bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein function prediction by massive integration of evolutionary analyses and multiple data sources
Authors: Cozzetto Domenico , Buchan Daniel WA , Bryson Kevin , Jones David T
Published: March 2013

Background

Accurate protein function annotation is a severe bottleneck when utilizing the deluge of high-throughput, next generation sequencing data. Keeping database annotations up-to-date has become a major scientific challenge that requires the development of reliable automatic predictors of protein function. The CAFA experiment provided a unique opportunity to undertake comprehensive 'blind testing' of many diverse approaches for automated function prediction. We report on the methodology we used for this challenge and on the lessons we learnt.

Methods

Our method integrates into a single framework a wide variety of biological information sources, encompassing sequence, gene expression and protein-protein interaction data, as well as annotations in UniProt entries. The methodology transfers functional categories based on the results from complementary homology-based and feature-based analyses. We generated the final molecular function and biological process assignments by combining the initial predictions in a probabilistic manner, which takes into account the Gene Ontology hierarchical structure.

Results

We propose a novel scoring function called COmbined Graph-Information Content similarity (COGIC) score for the comparison of predicted functional categories and benchmark data. We demonstrate that our integrative approach provides increased scope and accuracy over both the component methods and the naïve predictors. In line with previous studies, we find that molecular function predictions are more accurate than biological process assignments.

Conclusions

Overall, the results indicate that there is considerable room for improvement in the field. It still remains for the community to invest a great deal of effort to make automated function prediction a useful and routine component in the toolbox of life scientists. As already witnessed in other areas, community-wide blind testing experiments will be pivotal in establishing standards for the evaluation of prediction accuracy, in fostering advancements and new ideas, and ultimately in recording progress.
Pathway-focused bioassays and transcriptome analysis contribute to a better activity monitoring of complex herbal remedies
Authors: Klein Angela , Wrulich Oliver A , Jenny Marcel , Gruber Peter , Becker Kathrin , Fuchs Dietmar , Gostner Johanna M , Überall Florian
Published: February 2013

Background

Transcriptome analysis in combination with pathway-focused bioassays is suggested to be a helpful approach for gaining deeper insights into the complex mechanisms of action of herbal multicomponent preparations in living cells. The polyherbalism based concept of Tibetan and Ayurvedic medicine considers therapeutic efficacy through multi-target effects. A polyherbal Indo-Tibetan preparation, Padma 28, approved by the Swiss drug authorities (Swissmedic Nr. 58436), was applied to a more detailed dissection of mechanism of action in human hepatoma HepG2 cells. Cell-free and cell-based assays were employed to evaluate the antioxidant capacity. Genome-wide expression profiling was done by applying Human Genome U133 Plus 2.0 Affymetrix arrays. Pathway- and network-oriented analysis elucidated the affected biological processes. The results were validated using reporter gene assays and quantitative real-time PCR.

Results

To reveal the direct radical scavenging effects of the ethanolic extract of the Indo-Tibetan polyherbal remedy Padma 28, anin vitrooxygen radical absorbance capacity assay (ORAC) was employed, which resulted in a peroxyl-radical scavenging activity of 2006 ± 235 μmol TE/g. Furthermore, the antioxidant capacity of Padma 28 was analysed in living HepG2 cells, by measuring its scavenging potential against radical induced ROS. This formulation showed a considerable antioxidant capacity by significantly reducing ROS levels in a dose-dependent manner.

Integrated transcriptome analysis revealed a major influence on phase I and phase II detoxification and the oxidative stress response. Selected target genes, such as heme oxygenase 1, were validated in qPCR experiments. Network analysis showed 18 interrelated networks involved in important biological functions such as drug and bio-molecule metabolism, molecular transport and cellular communication. Some molecules are part of signaling cascades that are active during development and morphogenesis or are involved in pathological conditions and inflammatory response.

Conclusions

The identified molecular targets and pathways suggest several mechanisms that underlie the biological activity of the preparation. Although extrapolation of these findings to thein vivosituation is not possible, the results obtained might be the basis for further investigations and new hypotheses to be tested. This study demonstrates the potential of the combination of focused and unbiased research strategies in the mode of action analysis of multicomponent herbal mixtures.
Horizontal transfer of OC1 transposons in the Tasmanian devil
Authors: Gilbert Clement , Waters Paul , Feschotte Cedric , Schaack Sarah
Published: February 2013

Background

There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurrence, and prolific abundance of these elements in many eukaryotic genomes.

Results

Here, we provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) in the Tasmanian devil, Sarcophilus harrisii. Bioinformatic analyses of OC1 sequences in the Tasmanian devil genome suggest that this transposon infiltrated the common ancestor of the Dasyuridae family ~17 million years ago. This estimate is corroborated by a PCR-based screen for the presence/absence of this family in Tasmanian devils and closely-related species.

