bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetic Energy Budget for the Madden–Julian Oscillation in a Multiscale Framework
Authors: Zhou Lei , Sobel Adam H. , Murtugudde Raghu 
Published: March 2012

Abstract
A kinetic energy budget for the Madden–Julian oscillation (MJO) is established in a three-scale framework. The three scales are the zonal mean, the MJO scale with wavenumbers 1–4, and the small scale with wavenumbers larger than 4. In the composite budget, the dominant balance at the MJO scale is between conversion from potential energy and work done by the pressure gradient force (PGF). This balance is consistent with the view that the MJO wind perturbations can be viewed as a quasi-linear response to a slowly varying heat source. A large residual in the upper troposphere suggests that much kinetic energy dissipates there by cumulus friction. Kinetic energy exchange between different scales is not a large component of the composite budget. There is a transfer of kinetic energy from the MJO scale to the small scale; that is, this multiscale interaction appears to damp rather than strengthen the MJO. There is some variation in the relative importance of different terms from one event to the next. In particular, conversion from mean kinetic energy can be important in some events. In a few other events, the influence from the extratropics is pronounced.
Seasonal Variation of the Indonesian Throughflow in Makassar Strait
Authors: Shinoda Toshiaki , Han Weiqing , Metzger E. Joseph , Hurlburt Harley E. 
Published: March 2012

Abstract
The seasonal variation of Indonesian Throughflow (ITF) transport is investigated using ocean general circulation model experiments with the Hybrid Coordinate Ocean Model (HYCOM). Twenty-eight years (1981–2008) of ⅓° Indo-Pacific basin HYCOM simulations and three years (2004–06) from a global HYCOM simulation are analyzed. Both models are able to simulate the seasonal variation of upper-ocean currents and the total transport through Makassar Strait measured by International Nusantara Stratification and Transport (INSTANT) moorings reasonably well. The annual cycle of upper-ocean currents is then calculated from the Indo-Pacific HYCOM simulation. The reduction of southward currents at Makassar Strait during April–May and October–November is evident, consistent with the INSTANT observations. Analysis of the upper-ocean currents suggests that the reduction in ITF transport during April–May and October–November results from the wind variation in the tropical Indian Ocean through the generation of a Wyrtki jet and the propagation of coastal Kelvin waves, while the subsequent recovery during January–March originates from upper-ocean variability associated with annual Rossby waves in the Pacific that are enhanced by western Pacific winds. These processes are also found in the global HYCOM simulation during the period of the INSTANT observations. The model experiments forced with annual-mean climatological wind stress in the Pacific and 3-day mean wind stress in the Indian Ocean show the reduction of southward currents at Makassar Strait during October–November but no subsequent recovery during January–March, confirming the relative importance of wind variations in the Pacific and Indian Oceans for the ITF transport in each season.
Culture, context and therapeutic processes: delivering a parent-child intervention in a remote Aboriginal community
Authors: Mares Sarah , Robinson Gary 
Published: March 2012

Objective: Little is written about the process of delivering mainstream, evidence-based therapeutic interventions for Aboriginal children and families in remote communities. Patterns of interaction between parents and children and expectations about parenting and professional roles and responsibilities vary across cultural contexts. This can be a challenging experience for professionals accustomed to work in urban settings. Language is only a part of cultural difference, and the outsider in a therapeutic group in an Aboriginal community is outside not only in language but also in access to community relationships and a place within those relationships. Method: This paper uses examples from Let’s Start, a therapeutic parent-child intervention to describe the impact of distance, culture and relationships in a remote Aboriginal community, on the therapeutic framework, group processes and relationships. Results: Cultural and contextual factors influence communication, relationships and group processes in a therapeutic group program for children and parents in a remote Aboriginal community. Group leaders from within and from outside the community, are likely to have complementary skills. Conclusions: Cultural and contextual factors influence communication, relationships and group processes in a therapeutic group program for children and parents in a remote Aboriginal community. Group leaders from within and from outside the community, are likely to have complementary skills. Program adaptation, evaluation and staff training and support need to take these factors into account to ensure cultural accessibility without loss of therapeutic fidelity and efficacy.
A lightweight virtual machine monitor for Blue Gene/P
Authors: Stoess Jan , Steinberg Udo , Uhlig Volkmar , Kehne Jens , Appavoo Jonathan , Waterland Amos 
Published: March 2012

In this paper, we present a lightweight, micro-kernel-based virtual machine monitor (VMM) for the Blue Gene/P supercomputer. Our VMM comprises a small µ-kernel with virtualization capabilities and, atop, a user-level VMM component that manages virtual Blue Gene/P cores, memory, and interconnects; we also support running native applications directly atop the µ-kernel. Our design goal is to enable compatibility to standard operating systems such as Linux on BG/P via virtualization, but to also keep the amount of kernel functionality small enough to facilitate shortening the path to applications and lowering operating system noise. Our prototype implementation successfully virtualizes a Blue Gene/P version of Linux with support for Ethernet-based communication mapped onto Blue Gene/P’s collective and torus network devices. Our first experiences and experiments show that our VMM still shows a substantial performance hit, and that support for native application environments is a key requirement towards fully exploiting the capabilities of a supercomputer. Altogether, our approach poses an interesting operating system alternative for supercomputers, providing the convenience of a fully featured commodity software stack, while also promising to deliver the scalability and low latency of an HPC operating system.
Voxelwise analysis of conventional magnetic resonance imaging to predict future disability in early relapsing–remitting multiple sclerosis
Authors: Wybrecht Delphine , Reuter Françoise , Zaaraoui Wafaa , Faivre Anthony , Crespy Lydie , Rico Audrey , Malikova Irina , Confort-Gouny Sylviane , Soulier Elisabeth , Cozzone Patrick J , Pelletier Jean , Ranjeva Jean-Philippe , Audoin Bertrand 
Published: March 2012

