bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Authors: Cheng Chao , Yan Xiting , Sun Fengzhu , Li Lei M 
Published: November 2007

Abstract

Background
The identification of transcription factors (TFs) associated with a biological process is fundamental to understanding its regulatory mechanisms. From microarray data, however, the activity changes of TFs often cannot be directly observed due to their relatively low expression levels, post-transcriptional modifications, and other complications. Several approaches have been proposed to infer TF activity changes from microarray data. In some models, a linear relationship between gene expression and TF-gene binding strength is assumed. In some other models, the target genes of a TF are first determined by a significance cutoff to binding affinity scores, and then expression differentiation is checked between the target and other genes.

Results
We propose a novel method, referred to as BASE (binding association with sorted expression), to infer TF activity changes from microarray expression profiles with the help of binding affinity data. It searches the maximum association between bind affinity profile of a TF and expression change profile along the direction of sorted differentiation. The method does not make hard target gene selection, rather, the significances of TF activity changes are evaluated by permutation tests of binding association at the end. To show the effectiveness of this method, we apply it to three typical examples using different kinds of binding affinity data, namely, ChIP-chip data, motif discovery data, and positional weighted matrix scanning data, respectively. The implications obtained from all three examples are consistent with established biological results. Moreover, the inferences suggest new and biological meaningful hypotheses for further investigation.

Conclusion
The proposed method makes transcription inference from profiles of expression and binding affinity. The same machinery can be used to deal with various kinds of binding affinity data. The method does not require a linear assumption, and has the desirable property of scale-invariance with respect to TF-specific binding affinity. This method is easy to implement and can be routinely applied for transcriptional inferences in microarray studies.
Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats
Authors: Eugster Myriam , Roten Claude-Alain H , Greub Gilbert 
Published: November 2007

Abstract

Background
Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes.

Results
No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted α-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism.

Conclusion
Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.
N-myristoyltransferase: A potential novel diagnostic marker for colon cancer
Authors: Shrivastav Anuraag , Varma Shailly , Saxena Anurag , DeCoteau John , Sharma Rajendra K 
Published: November 2007

Abstract

Background
Colon cancer is the second leading cause of cancer deaths in the western world. If detected early, colorectal cancer is one of the most treatable forms of cancer. Unfortunately, very few people are screened. N-myristoyltransferase (NMT) catalyzes myristoylation of various proteins including oncoproteins. We have demonstrated earlier the alteration of NMT activity during the progression of colorectal cancer and established NMT as a putative therapeutic target for cancer.

Methods
Peripheral blood samples and bone marrow were collected from the colon cancer patients and azoxymethane induced colonic tumor rats and their controls respectively. NMT activity and expression was determined as reported earlier. Immunohistochemical studies were carried out using standard procedures.

Results
In this study we demonstrate for the first time altered expression and localization of NMT in the peripheral blood and bone marrow in colon cancer patients. Immunohistochemical analysis revealed weak to negative staining for NMT in peripheral blood mononuclear cells (PBMC) of controls, whereas strong positivity was observed in PBMC colon cancer patients. In addition, we observed that NMT was localized mostly in the nuclei of the bone marrow (BM) mononuclear cells of the colon cancer patients, whereas NMT remained cytoplasmic in the control bone marrow specimens.

Conclusion
The strikingly different NMT expression offers the basis of a potential adjunct investigative tool for screening or diagnosis of patients at risk for or suspected of having colon cancer. Furthermore, altered localization of NMT in BM of tumor bearing hosts may serve as an added investigative tool for the diagnostic purpose.
Parental attitudes and opinions on the use of psychotropic medication in mental disorders of childhood
Authors: Lazaratou Helen , Anagnostopoulos Dimitris C , Alevizos Elias V , Haviara Fotini , Ploumpidis Dimitris N 
Published: November 2007

Abstract

Background
The limited number of systematic, controlled studies that assess the safety and efficacy of psychotropic medications for children reinforce the hesitation and reluctance of parents to administer such medications. The aim of this study was to investigate the attitudes of parents of children with psychiatric disorders, towards psychotropic medication.

Methods
A 20-item questionnaire was distributed to 140 parents during their first contact with an outpatient child psychiatric service. The questionnaire comprised of questions regarding the opinions, knowledge and attitudes of parents towards children's psychotropic medication. Sociodemographic data concerning parents and children were also recorded. Frequency tables were created and the chi-square test and Fisher's exact tests were used for the comparison of the participants' responses according to sex, educational level, age and gender of the child and use of medication.