Conclusions

This case of HTT is the first to be reported in dasyurids. It brings the number of animal lineages independently invaded by OC1 to 12, and adds a fourth continent to the pandemic-like pattern of invasion of this transposon. In the context of these data, we discuss the evolutionary history of this transposon family and its potential impact on the diversification of marsupials.
A Drosophila functional evaluation of candidates from human genome-wide association studies of type 2 diabetes and related metabolic traits identifies tissue-specific roles for dHHEX
Authors: Pendse Jay , Ramachandran Prasanna V , Na Jianbo , Narisu Narisu , Fink Jill L , Cagan Ross L , Collins Francis S , Baranski Thomas J
Published: February 2013

Background

Genome-wide association studies (GWAS) identify regions of the genome that are associated with particular traits, but do not typically identify specific causative genetic elements. For example, while a large number of single nucleotide polymorphisms associated with type 2 diabetes (T2D) and related traits have been identified by human GWAS, only a few genes have functional evidence to support or to rule out a role in cellular metabolism or dietary interactions. Here, we use a recently developed Drosophila model in which high-sucrose feeding induces phenotypes similar to T2D to assess orthologs of human GWAS-identified candidate genes for risk of T2D and related traits.

Results

Disrupting orthologs of certain T2D candidate genes (HHEX, THADA, PPARG, KCNJ11) led to sucrose-dependent toxicity. Tissue-specific knockdown of the HHEX ortholog dHHEX (CG7056) directed metabolic defects and enhanced lethality; for example, fat-body-specific loss of dHHEX led to increased hemolymph glucose and reduced insulin sensitivity.

Conclusion

Candidate genes identified in human genetic studies of metabolic traits can be prioritized and functionally characterized using a simple Drosophila approach. To our knowledge, this is the first large-scale effort to study the functional interaction between GWAS-identified candidate genes and an environmental risk factor such as diet in a model organism system.
MicroRNA miR-30 family regulates non-attachment growth of breast cancer cells
Authors: Ouzounova Maria , Vuong Tri , Ancey Pierre-Benoit , Ferrand Mylène , Durand Geoffroy , Le-Calvez Kelm Florence , Croce Carlo , Matar Chantal , Herceg Zdenko , Hernandez-Vargas Hector
Published: March 2013

Background

A subset of breast cancer cells displays increased ability to self-renew and reproduce breast cancer heterogeneity. The characterization of these so-called putative breast tumor-initiating cells (BT-ICs) may open the road for novel therapeutic strategies. As microRNAs (miRNAs) control developmental programs in stem cells, BT-ICs may also rely on specific miRNA profiles for their sustained activity. To explore the notion that miRNAs may have a role in sustaining BT-ICs, we performed a comprehensive profiling of miRNA expression in a model of putative BT-ICs enriched by non-attachment growth conditions.

Results

We found breast cancer cells grown under non-attachment conditions display a unique pattern of miRNA expression, highlighted by a marked low expression of miR-30 family members relative to parental cells. We further show that miR-30a regulates non-attachment growth. A target screening revealed that miR-30 family redundantly modulates the expression of apoptosis and proliferation-related genes. At least one of these targets, the anti-apoptotic protein AVEN, was able to partially revert the effect of miR-30a overexpression. Finally, overexpression of miR-30a in vivo was associated with reduced breast tumor progression.

Conclusions

miR30-family regulates the growth of breast cancer cells in non-attachment conditions. This is the first analysis of target prediction in a whole family of microRNAs potentially involved in survival of putative BT-ICs.
CpG oligonucleotides bind TLR9 and RRM-Containing proteins in Atlantic Salmon (Salmo salar)
Authors: Iliev Dimitar B , Skjæveland Ingrid , Jørgensen Jorunn B
Published: March 2013

Background

Bacterial DNA is well-known for its potent immunostimulatory properties which have been attributed to the abundance of CpG dinucleotides within the genomes of prokaryotes. Research has found that mammalian TLR9 is a receptor which mediates the immune response to CpG DNA; however, its functional properties in non-mammalian vertebrates are still poorly characterized. Leukocytes isolated from lower vertebrates, including teleosts, respond to CpG DNA and TLR9 has been identified in many fish species; however, the ligand-binding properties of fish TLR9 have, so far, not been studied. The fact that some vertebrates, like chicken, lack TLR9 and use an alternative molecule (TLR21) as a receptor for CpGs has questioned the functional conservation of TLR9 within vertebrates.

Results

In the current study, TLR9 from Atlantic salmon (SsTLR9) has been found to interact with synthetic oligonucleotides via a CpG-independent but a pH-dependent mechanism. The endogenous receptor, expressed by primary mononuclear phagocytes colocalizes with CpG oligonucleotides (ODNs) in vesicles that appear to be endosomes. When overexpressed in salmonid cell lines, SsTLR9 spontaneously activates ISRE-containing promoters of genes involved in the IFN response; however, the transgenic receptor fails to translocate to CpG-containing endosomes. This indicates that only specific immune cell types have the ability to relocate the receptor to the appropriate cellular compartments where it may become activated by its ligand. In addition, through co-precipitation and mass spectrometry, two salmon proteins - hnRNPA0 and NCOA5, which both contain RNA-binding domains (RRM), were found to bind CpG ODNs, suggesting they may be involved in the CpG response in salmon leukocytes.

