bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic expression profiling of mature soybean (Glycine max) pollen
Authors: Haerizadeh Farzad , Wong Chui E , Bhalla Prem L , Gresshoff Peter M , Singh Mohan B 
Published: March 2009

AbstractBackgroundPollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant systemsArabidopsis thalianaandOryza sativawhich have tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip®to perform transcriptional profiling on mature bi-cellular soybean pollen.ResultsCompared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean transcripts addressed in this study, 10,299 transcripts (27.46%) are expressed in pollen. Of the pollen-expressed sequences, about 9,489 (92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), signal recognition receptors, transporters, heat shock-related proteins and members of the ubiquitin proteasome proteolytic pathway.ConclusionThis is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. A comparison between transcription factors up-regulated in soybean and those inArabidopsisrevealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.
Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia
Authors: Øyan Anne Margrete , Ånensen Nina , Bø Trond Hellem , Stordrange Laila , Jonassen Inge , Bruserud Øystein , Kalland Karl-Henning , Gjertsen Bjørn Tore 
Published: March 2009

Abstract

Background
The molecular changes in vivo in acute myeloid leukemia cells early after start of conventional genotoxic chemotherapy are incompletely understood, and it is not known if early molecular modulations reflect clinical response.

Methods
The gene expression was examined by whole genome 44 k oligo microarrays and 12 k cDNA microarrays in peripheral blood leukocytes collected from seven leukemia patients before treatment, 2–4 h and 18–24 h after start of chemotherapy and validated by real-time quantitative PCR. Statistically significantly upregulated genes were classified using gene ontology (GO) terms. Parallel samples were examined by flow cytometry for apoptosis by annexin V-binding and the expression of selected proteins were confirmed by immunoblotting.

Results
Significant differential modulation of 151 genes were found at 4 h after start of induction therapy with cytarabine and anthracycline, including significant overexpression of 31 genes associated with p53 regulation. Within 4 h of chemotherapy the BCL2/BAX and BCL2/PUMA ratio were attenuated in proapoptotic direction. FLT3 mutations indicated that non-responders (5/7 patients, 8 versus 49 months survival) are characterized by a unique gene response profile before and at 4 h. At 18–24 h after chemotherapy, the gene expression of p53 target genes was attenuated, while genes involved in chemoresistance, cytarabine detoxification, chemokine networks and T cell receptor were prominent. No signs of apoptosis were observed in the collected cells, suggesting the treated patients as a physiological source of pre-apoptotic cells.

Conclusion
Pre-apoptotic gene expression can be monitored within hours after start of chemotherapy in patients with acute myeloid leukemia, and may be useful in future determination of therapy responders. The low number of patients and the heterogeneity of acute myeloid leukemia limited the identification of gene expression predictive of therapy response. Therapy-induced gene expression reflects the complex biological processes involved in clinical cancer cell eradication and should be explored for future enhancement of therapy.
A pharmaco-economic analysis of patients with schizophrenia switching to generic risperidone involving a possible compliance loss
Authors: Treur Maarten , Heeg Bart , Möller Hans-Jürgen , Schmeding Annette , van Hout Ben 
Published: March 2009

Abstract

Background
As schizophrenia patients are typically suspicious of, or are hostile to changes they may be reluctant to accept generic substitution, possibly affecting compliance. This may counteract drug costs savings due to less symptom control and increased hospitalization risk. Although compliance losses following generic substitution have not been quantified so far, one can estimate the possible health-economic consequences. The current study aims to do so by considering the case of risperidone in Germany.

Methods
An existing DES model was adapted to compare staying on branded risperidone with generic substitution. Differences include the probability of non-compliance and medication costs. Incremental probability of non-compliance after generic substitution was varied between 2.5% and 10%, while generic medication costs were assumed to be 40% lower. Effect of medication price was assessed as well as the effect of applying compliance losses to all treatment settings. The probability of staying on branded risperidone being cost-effective was calculated for various outcomes of a hypothetical study that would investigate non-compliance following generic substitution of risperidone.

Results
If the incremental probability of non-compliance after generic substitution is 2.5%, 5.0%, 7.5% and 10% respectively, incremental effects of staying on branded risperidone are 0.004, 0.007, 0.011 and 0.015 Quality Adjusted Life Years (QALYs). Incremental costs are €757, €343, -€123 and -€554 respectively. Benefits of staying on branded risperidone include improved symptom control and fewer hospitalizations. If generic substitution results in a 5.2% higher probability of non-compliance, the model predicts staying on branded risperidone to be cost-effective (NICE threshold of ₤30,000 per QALY gained). Compliance losses of more than 6.9% makes branded risperidone the dominant alternative. Results are sensitive to the locations at which compliance loss is applied and the price of generic risperidone. The probability that staying on branded risperidone is cost-effective would increase with larger compliance differences and more patients included in the hypothetical study.

