bluuebunny/crossref_metadata_2025_split huggingface dataset:
The N@C60 nuclear spin qubit: Bang‐bang decoupling and ultrafast phase gates
Authors: Morton John J. L. , Tyryshkin Alexei M. , Ardavan Arzhang , Benjamin Simon C. , Porfyrakis Kyriakos , Lyon S. A. , Briggs G. Andrew D. 
Published: August 2006

AbstractNuclear spins have been proposed for the embodiment of quantum information and yielded the most complex demonstrations of quantum algorithms to date. However, the weak thermal polarisation of nuclear spins in experimentally accessible conditions has presented a barrier to further scaling. Here, we discuss the benefits of a coupled electron spin to the nuclear spin qubit and demonstrate the ideas using the 14N nuclear spin in the N@C60 molecule. In addition to providing a resource for nuclear spin polarisation and detection, the electron spin can be exploited to perform ultrafast nuclear spin phase gates, which can in turn be used to dynamically bang‐bang decouple the nuclear spin from unwanted interactions. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
‘Information‐Based‐Acquisition’ (IBA) technique with an ion‐trap/time‐of‐flight mass spectrometer for high‐throughput and reliable protein profiling
Authors: Yokosuka Toshiyuki , Yoshinari Kiyomi , Kobayashi Kinya , Ohtake Atsushi , Hirabayashi Atsumu , Hashimoto Yuichiro , Waki Izumi , Takao Toshifumi 
Published: August 2006

AbstractHighly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS). In an LC/MS run, intense peptide ions originating from high‐abundance proteins are preferentially analyzed using tandem mass spectrometry (MS2), so obtaining the MS2 spectra of peptide ions from low‐abundance proteins is difficult even if such ions are detected. Furthermore, the MS2 spectra may produce insufficient information to identify the peptides or proteins. To solve these problems, we have developed a real‐time optimization technique for MS2, called the Information‐Based‐Acquisition (IBA) system. In a preliminary LC/MS run, a few of the most intense ions detected in every MS spectrum are selected as precursors for MS2 and their masses, charge states and retention times are automatically registered in an internal database. In the next run, a sample similar to that used in the first run is analyzed using database searching. Then, the ions registered in the database are excluded from the precursor ion selection to avoid duplicate MS2 analyses. Furthermore, real‐time de novo sequencing is performed just after obtaining the MS2 spectrum, and an MS3 spectrum is obtained for accurate peptide identification when the number of interpreted amino acids in the MS2 spectrum is less than five. We applied the IBA system to a yeast cell lysate which is a typical crude sample, using a nanoLC/ion‐trap time‐of flight (IT/TOF) mass spectrometer, repeating the same LC/MS run five times. The obtained MS2 and MS3 spectra were analyzed by applying the Mascot® (Matrix Science, Boston, MA, USA) search engine to identify proteins from the sequence database. The total number of identified proteins in five LC/MS runs was three times higher than that in the first run and the ion scores for peptide identification also significantly increased, by about 70%, when the MS3 spectra were used, combined with the MS2 spectra, before being subjected to Mascot® analysis. Copyright © 2006 John Wiley & Sons, Ltd.
Histological and biological developmental characterization of the human cerebellar cortex
Authors: Lavezzi Anna Maria , Ottaviani Giulia , Terni Lorella , Matturri Luigi 
Published: August 2006

AbstractThe aim of this study was to investigate the histological and biological features of the human cerebellar cortex development and differentiation. We analyzed 52 brains of fetal and infant death victims, aged from 17 gestational weeks to 12th postnatal month. In particular, in the cerebellar cortex at different ages we evaluated, besides the structural aspects, the expression of several biomarkers implicated in proliferative processes (c‐fos, PCNA and apoptosis). We observed morphological patterns progressively evolving every month, from the indefinite structure of the second gestational trimester to the four‐layered structure (external granular layer, molecular layer, Purkinje cell layer, internal granular layer) of the late fetal cortex and subsequently to the three‐layered postnatal definitive morphology, due to involution of the external granular layer. The evaluation of the biological features of the cerebellar cortex showed high proliferative activity mainly confined to the transient external granular layer in prenatal life, and high apoptotic index after birth. Thus, the histological examination, better with the support of biomarker investigations, allows with accuracy to describe the dynamic sequence of steps that occur in human cerebellar cortex development and to establish in each case the age, namely the pre‐ or postnatal month of life. Consequently, we can diagnose delayed or altered processes of differentiation during the development of the human cerebellar cortex.
Kinetic Measurements of Protein Conformation in a Microchip
Authors: Kerby Matthew B. , Lee Jinkee , Ziperstein Joshua , Tripathi Anubhav 
Published: August 2006

