bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome
Authors: Smith Martin , Bringaud Frédéric , Papadopoulou Barbara 
Published: June 2009

Abstract

Background
We have recently identified two large families of extinct transposable elements termed Short Interspersed DEgenerated Retroposons (SIDERs) in the parasitic protozoan Leishmania major. The characterization of SIDER elements was limited to the SIDER2 subfamily, although members of both subfamilies have been shown to play a role in the regulation of gene expression at the post-transcriptional level. Apparent functional domestication of SIDERs prompted further investigation of their characterization, dissemination and evolution throughout the Leishmania genus, with particular attention to the disregarded SIDER1 subfamily.

Results
Using optimized statistical profiles of both SIDER1 and SIDER2 subgroups, we report the first automated and highly sensitive annotation of SIDERs in the genomes of L. infantum, L. braziliensis and L. major. SIDER annotations were combined to in-silico mRNA extremity predictions to generate a detailed distribution map of the repeat family, hence uncovering an enrichment of antisense-oriented SIDER repeats between the polyadenylation and trans-splicing sites of intergenic regions, in contrast to the exclusive sense orientation of SIDER elements within 3'UTRs. Our data indicate that SIDER elements are quite uniformly dispersed throughout all three genomes and that their distribution is generally syntenic. However, only 47.4% of orthologous genes harbor a SIDER element in all three species. There is evidence for species-specific enrichment of SIDERs and for their preferential association, especially for SIDER2s, with different metabolic functions. Investigation of the sequence attributes and evolutionary relationship of SIDERs to other trypanosomatid retroposons reveals that SIDER1 is a truncated version of extinct autonomous ingi-like retroposons (DIREs), which were functional in the ancestral Leishmania genome.

Conclusion
A detailed characterization of the sequence traits for both SIDER subfamilies unveils major differences. The SIDER1 subfamily is more heterogeneous and shows an evolutionary link with vestigial DIRE retroposons as previously observed for the ingi/RIME and L1Tc/NARTc couples identified in the T. brucei and T. cruzi genomes, whereas no identified DIREs are related to SIDER2 sequences. Although SIDER1s and SIDER2s display equivalent genomic distribution globally, the varying degrees of sequence conservation, preferential genomic disposition, and differential association to orthologous genes allude to an intricate web of SIDER assimilation in these parasitic organisms.
Probing the endosperm gene expression landscape in Brassica napus
Authors: Huang Yi , Chen Liang , Wang Liping , Vijayan Kannan , Phan Sieu , Liu Ziying , Wan Lianglu , Ross Andrew , Xiang Daoquan , Datla Raju , Pan Youlian , Zou Jitao 
Published: June 2009

Abstract

Background
In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and a significant portion of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species such as crucifer oilseeds.

Results
We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop Brassica napus. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that a transcription factor LEAFY COTYLEDON (LEC1) was highly expressed in the endosperm and that the regulatory cascade downstream of LEC1 operates in the endosperm.

Conclusion
The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the LEC1 regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development.
Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae
Authors: Zhang Lijuan , Zhu Zhaoqin , Jing Huaiqi , Zhang Jingyun , Xiong Yanwen , Yan Meiying , Gao Shouyi , Wu Long-Fei , Xu Jianguo , Kan Biao 
Published: June 2009

Abstract

Background
The Twin-arginine translocation (Tat) system serves to translocate folded proteins, including periplasmic enzymes that bind redox cofactors in bacteria. The Tat system is also a determinant of virulence in some pathogenic bacteria, related to pleiotropic effects including growth, motility, and the secretion of some virulent factors. The contribution of the Tat pathway to Vibrio cholerae has not been explored. Here we investigated the functionality of the Tat system in V. cholerae, the etiologic agent of cholera.