Conclusion

The presented data are the first to demonstrate that the DNA-binding properties of TLR9 are conserved between teleosts and mammals. The current study also identifies additional molecules which may function as mediators of the immunostimulatory properties of foreign DNA.
Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli
Authors: Kasari Villu , Mets Toomas , Tenson Tanel , Kaldalu Niilo
Published: March 2013

Background

Bacterial toxin-antitoxin (TA) systems are formed by potent regulatory or suicide factors (toxins) and their short-lived inhibitors (antitoxins). Antitoxins are DNA-binding proteins and auto-repress transcription of TA operons. Transcription of multiple TA operons is activated in temporarily non-growing persister cells that can resist killing by antibiotics. Consequently, the antitoxin levels of persisters must have been dropped and toxins are released of inhibition.

Results

Here, we describe transcriptional cross-activation between different TA systems of Escherichia coli. We find that the chromosomal relBEF operon is activated in response to production of the toxins MazF, MqsR, HicA, and HipA. Expression of the RelE toxin in turn induces transcription of several TA operons. We show that induction of mazEF during amino acid starvation depends on relBE and does not occur in a relBEF deletion mutant. Induction of TA operons has been previously shown to depend on Lon protease which is activated by polyphospate accumulation. We show that transcriptional cross-activation occurs also in strains deficient for Lon, ClpP, and HslV proteases and polyphosphate kinase. Furthermore, we find that toxins cleave the TA mRNA in vivo, which is followed by degradation of the antitoxin-encoding fragments and selective accumulation of the toxin-encoding regions. We show that these accumulating fragments can be translated to produce more toxin.

Conclusion

Transcriptional activation followed by cleavage of the mRNA and disproportionate production of the toxin constitutes a possible positive feedback loop, which can fire other TA systems and cause bistable growth heterogeneity. Cross-interacting TA systems have a potential to form a complex network of mutually activating regulators in bacteria.
Salinity tolerance, Na+ exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism?
Authors: Platten John Damien , Egdane James A , Ismail Abdelbagi M
Published: February 2013

Background

Cultivated rice species (Oryza sativa L. and O. glaberrima Steud.) are generally considered among the crop species most sensitive to salt stress. A handful of lines are known to be tolerant, and a small number of these have been used extensively as donors in breeding programs. However, these donors use many of the same genes and physiological mechanisms to confer tolerance. Little information is available on the diversity of mechanisms used by these species to cope with salt stress, and there is a strong need to identify varieties displaying additional physiological and/or genetic mechanisms to confer higher tolerance.

Results

Here we present data on 103 accessions from O. sativa and 12 accessions from O. glaberrima, many of which are identified as salt tolerant for the first time, showing moderate to high tolerance of high salinity. The correlation of salinity-induced senescence (as judged by the Standard Evaluation System for Rice, or SES, score) with whole-plant and leaf blade Na+ concentrations was high across nearly all accessions, and was almost identical in both O. sativa and O. glaberrima. The association of leaf Na+ concentrations with cultivar-groups was very weak, but association with the OsHKT1;5 allele was generally strong. Seven major and three minor alleles of OsHKT1;5 were identified, and their comparisons with the leaf Na+ concentration showed that the Aromatic allele conferred the highest exclusion and the Japonica allele the least. A number of exceptions to this association with the Oryza HKT1;5 allele were identified; these probably indicate the existence of additional highly effective exclusion mechanisms. In addition, two landraces were identified, one from Thailand and the other from Senegal, that show high tissue tolerance.

Conclusions

Significant variation in salinity tolerance exists within both cultivated Oryza species, and this is the first report of significant tolerance in O. glaberrima. The majority of accessions display a strong quantitative relationship between tolerance and leaf blade Na+ concentration, and thus the major tolerance mechanisms found in these species are those contributing to limiting sodium uptake and accumulation in active leaves. However, there appears to be genetic variation for several mechanisms that affect leaf Na+ concentration, and rare cases of accessions displaying different mechanisms also occur. These mechanisms show great promise for improving salt tolerance in rice over that available from current donors.
Designing and benchmarking the MULTICOM protein structure prediction system
Authors: Li Jilong , Deng Xin , Eickholt Jesse , Cheng Jianlin
Published: February 2013

Background

Predicting protein structure from sequence is one of the most significant and challenging problems in bioinformatics. Numerous bioinformatics techniques and tools have been developed to tackle almost every aspect of protein structure prediction ranging from structural feature prediction, template identification and query-template alignment to structure sampling, model quality assessment, and model refinement. How to synergistically select, integrate and improve the strengths of the complementary techniques at each prediction stage and build a high-performance system is becoming a critical issue for constructing a successful, competitive protein structure predictor.

Results

Over the past several years, we have constructed a standalone protein structure prediction system MULTICOM that combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model generation, model assessment, and model refinement. The system was blindly tested during the ninth Critical Assessment of Techniques for Protein Structure Prediction (CASP9) in 2010 and yielded very good performance. In addition to studying the overall performance on the CASP9 benchmark, we thoroughly investigated the performance and contributions of each component at each stage of prediction.

