bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins
Authors: Odronitz Florian , Becker Sebastian , Kollmar Martin 
Published: April 2009

Abstract

Background
Motor proteins have extensively been studied in the past and consist of large superfamilies. They are involved in diverse processes like cell division, cellular transport, neuronal transport processes, or muscle contraction, to name a few. Vertebrates contain up to 60 myosins and about the same number of kinesins that are spread over more than a dozen distinct classes.

Results
Here, we present the comparative genomic analysis of the motor protein repertoire of 21 completely sequenced arthropod species using the owl limpet Lottia gigantea as outgroup. Arthropods contain up to 17 myosins grouped into 13 classes. The myosins are in almost all cases clear paralogs, and thus the evolution of the arthropod myosin inventory is mainly determined by gene losses. Arthropod species contain up to 29 kinesins spread over 13 classes. In contrast to the myosins, the evolution of the arthropod kinesin inventory is not only determined by gene losses but also by many subtaxon-specific and species-specific gene duplications. All arthropods contain each of the subunits of the cytoplasmic dynein/dynactin complex. Except for the dynein light chains and the p150 dynactin subunit they contain single gene copies of the other subunits. Especially the roadblock light chain repertoire is very species-specific.

Conclusion
All 21 completely sequenced arthropods, including the twelve sequenced Drosophila species, contain a species-specific set of motor proteins. The phylogenetic analysis of all genes as well as the protein repertoire placed Daphnia pulex closest to the root of the Arthropoda. The louse Pediculus humanus corporis is the closest relative to Daphnia followed by the group of the honeybee Apis mellifera and the jewel wasp Nasonia vitripenni s. After this group the rust-red flour beetle Tribolium castaneum and the silkworm Bombyx mori diverged very closely from the lineage leading to the Drosophila species.
Gene set internal coherence in the context of functional profiling
Authors: Montaner David , Minguez Pablo , Al-Shahrour Fátima , Dopazo Joaquín 
Published: April 2009

AbstractBackgroundFunctional profiling methods have been extensively used in the context of high-throughput experiments and, in particular, in microarray data analysis. Such methods use available biological information to define different types of functional gene modules (e.g. gene ontology -GO-, KEGG pathways, etc.) whose representation in a pre-defined list of genes is further studied. In the most popular type of microarray experimental designs (e.g. up- or down-regulated genes, clusters of co-expressing genes, etc.) or in other genomic experiments (e.g. Chip-on-chip, epigenomics, etc.) these lists are composed by genes with a high degree of co-expression. Therefore, an implicit assumption in the application of functional profiling methods within this context is that the genes corresponding to the modules tested are effectively defining sets of co-expressing genes. Nevertheless not all the functional modules are biologically coherent entities in terms of co-expression, which will eventually hinder its detection with conventional methods of functional enrichment.ResultsUsing a large collection of microarray data we have carried out a detailed survey of internal correlation in GO terms and KEGG pathways, providing a coherence index to be used for measuring functional module co-regulation. An unexpected low level of internal correlation was found among the modules studied. Only around 30% of the modules defined by GO terms and 57% of the modules defined by KEGG pathways display an internal correlation higher than the expected by chance.This information on the internal correlation of the genes within the functional modules can be used in the context of a logistic regression model in a simple way to improve their detection in gene expression experiments.ConclusionFor the first time, an exhaustive study on the internal co-expression of the most popular functional categories has been carried out. Interestingly, the real level of coexpression within many of them is lower than expected (or even inexistent), which will preclude its detection by means of most conventional functional profiling methods. If the gene-to-function correlation information is used in functional profiling methods, the results obtained improve the ones obtained by conventional enrichment methods.
M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island
Authors: Panchaud Alexandre , Guy Lionel , Collyn François , Haenni Marisa , Nakata Masanobu , Podbielski Andreas , Moreillon Philippe , Roten Claude-Alain H 
Published: April 2009

Abstract

Background
The increasing number of completely sequenced bacterial genomes allows comparing their architecture and genetic makeup. Such new information highlights the crucial role of lateral genetic exchanges in bacterial evolution and speciation.