Results
Respondents were mostly mothers aged 25–45 years. Children for whom they asked for help with were mostly boys, aged between 6 and 12 years old. A total of 83% of the subjects stated that they knew psychotropic drugs are classified into categories, each having a distinct mechanism of action and effectiveness. A total of 40% believe that there is a proper use of psychotropic medication, while 20% believe that psychiatrists unnecessarily use high doses of psychotropic medication. A total of 80% fear psychotropic agents more than other types of medication. Most parents are afraid to administer psychotropic medication to their child when compared to any other medication, and believe that psychotherapy is the most effective method of dealing with every kind of mental disorders, including childhood schizophrenia (65%). The belief that children who take psychotropic medication from early childhood are more likely to develop drug addiction later is correlated with the parental level of education.

Conclusion
Parents' opinions and beliefs are not in line with scientific facts. This suggests a need to further inform the parents on the safety and efficacy of psychotropic medication in order to improve treatment compliance.
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models
Authors: Steinke Florian , Seeger Matthias , Tsuda Koji 
Published: November 2007

AbstractBackgroundIdentifying large gene regulatory networks is an important task, while the acquisition of data through perturbation experiments (e.g., gene switches, RNAi, heterozygotes) is expensive. It is thus desirable to use an identification method that effectively incorporates available prior knowledge – such as sparse connectivity – and that allows to design experiments such that maximal information is gained from each one.ResultsOur main contributions are twofold: a method for consistent inference of network structure is provided, incorporating prior knowledge about sparse connectivity. The algorithm is time efficient and robust to violations of model assumptions. Moreover, we show how to use it for optimal experimental design, reducing the number of required experiments substantially. We employ sparse linear models, and show how to perform full Bayesian inference for these. We not only estimate a single maximum likelihood network, but compute a posterior distribution over networks, using a novel variant of the expectation propagation method. The representation of uncertainty enables us to do effective experimental design in a standard statistical setting: experiments are selected such that the experiments are maximally informative.ConclusionFew methods have addressed the design issue so far. Compared to the most well-known one, our method is more transparent, and is shown to perform qualitatively superior. In the former, hard and unrealistic constraints have to be placed on the network structure for mere computational tractability, while such are not required in our method. We demonstrate reconstruction and optimal experimental design capabilities on tasks generated from realistic non-linear network simulators.The methods described in the paper are available as a Matlab package athttp://www.kyb.tuebingen.mpg.de/sparselinearmodel.
Quantification of ortholog losses in insects and vertebrates
Authors: Wyder Stefan , Kriventseva Evgenia V , Schröder Reinhard , Kadowaki Tatsuhiko , Zdobnov Evgeny M 
Published: November 2007

Abstract
Background
The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits.

Results
To consistently quantify losses of orthologous groups of genes, we compared the gene repertoires of five vertebrates and five insects, including honeybee and Tribolium beetle, that represent insect orders outside the previously sequenced Diptera. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes.

Conclusion
Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their two- to three-fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.
The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z
Authors: Rens Willem , O'Brien Patricia CM , Grützner Frank , Clarke Oliver , Graphodatskaya Daria , Tsend-Ayush Enkhjargal , Trifonov Vladimir A , Skelton Helen , Wallis Mary C , Johnston Steve , Veyrunes Frederic , Graves Jennifer AM , Ferguson-Smith Malcolm A 
Published: November 2007

Abstract
Background
Sex-determining systems have evolved independently in vertebrates. Placental mammals and marsupials have an XY system, birds have a ZW system. Reptiles and amphibians have different systems, including temperature-dependent sex determination, and XY and ZW systems that differ in origin from birds and placental mammals. Monotremes diverged early in mammalian evolution, just after the mammalian clade diverged from the sauropsid clade. Our previous studies showed that male platypus has five X and five Y chromosomes, no SRY, and DMRT1 on an X chromosome. In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping.

