bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Weighting of Multimodel Ensembles in Seasonal and Short-Range Weather Forecasting
Authors: Casanova Sophie , Ahrens Bodo
Published: May 2009

The performance of multimodel ensemble forecasting depends on the weights given to the different models of the ensemble in the postprocessing of the direct model forecasts. This paper compares the following different weighting methods with or without taking into account the single-model performance: equal weighting of models (EW), simple skill-based weighting (SW), using a simple model performance indicator, and weighting by Bayesian model averaging (BMA). These methods are tested for both short-range weather and seasonal temperature forecasts. The prototype seasonal multimodel ensemble is the Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) system, with four different models and nine forecasts per model. The short-range multimodel prototype system is the European Meteorological Services (EUMETNET) Poor-Man’s Ensemble Prediction System (PEPS), with 14 models and one forecast per model. It is shown that despite the different forecast ranges and spatial scales, the impact of weighting is comparable for both forecast systems and is related to the same ensemble characteristics. In both cases the added value of ensemble forecasting over single-model forecasting increases considerably with the decreasing correlation of the models’ forecast errors, with a relation depending only on the number of models. Also, in both cases a larger spread in model performance increases the added value of combining model forecasts using the performance-based SW or BMA weighting instead of EW. Finally, the more complex BMA weighting adds value over SW only if the best model performs better than the ensemble with EW weighting.
System dynamics approach to immunization healthcare issues in developing countries: a case study of Uganda
Authors: Rwashana Agnes S. , Williams Ddembe W. , Neema Stella
Published: May 2009

This article critically examines the challenges associated with demand for immunization, including the interplay of political, social, economic and technological forces that influence the level of immunization coverage. The article suggests a framework to capture the complex and dynamic nature of the immunization process and tests its effectiveness using a case study of Ugandan healthcare provision. Field study research methods and qualitative system dynamics, a feedback and control theory based modelling approach, are used to capture the complexity and dynamic nature of the immunization process, to enhance a deeper understanding of the immunization organizational environment. A model showing the dynamic influences associated with demand and provision of immunization services, with the aim of facilitating the decision making process as well as healthcare policy interventions, is presented.
Reflections on the use of electronic health record data for clinical research
Authors: West Suzanne L. , Blake Catherine , Zhiwen Liu  , McKoy J. Nikki , Oertel Maryann D. , Carey Timothy S.
Published: May 2009

The adoption of electronic health records (EHRs) offers the potential to improve the delivery, quality, and continuity of clinical care, but widespread use has not yet occurred. In this article, we describe our use of clinical (production) data that were derived from outpatient and inpatient visits at a university teaching hospital for clinical research, a use for which the data and their structure were not originally designed. Similar data exist at many outpatient and inpatient clinical facilities, and we believe that our insights are relevant to electronically captured medical data regardless of their origin. We describe the approaches taken to ensure compliance with the Health Insurance Portability and Accountability Act (HIPAA) and to leverage the vast stores of structured and unstructured data that are currently underused. We conclude by reflecting on what we would have done differently and by making recommendations to streamline the process.
Differential expression of NADPH oxidases in megakaryocytes and their role in polyploidy
Authors: McCrann Donald J. , Eliades Alexia , Makitalo Maria , Matsuno Kuniharu , Ravid Katya
Published: May 2009

Megakaryocytes (MKs) undergo an endomitotic cell cycle, leading to polyploidy. We examined the expression of the flavoproteins and oxidative stress-promoting enzymes, NADPH oxidases (Nox's), in MKs because of their known role in promoting the cell cycle. Although the expression of Nox isoforms varies between cell types, they are induced at the mRNA level by mitogenic stimuli. Western blotting or reverse transcription–polymerase chain reaction of purified mouse MKs isolated from thrombopoietin (TPO)–treated bone marrow (BM) cultures indicated high expression of Nox1, a weak expression of Nox4, and no significant expression of Nox2. Immunofluorescence of freshly isolated MKs confirmed strong expression of Nox1 in one-third of MKs, whereas Nox1 staining was detected in nearly all MKs in TPO-stimulated BM cultures. Treatment of mouse BM cultures with Nox inhibitors resulted in accumulation of MKs with low DNA content levels and significant reduction of higher ploidy MKs. Purified, Nox-inhibited MKs showed a notable decrease in the level of the G1 phase cyclin E, a cyclin associated with MK polyploidy, and its up-regulation restored most of the effect of Nox inhibitors. Hence, this study shows the expression of Nox isoforms in MKs and highlights a potential role of flavoproteins in promoting polyploidization in this lineage.
Apoptosis signal-regulating kinase 1 mediates denbinobin-induced apoptosis in human lung adenocarcinoma cells
Authors: Kuo Chen-Tzu , Chen Bing-Chang , Yu Chung-Chi , Weng Chih-Ming , Hsu Ming-Jen , Chen Chien-Chih , Chen Mei-Chieh , Teng Che-Ming , Pan Shiow-Lin , Bien Mauo-Ying , Shih Chung-Hung , Lin Chien-Huang
Published: May 2009