Conclusions

Our comprehensive and comparative study not only provides useful and practical insights about how to select, improve, and integrate complementary methods to build a cutting-edge protein structure prediction system but also identifies a few new sources of information that may help improve the design of a protein structure prediction system. Several components used in the MULTICOM system are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.
Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study
Authors: Fehr Jan , Glass Tracy R , Louvel Séverine , Hamy François , Hirsch Hans H , von Wyl Viktor , Böni Jürg , Yerly Sabine , Bürgisser Philippe , Cavassini Matthias , Fux Christoph A , Hirschel Bernard , Vernazza Pietro , Martinetti Gladys , Bernasconi Enos , Günthard Huldrych F , Battegay Manuel , Bucher Heiner C , Klimkait Thomas ,   the Swiss HIV Cohort Study
Published: March 2013

Background

Replicative phenotypic HIV resistance testing (rPRT) uses recombinant infectious virus to measure viral replication in the presence of antiretroviral drugs. Due to its high sensitivity of detection of viral minorities and its dissecting power for complex viral resistance patterns and mixed virus populations rPRT might help to improve HIV resistance diagnostics, particularly for patients with multiple drug failures. The aim was to investigate whether the addition of rPRT to genotypic resistance testing (GRT) compared to GRT alone is beneficial for obtaining a virological response in heavily pre-treated HIV-infected patients.

Methods

Patients with resistance tests between 2002 and 2006 were followed within the Swiss HIV Cohort Study (SHCS). We assessed patients' virological success after their antiretroviral therapy was switched following resistance testing. Multilevel logistic regression models with SHCS centre as a random effect were used to investigate the association between the type of resistance test and virological response (HIV-1 RNA <50 copies/mL or ≥1.5log reduction).

Results

Of 1158 individuals with resistance tests 221 with GRT+rPRT and 937 with GRT were eligible for analysis. Overall virological response rates were 85.1% for GRT+rPRT and 81.4% for GRT. In the subgroup of patients with >2 previous failures, the odds ratio (OR) for virological response of GRT+rPRT compared to GRT was 1.45 (95% CI 1.00-2.09). Multivariate analyses indicate a significant improvement with GRT+rPRT compared to GRT alone (OR 1.68, 95% CI 1.31-2.15).

Conclusions

In heavily pre-treated patients rPRT-based resistance information adds benefit, contributing to a higher rate of treatment success.
Respiratory infection of mice with mammalian reoviruses causes systemic infection with age and strain dependent pneumonia and encephalitis
Authors: Gauvin Lianne , Bennett Steffany , Liu Hong , Hakimi Mansoureh , Schlossmacher Michael , Majithia Jay , Brown Earl G
Published: March 2013

Background

Because mammalian reoviruses are isolated from the respiratory tract we modeled the natural history of respiratory infection of adult and suckling mice with T1 Lang (T1L) and T3 Dearing (T3D) reoviruses.

Methods

Adult and suckling Balb/c mice were infected by the intranasal route and were assessed for dose response of disease as well as viral replication in the lung and other organs. Viral antigen was assessed by immunofluorescence and HRP staining of tissue sections and histopathology was assessed on formalin fixed, H + E stained tissue sections.

Results

Intranasal infection of adult mice resulted in fatal respiratory distress for high doses (107 pfu) of T1L but not T3D. In contrast both T1L and T3D killed suckling mice at moderate viral dosages (105 pfu) but differed in clinical symptoms where T1L induced respiratory failure and T3D caused encephalitis. Infections caused transient viremia that resulted in spread to peripheral tissues where disease correlated with virus replication, and pathology. Immunofluorescent staining of viral antigens in the lung showed reovirus infection was primarily associated with alveoli with lesser involvement of bronchiolar epithelium. Immunofluorescent and HRP staining of viral antigens in brain showed infection of neurons by T3D and glial cells by T1L.

Conclusions

These mouse models of reovirus respiratory infection demonstrated age and strain dependent disease that are expected to be relevant to understanding and modulating natural and therapeutic reovirus infections in humans.
CognitionMaster: an object-based image analysis framework
Authors: Wienert Stephan , Heim Daniel , Kotani Manato , Lindequist Björn , Stenzinger Albrecht , Ishii Masaru , Hufnagl Peter , Beil Michael , Dietel Manfred , Denkert Carsten , Klauschen Frederick
Published: February 2013

Background

Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired.

Results

In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept.

Conclusions

We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis.
Distribution of high and low risk HPV types by cytological status: a population based study from Italy
Authors: Giorgi Rossi Paolo , Chini Francesco , Bisanzi Simonetta , Burroni Elena , Carillo Giuseppe , Lattanzi Amedeo , Angeloni Claudio , Scalisi Aurora , Macis Rosalba , Pini Maria T , Capparucci Paola , Guasticchi Gabriella , Carozzi Francesca M ,   the Prevalence Italian Working Group.HPV
Published: March 2013

Background

HPV type distribution by cytological status represents useful information to predict the impact of mass vaccination on screening programs.

