistant patients had mutations of BCR-ABL1, including 2 T315I mutations. Besides known TKI resistance-associated genomic lesions, such as duplication of the BCR-ABL1 gene (n = 8) and trisomy 8 (n = 3), recurrent submicroscopic alterations, including acquired uniparental disomy, were detectable on chromosomes 1, 8, 9, 17, 19, and 22. On chromosome 22, newly acquired and recurrent deletions of the IGLC1 locus were detected in 3 patients, who had previously presented with lymphoid or myeloid blast crisis. This may support a hypothesis of TKI-induced selection of subclones differentiating into immature B-cell progenitors as a mechanism of disease progression and evasion of TKI sensitivity.
Alterations of the systemic environment are the primary cause of impaired B and T lymphopoiesis in telomere-dysfunctional mice
Authors: Song Zhangfa , Wang Jianwei , Guachalla Luis Miguel , Terszowski Grzegorz , Rodewald Hans-Reimer , Ju Zhenyu , Rudolph K. Lenhard 
Published: December 2009

AbstractThere is growing evidence that telomere dysfunction can contribute to human aging. Telomere dysfunction limits lymphopoiesis in aging telomerase knockout (mTerc−/−) mice primarily by the induction of stem cell–extrinsic alterations. The relative contribution of alterations in the stem cell niche and the systemic environment to the impairment of lymphopoiesis in response to telomere dysfunction is currently unknown. This study reveals a minor impact of stem cell–intrinsic defects on the impairment of B and T lymphopoiesis in response to telomere dysfunction. The impairment in B and T lymphopoiesis in aging telomere-dysfunctional mice was mainly due to alterations of the systemic environment. Telomere dysfunction had no significant cell-autonomous effects impairing the function of thymic or bone marrow niches in supporting B and T lymphopoiesis. Moreover, age-related alterations in the cellular composition of the thymic epithelium in telomere-dysfunctional mice were rescued by transplantation of the thymus into a wild-type environment; these rejuvenated thymi supported normal T lymphopoiesis in recipient mice. Together, these data place alterations in the systemic environment on top of the hierarchy of events limiting lymphopoiesis in response to telomere dysfunction.
An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops
Authors: Totir Liviu R , Fernando Rohan L , Abraham Joseph 
Published: December 2009

Abstract

Background
Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species.

Methods
In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood.

Examples
A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree.
Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100
Authors: Dastidar Shubhra Ghosh , Lane David P , Verma Chandra S 
Published: December 2009

Abstract

Background
The tumor suppressor protein p53 is regulated by the ubiquitin ligase MDM2 which down-regulates p53. In tumours with overexpressed MDM2, the p53-MDM2 interaction can be interrupted by a peptide or small molecule to stabilize p53 as a therapeutic strategy. Structural and biochemical/mutagenesis data show that p53 has 3 hydrophobic residues F19, W23 and L26 that embed into the ligand binding pocket of MDM2 which is highly plastic in nature and can modulate its size to accommodate a variety of ligands. This binding pocket is primarily dependent on the orientation of a particular residue, Y100. We have studied the role of the dynamics of Y100 in p53 recognition.

Results
Molecular dynamics simulations show that the Y100 side chain can be in "open" or "closed" states with only the former enabling complex formation. When both p53 and MDM2 are in near native conformations, complex formation is rapid and is driven by the formation of a hydrogen bond between W23 of p53 and L54 of MDM2 or by the embedding of F19 of p53 into MDM2. The transition of Y100 from "closed" to "open" can increase the size of the binding site. Interconversions between these two states can be induced by the N-terminal region of MDM2 or by the conformations of the p53 peptides.