Results
Chromosome painting reveals a meiotic chain of nine sex chromosomes in the male echidna and establishes their order in the chain. Two of those differ from those in the platypus, three of the platypus sex chromosomes differ from those of the echidna and the order of several chromosomes is rearranged. Comparative gene mapping shows that, in addition to bird autosome regions, regions of bird Z chromosomes are homologous to regions in four platypus X chromosomes, that is, X1, X2, X3, X5, and in chromosome Y1.

Conclusion
Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z.
ERCC1 Genotype and Phenotype in Epithelial Ovarian Cancer Identify Patients Likely to Benefit From Paclitaxel Treatment in Addition to Platinum-Based Therapy
Authors: Smith Stephanie , Su Dan , Rigault de la Longrais Irene A. , Schwartz Peter , Puopolo Manuela , Rutherford Thomas J. , Mor Gil , Yu Herbert , Katsaros Dionyssios 
Published: November 2007

Purpose To investigate the effect of excision repair cross-complementation group 1 (ERCC1) on treatment response and survival of patients treated with platinum chemotherapy with or without paclitaxel. Patients and Methods Tumor samples from epithelial ovarian cancer patients were evaluated for ERCC1 mRNA expression and a single nucleotide polymorphism at codon 118 (C>T). Of 178 patients treated with postoperative platinum-based chemotherapy, 75 were also given paclitaxel. For all of these patients, ERCC1 expression and genotype were analyzed for associations with treatment response and survival. Results Among the 103 patients treated with platinum without paclitaxel, the C/C genotype, compared with C/T and T/T, was associated with greater risk of disease progression and death (hazard ratio [HR], 1.95, P = .051; HR, 2.01, P = .033, respectively); high levels of ERCC1 mRNA, compared with low levels, were associated with greater risk of disease progression (HR, 2.41; P = .014). Similarly, when the ERCC1 data were combined, patients with the C/C genotype and high ERCC1 expression had greater risk for disease progression (HR, 3.73; P = .003) compared with those with low expression and non-C/C genotype. However, for the 75 patients treated with platinum plus paclitaxel, the C/C genotype and high ERCC1 expression were not associated with poor prognosis, suggesting that paclitaxel may help to alleviate ERCC1-related platinum resistance. Conclusion Ovarian cancer patients with high ERCC1 expression or the C/C genotype at codon 118 may benefit from the combination of platinum and paclitaxel, while those with low ERCC1 expression or the C/T or T/T genotype may respond well to platinum without paclitaxel.
Disability in Adult Survivors of Childhood Cancer: A Swedish National Cohort Study
Authors: Hjern Anders , Lindblad Frank , Boman Krister K. 
Published: November 2007

Purpose We studied the effects of childhood or adolescent cancer and cancer treatment on disability as indicated by persistent aid needs in adult life. Patients and Methods A group of 2,503 survivors of childhood cancer diagnosed before their 16th birthday were studied with data from registers in a national cohort of 1.91 million Swedish residents. Disability indicators were created from information in national registers about income (sickness pension, handicap allowance), personal assistance, and family situation in 2002. Multivariate logistic regression on the log scale was used to estimate relative risk (RR) ratios. Results A total of 7.6% of survivors received handicap allowance indicating permanent disability, including brain tumors (14.0%), other solid tumors (6.3), and leukemias/lymphomas (2.9%), compared with 0.6% in the general population. Twenty-six percent of survivors of CNS tumor and 10% of survivors of solid tumors had at least one indication of a disability. Younger age at diagnosis suggested a higher risk for disability. CNS tumor survivors had an RR of 10.7 (95% CI, 9.3 to 12.8) for having at least one disability indication compared with the noncancer population, whereas leukemia and lymphoma survivors had an RR of 3.0, and survivors of other cancers had an RR of 3.8. Survivors of CNS tumor only had an increased RR for living in the parental household (RR = 1.6; 95% CI, 1.4 to 1.9). Conclusion Childhood cancer survivors more often have persistent needs of supportive measures provided by community and/or the parental household. The survivors of CNS tumors were at particular risk, indicating a need of safer treatment protocols, and tailored follow-up, prevention, and rehabilitation to address this persistent social disability.
Preparation of Nanostructured Conjugated Polymers Using Template Electrochemical Polymerization in Supercritical Fluids
Authors: Atobe Mahito , Iizuka Shinya , Fuchigami Toshio , Yamamoto Hikaru 
Published: November 2007