In the present study, we explore the role of apoptosis signal-regulating kinase 1 (ASK1) in denbinobin-induced apoptosis in human lung adenocarcinoma (A549) cells. Denbinobin-induced cell apoptosis was attenuated by an ASK1 dominant-negative mutant (ASK1DN), two antioxidants (N-acetyl-L-cysteine (NAC) and glutathione (GSH)), a c-Jun N-terminal kinase (JNK) inhibitor (SP600125), and an activator protein-1 (AP-1) inhibitor (curcumin). Treatment of A549 cells with denbinobin caused increases in ASK1 activity and reactive oxygen species (ROS) production, and these effects were inhibited by NAC and GSH. Stimulation of A549 cells with denbinobin caused JNK activation; this effect was markedly inhibited by NAC, GSH, and ASK1DN. Denbinobin induced c-Jun phosphorylation, the formation of an AP-1-specific DNA-protein complex, and Bim expression. Bim knockdown using a bim short interfering RNA strategy also reduced denbinobin-induced A549 cell apoptosis. The denbinobin-mediated increases in c-Jun phosphorylation and Bim expression were inhibited by NAC, GSH, SP600125, ASK1DN, JNK1DN, and JNK2DN. These results suggest that denbinobin might activate ASK1 through ROS production to cause JNK/AP-1 activation, which in turn induces Bim expression, and ultimately results in A549 cell apoptosis.
Molecular characterization of a fungal gene paralogue of the penicillin penDE gene of Penicillium chrysogenum
Authors: García-Estrada Carlos , Vaca Inmaculada , Ullán Ricardo V , van den Berg Marco A , Bovenberg Roel AL , Martín Juan Francisco
Published: May 2009

Background

Penicillium chrysogenum converts isopenicillin N (IPN) into hydrophobic penicillins by means of the peroxisomal IPN acyltransferase (IAT), which is encoded by the penDE gene. In silico analysis of the P. chrysogenum genome revealed the presence of a gene, Pc13g09140, initially described as paralogue of the IAT-encoding penDE gene. We have termed this gene ial because it encodes a protein with high similarity to IAT (IAL for IAT-Like). We have conducted an investigation to characterize the ial gene and to determine the role of the IAL protein in the penicillin biosynthetic pathway.

Results

The IAL contains motifs characteristic of the IAT such as the processing site, but lacks the peroxisomal targeting sequence ARL. Null ial mutants and overexpressing strains indicated that IAL lacks acyltransferase (penicillin biosynthetic) and amidohydrolase (6-APA forming) activities in vivo. When the canonical ARL motif (leading to peroxisomal targeting) was added to the C-terminus of the IAL protein (IALARL) by site-directed mutagenesis, no penicillin biosynthetic activity was detected. Since the IAT is only active after an accurate self-processing of the preprotein into α and β subunits, self-processing of the IAL was tested in Escherichia coli. Overexpression experiments and SDS-PAGE analysis revealed that IAL is also self-processed in two subunits, but despite the correct processing, the enzyme remained inactive in vitro.

Conclusion

No activity related to the penicillin biosynthesis was detected for the IAL. Sequence comparison among the P. chrysogenum IAL, the A. nidulans IAL homologue and the IAT, revealed that the lack of enzyme activity seems to be due to an alteration of the essential Ser309 in the thioesterase active site. Homologues of the ial gene have been found in many other ascomycetes, including non-penicillin producers. Our data suggest that like in A. nidulans, the ial and penDE genes might have been formed from a single ancestral gene that became duplicated during evolution, although a separate evolutive origin for the ial and penDE genes, is also discussed.
DNA methylation-histone modification relationships across the desmin locus in human primary cells
Authors: Lindahl Allen Marianne , Koch Christoph M , Clelland Gayle K , Dunham Ian , Antoniou Michael
Published: May 2009

Background

We present here an extensive epigenetic analysis of a 500 kb region, which encompasses the human desmin gene (DES) and its 5' locus control region (LCR), the only muscle-specific transcriptional regulatory element of this type described to date. These data complement and extend Encyclopaedia of DNA Elements (ENCODE) studies on region ENr133. We analysed histone modifications and underlying DNA methylation patterns in physiologically relevant DES expressing (myoblast/myotube) and non-expressing (peripheral blood mononuclear) primary human cells.

Results

We found that in expressing myoblast/myotube but not peripheral blood mononuclear cell (PBMC) cultures, histone H4 acetylation displays a broadly distributed enrichment across a gene rich 200 kb region whereas H3 acetylation localizes at the transcriptional start site (TSS) of genes. We show that the DES LCR and TSS of DES are enriched with hyperacetylated domains of acetylated histone H3, with H3 lysine 4 di- and tri-methylation (H3K4me2 and me3) exhibiting a different distribution pattern across this locus. The CpG island that extends into the first intron of DES is methylation-free regardless of the gene's expression status and in non-expressing PBMCs is marked with histone H3 lysine 27 tri-methylation (H3K27me3).

Conclusion

Overall, our results constitute the first study correlating patterns of histone modifications and underlying DNA methylation of a muscle-specific LCR and its associated downstream gene region whilst additionally placing this within a much broader genomic context. Our results clearly show that there are distinct patterns of histone H3 and H4 acetylation and H3 methylation at the DES LCR, promoter and intragenic region. In addition, the presence of H3K27me3 at the DES methylation-free CpG only in non-expressing PBMCs may serve to silence this gene in non-muscle tissues. Generally, our work demonstrates the importance of using multiple, physiologically relevant tissue types that represent different expressing/non-expressing states when investigating epigenetic marks and that underlying DNA methylation status should be correlated with histone modification patterns when studying chromatin structure.
Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain
Authors: Liefhebber Jolanda MP , Brandt Bernd W , Broer Rene , Spaan Willy JM , van Leeuwen Hans C
Published: May 2009

Background

Hepatitis C virus (HCV) induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B) has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD) of NS4B is highly conserved in Hepaciviruses, though its function remains unknown.