Methods

women aged from 25 to 64 who attended cervical cancer screening in five different Italian regions were tested for HPV infection with Hybrid Capture II (HCII) low and high risk probes. Women repeating Pap-test upon unsatisfactory or positive results, or as a post-treatment and post-colposcopy follow-up analysis, were excluded from our study. High risk (HR) HPV positive samples were typed using GP5+/GP6+ primed PCR, followed by Reverse Line Blot for 18 high/intermediate risk HPV types, while low risk (LR) HPV positive samples were tested with type specific primers for HPV6 and HPV11.

Results

3410 women had a valid HCII and Pap-test. The prevalence of HR and LR infections was 7.0% and 3.6%, 29.1% and 13.7%, 68.1% and 31.9%, 60.0% and 0.0%, 65.0% and 12.0%, for negative, ASC-US, L-SIL, ASC-H and H-SIL cytology, respectively. The fraction of ASC-US+ cytology due to HPV 16 and 18 ranged from 11.2 (HPV 16/18 alone) to 15.4% (including HPV 16/18 in co-infection with other virus strains), and that due to HPV 6 and 11 ranged from 0.2% (HPV 6/11 alone) to 0.7% (including HPV 6/11 in co-infection with other LR virus strains).

Conclusions

mass vaccination with bivalent or quadrivalent HPV vaccine would modestly impact on prevalence of abnormal Pap-test in screening.
A real-time PCR assay with improved specificity for detection and discrimination of all clinically relevant Bordetella species by the presence and distribution of three Insertion Sequence elements
Authors: Roorda Lieuwe , Buitenwerf Johannes , Ossewaarde Jacobus M , van der Zee Anneke
Published: March 2013

Background

In Dutch laboratories molecular detection of B. pertussis and B. parapertussis is commonly based on insertion sequences IS 481 and IS 1001, respectively. Both IS elements are more widely spread among Bordetella species. Both Bordetella
holmesii, and B. bronchiseptica can harbour IS 481. Also, IS 1001 is found among B. bronchiseptica. IS 481, and IS 1001 based PCR thus lacks specificity when used for detection of specific Bordetella spp.

Findings

We designed a PCR based on IS 1002, another IS element that is present among Bordetella species, and exploited it as a template in combination with PCR for IS 481, and IS 1001. In combining the PCRs for IS 481, IS 1001, and IS 1002, and including an inhibition control, we were able to detect and discriminate all clinically relevant Bordetella species.

Conclusions

We developed an improved PCR method for specific detection of B. pertussis, B. parapertussis, B. holmesii, and B. bronchiseptica.
The efficacy of incretin therapy in patients with type 2 diabetes undergoing hemodialysis
Authors: Terawaki Yuichi , Nomiyama Takashi , Akehi Yuko , Takenoshita Hiromasa , Nagaishi Ryoko , Tsutsumi Yoko , Murase Kunitaka , Nagasako Hisahiro , Hamanoue Nobuya , Sugimoto Kaoru , Takada Ayako , Ito Kenji , Abe Yasuhiro , Sasatomi Yoshie , Ogahara Satoru , Nakashima Hitoshi , Saito Takao , Yanase Toshihiko
Published: March 2013

Background

Although incretin therapy is clinically available in patients with type 2 diabetes undergoing hemodialysis, no study has yet examined whether incretin therapy is capable of maintaining glycemic control in this group of patients when switched from insulin therapy. In this study, we examined the efficacy of incretin therapy in patients with insulin-treated type 2 diabetes undergoing hemodialysis.

Methods

Ten type 2 diabetic patients undergoing hemodialysis received daily 0.3 mg liraglutide, 50 mg vildagliptin, and 6.25 mg alogliptin switched from insulin therapy on both the day of hemodialysis and the non-hemodialysis day. Blood glucose level was monitored by continuous glucose monitoring. After blood glucose control by insulin, patients were treated with three types of incretin therapy in a randomized crossover manner, with continuous glucose monitoring performed for each treatment.

Results

During treatment with incretin therapies, severe hyperglycemia and ketosis were not observed in any patients. Maximum blood glucose and mean blood glucose on the day of hemodialysis were significantly lower after treatment with liraglutide compared with treatment with alogliptin (p < 0.05), but not with vildagliptin. The standard deviation value, a marker of glucose fluctuation, on the non-hemodialysis day was significantly lower after treatment with liraglutide compared with treatment with insulin and alogliptin (p < 0.05), but not with vildagliptin. Furthermore, the duration of hyperglycemia was significantly shorter after treatment with liraglutide on both the hemodialysis and non-hemodialysis days compared with treatment with alogliptin (p < 0.05), but not with vildagliptin.