Abstract
The electrochemical coating and filling with conjugated polymers in porous templates were carried out in supercritical fluids. The use of the special properties of the fluids such as higher diffusivity and lower viscosity enabled the effective monomer transport into the porous template and the nanoprecise coating and filling with the polymers.
New Facile Preparation of a Poly(vinyl chloride)/Layered Double Hydroxide Nanocomposite via Solution Intercalation
Authors: Liu Jun , Chen Guangming , Yang Jiping , Ma Yongmei 
Published: November 2007

Abstract
A poly(vinyl chloride)/layered double hydroxide (PVC/LDH) nanocomposite was successfully prepared via solution intercalation for the first time. Its microstructure was characterized by XRD, TEM, TGA, and IR, which clearly demonstrates that LDH particles were exfoliated into nanometer scale and homogeneously dispersed in the PVC matrix.
One-dimensional Strands of Trigonellinium Constructed by Intermolecular Strong O–H···O and Weak C–H···O Hydrogen Bonds in the Crystal of Partially Oxidized Ni(dmit)2 Salt
Authors: Tomono Kazuaki , Miyamura Kazuo 
Published: November 2007

Abstract
The trigonellinium cations in the partially oxidized Ni(dmit)2 complex salt 1 formed strong O–H···O hydrogen-bridged dimers, and the dimers are held together by the weak C(sp2 and sp3)–H···O hydrogen bond to form 1D strands. Further assembly through weak C(sp3)–H···O hydrogen bond and π···π interaction resulted in the formation of Ni(dmit)2 column structure.
Hormonal, pH, and Calcium Regulation of Connexin 43–Mediated Dye Transfer in Osteocytes in Chick Calvaria
Authors: Ishihara Yoshihito , Kamioka Hiroshi , Honjo Tadashi , Ueda Hirotaka , Takano-Yamamoto Teruko , Yamashiro Takashi 
Published: November 2007

Abstract
Gap junctional intercellular communication among osteocytes in chick calvaria, their natural 3D environment, was examined using FRAP analysis. Cell–cell communication among osteocytes in chick calvaria was mediated by Cx43 and was regulated by extracellular pH, extracellular calcium ion concentration, and PTH.
Introduction: The intercellular network of communication among osteocytes is mediated by gap junctions. Gap junctional intercellular communication (GJIC) is thought to play an important role in integration and synchronization of bone remodeling. We hypothesized that extracellular pH (pHo) and extracellular calcium ion concentration ([Ca2+]e), both of which are dynamically altered by osteoclasts during bone remodeling, affect GJIC among osteocytes. Using fluorescence replacement after photobleaching (FRAP) analysis, we examined the effect of changes in pHo and [Ca2+]e and addition of PTH on GJIC in osteocytes in chick calvaria. Additionally, we examined the role of intracellular calcium on the regulation of GJIC among osteocytes.
Materials and Methods: Anti-Connexin43 (Cx43) immunolabeling was used to localize gap junctions in chick calvaria. GJIC among osteocytes in chick calvariae was assessed using FRAP.
Results: Cx43 immunoreactivity was detected in most of the osteocyte processes. FRAP analysis showed dye-coupling among osteocytes in chick calvariae. In untreated osteocytes, fluorescence intensity recovered 43.7 ± 2.2% within 5 min after photobleaching. Pretreatment of osteocytes with 18 α-GA, a reversible inhibitor of GJIC, significantly decreased fluorescence recovery to 10.7 ± 2.2%. When pHo was decreased from 7.4 to 6.9, fluorescence recovery significantly decreased from 43.3 ± 2.9% to 19.7 ± 2.3%. Conversely, when pHo was increased from 7.4 to 8.0, fluorescence recovery was significantly increased to 61.9 ± 4.5%. When [Ca2+]e was increased from 1 to 25 mM, fluorescence recovery was significantly decreased from 47.0 ± 6.1% to 16.1 ± 2.1%. In bone fragments exposed to 1.0–10 nM rPTH for 3 h, replacement of fluorescence was significantly increased to 60.7 ± 7.2%. Chelating intracellular calcium ions affected GJIC regulation by [Ca2+]e and PTH.
Conclusions: Our study of cell–cell communication between osteocytes in chick calvaria showed for the first time that GJIC among osteocytes is regulated by the extracellular environment and by hormonal stimulation during bone remodeling. This method may be more biologically relevant to living bone than current methods.