Results

A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH). The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD) of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system.

Conclusion

Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.
Properties of virion transactivator proteins encoded by primate cytomegaloviruses
Authors: Nicholson Iain P , Sutherland Jane S , Chaudry Tanya N , Blewett Earl L , Barry Peter A , Nicholl Mary Jane , Preston Chris M
Published: May 2009

Background

Human cytomegalovirus (HCMV) is a betaherpesvirus that causes severe disease in situations where the immune system is immature or compromised. HCMV immediate early (IE) gene expression is stimulated by the virion phosphoprotein pp71, encoded by open reading frame (ORF) UL82, and this transactivation activity is important for the efficient initiation of viral replication. It is currently recognized that pp71 acts to overcome cellular intrinsic defences that otherwise block viral IE gene expression, and that interactions of pp71 with the cell proteins Daxx and ATRX are important for this function. A further property of pp71 is the ability to enable prolonged gene expression from quiescent herpes simplex virus type 1 (HSV-1) genomes. Non-human primate cytomegaloviruses encode homologs of pp71, but there is currently no published information that addresses their effects on gene expression and modes of action.

Results

The UL82 homolog encoded by simian cytomegalovirus (SCMV), strain Colburn, was identified and cloned. This ORF, named S82, was cloned into an HSV-1 vector, as were those from baboon, rhesus monkey and chimpanzee cytomegaloviruses. The use of an HSV-1 vector enabled expression of the UL82 homologs in a range of cell types, and permitted investigation of their abilities to direct prolonged gene expression from quiescent genomes. The results show that all UL82 homologs activate gene expression, and that neither host cell type nor promoter target sequence has major effects on these activities. Surprisingly, the UL82 proteins specified by non-human primate cytomegaloviruses, unlike pp71, did not direct long term expression from quiescent HSV-1 genomes. In addition, significant differences were observed in the intranuclear localization of the UL82 homologs, and in their effects on Daxx. Strikingly, S82 mediated the release of Daxx from nuclear domain 10 substructures much more rapidly than pp71 or the other proteins tested. All UL82 homologs stimulated the early release of ATRX from nuclear domain 10.

Conclusion

All of the UL82 homolog proteins analysed activated gene expression, but surprising differences in other aspects of their properties were revealed. The results provide new information on early events in infection with cytomegaloviruses.
Lessons from dynamic cadaver and invasive bone pin studies: do we know how the foot really moves during gait?
Authors: Nester Christopher J
Published: May 2009

Background

This paper provides a summary of a Keynote lecture delivered at the 2009 Australasian Podiatry Conference. The aim of the paper is to review recent research that has adopted dynamic cadaver and invasive kinematics research approaches to better understand foot and ankle kinematics during gait. It is not intended to systematically cover all literature related to foot and ankle kinematics (such as research using surface mounted markers). Since the paper is based on a keynote presentation its focuses on the authors own experiences and work in the main, drawing on the work of others where appropriate

Methods

Two approaches to the problem of accessing and measuring the kinematics of individual anatomical structures in the foot have been taken, (i) static and dynamic cadaver models, and (ii) invasive in‐vivo research. Cadaver models offer the advantage that there is complete access to all the tissues of the foot, but the cadaver must be manipulated and loaded in a manner which replicates how the foot would have performed when in‐vivo. The key value of invasive in‐vivo foot kinematics research is the validity of the description of foot kinematics, but the key difficulty is how generalisable this data is to the wider population.

Results

Through these techniques a great deal has been learnt. We better understand the valuable contribution mid and forefoot joints make to foot biomechanics, and how the ankle and subtalar joints can have almost comparable roles. Variation between people in foot kinematics is high and normal. This includes variation in how specific joints move and how combinations of joints move. The foot continues to demonstrate its flexibility in enabling us to get from A to B via a large number of different kinematic solutions.

Conclusion

Rather than continue to apply a poorly founded model of foot type whose basis is to make all feet meet criteria for the mechanical ‘ideal’ or ‘normal’ foot, we should embrace variation between feet and identify it as an opportunity to develop patient‐specific clinical models of foot function.
Infra-red thermometry: the reliability of tympanic and temporal artery readings for predicting brain temperature after severe traumatic brain injury
Authors: Kirk Danielle , Rainey Timothy , Vail Andy , Childs Charmaine
Published: May 2009

Introduction

Temperature measurement is important during routine neurocritical care especially as differences between brain and systemic temperatures have been observed. The purpose of the study was to determine if infra-red temporal artery thermometry provides a better estimate of brain temperature than tympanic membrane temperature for patients with severe traumatic brain injury.

Methods

Brain parenchyma, tympanic membrane and temporal artery temperatures were recorded every 15–30 min for five hours during the first seven days after admission.

Results

Twenty patients aged 17–76 years were recruited. Brain and tympanic membrane temperature differences ranged from -0.8 °C to 2.5 °C (mean 0.9 °C). Brain and temporal artery temperature differences ranged from -0.7 °C to 1.5 °C (mean 0.3 °C). Tympanic membrane temperature differed from brain temperature by an average of 0.58 °C more than temporal artery temperature measurements (95% CI 0.31 °C to 0.85 °C, P < 0.0001).