Results
Here we analyzed the twelve sequenced genomes of Streptococcus pyogenes by a naïve approach that examines the preferential nucleotide usage along the chromosome, namely the usage of G versus C (GC-skew) and T versus A (TA-skew). The cumulative GC-skew plot presented an inverted V-shape composed of two symmetrical linear segments, where the minimum and maximum corresponded to the origin and terminus of DNA replication. In contrast, the cumulative TA-skew presented a V-shape, which segments were interrupted by several steep slopes regions (SSRs), indicative of a different nucleotide composition bias. Each S. pyogenes genome contained up to nine individual SSRs, encompassing all described strain-specific prophages. In addition, each genome contained a similar unique non-phage SSR, the core of which consisted of 31 highly homologous genes. This core includes the M-protein, other mga-related factors and other virulence genes, totaling ten intrinsic virulence genes. In addition to a high content in virulence-related genes and to a peculiar nucleotide bias, this SSR, which is 47 kb-long in a M1GAS strain, harbors direct repeats and a tRNA gene, suggesting a mobile element. Moreover, its complete absence in a M-protein negative group A Streptococcus natural isolate demonstrates that it could be spontaneously lost, but in vitro deletion experiments indicates that its excision occurred at very low rate. The stability of this SSR, combined to its presence in all sequenced S. pyogenes sequenced genome, suggests that it results from an ancient acquisition.

Conclusion
Thus, this non-phagic SSR is compatible with a pathogenicity island, acquired before S. pyogenes speciation. Its potential excision might bear relevance for vaccine development, because vaccines targeting M-protein might select for M-protein-negative variants that still carry other virulence determinants.
Tumor-directed gene therapy in mice using a composite nonviral gene delivery system consisting of the piggyBac transposon and polyethylenimine
Authors: Kang Yu , Zhang Xiaoyan , Jiang Wei , Wu Chaoqun , Chen Chunmei , Zheng Yufang , Gu Jianren , Xu Congjian 
Published: April 2009

Abstract

Background
Compared with viral vectors, nonviral vectors are less immunogenic, more stable, safer and easier to replication for application in cancer gene therapy. However, nonviral gene delivery system has not been extensively used because of the low transfection efficiency and the short transgene expression, especially in vivo. It is desirable to develop a nonviral gene delivery system that can support stable genomic integration and persistent gene expression in vivo. Here, we used a composite nonviral gene delivery system consisting of the piggyBac (PB) transposon and polyethylenimine (PEI) for long-term transgene expression in mouse ovarian tumors.

Methods
A recombinant plasmid PB [Act-RFP, HSV-tk] encoding both the herpes simplex thymidine kinase (HSV-tk) and the monomeric red fluorescent protein (mRFP1) under PB transposon elements was constructed. This plasmid and the PBase plasmid were injected into ovarian cancer tumor xenografts in mice by in vivo PEI system. The antitumor effects of HSV-tk/ganciclovir (GCV) system were observed after intraperitoneal injection of GCV. Histological analysis and TUNEL assay were performed on the cryostat sections of the tumor tissue.

Results
Plasmid construction was confirmed by PCR analysis combined with restrictive enzyme digestion. mRFP1 expression could be visualized three weeks after the last transfection of pPB/TK under fluorescence microscopy. After GCV admission, the tumor volume of PB/TK group was significantly reduced and the tumor inhibitory rate was 81.96% contrasted against the 43.07% in the TK group. Histological analysis showed that there were extensive necrosis and lymphocytes infiltration in the tumor tissue of the PB/TK group but limited in the tissue of control group. TUNEL assays suggested that the transfected cells were undergoing apoptosis after GCV admission in vivo.

Conclusion
Our results show that the nonviral gene delivery system coupling PB transposon with PEI can be used as an efficient tool for gene therapy in ovarian cancer.
Bipolar disorder and dopamine dysfunction: an indirect approach focusing on tardive movement syndromes in a naturalistic setting
Authors: van Rossum Inge , Tenback Diederik , van Os Jim 
Published: April 2009

Abstract

Background
It has been suggested that dopamine dysfunction may play a role in bipolar disorder (BD). An indirect approach to examine this issue was developed, focusing on associations between dopamine proxy measures observed in BD (dopamine-related clinical traits using tardive movement syndromes as dopamine proxy measure of reference).