AbstractThis paper presents a microchip‐based system for collecting kinetic time‐based information on protein refolding and unfolding. Dynamic protein conformational change pathways were studied in microchannel flow using a microfluidic device. We present a protein‐conserving approach for quantifying refolding by dynamically varying the concentration of the chemical denaturants, guanidine hydrochloride and urea. Short diffusion distances in the microchannel result in rapid equilibrium between protein and titrating solutions. Dilutions on the chip were tightly regulated using pressure controls rather than syringe‐based flow, as verified with extensive on‐chip tracer dye controls. To validate this protein assay method, folding transition experiments were performed using two well‐characterized proteins, human serum albumin (HSA) and bovine carbonic anhydrase (BCA). Transition events were monitored through fluorescence intensity shifts of the protein dye 8‐anilino‐1‐naphthalenesulfonic acid (ANS) during dilutions of protein from urea or guanidine hydrochloride solutions. The enzymatic activity of refolded BCA was measured by UV absorption through the conversion of p‐nitrophenyl acetate (p‐NPA). The microchip protein refolding transitions using ANS were well‐correlated with conventional plate‐based experiments. The microfluidic platform enables refolding studies to identify rapidly the optimal folding strategy for a protein using small quantities of material.
HiRes—a tool for comprehensive assessment and interpretation of metabolomic data
Authors: Zhao Qi , Stoyanova Radka , Du Shuyan , Sajda Paul , Brown Truman R. 
Published: August 2006

Abstract
Summary: The increasing role of metabolomics in system biology is driving the development of tools for comprehensive analysis of high-resolution NMR spectral datasets. This task is quite challenging since unlike the datasets resulting from other ‘omics’, a substantial preprocessing of the data is needed to allow successful identification of spectral patterns associated with relevant biological variability. HiRes is a unique stand-alone software tool that combines standard NMR spectral processing functionalities with techniques for multi-spectral dataset analysis, such as principal component analysis and non-negative matrix factorization. In addition, HiRes contains extensive abilities for data cleansing, such as baseline correction, solvent peak suppression, removal of frequency shifts owing to experimental conditions as well as auxiliary information management. Integration of these components together with multivariate analytical procedures makes HiRes very capable of addressing the challenges for assessment and interpretation of large metabolomic datasets, greatly simplifying this otherwise lengthy and difficult process and assuring optimal information retrieval.
Availability: HiRes is freely available for research purposes at
Contact: qz2106@columbia.edu
A large quantity of novel human antisense transcripts detected by LongSAGE
Authors: Ge Xijin , Wu Qingfa , Jung Yong-Chul , Chen Jun , Wang San Ming 
Published: August 2006

Abstract
Motivation: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632 813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts.
Results: Our study identified 45 321 tags that match the antisense strand of 9804 known mRNA sequences, 6606 of which contain antisense ESTs and 3198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database.
Conclusions: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome.
Contact: swang1@northwestern.edu
Supplementary information: Supplementary data are available at Bioinformatics online
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
Authors: Bekaert Michaël , Atkins John F , Baranov Pavel V 
Published: August 2006

Abstract
Summary: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.
Availability: The PHP based web interface of ARFA and the source code are located at
Contact: baranov@genetics.utah.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network
Authors: Stoll Gautier , Rougemont Jacques , Naef Félix 
Published: August 2006

Abstract
Motivation: The ability of cells to complete mitosis with high fidelity relies on elaborate checkpoint mechanisms. We study S- and M-phase checkpoint responses in silico in the budding yeast with a stochastic dynamical model for the cell-cycle. We aim to provide an unbiased functional classification of network interactions that reflect the contribution of each link to checkpoint efficiency in the presence of cellular fluctuations.
Results: We developed an algorithm BNetDyn to compute stochastic dynamical trajectories for an input gene network and its structural perturbations. User specified output measures like the mutual information between trigger and output nodes are then evaluated on the stationary state of the Markov process. Systematic perturbations of the yeast cell-cycle model by Li et al. classify each link according to its effect on checkpoint efficiencies and stabilities of the main cell-cycle phases. This points to the crosstalk in the cascades downstream of the SBF/MBF transcription activator complexes as determinant for checkpoint optimality; a finding that consistently reflects recent experiments. Finally our stochastic analysis emphasizes how dynamical stability in the yeast cell-cycle network crucially relies on backward inhibitory circuits next to forward induction.
Availability: C++ source code and network models can be downloaded at
Contact: felix.naef@isrec.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
COPA—cancer outlier profile analysis
Authors: MacDonald James W. , Ghosh Debashis 
Published: August 2006