Conclusions

At temperatures within the normal to febrile range, temporal artery temperature is closer to brain temperature than is tympanic membrane temperature.
The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress
Authors: Alejandro-Osorio Adriana L , Huebert Dana J , Porcaro Dominic T , Sonntag Megan E , Nillasithanukroh Songdet , Will Jessica L , Gasch Audrey P
Published: May 2009

Background

Yeast responding to stress activate a large gene expression program called the Environmental Stress Response that consists of approximately 600 repressed genes and approximately 300 induced genes. Numerous factors are implicated in regulating subsets of Environmental Stress Response genes; however, a complete picture of Environmental Stress Response regulation remains unclear. We investigated the role of the histone deacetylase Rpd3p, previously linked to the upstream regions of many Environmental Stress Response genes, in producing Environmental Stress Response gene expression changes in response to stress.

Results

We found that the Rpd3-Large complex is required for proper expression of both induced and repressed Environmental Stress Response genes under multiple stress conditions. Cells lacking RPD3 or the Rpd3-Large subunit PHO23 had a major defect in Environmental Stress Response initiation, particularly during the transient phase of expression immediately after stress exposure. Chromatin-immunoprecipitation showed a direct role for Rpd3-Large at representative genes; however, there were different effects on nucleosome occupancy and histone deacetylation at different promoters. Computational analysis implicated regulators that may act with Rpd3p at Environmental Stress Response genes. We provide genetic and biochemical evidence that Rpd3p is required for binding and action of the stress-activated transcription factor Msn2p, although the contribution of these factors differs for different genes.

Conclusions

Our results implicate Rpd3p as an important co-factor in the Environmental Stress Response regulatory network, and suggest the importance of histone modification in producing transient changes in gene expression triggered by stress.
Dose-Modified Oral Chemotherapy in the Treatment of AIDS-Related Non-Hodgkin's Lymphoma in East Africa
Authors: Mwanda Walter O. , Orem Jackson , Fu Pingfu , Banura Cecilia , Kakembo Joweria , Onyango Caren Auma , Ness Anne , Reynolds Sherrie , Johnson John L. , Subbiah Vivek , Bako Jacob , Wabinga Henry , Abdallah Fatuma K. , Meyerson Howard J. , Whalen Christopher C. , Lederman Michael M. , Black Jodi , Ayers Leona W. , Katongole-Mbidde Edward , Remick Scot C.
Published: May 2009

Purpose

Africa is burdened by the AIDS epidemic and attendant increase in HIV/AIDS-related malignancies. Pragmatic approaches to therapeutic intervention could be of great value. Dose-modified oral chemotherapy for AIDS-related non-Hodgkin's lymphoma is one such approach.

Patients and Methods

The oral regimen consisted of lomustine 50 mg/m2on day 1 (cycle 1 only), etoposide 100 mg/m2on days 1 to 3, and cyclophosphamide/procarbazine 50 mg/m2each on days 22 to 26 at 6-week intervals (one cycle) for two total cycles in HIV-infected patients with biopsy-proven non-Hodgkin's lymphoma.

Results

Forty-nine patients (21 in Uganda and 28 in Kenya) were treated. The majority of patients were female (59%) and had a poor performance status (63%); 69% of patients had advanced-stage disease; and 18 patients (37%) had access to antiretroviral therapy. In total, 79.5 cycles of therapy were administered. The regimen was well tolerated, had modest effects (decline) on CD4+lymphocyte counts (P = .077), and had negligible effects on HIV-1 viral replication. Four febrile neutropenia episodes and three treatment-related deaths (6% mortality rate) occurred. The overall objective response rate was 78% (95% CI, 62% to 88%); median follow-up time was 8.2 months (range, 0.1 to 71 months); median event-free and overall survival times were 7.9 months (95% CI, 3.3 to 13.0 months) and 12.3 months (95% CI, 4.9 to 32.4 months), respectively; and 33% of patients survived 5 years.

Conclusion

Dose-modified oral chemotherapy is efficacious, has comparable outcome to that in the United States in the pre–highly active antiretroviral therapy setting, has an acceptable safety profile, and is pragmatic in sub-Saharan Africa. The international collaboration has been highly successful, and subsequent projects should focus on strategies to optimize combination antiretroviral therapy and chemotherapy and follow-up tissue correlative studies.
Japanese-US Common-Arm Analysis of Paclitaxel Plus Carboplatin in Advanced Non–Small-Cell Lung Cancer: A Model for Assessing Population-Related Pharmacogenomics
Authors: Gandara David R. , Kawaguchi Tomoya , Crowley John , Moon James , Furuse Kiyoyuki , Kawahara Masaaki , Teramukai Satoshi , Ohe Yuichiro , Kubota Kaoru , Williamson Stephen K. , Gautschi Oliver , Lenz Heinz Josef , McLeod Howard L. , Lara Primo N. , Coltman Charles Arthur , Fukuoka Masahiro , Saijo Nagahiro , Fukushima Masanori , Mack Philip C.
Published: May 2009

Purpose

To explore whether population-related pharmacogenomics contribute to differences in patient outcomes between clinical trials performed in Japan and the United States, given similar study designs, eligibility criteria, staging, and treatment regimens.