Methods
3459 eligible bipolar patients were enrolled in an observational study. Incidence rates of tardive movement syndromes (tardive dyskinesia and tardive dystonia; TDD) were examined. A priori hypothesized associations between incident TDD and other dopamine proxies (e.g. prolactin-related adverse effects, bipolar symptoms) were tested over a 2 year follow-up period.

Results
The incidence rate of tardive syndromes was 4.1 %. Incident TDD was independently associated not only with use of antipsychotics, but also with more severe bipolar symptoms, other extrapyramidal symptoms and prolactin-related adverse effects of medication.

Conclusion
Apart from the well-known association with antipsychotics, development of TDD was associated with various other dopamine proxy measures, indirectly supporting the notion of generalised dopamine dysregulation in BD.
Knowledge and attitude on maternal health care among rural-to-urban migrant women in Shanghai, China
Authors: Zhao Qi , Kulane Asli , Gao Yi , Xu Biao 
Published: April 2009

AbstractBackgroundIn China, with the urbanization, women migrated from rural to big cities presented much higher maternal mortality rates than local residents. Health knowledge is one of the key factors enabling women to be aware of their rights and health status in order to seek appropriate health services. This study aims to assess the knowledge and attitude on maternal health care and the contributing factors to being knowledgeable among rural-to-urban migrant women in Shanghai.MethodsA cross-sectional study was conducted in a district center hospital in Shanghai where migrants gathered. Totally 475 rural-to-urban migrant pregnant women were interviewed and completed the self-administered questionnaire after obtaining informed consent.ResultsThe mean score of knowledge on maternal health care was 8.28 out of 12. However, only 36.6% women had attended the required 5 antenatal checks, and 58.3% of the subjects thought financial constrains being the main reason for not attending antenatal care. It was found that higher level of education (OR = 3.3, 95%CI: 1.8–3.8), husbands' Shanghai residence (OR = 4.0, 95%CI: 1.3–12.1) and better family income (OR = 3.3, 95%CI: 1.4–8.2) were associated with better knowledge.ConclusionsRural-to-urban migrant women's unawareness of maternal health service, together with their vulnerable living status, influences their utilization of maternal health care. Tailored maternal health education and accessible services are in demands for this population.
Rasch scaling procedures for informing development of a valid Fetal Surveillance Education Program multiple-choice assessment
Authors: Zoanetti Nathan , Griffin Patrick , Beaves Mark , Wallace Euan M 
Published: April 2009

Abstract

Background
It is widely recognised that deficiencies in fetal surveillance practice continue to contribute significantly to the burden of adverse outcomes. This has prompted the development of evidence-based clinical practice guidelines by the Royal Australian and New Zealand College of Obstetricians and Gynaecologists and an associated Fetal Surveillance Education Program to deliver the associated learning. This article describes initial steps in the validation of a corresponding multiple-choice assessment of the relevant educational outcomes through a combination of item response modelling and expert judgement.

Methods
The Rasch item response model was employed for item and test analysis and to empirically derive the substantive interpretation of the assessment variable. This interpretation was then compared to the hierarchy of competencies specified a priori by a team of eight subject-matter experts. Classical Test Theory analyses were also conducted.

Results
A high level of agreement between the hypothesised and derived variable provided evidence of construct validity. Item and test indices from Rasch analysis and Classical Test Theory analysis suggested that the current test form was of moderate quality. However, the analyses made clear the required steps for establishing a valid assessment of sufficient psychometric quality. These steps included: increasing the number of items from 40 to 50 in the first instance, reviewing ineffective items, targeting new items to specific content and difficulty gaps, and formalising the assessment blueprint in light of empirical information relating item structure to item difficulty.

Conclusion
The application of the Rasch model for criterion-referenced assessment validation with an expert stakeholder group is herein described. Recommendations for subsequent item and test construction are also outlined in this article.
Host immune responses to chlamydial inclusion membrane proteins B and C in Chlamydia trachomatis infected women with or without fertility disorders
Authors: Gupta Rishein , Srivastava Pragya , Vardhan Harsh , Salhan Sudha , Mittal Aruna 
Published: April 2009