Results
In V. cholerae, the tatABC genes function in the translocation of TMAO reductase. Deletion of the tatABC genes led to a significant decrease in biofilm formation, the ability to attach to HT-29 cells, and the ability to colonize suckling mouse intestines. In addition, we observed a reduction in the output of cholera toxin, which may be due to the decreased transcription level of the toxin gene in tatABC mutants, suggesting an indirect effect of the mutation on toxin production. No obvious differences in flagellum biosynthesis and motility were found between the tatABC mutant and the parental strain, showing a variable effect of Tat in different bacteria.

Conclusion
The Tat system contributes to the survival of V. cholerae in the environment and in vivo, and it may be associated with its virulence.
Epidemiologic heterogeneity of common mood and anxiety disorders over the lifecourse in the general population: a systematic review
Authors: Nandi Arijit , Beard John R , Galea Sandro 
Published: June 2009

Abstract

Background
Clinical evidence has long suggested there may be heterogeneity in the patterns and predictors of common mood and anxiety disorders; however, epidemiologic studies have generally treated these outcomes as homogenous entities. The objective of this study was to systematically review the epidemiologic evidence for potential patterns of heterogeneity of common mood and anxiety disorders over the lifecourse in the general population.

Methods
We reviewed epidemiologic studies examining heterogeneity in either the nature of symptoms experienced ("symptom syndromes") or in patterns of symptoms over time ("symptom trajectories"). To be included, studies of syndromes were required to identify distinct symptom subtypes, and studies of trajectories were required to identify distinct longitudinal patterns of symptoms in at least three waves of follow-up. Studies based on clinical or patient populations were excluded.

Results
While research in this field is in its infancy, we found growing evidence that, not only can mood and anxiety disorders be differentiated by symptom syndromes and trajectories, but that the factors associated with these disorders may vary between these subtypes. Whether this reflects a causal pathway, where genetic or environmental factors influence the nature of the symptom or trajectory subtype experienced by an individual, or whether individuals with different subtypes differed in their susceptibility to different environmental factors, could not be determined. Few studies addressed issues of comorbidity or transitions in symptoms between common disorders.

Conclusion
Understanding the diversity of these conditions may help us identify preventable factors that are only associated with some subtypes of these common disorders.
Integrated application of uniform design and least-squares support vector machines to transfection optimization
Authors: Pan Jin-Shui , Hong Mei-Zhu , Zhou Qi-Feng , Cai Jia-Yan , Wang Hua-Zhen , Luo Lin-Kai , Yang De-Qiang , Dong Jing , Shi Hua-Xiu , Ren Jian-Lin 
Published: June 2009

AbstractBackgroundTransfection in mammalian cells based on liposome presents great challenge for biological professionals. To protect themselves from exogenous insults, mammalian cells tend to manifest poor transfection efficiency. In order to gain high efficiency, we have to optimize several conditions of transfection, such as amount of liposome, amount of plasmid, and cell density at transfection. However, this process may be time-consuming and energy-consuming. Fortunately, several mathematical methods, developed in the past decades, may facilitate the resolution of this issue. This study investigates the possibility of optimizing transfection efficiency by using a method referred to as least-squares support vector machine, which requires only a few experiments and maintains fairly high accuracy.ResultsA protocol consists of 15 experiments was performed according to the principle of uniform design. In this protocol, amount of liposome, amount of plasmid, and the number of seeded cells 24 h before transfection were set as independent variables and transfection efficiency was set as dependent variable. A model was deduced from independent variables and their respective dependent variable. Another protocol made up by 10 experiments was performed to test the accuracy of the model. The model manifested a high accuracy. Compared to traditional method, the integrated application of uniform design and least-squares support vector machine greatly reduced the number of required experiments. What's more, higher transfection efficiency was achieved.ConclusionThe integrated application of uniform design and least-squares support vector machine is a simple technique for obtaining high transfection efficiency. Using this novel method, the number of required experiments would be greatly cut down while higher efficiency would be gained. Least-squares support vector machine may be applicable to many other problems that need to be optimized.
Effective and cheap removal of leukocytes and platelets from Plasmodium vivax infected blood
Authors: Sriprawat Kanlaya , Kaewpongsri Supaporn , Suwanarusk Rossarin , Leimanis Mara L , Lek-Uthai Usa , Phyo Aung Pyae , Snounou Georges , Russell Bruce , Renia Laurent , Nosten François 
Published: June 2009