Methods

We prospectively designed and conducted three phase III trials (Four-Arm Cooperative Study, LC00-03, and S0003) in advanced-stage, non–small-cell lung cancer, each with a common arm of paclitaxel plus carboplatin. Genomic DNA was collected from patients in LC00-03 and S0003 who received paclitaxel (225 mg/m2) and carboplatin (area under the concentration-time curve, 6). Genotypic variants of CYP3A4, CYP3A5, CYP2C8, NR1I2-206, ABCB1, ERCC1, and ERCC2 were analyzed by pyrosequencing or by PCR restriction fragment length polymorphism. Results were assessed by Cox model for survival and by logistic regression for response and toxicity.

Results

Clinical results were similar in the two Japanese trials, and were significantly different from the US trial, for survival, neutropenia, febrile neutropenia, and anemia. There was a significant difference between Japanese and US patients in genotypic distribution for CYP3A4*1B (P = .01), CYP3A5*3C (P = .03), ERCC1 118 (P < .0001), ERCC2 K751Q (P < .001), and CYP2C8 R139K (P = .01). Genotypic associations were observed between CYP3A4*1B for progression-free survival (hazard ratio [HR], 0.36; 95% CI, 0.14 to 0.94; P = .04) and ERCC2 K751Q for response (HR, 0.33; 95% CI, 0.13 to 0.83; P = .02). For grade 4 neutropenia, the HR for ABCB1 3425C→T was 1.84 (95% CI, 0.77 to 4.48; P = .19).

Conclusion

Differences in allelic distribution for genes involved in paclitaxel disposition or DNA repair were observed between Japanese and US patients. In an exploratory analysis, genotype-related associations with patient outcomes were observed for CYP3A4*1B and ERCC2 K751Q. This common-arm approach facilitates the prospective study of population-related pharmacogenomics in which ethnic differences in antineoplastic drug disposition are anticipated.
Prevailing Ethical Dilemmas in Terminal Care for Patients With Cancer in Taiwan
Authors: Chiu Tai-Yuan , Hu Wen-Yu , Huang Hsien-Liang , Yao Chien-An , Chen Ching-Yu
Published: May 2009

Purpose

The study aimed to investigate prevailing ethical dilemmas in terminal care for patients with cancer nationwide and identify related factors after the enactment of the Natural Death Act in Taiwan.

Methods

This multicenter study surveyed 800 physicians and nursing staff of oncology wards and hospices through a set questionnaire. A total of 505 respondents (63.1%) who had taken care of patients with terminal cancer were analyzed.

Results

The most frequently encountered ethical dilemmas were truth-telling (mean ± SD = 1.30 ± 0.63; range [never, occasional, often], 0 to 2) and place of care (1.19 ± 0.69), both of which were related to communication issues. Dilemmas related to clinical management were artificial nutrition and hydration (1.04 ± 0.66) and use of antimicrobial agents (0.94 ± 0.70). Logistic regression analyses revealed that positive attitudes about the Natural Death Act was negatively related to the extent of ethical dilemmas (odds ratio, 0.426; 95% CI, 0.256 to 0.710].

Conclusion

The enactment of the Natural Death Act in Taiwan would contribute to improving the quality of end-of-life care, which suggests that this kind of law should be adopted in other countries. Educating cancer care professionals in building positive beliefs toward the act is strongly encouraged.
Rapamycin suppresses seizures and neuronal hypertrophy in a mouse model of cortical dysplasia
Authors: Ljungberg M. Cecilia , Sunnen C. Nicole , Lugo Joaquin N. , Anderson Anne E. , D’Arcangelo Gabriella
Published: May 2009

Malformations of the cerebral cortex known as cortical dysplasia account for the majority of cases of intractable childhood epilepsy. With the exception of the tuberous sclerosis complex, the molecular basis of most types of cortical dysplasia is completely unknown. Currently, there are no good animal models available that recapitulate key features of the disease, such as structural cortical abnormalities and seizures, hindering progress in understanding and treating cortical dysplasia. At the neuroanatomical level, cortical abnormalities may include dyslamination and the presence of abnormal cell types, such as enlarged and misoriented neurons and neuroglial cells. Recent studies in resected human brain tissue suggested that a misregulation of the PI3K (phosphoinositide 3-kinase)-Akt-mTOR (mammalian target of rapamycin) signaling pathway might be responsible for the excessive growth of dysplastic cells in this disease. Here, we characterize neuronal subset (NS)-Pten mutant mice as an animal model of cortical dysplasia. In these mice, the Pten gene, which encodes a suppressor of the PI3K pathway, was selectively disrupted in a subset of neurons by using Cre-loxP technology. Our data indicate that these mutant mice, like cortical dysplasia patients, exhibit enlarged cortical neurons with increased mTOR activity, and abnormal electroencephalographic activity with spontaneous seizures. We also demonstrate that a short-term treatment with the mTOR inhibitor rapamycin strongly suppresses the severity and the duration of the seizure activity. These findings support the possibility that this drug may be developed as a novel antiepileptic treatment for patients with cortical dysplasia and similar disorders.
An ENU-induced mutation in mouse glycyl-tRNA synthetase (GARS) causes peripheral sensory and motor phenotypes creating a model of Charcot-Marie-Tooth type 2D peripheral neuropathy
Authors: Achilli Francesca , Bros-Facer Virginie , Williams Hazel P. , Banks Gareth T. , AlQatari Mona , Chia Ruth , Tucci Valter , Groves Michael , Nickols Carole D. , Seburn Kevin L. , Kendall Rachel , Cader Muhammed Z. , Talbot Kevin , van Minnen Jan , Burgess Robert W. , Brandner Sebastian , Martin Joanne E. , Koltzenburg Martin , Greensmith Linda , Nolan Patrick M. , Fisher Elizabeth M. C.
Published: May 2009