AbstractBackgroundWith an increase in the number of putative inclusion membrane proteins (incs) in chlamydial genomes, there is a need for understanding their contribution in host-pathogen interactions. Thus in this study we determined the host mucosal and peripheral immune responses to incs (IncB and IncC) of Chlamydia trachomatis (CT).MethodsFemale patients (n = 296) attending the gynaecology out patient department of Safdarjung hospital, New Delhi were enrolled for the study and were clinically characterized into two groups; CT-positive fertile women (n = 38) and CT-positive women with fertility disorders (n = 29). Uninfected healthy fertile women were enrolled as controls (n = 31). Gene specific PCRs were used for detection of incB and incC genes in endocervical samples of CT-positive patients. ELISA and Western blot assay were used for detection of IgA and IgG antibodies to IncB and IncC in cervical washes and sera. Effect of IncB and IncC stimulation of cervical cells and PBMCs on cellular proliferation and cytotoxity was determined using MTT assay and Lactate dehydrogenase (LDH)-cytotoxicity assay respectively. Modulation of cytokines (Interleukin (IL)-1 Beta, IL-4, IL-5, IL-6, IL-10, Interferon-gamma, IL-12, Tumor Necrosis Factor-alpha and Granulocyte macrophage colony-stimulating factor (GM-CSF)) in cervical cells and PBMCs upon stimulation with IncB and IncC was determined by real-time reverse-transcriptase (RT)-PCR and ELISA. Further, CD4 positive T cells were purified from cervical cells and peripheral blood mononuclear cells (PBMCs) and secreted cytokines (Interferon-gamma and IL-4) were evaluated by ELISPOT and real-time RT-PCR.ResultsUsing MTT assay, significantly high proliferative responses (P < 0.05) were observed in inc-stimulated cervical cells and PBMCs from CT-positive fertile women compared to CT-positive women with fertility disorders and controls. Interferon-gamma, IL-12 and GM-CSF were found to be elevated in inc-stimulated cervical cells and PBMCs of CT-positive fertile women compared to CT-positive women with fertility disorders and controls (P < 0.05). In contrast, IL-1 Beta, IL-4, IL-5, IL-6 and IL-10 levels were found to be higher in CT-positive women with fertility disorders compared to CT-positive fertile women and controls (P < 0.05). Interferon-gamma secreting cells and mRNA expression in inc-stimulated cervical and peripheral CD4 positive T cells were significantly higher (P < 0.05) in CT positive fertile women compared to CT-positive women with fertility disorders.ConclusionOur data overall suggests that CT incs, IncB and IncC modulate host immune responses and may have a role in protection/pathogenesis of genital chlamydial infection in women.
Influencing factors and clinical significance of the metastatic lymph nodes ratio in gastric adenocarcinoma
Authors: Yu Ji-wei , Wu Ju-gang , Zheng Lin-hai , Zhang Biao , Ni Xiao-chun , Li Xiao-qiang , Jiang Bo-jian 
Published: April 2009

Abstract

Background
To investigate influencing factors of the metastatic lymph nodes ratio (MLR) and whether it is related to survival in patients with gastric adenocarcinoma.

Methods
We retrospectively evaluated the clinical features of 121 patients with gastric adenocarcinoma enrolled in our hospital between 2000 and 2007. The receiver operating characteristic (ROC) curve was used to determine the cutoff of the MLR, and CK20 immunohistochemical staining was used to detect micrometastasis of the lymph nodes.

Results
The areas under the ROC curve of MLR used to predict the death of 3-year and 5-year postoperative patients were 0.826 ± 0.053 and 0.896 ± 0.046. Thus MLR = 30.95% and MLR = 3.15% were designated as cutoffs. The MLR was then classified into three groups: MLR1 (MLR<3.15%); MLR2(3.15% ≤ MLR ≤ 30.95%); and MLR3 (MLR>30.95%). We found that patients with a higher MLR demonstrated a much poorer survival period after radical operation than those patients with a lower MLR (P = 0.000). The COX model showed that MLR was an independent prognostic factor (P = 0.000). The MLR could also discriminate between subsets of patients with different 5-year survival periods within the same N stage (P < 0.05). The MLR has been shown to be 34.7% (242/697) by HE staining and 43.5% (303/697) by CK staining (P = 0.001). The clinicopathological characteristics of lymph vessel invasion and the depth of invasion could significantly affect the MLR.