Conclusion
Molecular dynamics simulations have revealed how the binding of p53 to MDM2 is modulated by the conformational mobility of Y100 which is the gatekeeper residue in MDM2. The mobility of this residue can be modulated by the conformations of p53 and the Nterminal lid region of MDM2.
BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature
Authors: Kuo Cheng-Ju , Ling Maurice HT , Lin Kuan-Ting , Hsu Chun-Nan 
Published: December 2009

Abstract

Background
To automatically process large quantities of biological literature for knowledge discovery and information curation, text mining tools are becoming essential. Abbreviation recognition is related to NER and can be considered as a pair recognition task of a terminology and its corresponding abbreviation from free text. The successful identification of abbreviation and its corresponding definition is not only a prerequisite to index terms of text databases to produce articles of related interests, but also a building block to improve existing gene mention tagging and gene normalization tools.

Results
Our approach to abbreviation recognition (AR) is based on machine-learning, which exploits a novel set of rich features to learn rules from training data. Tested on the AB3P corpus, our system demonstrated a F-score of 89.90% with 95.86% precision at 84.64% recall, higher than the result achieved by the existing best AR performance system. We also annotated a new corpus of 1200 PubMed abstracts which was derived from BioCreative II gene normalization corpus. On our annotated corpus, our system achieved a F-score of 86.20% with 93.52% precision at 79.95% recall, which also outperforms all tested systems.

Conclusion
By applying our system to extract all short form-long form pairs from all available PubMed abstracts, we have constructed BIOADI. Mining BIOADI reveals many interesting trends of bio-medical research. Besides, we also provide an off-line AR software in the download section on http://bioagent.iis.sinica.edu.tw/BIOADI/.
Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study
Authors: Regier Jerome C , Zwick Andreas , Cummings Michael P , Kawahara Akito Y , Cho Soowon , Weller Susan , Roe Amanda , Baixeras Joaquin , Brown John W , Parr Cynthia , Davis Donald R , Epstein Marc , Hallwachs Winifred , Hausmann Axel , Janzen Daniel H , Kitching Ian J , Solis M Alma , Yen Shen-Horn , Bazinet Adam L , Mitter Charles 
Published: December 2009

AbstractBackgroundIn the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.ResultsOur trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P< 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P≤ 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P< 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data.ConclusionOur results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.
MitoVariome: a variome database of human mitochondrial DNA
Authors: Lee Yong Seok , Kim Woo-Yeon , Ji Mihyun , Kim Ji Han , Bhak Jong 
Published: December 2009

Abstract

Background
Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forensics, degenerative diseases, cancers, and aging process. Typically, human mitochondrial DNA has various features such as HVSI, HVSII, single-nucleotide polymorphism (SNP), restriction enzyme sites, and short tandem repeat (STR).

Results
We present a variome database (MitoVariome) of human mitochondrial DNA sequences. Queries against MitoVariome can be made using accession numbers or haplogroup/continent. Query results are presented not only in text but also in HTML tables to report extensive mitochondrial sequence variation information. The variation information includes repeat pattern, restriction enzyme site polymorphism, short tandem repeat, disease information as well as single nucleotide polymorphism. It also provides a graphical interface as Gbrowse displaying all variations at a glance. The web interface also provides the tool for assigning haplogroup based on the haplogroup-diagnostic system with complete human mitochondrial SNP position list and for retrieving sequences that users query against by using accession numbers.

Conclusion
MitoVariome is a freely accessible web application and database that enables human mitochondrial genome researchers to study genetic variation in mitochondrial genome with textual and graphical views accompanied by assignment function of haplogrouping if users submit their own data. Hence, the MitoVariome containing many kinds of variation features in the human mitochondrial genome will be useful for understanding mitochondrial variations of each individual, haplogroup, or geographical location to elucidate the history of human evolution.
Improving gene expression similarity measurement using pathway-based analytic dimension
Authors: Keum Changwon , Woo Jung Hoon , Oh Won Seok , Park Sue-Nie , No Kyoung Tai 
Published: December 2009

Abstract

Background
Gene expression similarity measuring methods were developed and applied to search rapidly growing public microarray databases. However, current expression similarity measuring methods need to be improved to accurately measure similarity between gene expression profiles from different platforms or different experiments.