Mutations in the enzyme glycyl-tRNA synthetase (GARS) cause motor and sensory axon loss in the peripheral nervous system in humans, described clinically as Charcot-Marie-Tooth type 2D or distal spinal muscular atrophy type V. Here, we characterise a new mouse mutant, GarsC201R, with a point mutation that leads to a non-conservative substitution within GARS. Heterozygous mice with a C3H genetic background have loss of grip strength, decreased motor flexibility and disruption of fine motor control; this relatively mild phenotype is more severe on a C57BL/6 background. Homozygous mutants have a highly deleterious set of features, including movement difficulties and death before weaning. Heterozygous animals have a reduction in axon diameter in peripheral nerves, slowing of nerve conduction and an alteration in the recovery cycle of myelinated axons, as well as innervation defects. An assessment of GARS levels showed increased protein in 15-day-old mice compared with controls; however, this increase was not observed in 3-month-old animals, indicating that GARS function may be more crucial in younger animals. We found that enzyme activity was not reduced detectably in heterozygotes at any age, but was diminished greatly in homozygous mice compared with controls; thus, homozygous animals may suffer from a partial loss of function. The GarsC201R mutation described here is a contribution to our understanding of the mechanism by which mutations in tRNA synthetases, which are fundamentally important, ubiquitously expressed enzymes, cause axonopathy in specific sets of neurons.
Integrin α9β1 mediates enhanced cell migration through nitric oxide synthase activity regulated by Src tyrosine kinase
Authors: Gupta Shiv K. , Vlahakis Nicholas E.
Published: May 2009

Integrins are important mediators of cell adhesion and migration, which in turn are essential for diverse biological functions, including wound healing and cancer metastasis. The integrin α9β1 is expressed on numerous mammalian tissues and can mediate accelerated cell migration. As the molecular signaling mechanisms that transduce this effect are poorly defined, we investigated the pathways by which activated integrin α9β1 signals migration. We found for the first time that specific ligation of integrin α9β1 rapidly activates Src tyrosine kinase, with concomitant tyrosine phosphorylation of p130Cas and activation of Rac-1. Furthermore, activation of integrin α9β1 also enhanced NO production through activation of inducible nitric oxide synthase (iNOS). Inhibition of Src tyrosine kinase or NOS decreased integrin-α9β1-dependent cell migration. Src appeared to function most proximal in the signaling cascade, in a FAK-independent manner to facilitate iNOS activation and NO-dependent cell migration. The cytoplasmic domain of integrin α9 was crucial for integrin-α9β1-induced Src activation, subsequent signaling events and cell migration. When taken together, our results describe a novel and unique mechanism of coordinated interactions of the integrin α9 cytoplasmic domain, Src tyrosine kinase and iNOS to transduce integrin-α9β1-mediated cell migration.
Robust heat shock induces eIF2α-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast,Saccharomyces cerevisiae
Authors: Groušl Tomáš , Ivanov Pavel , Frydlová Ivana , Vašicová Pavla , Janda Filip , Vojtová Jana , Malínská Kateřina , Malcová Ivana , Nováková Lenka , Janošková Dana , Valášek Leoš , Hašek Jiří
Published: May 2009

Environmental stresses inducing translation arrest are accompanied by the deposition of translational components into stress granules (SGs) serving as mRNA triage sites. It has recently been reported that, in Saccharomyces cerevisiae, formation of SGs occurs as a result of a prolonged glucose starvation. However, these SGs did not contain eIF3, one of hallmarks of mammalian SGs. We have analyzed the effect of robust heat shock on distribution of eIF3a/Tif32p/Rpg1p and showed that it results in the formation of eIF3a accumulations containing other eIF3 subunits, known yeast SG components and small but not large ribosomal subunits and eIF2α/Sui2p. Interestingly, under these conditions, Dcp2p and Dhh1p P-body markers also colocalized with eIF3a. Microscopic analyses of the edc3Δlsm4ΔC mutant demonstrated that different scaffolding proteins are required to induce SGs upon robust heat shock as opposed to glucose deprivation. Even though eIF2α became phosphorylated under these stress conditions, the decrease in polysomes and formation of SGs occurred independently of phosphorylation of eIF2α. We conclude that under specific stress conditions, such as robust heat shock, yeast SGs do contain eIF3 and 40S ribosomes and utilize alternative routes for their assembly.
Linear Regression Models for Predicting Liquefaction during Cyclic Triaxial Testing
Authors: Polito Carmine
Published: May 2009

Cyclic triaxial tests are commonly used in research and engineering practice to evaluate soil liquefaction potential and the factors that influence it. During testing it is necessary to estimate the level of loading to be applied to the specimen. This can be a difficult task unless the engineer has previously acquired a reasonable amount of experience with this type of testing. In order to provide guidance in selecting an appropriate level of loading, a series of four linear regression models have been developed to predict liquefaction in sands and soils with nonplastic silts. The models were separated by the soil type and the method of specimen preparation. These models were developed using the data from over 750 tests collected from the author’s files and the literature. The validity of each model was assessed by examining the statistical parameters of the model, an analysis of residuals, and predictions made using additional data obtained from the literature.
Pregnanolone Sulfate Promotes Desensitization of Activated NMDA Receptors
Authors: Kussius Cassandra L. , Kaur Navjot , Popescu Gabriela K.
Published: May 2009