Conclusions

The data presented here suggest that patients with type 2 diabetes undergoing hemodialysis and insulin therapy could be treated with incretin therapy in some cases.
Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration
Authors: Weber Beatrice , Heitkam Tony , Holtgräwe Daniela , Weisshaar Bernd , Minoche André E , Dohm Juliane C , Himmelbauer Heinz , Schmidt Thomas
Published: March 2013

Background

Chromoviruses are one of the three genera of Ty3-gypsy long terminal repeat (LTR) retrotransposons, and are present in high copy numbers in plant genomes. They are widely distributed within the plant kingdom, with representatives even in lower plants such as green and red algae. Their hallmark is the presence of a chromodomain at the C-terminus of the integrase. The chromodomain exhibits structural characteristics similar to proteins of the heterochromatin protein 1 (HP1) family, which mediate the binding of each chromovirus type to specific histone variants. A specific integration via the chromodomain has been shown for only a few chromoviruses. However, a detailed study of different chromoviral clades populating a single plant genome has not yet been carried out.

Results

We conducted a comprehensive survey of chromoviruses within the Beta vulgaris (sugar beet) genome, and found a highly diverse chromovirus population, with significant differences in element size, primarily caused by their flanking LTRs. In total, we identified and annotated full-length members of 16 families belonging to the four plant chromoviral clades: CRM, Tekay, Reina, and Galadriel. The families within each clade are structurally highly conserved; in particular, the position of the chromodomain coding region relative to the polypurine tract is clade-specific. Two distinct groups of chromodomains were identified. The group II chromodomain was present in three chromoviral clades, whereas families of the CRM clade contained a more divergent motif. Physical mapping using representatives of all four clades identified a clade-specific integration pattern. For some chromoviral families, we detected the presence of expressed sequence tags, indicating transcriptional activity.

Conclusions

We present a detailed study of chromoviruses, belonging to the four major clades, which populate a single plant genome. Our results illustrate the diversity and family structure of B. vulgaris chromoviruses, and emphasize the role of chromodomains in the targeted integration of these viruses. We suggest that the diverse sets of plant chromoviruses with their different localization patterns might help to facilitate plant-genome organization in a structural and functional manner.
Lack of clinically evident signs of organ failure affects ED treatment of patients with severe sepsis
Authors: Kakebeeke Dirkjan , Vis Alice , de Deckere Ernie RJT , Sandel Maro H , de Groot Bas
Published: February 2013

Background

It is not known whether lack of recognition of organ failure explains the low compliance with the “Surviving Sepsis Campaign” (SSC) guidelines. We evaluated whether compliance was higher in emergency department (ED) sepsis patients with clinically recognizable signs of organ failure compared to patients with only laboratory signs of organ failure.

Methods

Three hundred twenty-three ED patients with severe sepsis and septic shock were prospectively included. Multivariable binary logistic regression was used to assess if clinical and biochemical signs of organ failure were associated with compliance to a SSC-based resuscitation bundle. In addition, two-way analysis of variance was used to investigate the relation between the predisposition, infection, response and organ failure (PIRO) score (3 groups: 1–7, 8–14, 15–24) as a measure of illness severity and time to antibiotics with disposition to ward or ICU as effect modifier.

Results

One hundred twenty-five of 323 included sepsis patients with new-onset organ failure were admitted to the ICU, and in all these patients the SSC resuscitation bundle was started. Respiratory difficulty, hypotension and altered mental status as clinically recognizable signs of organ failure were independent predictors of 100% compliance and not illness severity per se. Corrected ORs (95% CI) were 3.38 (1.08–10.64), 2.37 (1.07–5.23) and 4.18 (1.92–9.09), respectively. Septic ED patients with clinically evident organ failure were more often admitted to the ICU compared to a ward (125 ICU admissions, P < 0.05), which was associated with shorter time to antibiotics [ward: 127 (113–141) min; ICU 94 (80–108) min (P = 0.005)].

Conclusions

The presence of clinically evident compared to biochemical signs of organ failure was associated with increased compliance with a SSC-based resuscitation bundle and admission to the ICU, suggesting that recognition of severe sepsis is an important barrier for successful implementation of quality improvement programs for septic patients. In septic ED patients admitted to the ICU, the time to antibiotics was shorter compared to patients admitted to a normal ward.
The labour supply effects of a partial cash-out of in-kind transfers to single mothers
Authors: Bingley Paul , Walker Ian
Published: March 2013

We estimate a model of labour supply and participation in multiple cash and in-kind welfare programmes. The modeling exploits a reform that affected U.K. single mothers. In-work cash entitlements increased under this reform but eligibility to in-kind child nutrition programmes was lost for some households. When we allow for differences in the costs associated with each welfare programme we find that in-work cash and in-work in-kind transfers both have large positive labour supply effects. There is, however, a utility loss from programme participation which is estimated to be larger for the cash programme than for the child nutrition programmes. Our findings imply that the partial cash out of the in-kind transfers reduced labour supply and suggest that there may be a place in policy portfolios for in-kind programmes despite their “inefficiency”.