Conclusion
The model predicts that it is cost-effective to keep a patient with schizophrenia in Germany on branded risperidone instead of switching him/her to generic risperidone (assuming a 40% reduction in medication costs), if the incremental probability of becoming non-compliant after generic substitution exceeds 5.2%.
Ciliary neurotrophic factor (CNTF) plus soluble CNTF receptor α increases cyclooxygenase-2 expression, PGE2release and interferon-γ-induced CD40 in murine microglia
Authors: Lin Hsiao-Wen , Jain Mohit Raja , Li Hong , Levison Steven W 
Published: March 2009

AbstractBackgroundCiliary neurotrophic factor (CNTF) has been regarded as a potent trophic factor for motor neurons. However, recent studies have shown that CNTF exerts effects on glial cells as well as neurons. For instance, CNTF stimulates astrocytes to secrete FGF-2 and rat microglia to secrete glial cell line-derived neurotrophic factor (GDNF), which suggest that CNTF exerts effects on astrocytes and microglia to promote motor neuron survival indirectly. As CNTF is structurally related to IL-6, which can stimulate immune functions of microglia, we hypothesized that CNTF might exert similar effects.MethodsWe performed 2-D and 1-D proteomic experiments with western blotting and flow cytometry to examine effects of CNTF on primary microglia derived from neonatal mouse brains.ResultsWe show that murine microglia express CNTF receptor α (CNTFRα), which can be induced by interferon-γ (IFNγ). Whereas IL-6 activated STAT-3 and ERK phosphorylation, CNTF did not activate these pathways, nor did CNTF increase p38 MAP kinase phosphorylation. Using 2-D western blot analysis, we demonstrate that CNTF induced the dephosphorylation of a set of proteins and phosphorylation of a different set. Two proteins that were phosphorylated upon CNTF treatment were the LYN substrate-1 and β-tubulin 5. CNTF weakly stimulated microglia, whereas a stronger response was obtained by adding exogenous soluble CNTFRα (sCNTFRα) as has been observed for IL-6. When used in combination, CNTF and sCNTFRα collaborated with IFNγ to increase microglial surface expression of CD40 and this effect was quite pronounced when the microglia were differentiated towards dendritic-like cells. CNTF/sCNTFRα complex, however, failed to increase MHC class II expression beyond that induced by IFNγ. The combination of CNTF and sCNTFRα, but not CNTF alone, enhanced microglial Cox-2 protein expression and PGE2secretion (although CNTF was 30 times less potent than LPS). Surprisingly, Cox-2 production was enhanced 2-fold, rather than being inhibited, upon addition of a gp130 blocking antibody.ConclusionOur studies indicate that CNTF can activate microglia and dendritic-like microglia similar to IL-6; however, unlike IL-6, CNTF does not stimulate the expected signaling pathways in microglia, nor does it appear to require gp130.
Trend tests for the evaluation of exposure-response relationships in epidemiological exposure studies
Authors: Hothorn Ludwig A , Vaeth Michael , Hothorn Torsten 
Published: March 2009

AbstractOne possibility for the statistical evaluation of trends in epidemiological exposure studies is the use of a trend test for data organized in a 2 × k contingency table. Commonly, the exposure data are naturally grouped or continuous exposure data are appropriately categorized. The trend test should be sensitive to any shape of the exposure-response relationship. Commonly, a global trend test only determines whether there is a trend or not. Once a trend is seen it is important to identify the likely shape of the exposure-response relationship. This paper introduces a best contrast approach and an alternative approach based on order-restricted information criteria for the model selection of a particular exposure-response relationship. For the simple change point alternative H1 : π1 = ...= π
q
<πq+1 = ... = π
k
an appropriate approach for the identification of a global trend as well as for the most likely shape of that exposure-response relationship is characterized by simulation and demonstrated for real data examples. Power and simultaneous confidence intervals can be estimated as well. If the conditions are fulfilled to transform the exposure-response data into a 2 × k table, a simple approach for identification of a global trend and its elementary shape is available for epidemiologists.
Long-term surveillance of sulfate-reducing bacteria in highly saline industrial wastewater evaporation ponds
Authors: Ben-Dov Eitan , Kushmaro Ariel , Brenner Asher 
Published: March 2009