Neurosteroids are potent neuromodulators which act in part by binding to and modifying the activity of neurotransmitter-gated channels. Pregnanolone sulfate (PAS) is an endogenous neurosteroid that inhibits NMDA receptors and is neuroprotectivein vivo. To delineate the mechanism of NMDA receptor inhibition by pregnanolone sulfate we used kinetic analyses of equilibrium single-channel currents recorded from individual GluN1/GluN2A receptors. Results show that PAS (0.1 mm) reduces single-channel open probability by 50% solely by increasing ∼5-fold the mean time spent by receptors in closed conformations. From these data we derive a kinetic scheme that summarizes the effects of PAS on single channel kinetics, accounts for the PAS effects on macroscopic responses and leads us to propose that PAS inhibits NMDA receptor activity by shifting active receptors into desensitized conformations. These findings highlight the neurosteroid inhibitory site on NMDA receptors as a valuable therapeutic target against excitotoxic pathologies including acute and chronic neurodegeneration.
Regulation of Mn-Superoxide Dismutase Activity and Neuroprotection by STAT3 in Mice after Cerebral Ischemia
Authors: Jung Joo Eun , Kim Gab Seok , Narasimhan Purnima , Song Yun Seon , Chan Pak H.
Published: May 2009

Cerebral ischemia and reperfusion increase superoxide anions (O2·−) in brain mitochondria. Manganese superoxide dismutase (Mn-SOD; SOD2), a primary mitochondrial antioxidant enzyme, scavenges superoxide radicals and its overexpression provides neuroprotection. However, the regulatory mechanism of Mn-SOD expression during cerebral ischemia and reperfusion is still unclear. In this study, we identified the signal transducer and activator of transcription 3 (STAT3) as a transcription factor of the mouse Mn-SOD gene, and elucidated the mechanism of O2·−overproduction after transient focal cerebral ischemia (tFCI). We found that Mn-SOD expression is significantly reduced by reperfusion in the cerebral ischemic brain. We also found that activated STAT3 is usually recruited into the mouse Mn-SOD promoter and upregulates transcription of the mouse Mn-SOD gene in the normal brain. However, at early postreperfusion periods after tFCI, STAT3 was rapidly downregulated, and its recruitment into the Mn-SOD promoter was completely blocked. In addition, transcriptional activity of the mouse Mn-SOD gene was significantly reduced by STAT3 inhibition in primary cortical neurons. Moreover, we found that STAT3 deactivated by reperfusion induces accumulation of O2·−in mitochondria. The loss of STAT3 activity induced neuronal cell death by reducing Mn-SOD expression. Using SOD2−/+ heterozygous knock-out mice, we found that Mn-SOD is a direct target of STAT3 in reperfusion-induced neuronal cell death. Our study demonstrates that STAT3 is a novel transcription factor of the mouse Mn-SOD gene and plays a crucial role as a neuroprotectant in regulating levels of reactive oxygen species in the mouse brain.
Prolonged Withdrawal from Repeated Noncontingent Cocaine Exposure Increases NMDA Receptor Expression and ERK Activity in the Nucleus Accumbens
Authors: Schumann Johanna , Yaka Rami
Published: May 2009

Cocaine-induced changes in glutamatergic synaptic transmission in the ventral tegmental area (VTA) and the nucleus accumbens (NAc) play a key role in cocaine behavioral effects. Activation of ionotropic glutamate receptor NMDA receptor (NMDAR) in the VTA is critical for the development of cocaine psychomotor sensitization. However, the role of NMDAR in the NAc, a brain area critical for the expression of cocaine psychomotor sensitization, remains to be explored. Here, we show that repeated noncontingent cocaine injections increased NAc NMDAR subunits, NR1, NR2A, and NR2B 21 d, but not 1 d, after withdrawal from cocaine. These changes were associated with an increase in the GluR1 subunit of the AMPA receptor. We also found a time-dependent increase in extracellular signal-regulated kinase (ERK) activity which correlated with the increased expression of NMDAR subunits. Furthermore, the increase in GluR1 and ERK activity was blocked after inhibition of NR2B-containing NMDAR during the development of cocaine psychomotor sensitization or when the MEK (mitogen-activated protein/ERK kinase) inhibitor was microinjected into the NAc 21 d after withdrawal from cocaine. Together, these results suggest that the development of cocaine psychomotor sensitization triggers a delayed increase in the expression of NMDAR subunits in the NAc, which in turn enhances the activity of ERK. Enhanced ERK activity drives the increased expression of the GluR1 subunits, which increases the excitability of NAc neurons after prolonged withdrawal from cocaine and results in enduring expression of psychomotor sensitization.
Short-Latency Influence of Medial Frontal Cortex on Primary Motor Cortex during Action Selection under Conflict
Authors: Mars Rogier B. , Klein Miriam C. , Neubert Franz-Xaver , Olivier Etienne , Buch Ethan R. , Boorman Erie D. , Rushworth Matthew F. S.
Published: May 2009