Abstract

Background
Investigations of Plasmodium vivax are restricted to samples collected from infected persons or primates, because this parasite cannot be maintained in in vitro cultures. Contamination of P. vivax isolates with host leukocytes and platelets is detrimental to a range of ex vivo and molecular investigations. Easy-to-produce CF11 cellulose filters have recently provided us with an inexpensive method for the removal of leukocytes and platelets. This contrasted with previous reports of unacceptably high levels of infected red blood cell (IRBC) retention by CF11. The aims of this study were to compare the ability of CF11 cellulose filters and the commercial filter Plasmodipur at removing leukocyte and platelet, and to investigate the retention of P. vivax IRBCs by CF11 cellulose filtration.

Methods and Results
Side-by-side comparison of six leukocyte removal methods using blood samples from five healthy donor showed that CF11 filtration reduced the mean initial leukocyte counts from 9.4 × 103 per μl [95%CI 5.2–13.5] to 0.01 × 103 [95%CI 0.01–0.03]. The CF11 was particularly effective at removing neutrophils. CF11 treatment also reduced initial platelet counts from 211.6 × 103 per μl [95%CI 107.5–315.7] to 0.8 × 103 per μl [95%CI -0.7–2.2]. Analysis of 30 P. vivax blood samples before and after CF11 filtration showed only a minor loss in parasitaemia (≤ 7.1% of initial counts). Stage specific retention of P. vivax IRBCs was not observed.

Conclusion
CF11 filtration is the most cost and time efficient method for the production of leukocyte- and platelet-free P. vivax-infected erythrocytes from field isolates.
An exo-cell assay for examining real-time γ-secretase activity and inhibition
Authors: Shelton Christopher C , Tian Yuan , Frattini Mark G , Li Yue-Ming 
Published: June 2009

Abstract
γ-Secretase is an aspartyl protease that cleaves multiple substrates that are involved in broad biological processes ranging from stem cell development to neurodegeneration. The investigation of γ-secretase has been limited by currently available assays that require genetic or biochemical manipulation in the form of substrate transfection or membrane preparation. Here we report an exo-cell assay that is capable of characterizing γ-secretase activity in any cellular system without limitation. Using a highly active, recombinant substrate this assay can quickly and easily ascertain the status of γ-secretase activity in cell systems and patient samples. We have applied this method to determine the activity of γ-secretase in primary cell samples where transfection and/or membrane isolation are not viable options. Importantly, it allows for the detection of real time γ-secretase activity after inhibitor or drug treatment. The application of this assay to determine the role of γ-secretase in physiological and pathological conditions will greatly facilitate our characterization of this complex protease and help in the development and evaluation of γ-secretase-targeted therapies in Alzheimer's disease or a variety of neoplasms.
The bioactivity of plant extracts against representative bacterial pathogens of the lower respiratory tract
Authors: Bocanegra-García Virgilio , del Rayo Camacho-Corona María , Ramírez-Cabrera Mónica , Rivera Gildardo , Garza-González Elvira 
Published: June 2009

Abstract

Background
Lower respiratory tract infections are a major cause of illness and death. Such infections are common in intensive care units (ICU) and their lethality persists despite advances in diagnosis, treatment and prevention. In Mexico, some plants are used in traditional medicine to treat respiratory diseases or ailments such as cough, bronchitis, tuberculosis and other infections. Medical knowledge derived from traditional societies has motivated searches for new bioactive molecules derived from plants that show potent activity against bacterial pathogens. Therefore, the aim of this study was to evaluate the effect of hexanic, chloroformic (CLO), methanolic (MET) and aqueous extracts from various plants used in Mexican traditional medicine on various microorganisms associated with respiratory disease.