Abstract
Abundance and seasonal dynamics of sulfate-reducing bacteria (SRB), in general, and of extreme halophilic SRB (belonging to Desulfocella halophila) in particular, were examined in highly saline industrial wastewater evaporation ponds over a forty one month period. Industrial wastewater was sampled and the presence of SRB was determined by quantitative real-time PCR (qPCR) with a set of primers designed to amplify the dissimilatory sulfite reductase (dsrA) gene. SRB displayed higher abundance during the summer (106–108 targets ml-1) and lower abundance from the autumn-spring (103–105 targets ml-1). However, addition of concentrated dissolved organic matter into the evaporation ponds during winter immediately resulted in a proliferation of SRB, despite the lower wastewater temperature (12–14°C). These results indicate that the qPCR approach can be used for rapid measurement of SRB to provide valuable information about the abundance of SRB in harsh environments, such as highly saline industrial wastewaters. Low level of H2S has been maintained over five years, which indicates a possible inhibition of SRB activity, following artificial salination (≈16% w/v of NaCl) of wastewater evaporation ponds, despite SRB reproduction being detected by qPCR.
Amino acid racemization reveals differential protein turnover in osteoarthritic articular and meniscal cartilages
Authors: Stabler Thomas V , Byers Samuel S , Zura Robert D , Kraus Virginia Byers 
Published: March 2009

Abstract
Introduction
Certain amino acids within proteins have been reported to change from the L form to the D form over time. This process is known as racemization and is most likely to occur in long-lived low-turnover tissues such as normal cartilage. We hypothesized that diseased tissue, as found in an osteoarthritic (OA) joint, would have increased turnover reflected by a decrease in the racemized amino acid content.

Methods
Using high-performance liquid chromatography methods, we quantified the L and D forms of amino acids reported to racemize in vivo on a biological timescale: alanine, aspartate (Asp), asparagine (Asn), glutamate, glutamine, isoleucine, leucine (Leu), and serine (Ser). Furthermore, using a metabolically inactive control material (tooth dentin) and a control material with normal metabolism (normal articular cartilage), we developed an age adjustment in order to make inferences about the state of protein turnover in cartilage and meniscus.

Results
In the metabolically inactive control material (n = 25, ages 13 to 80 years) and the normal metabolizing control material (n = 19, ages 17 to 83 years), only Asp + Asn (Asx), Ser, and Leu showed a significant change (increase) in racemization with age (P < 0.01). The age-adjusted proportions of racemized to total amino acid (D/D+L expressed as a percentage of the control material) for Asx, Ser, and Leu when compared with the normal articular cartilage control were 97%, 74%, and 73% in OA meniscal cartilage and 97%, 70%, and 78% in OA articular cartilage. We also observed lower amino acid content in OA articular and meniscal cartilages compared with normal articular cartilage as well as a loss of total amino acids with age in the OA meniscal but not the OA articular cartilage.

Conclusions
These data demonstrate comparable anabolic responses for non-lesioned OA articular cartilage and OA meniscal cartilage but an excess of catabolism over anabolism for the meniscal cartilage.
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
Authors: Lemmens Karen , De Bie Tijl , Dhollander Thomas , De Keersmaecker Sigrid C , Thijs Inge M , Schoofs Geert , De Weerdt Ami , De Moor Bart , Vanderleyden Jos , Collado-Vides Julio , Engelen Kristof , Marchal Kathleen 
Published: March 2009

AbstractWe present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.
Aripiprazole for schizophrenia
Authors: El-Sayeh H. G. , Morganti C. , Adams C. E. 
Published: March 2009

BackgroundAripiprazole is an atypical antipsychotic that is reported to be
effective in the treatment of schizophrenia.AimsTo investigate the effects of aripiprazole on patients with schizophrenia
and schizophrenia-like psychoses by conducting a systematic review of
randomised controlled trials (RCTs).MethodDatabase and manual searches and direct contact were used to identify
relevant RCTs.ResultsWe included 10 randomised controlled studies (involving a total of 4125
patients), but study attrition was large and the standard of data
reporting was poor. Compared with placebo, aripiprazole treatment was
associated with a significant decrease in relapse rates, increased
compliance with the study protocol, and a decrease in prolactin levels
below the expected values. Compared with risperidone, aripiprazole caused
less elevation of prolactin levels and less prolongation of the average
QTc interval.ConclusionsAripiprazole has been licensed despite the fact that few reliable data on
this drug are publicly available. It may be effective for treatment of
schizophrenia, but in terms of tolerability and global outcomes it shows
little difference from existing antipsychotics.
Health service use by adults with depression: community survey in five European countries
Authors: McCracken Cherie , Dalgard Odd Steffen , Ayuso-Mateos Jose Luis , Casey Patricia , Wilkinson Greg , Lehtinen Ville , Dowrick Christopher 
Published: March 2009