Medial frontal cortex (MFC) is crucial when actions have to be inhibited, reprogrammed, or selected under conflict, but the precise mechanism by which it operates is unclear. Importantly, how and when the MFC influences the primary motor cortex (M1) during action selection is unknown. Using paired-pulse transcranial magnetic stimulation, we investigated functional connectivity between the presupplementary motor area (pre-SMA) part of MFC and M1. We found that functional connectivity increased in a manner dependent on cognitive context: pre-SMA facilitated the motor evoked-potential elicited by M1 stimulation only during action reprogramming, but not when otherwise identical actions were made in the absence of conflict. The effect was anatomically specific to pre-SMA; it was not seen when adjacent brain regions were stimulated. We discuss implications for the anatomical pathways mediating the observed effects.
UBXD4, a UBX-Containing Protein, Regulates the Cell Surface Number and Stability of α3-Containing Nicotinic Acetylcholine Receptors
Authors: Rezvani Khosrow , Teng Yanfen , Pan Yaping , Dani John A. , Lindstrom Jon , García Gras Eduardo A. , McIntosh J. Michael , De Biasi Mariella
Published: May 2009

Adaptor proteins are likely to modulate spatially and temporally the trafficking of a number of membrane proteins, including neuronal nicotinic acetylcholine receptors (nAChRs). A yeast two-hybrid screen identified a novel UBX-containing protein, UBXD4, as one of the cytosolic proteins that interact directly with the α3 and α4 nAChR subunits. The function of UBX-containing proteins is largely unknown. Immunoprecipitation and confocal microscopy confirmed the interaction of UBXD4 with α3-containing nAChRs (α3* nAChRs) expressed in HEK293 cells, PC12 cells, and rat cortical neurons. Overexpression of UBXD4 in differentiated PC12 cells (dPC12) increased nAChR cell surface expression, especially that of the α3β2 subtype. These findings were corroborated by electrophysiology, immunofluorescent staining, and biotinylation of surface receptors. Silencing of UBXD4 led to a significant reduction of α3* nAChRs in rat cortical neurons and dPC12 cells. Biochemical and immunofluorescence studies of endogenous UBXD4 showed that the protein is located in both the ER andcis-Golgi compartments. Our investigations also showed that the α3 subunit is ubiquitinated and that UBXD4 can interfere with its ubiquitination and consequent degradation by the proteasome. Our data suggest that UBXD4 modulates the distribution of α3* nAChRs between specialized intracellular compartments and the plasma membrane. This effect is achieved by controlling the stability of the α3 subunit and, consequently, the number of receptors at the cell surface.
Effects of Restricted Basilar Papillar Lesions and Hair Cell Regeneration on Auditory Forebrain Frequency Organization in Adult European Starlings
Authors: Irvine Dexter R. F. , Brown Mel , Kamke Marc R. , Rubel Edwin W
Published: May 2009

The frequency organization of neurons in the forebrain Field L complex (FLC) of adult starlings was investigated to determine the effects of hair cell (HC) destruction in the basal portion of the basilar papilla (BP) and of subsequent HC regeneration. Conventional microelectrode mapping techniques were used in normal starlings and in lesioned starlings either 2 d or 6–10 weeks after aminoglycoside treatment. Histological examination of the BP and recordings of auditory brainstem evoked responses confirmed massive loss of HCs in the basal portion of the BP and hearing losses at frequencies >2 kHz in starlings tested 2 d after aminoglycoside treatment. In these birds, all neurons in the region of the FLC in which characteristic frequencies (CFs) normally increase from 2 to 6 kHz had CF in the range of 2–4 kHz. The significantly elevated thresholds of responses in this region of altered tonotopic organization indicated that they were the residue of prelesion responses and did not reflect CNS plasticity. In the long-term recovery birds, there was histological evidence of substantial HC regeneration. The tonotopic organization of the high-frequency region of the FLC did not differ from that in normal starlings, but the mean threshold at CF in this frequency range was intermediate between the values in the normal and lesioned short-recovery groups. The recovery of normal tonotopicity indicates considerable stability of the topography of neuronal connections in the avian auditory system, but the residual loss of sensitivity suggests deficiencies in high-frequency HC function.
Membrane Potential Changes in Dendritic Spines during Action Potentials and Synaptic Input
Authors: Palmer Lucy M. , Stuart Greg J.
Published: May 2009

Excitatory input onto many neurons in the brain occurs onto specialized projections called dendritic spines. Despite their potential importance in neuronal function, direct experimental evidence on electrical signaling in dendritic spines is lacking as their small size makes them inaccessible to standard electrophysiological techniques. Here, we investigate electrical signaling in dendritic spines using voltage-sensitive dye imaging in cortical pyramidal neurons during backpropagating action potentials and synaptic input. Backpropagating action potentials were found to fully invade dendritic spines without voltage loss. The voltage change in dendritic spines during synaptic input ranged from a few millivolts up to ∼20 mV. During hyperpolarization of the membrane potential, the amplitude of the synaptic voltage in spines was increased, consistent with the expected change resulting from the increased driving force. This observation suggests that voltage-activated channels do not significantly boost the voltage response in dendritic spines during synaptic input. Finally, we used simulations of our experimental observations in morphologically realistic models to estimate spine neck resistance. These simulations indicated that spine neck resistance ranges up to ∼500 MΩ. Spine neck resistances of this magnitude reduce somatic EPSPs by <15%, indicating that the spine neck is unlikely to act as a physical device to significantly modify synaptic strength.