Conclusion
MLR is an independent prognostic factor in gastric cancer. The combined ROC curve with MLR is an effective strategy to produce a curve to predict the 3-year and 5-year survival rates.
Flow cytometric analysis of CK19 expression in the peripheral blood of breast carcinoma patients: relevance for circulating tumor cell detection
Authors: Wang Lili , Wang Yanyan , Liu Yajing , Cheng Min , Wu Xu , Wei Haiming 
Published: April 2009

Abstract

Background
Immunocytochemistry and RT-PCR have been widely used for the detection of circulating tumor cells in patients with breast cancer but their specificity is limited. Our purpose is to utilize a convenient and specific technology to detect circulating tumor cells in breast cancer patients.

Methods
To determine the sensitivity and specificity of our method, A431 cells were serially diluted with human peripheral blood leukocytes and stained with CK19. A total of 73 blood specimens including 25 healthy volunteers and 48 patients with breast carcinoma and benign tumor were tested by flow cytometry to quantify the expression of CK19.

Results
The detectable upper limit of A431 cells was 1 cancer cell among 104 human white blood cells. CK19 was detected in 27% of breast cancer patients but none control gives positive result. The number of cancer cells increased gradually along with the disease stages for it was the least in stage I (0%) and the most in stage IV (1.29%). Fifteen patients were observed during three month chemotherapy after surgery, and most of their CK19 expression levels declined after treatment.

Conclusion
Our research convinces that the detection of CK19 in peripheral blood by flow cytometry is also a specific and feasible method to monitor circulating tumor cells in breast cancer.
Subtelomeric FISH analysis in 76 patients with syndromic developmental delay/intellectual disability
Authors: Belligni Elga F , Biamino Elisa , Molinatto Cristina , Messa Jole , Pierluigi Mauro , Faravelli Francesca , Zuffardi Orsetta , Ferrero Giovanni B , Silengo Margherita Cirillo 
Published: April 2009

Abstract

Background
Intellectual disability affects approximately 1 to 3% of the general population. The etiology is still poorly understood and it is estimated that one-half of the cases are due to genetic factors. Cryptic subtelomeric aberrations have been found in roughly 5 to 7% of all cases.

Methods
We performed a subtelomeric FISH analysis on 76 unrelated children with normal standard karyotype ascertained by developmental delay or intellectual disability, associated with congenital malformations, and/or facial dysmorphisms.

Results
Ten cryptic chromosomal anomalies have been identified in the whole cohort (13,16%), 8 in the group of patients characterized by developmental delay or intellectual disability associated with congenital malformations and facial dysmorphisms, 2 in patients with developmental delay or intellectual disability and facial dysmorphisms only.

Conclusion
We demonstrate that a careful clinical examination is a very useful tool for pre-selection of patients for genomic analysis, clearly enhancing the chromosomal anomaly detection rate. Clinical features of most of these patients are consistent with the corresponding emerging chromosome phenotypes, pointing out these new clinical syndromes associated with specific genomic imbalances.
Propofol: neuroprotection in an in vitro model of traumatic brain injury
Authors: Rossaint Jan , Rossaint Rolf , Weis Joachim , Fries Michael , Rex Steffen , Coburn Mark 
Published: April 2009

Abstract
Introduction
The anaesthetic agent propofol (2,6-diisopropylphenol) has been shown to be an effective neuroprotective agent in different in vitro models of brain injury induced by oxygen and glucose deprivation. We examined its neuroprotective properties in an in vitro model of traumatic brain injury.

Methods
In this controlled laboratory study organotypic hippocampal brain-slice cultures were gained from six- to eight-day-old mice pups. After 14 days in culture, hippocampal brain slices were subjected to a focal mechanical trauma and subsequently treated with different molar concentrations of propofol under both normo- and hypothermic conditions. After 72 hours of incubation, tissue injury assessment was performed using propidium iodide (PI), a staining agent that becomes fluorescent only when it enters damaged cells via perforated cell membranes. Inside the cell, PI forms a fluorescent complex with nuclear DNA.

Results
A dose-dependent reduction of both total and secondary tissue injury could be observed in the presence of propofol under both normo- and hypothermic conditions. This effect was further amplified when the slices were incubated at 32°C after trauma.

Conclusions
When used in combination, the dose-dependent neuroprotective effect of propofol is additive to the neuroprotective effect of hypothermia in an in vitro model of traumatic brain injury.