BackgroundLittle is known about patterns of healthcare use by people with depression in Europe.AimsTo examine the use and cost of services by adults with depressive or adjustment disorders in five European countries, and predictive factors.MethodPeople aged 18–65 years with depressive or adjustment disorders (n=427) in Ireland, Finland, Norway, Spain and the UK provided information on predisposition (demographics, social support), enablement (country, urban/rural, social function) and need (symptom severity, perceived health status) for services. Outcome measures were self-reported use Client Services Receipt Interview and costs of general practice, generic, psychiatric or social services in the past 6 months.ResultsLess frequent use was made of generic services in Norway and psychiatric services in the UK. Severity of depression, perceived health status, social functioning and level of social support were significant predictors of use; the number of people able to provide support was positively associated with greater health service use.ConclusionsIndividual participant factors provided greater explanatory power than national differences in healthcare delivery. The association between social support and service use suggests that interventions may be needed for those who lack social support.
Generic clozapine: outcomes after switching
formulations
Authors: Paton Carol 
Published: March 2009

SummaryTwo generic preparations of clozapine have been licensed in the UK. The
bioequivalence of these products compared with Clozaril® has not
been unequivocally demonstrated. Clinical equivalence has also been
questioned. The objective of this study was to determine clinical outcomes
for all patients switched from Clozaril® to a generic formulation
in one mental health service. We examined dosage data and Clinical Global
Impression (CGI) of Severity of Illness scores for 337 patients before and
after the switch and CGI change scores after the switch. There was no
evidence of clinical deterioration or need to use higher dosages. Generic
clozapine is not inferior to Clozaril®.
Simulation of CO2 storage in a heterogeneous aquifer
Authors: Ukaegbu C , Gundogan O , Mackay E , Pickup G , Todd A , Gozalpour F 
Published: March 2009

The fate of carbon dioxide (CO2) injected into a deep saline aquifer depends largely on the geological structure within the aquifer. For example, low permeability layers, such as shales or mudstones, will act as barriers to vertical flow of CO2 gas, whereas high permeability channels may assist the lateral migration of CO2. It is therefore important to include permeability heterogeneity in models for numerical flow simulation As an example of a heterogeneous system, a model of fluvial-incised valley deposits was used. Flow simulations were performed using the generalized equation-of-state model—greenhouse gas software package from Computer Modelling Group, which is a compositional simulator, specially adapted for CO2 storage. The impacts of residual gas and water saturations, gas diffusion in the aqueous phase, hysteresis, and permeability anisotropy on the distribution of CO2 between the gaseous and aqueous phases were examined. Gas diffusion in the aqueous phase was found to significantly enhance solubility trapping of CO2, even when hysteretic trapping of CO2 as a residual phase is taken into account.
Catalytic Use of Strontium Hexamethyldisilazide in the Asymmetric Michael Addition of Malonate to Chalcone Derivatives
Authors: Kobayashi Shu , Yamaguchi Miyuki , Agostinho Magno , Schneider Uwe 
Published: March 2009

Abstract
Strontium hexamethyldisilazide, combined with a chiral bis(sulfonamide) ligand, was found to be very effective for the catalytic asymmetric Michael addition of malonate to chalcone derivatives.
Autoantibodies to Cardiac Troponin Associate with Higher Initial Concentrations and Longer Release of Troponin I in Acute Coronary Syndrome Patients
Authors: Pettersson Kim , Eriksson Susann , Wittfooth Saara , Engström Emilia , Nieminen Markku , Sinisalo Juha 
Published: March 2009

AbstractBackground: Cardiac troponin (cTn) is an established marker of myocardial infarction. Pronounced heterogeneity and the minute amounts released into the circulation constitute significant challenges for cTn detection. Recently, autoantibody formation to cTn was shown to be common and to interfere with immunoassay performance. In this study, we investigated cTn autoantibodies and cardiac troponin I (cTnI) in acute coronary syndrome (ACS) patients over a 1-year period after the index event.Methods: We used a second-generation cTnI assay designed to reduce the interference of cTn autoantibodies. The assay for cTn autoantibodies used 2 anti-cTnI antibodies to capture the ternary cTnI-complex, enabling unrestricted binding of the autoantibodies, which were detected with a labeled antihuman IgG antibody. We analyzed serum samples from 81 non–ST-elevation ACS patients taken at admission and after 1 week and 3 and 12 months.Results: We found 14 cTn autoantibody–positive patients (21%) among the 67 cTnI-positive and none among the 14 cTnI-negative patients. Nine were autoantibody-positive at admission, and 5 became positive at 1 week. Autoantibody signals significantly increased in the 1-week and 3-month samples. At all time points, cTnI was significantly increased in the autoantibody-positive group relative to the negative group. Persistent cTnI elevations at 3 and 12 months were seen in the patients already autoantibody positive at admission.Conclusions: During ACS, patients with cTn autoantibodies have higher cTnI release and therefore larger myocardial damage than patients without autoantibodies. Their cTnI release also lasts longer, at least months. The possible prognostic impact of these observations must be evaluated in larger clinical cohorts.