JEL Codes

C31, C35, D12, J22
Evaluation of the novel folate receptor ligand [18F]fluoro-PEG-folate for macrophage targeting in a rat model of arthritis
Authors: Gent Yoony YJ , Weijers Karin , Molthoff Carla FM , Windhorst Albert D , Huisman Marc C , Smith Desirée EC , Kularatne Sumith A , Jansen Gerrit , Low Philip S , Lammertsma Adriaan A , van der Laken Conny J
Published: March 2013

Introduction

Detection of (subclinical) synovitis is relevant for both early diagnosis and monitoring of therapy of rheumatoid arthritis (RA). Previously, the potential of imaging (sub)clinical arthritis was demonstrated by targeting the translocator protein in activated macrophages using (R)-[11C]PK11195 and positron emission tomography (PET). Images, however, also showed significant peri-articular background activity. The folate receptor (FR)-β is a potential alternative target for imaging activated macrophages. Therefore, the PET tracer [18F]fluoro-PEG-folate was synthesized and evaluated in both in vitro and ex vivo studies using a methylated BSA induced arthritis model.

Methods

[18F]fluoro-PEG-folate was synthesized in a two-step procedure. Relative binding affinities of non-radioactive fluoro-PEG-folate, folic acid and naturally circulating 5-methyltetrahydrofolate (5-Me-THF) to FR were determined using KB cells with high expression of FR. Both in vivo [18F]fluoro-PEG-folate PET and ex vivo tissue distribution studies were performed in arthritic and normal rats and results were compared with those of the established macrophage tracer (R)-[11C]PK11195.

Results

[18F]fluoro-PEG-folate was synthesized with a purity >97%, a yield of 300 to 1,700 MBq and a specific activity between 40 and 70 GBq/µmol. Relative in vitro binding affinity for FR of F-PEG-folate was 1.8-fold lower than that of folic acid, but 3-fold higher than that of 5-Me-THF . In the rat model, [18F]fluoro-PEG-folate uptake in arthritic knees was increased compared with both contralateral knees and knees of normal rats. Uptake in arthritic knees could be blocked by an excess of glucosamine-folate, consistent with [18F]fluoro-PEG-folate being specifically bound to FR. Arthritic knee-to-bone and arthritic knee-to-blood ratios of [18F]fluoro-PEG-folate were increased compared with those of (R)-[11C]PK11195. Reduction of 5-Me-THF levels in rat plasma to those mimicking human levels increased absolute [18F]fluoro-PEG-folate uptake in arthritic joints, but without improving target-to-background ratios.

Conclusions

The novel PET tracer [18F]fluoro-PEG-folate, designed to target FR on activated macrophages provided improved contrast in a rat model of arthritis compared with the accepted macrophage tracer (R)-[11C]PK11195. These results warrant further exploration of [18F]fluoro-PEG-folate as a putative PET tracer for imaging (sub)clinical arthritis in RA patients.
Cultural factors and sexual dysfunction in clinical practice
Authors: Bhavsar Vishal , Bhugra Dinesh
Published: March 2013

Attitudes to sex and the perceived role of sexual activity are very strongly influenced by cultural values. Culturally determined gender roles influence relationships between different-sex partners, and cultural values affect attitudes towards sexual variation. Cultures define what is deviant and from where help is sought. Through differing patterns of child-rearing, cultures also affect individuals' cognitive development, world views and explanatory models of emotional distress. It is critical that clinicians are aware of the role of culture in defining sexual dysfunction and how cultural factors can be used in initiating treatment as well as in therapeutic engagement and alliance. Although epidemiological data on prevalence of sexual dysfunction across cultures are scanty, it is likely that prevalences vary, as will pathways into care and patterns of help-seeking. In this article we discuss the potential impact of culture on sexual dysfunction, and issues that clinicians, whether in specialist or in general services, need to be aware of in assessing and treating patients who present with sexual dysfunction.
The mental state examination
Authors: Huline-Dickens Sarah
Published: March 2013

The mental state examination is unlike any other assessment in medicine. Karl Jaspers is largely attributed with describing the structure and method of its use. In the centenary year of Jaspers' seminal workGeneral Psychopathology, psychiatry can celebrate the mental state examination as part of its rational and secular heritage.
Clinical dashboard: use in older adult mental health wards
Authors: Daley Kate , Richardson Jonathan , James Ian , Chambers Annette , Corbett David
Published: March 2013

Aims and method

To explore the experiences and attitudes of mental health professionals working in acute elderly care to a new clinical dashboard system. Metrics were identified from the Royal College of Psychiatrists' Accreditation for Inpatient Mental Health Services – Older People (AIMS-OP); these were tracked from baseline to 6 months. A questionnaire was developed and distributed across the three clinical areas involved in the clinical dashboard mental health pilot.

Results

Staff completed the questionnaire 3 months after the initial implementation. At this point the benefits of the introduction of the dashboard were suggested as: improved access to information, increased communication and information-sharing, increased staff awareness, and data quality.