Methods
thirty-five extracts prepared from nine plants used in Mexican traditional medicine for the treatment of respiratory infections were evaluated against 15 control bacterial species and clinical isolates.

Results
Both chloroformic (CLO) and methanolic (MET) extracts of Larrea tridentata were active against Methicillin-resistant S. aureus, B. subtilis and L. monocytogenes. A MET extract of L. tridentata was also active against S. aureus, S. pneumoniae, S. maltophilia, E. faecalis and H. influenzae and the CLO extract was active against A. baumannii. An Aqueous extract of M. acumitata and a MET extract of N. officinale were active against S. pneumoniae. CLO and MET extracts of L. tridentata were active against clinical isolates of S. aureus, S. pneumoniae and E. faecalis.

Conclusion
Overall, our results support the potential use of L. tridentata as a source of antibacterial compounds.
Nerve growth factor and receptor expression in rheumatoid arthritis and spondyloarthritis
Authors: Barthel Christian , Yeremenko Nataliya , Jacobs Roland , Schmidt Reinhold E , Bernateck Michael , Zeidler Henning , Tak Paul-Peter , Baeten Dominique , Rihl Markus 
Published: June 2009

Abstract
Introduction
We previously described the presence of nerve growth factor receptors in the inflamed synovial compartment. Here we investigated the presence of the corresponding nerve growth factors, with special focus on nerve growth factor (NGF).

Methods
mRNA expression levels of four ligands (NGF, brain derived growth factor (BDNF), neurotrophin (NT)-3, NT-4) and their four corresponding receptors (tyrosine kinase (trk) A, trkB, trkC, NGFRp75) were determined in the synovial fluid (SF) cells of 9 patients with rheumatoid arthritis (RA) and 16 with spondyloarthritis (SpA) and compared with 7 osteoarthritis (OA) patients. NGF was also determined in synovial tissue (ST) biopsies of 10 RA and 10 SpA patients. The production of NGF by monocytes and lymphocytes was assessed by flow cytometry of SF cells, synovial tissue derived fibroblast-like synoviocytes (FLS) were assessed by ELISA on culture supernatant.

Results
SF cell analysis revealed a clear BDNF and NGF mRNA expression, with significantly higher NGF expression in RA and SpA patients than in the OA group. NGF expression was higher in ST samples of RA as compared to SpA. Using intracellular FACS analysis, we could demonstrate the presence of the NGF protein in the two inflammatory arthritis groups on both CD3+ T lymphocytes and CD14+ cells, i.e. monocytes/macrophages, whereas cultured FLS did not produce NGF in vitro.

Conclusions
Neurotrophins and especially NGF are expressed in the synovial fluid and tissue of patients with peripheral synovitis. The presence of neurotrophins as well as their receptors, in particular the NGF/trkA-p75 axis in peripheral synovitis warrants further functional investigation of their active involvement in chronic inflammatory arthritis.
The spatial distribution of radiodense breast tissue: a longitudinal study
Authors: Pinto Pereira Snehal M , McCormack Valerie A , Moss Sue M , dos Santos Silva Isabel 
Published: June 2009

Abstract
Introduction
Mammographic breast density is one of the strongest known markers of susceptibility to breast cancer. To date research into density has relied on a single measure (for example, percent density (PD)) summarising the average level of density for the whole breast, with no consideration of how the radiodense tissue may be distributed. This study aims to investigate the spatial distribution of density within the breast using 493 mammographic images from a sample of 165 premenopausal women (~3 medio-lateral oblique views per woman).