Results
We devised new gene expression similarity measuring method based on pathway information. In short, newly devised method measure similarity between gene expression profiles after converting them into pathway based expression profiles. To evaluate pathway based gene expression similarity measuring method, we conducted cell type classification test. Pathway based similarity measuring method shows higher classification accuracy. Especially, pathway based methods outperform at most 50% and 10% over conventional gene expression similarity method when search databases are limited to cross-platform profiles and cross-experiment profiles.

Conclusion
The pathway based gene expression similarity measuring method outperforms commonly used similarity measuring methods. Considering the fact that public microarray database is consist of gene expression profiles of various experiments with various type of platform, pathway based gene expression similarity measuring method could be successfully applied for searching large public microarray databases.
BOAT: Basic Oligonucleotide Alignment Tool
Authors: Zhao Shu-Qi , Wang Jun , Zhang Li , Li Jiong-Tang , Gu Xiaocheng , Gao Ge , Wei Liping 
Published: December 2009

Abstract

Background
Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together.

Results
We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control.

Conclusion
Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies.
MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis
Authors: Reja Rohit , Venkatakrishnan AJ , Lee Jungwoo , Kim Byoung-Chul , Ryu Jea-Woon , Gong Sungsam , Bhak Jong , Park Daeui 
Published: December 2009

Abstract

Background
Mitochondria play a vital role in the energy production and apoptotic process of eukaryotic cells. Proteins in the mitochondria are encoded by nuclear and mitochondrial genes. Owing to a large increase in the number of identified mitochondrial protein sequences and completed mitochondrial genomes, it has become necessary to provide a web-based database of mitochondrial protein information.

Results
We present 'MitoInteractome', a consolidated web-based portal containing a wealth of information on predicted protein-protein interactions, physico-chemical properties, polymorphism, and diseases related to the mitochondrial proteome. MitoInteractome contains 6,549 protein sequences which were extracted from the following databases: SwissProt, MitoP, MitoProteome, HPRD and Gene Ontology database. The first general mitochondrial interactome has been constructed based on the concept of 'homologous interaction' using PSIMAP (Protein Structural Interactome MAP) and PEIMAP (Protein Experimental Interactome MAP). Using the above mentioned methods, protein-protein interactions were predicted for 74 species. The mitochondrial protein interaction data of humans was used to construct a network for the aging process. Analysis of the 'aging network' gave us vital insights into the interactions among proteins that influence the aging process.

Conclusion
MitoInteractome is a comprehensive database that would (1) aid in increasing our understanding of the molecular functions and interaction networks of mitochondrial proteins, (2) help in identifying new target proteins for experimental research using predicted protein-protein interaction information, and (3) help in identifying biomarkers for diagnosis and new molecular targets for drug development related to mitochondria. MitoInteractome is available at http://mitointeractome.kobic.kr/.
Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin
Authors: Jongkon Nipa , Mokmak Wanwimon , Chuakheaw Daungmanee , Shaw Philip J , Tongsima Sissades , Sangma Chak 
Published: December 2009

Abstract

Background
It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barrier to viral transmission from birds to humans. However, strains may emerge with mutated hemagglutinin, potentially changing the receptor binding preference from avian to human-type. This hypothesis has been proven correct, since viral isolates from Vietnam and Thailand have been found which have increased selectivity toward the human cell receptor. The change in binding preference is due to mutation, which can be computationally modelled. The aim of this study is to further explore whether computational simulation could be used as a prediction tool for host type selectivity in emerging variants.

Results
Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). The avian receptor was represented by Siaα(2,3)Gal substructure and human receptor by Siaα(2,6)Gal. The glycoside binding conformation was monitored throughout the simulations since high selectivity toward a particular host occurs when the sialoside bound with the near-optimized conformation.

Conclusion
The simulation results showed all hemagglutinin proteins used the same set of amino acid residues to bind with the glycoside; however, some mutations alter linkage preferences. Preference toward human-type receptors is associated with a positive torsion angle, while avian-type receptor preference is associated with a negative torsion angle. According to the conformation analysis of the bound receptors, we could predict the relative selectivity in accordance with in vitro experimental data when disaccharides receptor analogs were used.