Clinical implications

The introduction of the clinical dashboard in older adult mental health services allowed for better data availability and resulted in better data quality.
Functional Plasticity of the Human Infant β-Cell Exocytotic Phenotype
Authors: Fox Jocelyn E. Manning , Seeberger Karen , Dai Xiao Qing , Lyon James , Spigelman Aliya F. , Kolic Jelena , Hajmrle Catherine , Joseph Jamie W. , Kin Tatsuya , Shapiro A.M. James , Korbutt Gregory , MacDonald Patrick E.
Published: March 2013

Our understanding of adult human β-cells is advancing, but we know little about the function and plasticity of β-cells from infants. We therefore characterized islets and single islet cells from human infants after isolation and culture. Although islet morphology in pancreas biopsies was similar to that in adults, infant islets after isolation and 24–48 hours of culture had less insulin staining, content, and secretion. The cultured infant islets expressed pancreatic and duodenal homeobox 1 and several (Glut1, Cav1.3, Kir6.2) but not all (syntaxin 1A and synaptosomal-associated protein 25) markers of functional islets, suggesting a loss of secretory phenotype in culture. The activity of key ion channels was maintained in isolated infant β-cells, whereas exocytosis was much lower than in adults. We examined whether a functional exocytotic phenotype could be reestablished under conditions thought to promote β-cell differentiation. After a 24- to 28-day expansion and maturation protocol, we found preservation of endocrine markers and hormone expression, an increased proportion of insulin-positive cells, elevated expression of syntaxin 1A and synaptosomal-associated protein 25, and restoration of exocytosis to levels comparable with that in adult β-cells. Thus, human infant islets are prone to loss of their exocytotic phenotype in culture but amenable to experimental approaches aimed at promoting expansion and functional maturation. Control of exocytotic protein expression may be an important mechanism underlying the plasticity of the secretory machinery, an increased understanding of which may lead to improved regenerative approaches to treat diabetes.
PTP1B promotes focal complex maturation, lamellar persistence and directional migration
Authors: Burdisso Juan E. , González Ángela , Arregui Carlos O.
Published: February 2013

Previous findings established that ER-bound PTP1B targets peripheral cell-matrix adhesions and regulates positively cell adhesion to fibronectin. Here we show that PTP1B enhances focal complex lifetime at the lamellipodium base, delaying their turnover and facilitating α-actinin incorporation. We demonstrate the presence of catalytic PTP1BD181A-α-actinin complexes at focal complexes. Kymograph analysis reveals that PTP1B contributes to lamellar protrusion persistence and directional cell migration. Pull down and FRET analysis also shows that PTP1B is required for efficient integrin-dependent downregulation of RhoA and upregulation of Rac1 during spreading. A substrate trap strategy revealed that FAK/Src recruitment and Src activity were essential for the generation of PTP1B substrates in adhesions. PTP1B targets the negative regulatory site of Src (phosphotyrosine 529), paxillin and p130Cas at peripheral cell-matrix adhesions. We postulate that PTP1B modulates more than one pathway required for focal complex maturation and membrane protrusion, including α-actinin-mediated cytoskeletal anchorage, integrin-dependent activation of the FAK/Src signaling pathway, and RhoA and Rac1 GTPase activity. By doing so, PTP1B contributes to coordinate adhesion turnover, lamellar stability and directional cell migration.
Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites
Authors: Larkin Joshua D. , Papantonis Argyris , Cook Peter R.
Published: February 2013

Both the sequence of a promoter and the position of a gene in 3D nuclear space play critical roles in gene regulation, but few studies address their inter-relationship. Using human and viral promoters on minichromosomes and RNA fluorescence in situ hybridization coupled to “high-precision” localization, we show that promoters binding the same transcription factors and responding to the same signaling pathways tend to be co-transcribed in the same transcription factories. We go on to suggest how such spatial co-association might drive co-regulation of genes under the control of similar cis-elements.
Evaluation of a mobile clinical pathology laboratory developed for the home care of pediatric patients following transplantation of peripheral blood precursor cells
Authors: Facco Fabio , Agazzi Alessia , Manfredini Luca , Dallorso Sandro , Melioli Giovanni
Published: February 2013

Background: A mobile clinical pathology laboratory (MoLab) was designed, outfitted and evaluated to improve the turnaround time (TAT) of laboratory tests performed in patients who receive follow-up care at home.

Methods: Full blood counts (FBCs), basic clinical biochemistry tests on blood and urine, and basic coagulation and blood gases were measured using bench-top laboratory analyzers to perform point-of-care tests in a mobile setting. The quality of the results was evaluated on the instruments both while the vehicle was at rest and following movement during the course of routine activity.

Results: The equivalence of the values produced by the point-of-care testing (POCT) and central laboratory (CL) measurement procedures was demonstrated and remained stable after movement in city traffic. The TATs ranged from a few minutes for FBCs to <20 min for extended clinical biochemistry tests.

Conclusions: During the first 6 months of activity, the MoLab assured the provision of laboratory results for home care patients in a matter of minutes. This approach not only allowed for real-time modifications in therapy but also reduced the number of second visits by the home care medical team. Point-of-care tests performed on the MoLab were significantly more expensive than the same tests performed in the CL. However, the savings in patient hospitalization expenses and the reduced costs resulting from fewer second daily visits completely offset the costs of using the MoLab during the first 6-month pilot phase.