Abstract
Summary: Chromosomal translocations are common in cancer, and in some cases may be causal in the progression of the disease. Using microarrays, in which the expression of thousands of genes are simultaneously measured, could potentially allow one to detect recurrent translocations for a particular cancer type. Standard statistical tests, such as the t-test are not suited for detecting these translocations, but a simple test based on robust centering and scaling of the data to help detect outlier samples, followed by a search for pairs of samples with mutually exclusive outliers, may be used to find genes involved in recurrent translocations. We have implemented this method, termed Cancer Outlier Profile Analysis (COPA) in an R package (that we call the copa package), and show its applicability on a publicly available dataset.
Availability:
Contact: jmacdon@med.umich.edu
A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato
Authors: Moco Sofia , Bino Raoul J. , Vorst Oscar , Verhoeven Harrie A. , de Groot Joost , van Beek Teris A. , Vervoort Jacques , de Vos C.H. Ric 
Published: August 2006

AbstractFor the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and α-tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue.
Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis
Authors: Li Xiaoxing , Duan Xuepeng , Jiang Haixiong , Sun Yujin , Tang Yuanping , Yuan Zheng , Guo Jingkang , Liang Wanqi , Chen Liang , Yin Jingyuan , Ma Hong , Wang Jian , Zhang Dabing 
Published: August 2006

AbstractThe basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.
Consensus by Democracy. Using Meta-Analyses of Microarray and Genomic Data to Model the Cold Acclimation Signaling Pathway in Arabidopsis
Authors: Benedict Catherine , Geisler Matt , Trygg Johan , Huner Norman , Hurry Vaughan 
Published: August 2006

Abstract
The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (−1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.
Impact of comorbid autism spectrum disorders on stimulant response in children with attention deficit hyperactivity disorder: a retrospective and prospective effectiveness study
Authors: Santosh P. J. , Baird G. , Pityaratstian N. , Tavare E. , Gringras P. 
Published: August 2006

AbstractBackground  In the recent past, psychiatrists and paediatricians have avoided prescribing stimulant medication, such as methylphenidate and dexamphetamine to patients with autism spectrum disorders (ASD) because of both doubts about efficacy and concern that these medications make stereotypies worse. Recently, a number of small trials have suggested that methyphenidate does have a role in the management of hyperactivity in children with autistic spectrum disorders.Methods  Children with ASD and attention deficit hyperactivity disorder (ADHD), and children with ADHD without ASD received standard treatment with methyphenidate from one specialist centre. A combination of standardized and novel outcome tools was used to allow both an exploratory retrospective study of 174 children and then a prospective study of a further 52 children to be carried out.Results  After treatment with stimulants, the subjects in both groups showed statistically significant improvements in target symptoms of ‘hyperactivity’, ‘impulsivity’, ‘inattention’, ‘oppositionality’, ‘aggression’ and ‘intermittent explosive rage’. The Clinical Global Impression‐Improvement and efficacy index measures also improved in each group. In both the retrospective and the prospective studies, there was no statistically significant difference in the degree of improvements between each group. Importantly, neither tics nor repetitive behaviours worsened in either group. Children in the ‘ADHD‐only’ group who were prescribed stimulants experienced significant ‘nausea’, ‘giddiness’, ‘headaches’ and ‘sleep difficulties’, whereas sleep difficulties were the only side effect that emerged in children in the ASD with ADHD group.Conclusions  Both studies presented here support previous findings from smaller studies that show children with autism and ADHD can respond as well to stimulants as children with ADHD alone. Although randomized controlled trials remain the gold standard for efficacy studies, systems like this that allow clinicians to continue rigorous and consistent monitoring for many years have a valuable role to play. Furthermore, such monitoring systems which now exist electronically can easily accumulate large data sets and reveal details about long‐term effectiveness and long‐term side effects of medication that are unlikely to be discovered in short‐term trials.
Families in a state of flux: the experience of grandparents in autism spectrum disorder
Authors: Margetts J. K. , Le Couteur A. , Croom S. 
Published: August 2006

AbstractBackground  The experience of being a grandparent of a grandchild with autism spectrum disorder (ASD) is a previously under‐researched area. This study sets out to examine the grandparents’ own perspective in an exploratory way using a qualitative approach to answer the question, ‘What is the experience like?’Method  A qualitative research project, using a purposive sampling technique and semi‐structured interviews to examine the experiences of six grandparents of children with ASD diagnosed by a specialist team in a second opinion Tier 4 Child and Adolescent Mental Health Service.Results  The experiences of the grandparents were characterized by three Key Themes which emerged from the interviews: (1) The Parental Bond (protective bonding towards grandchild and adult child); (2) Striving for Answers (searching for meaning); (3) Keeping Intact (holding the family together).Conclusion  The study suggests some interesting insights and confirms the need for more attention to this area. A key question raised by the study is how a child‐focused multidisciplinary team can embrace its role in delivering a family‐centred service. The clinical implications of this project have led to a change of practice in the specialist team. Further research would be appropriate to investigate the therapeutic effectiveness and cost effectiveness of involving grandparents as part of the assessment process.