Methods
Each breast image was divided into 48 regions and the PD for the whole breast (overall PD) and for each one of its regions (regional PD) was estimated. The spatial autocorrelation (Moran's I value) of regional PD for each image was calculated to investigate spatial clustering of density, whether the degree of clustering varied between a woman's two breasts and whether it was affected by age and other known density correlates.

Results
The median Moran's I value for 165 women was 0.31 (interquartile range: 0.26, 0.37), indicating a clustered pattern. High-density areas tended to cluster in the central regions of the breast, regardless of the level of overall PD, but with considerable between-woman variability in regional PD. The degree of clustering was similar between a woman's two breasts (mean within-woman difference in Moran's I values between left and right breasts = 0.00 (95% confidence interval (CI) = -0.01, 0.01); P = 0.76) and did not change with aging (mean within-woman difference in I values between screens taken on average 8 years apart = 0.01 (95% CI = -0.01, 0.02); P = 0.30). Neither parity nor age at first birth affected the level of spatial autocorrelation of density, but increasing body mass index (BMI) was associated with a decrease in the degree of spatial clustering.

Conclusions
This study is the first to demonstrate that the distribution of radiodense tissue within the breast is spatially autocorrelated, generally with the high-density areas clustering in the central regions of the breast. The degree of clustering was similar within a woman's two breasts and between women, and was little affected by age or reproductive factors although it declined with increasing BMI.
Implementation of the Quality Oncology Practice Initiative at a University Comprehensive Cancer Center
Authors: Blayney Douglas W. , McNiff Kristen , Hanauer David , Miela Gretchen , Markstrom Denise , Neuss Michael 
Published: June 2009

Purpose
The Quality Oncology Practice Initiative (QOPI) is a voluntary program developed by the American Society of Clinical Oncology (ASCO) to aid oncology practices in quality self-assessment. Few academic cancer centers have been QOPI participants.

Methods
We implemented the QOPI process at the University of Michigan Comprehensive Cancer Center, a large, hospital-based academic cancer center, and report our experience with five rounds of data collection. Patient medical records were selected using QOPI-specified procedures and abstracted locally; results were entered into an ASCO-maintained database and analyzed.

Results
Abstractors who were not directly involved with patient care required an average of 62.3 minutes per medical record (4.7 minutes per data element) to abstract data. We found that compliance with quality measures was uniformly high when measures were structured into our electronic medical record. Results from other measures, including those measuring chemotherapy administration in the last 2 weeks of life, were initially markedly different from those reported by other QOPI participants. Our practice changed toward the QOPI national practice norm after a presentation of the results at a faculty research conference. We found that other measures were consistently greater than 90%, including disease-specific diagnosis and treatment measures.

Conclusion
Measuring and showing performance data to physicians was sufficient to change some aspects of physician behavior. Improvement in other measures requires structural practice changes. QOPI, an oncologist-developed system, can be adapted for use in practice improvement at an academic medical center.
Tumour markers requesting pattern with regards to different organizational settings in Italy: a survey of hospital laboratories
Authors: Franceschini Roberta , Trevisiol Chiara , Dittadi Ruggero , Gion Massimo 
Published: June 2009

Background Tumour markers are frequently used in clinical practice and the reason for ordering varies considerably and often seems to be inappropriate. We carried out a survey of Italian laboratories on their current pattern of use. Methods Forty-four laboratories located in health-care institutions with inpatient beds were surveyed about the organizational, clinical and methodological aspects of tumour markers ordering. Results Thirty-one laboratories (70%) filled in and returned the questionnaire. Overall, 977,786 tumour marker tests were scrutinized. The pattern of tumour marker use did not seem to be influenced by the institutional setting, by availability of oncology facilities or by adoption of clinical guidelines. In addition, the information flow from clinicians to the laboratory and vice versa was poor and informal. Conclusions Monitoring tumour marker pattern use can provide valuable information for health-care decision makers, highlighting potential inadequacies in laboratory services but also identifying problems in other areas of health-care delivery that could benefit from educational programmes.