Background: The ability of conventional magnetic resonance imaging (MRI) to predict subsequent physical disability and cognitive deterioration after a clinically isolated syndrome (CIS) is weak. Objectives: We aimed to investigate whether conventional MRI changes over 1 year could predict cognitive and physical disability 5 years later in CIS. We performed analyses using a global approach (T2 lesion load, number of T2 lesions), but also a topographic approach. Methods: This study included 38 patients with a CIS. At inclusion, 10 out of 38 patients fulfilled the 2010 revised McDonald’s criteria for the diagnosis of multiple sclerosis. Expanded Disability Status Scale (EDSS) evaluation was performed at baseline, year 1 and year 5, and cognitive evaluation at baseline and year 5. T2-weighted MRI was performed at baseline and year 1. We used voxelwise analysis to analyse the predictive value of lesions location for subsequent disability. Results: Using the global approach, no correlation was found between MRI and clinical data. The occurrence or growth of new lesions in the brainstem was correlated with EDSS changes over the 5 years of follow-up. The occurrence or growth of new lesions in cerebellum, thalami, corpus callosum and frontal lobes over 1 year was correlated with cognitive impairment at 5 years. Conclusion: The assessment of lesion location at the first stage of multiple sclerosis may be of value to predict future clinical disability.
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
Authors: Chang Jia-Ming , Di Tommaso Paolo , Taly Jean-François , Notredame Cedric 
Published: March 2012

Abstract

Background
Transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7.

Methods
We show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension.

Results
Our benchmarking on BAliBASE2-ref7 alpha-helical TMPs shows a significant improvement over the most accurate methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. We also estimated the influence of the database used for homology extension and show that highly non-redundant UniRef databases can be used to obtain similar results at a significantly reduced computational cost over full protein databases. TM-Coffee is part of the T-Coffee package, a web server is also available from http://tcoffee.crg.cat/tmcoffee and a freeware open source code can be downloaded from http://www.tcoffee.org/Packages/Stable/Latest.
Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome
Authors: Cornero Andrea , Acquaviva Massimo , Fardin Paolo , Versteeg Rogier , Schramm Alexander , Eva Alessandra , Bosco Maria Carla , Blengio Fabiola , Barzaghi Sara , Varesio Luigi 
Published: March 2012

AbstractBackgroundNeuroblastoma is the most common pediatric solid tumor of the sympathetic nervous system. Development of improved predictive tools for patients stratification is a crucial requirement for neuroblastoma therapy. Several studies utilized gene expression-based signatures to stratify neuroblastoma patients and demonstrated a clear advantage of adding genomic analysis to risk assessment. There is little overlapping among signatures and merging their prognostic potential would be advantageous. Here, we describe a new strategy to merge published neuroblastoma related gene signatures into a single, highly accurate, Multi-Signature Ensemble (MuSE)-classifier of neuroblastoma (NB) patients outcome.MethodsGene expression profiles of 182 neuroblastoma tumors, subdivided into three independent datasets, were used in the various phases of development and validation of neuroblastoma NB-MuSE-classifier. Thirty three signatures were evaluated for patients' outcome prediction using 22 classification algorithms each and generating 726 classifiers and prediction results. The best-performing algorithm for each signature was selected, validated on an independent dataset and the 20 signatures performing with an accuracy > = 80% were retained.ResultsWe combined the 20 predictions associated to the corresponding signatures through the selection of the best performing algorithm into a single outcome predictor. The best performance was obtained by the Decision Table algorithm that produced the NB-MuSE-classifier characterized by an external validation accuracy of 94%. Kaplan-Meier curves and log-rank test demonstrated that patients with good and poor outcome prediction by the NB-MuSE-classifier have a significantly different survival (p < 0.0001). Survival curves constructed on subgroups of patients divided on the bases of known prognostic marker suggested an excellent stratification of localized and stage 4s tumors but more data are needed to prove this point.ConclusionsThe NB-MuSE-classifier is based on an ensemble approach that merges twenty heterogeneous, neuroblastoma-related gene signatures to blend their discriminating power, rather than numeric values, into a single, highly accurate patients' outcome predictor. The novelty of our approach derives from the way to integrate the gene expression signatures, by optimally associating them with a single paradigm ultimately integrated into a single classifier. This model can be exported to other types of cancer and to diseases for which dedicated databases exist.
An ICT infrastructure to integrate clinical and molecular data in oncology research
Authors: Segagni Daniele , Tibollo Valentina , Dagliati Arianna , Zambelli Alberto , Priori Silvia G , Bellazzi Riccardo 
Published: March 2012

Abstract

Background
The ONCO-i2b2 platform is a bioinformatics tool designed to integrate clinical and research data and support translational research in oncology. It is implemented by the University of Pavia and the IRCCS Fondazione Maugeri hospital (FSM), and grounded on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) research center. I2b2 has delivered an open source suite based on a data warehouse, which is efficiently interrogated to find sets of interesting patients through a query tool interface.

Methods
Onco-i2b2 integrates data coming from multiple sources and allows the users to jointly query them. I2b2 data are then stored in a data warehouse, where facts are hierarchically structured as ontologies. Onco-i2b2 gathers data from the FSM pathology unit (PU) database and from the hospital biobank and merges them with the clinical information from the hospital information system.
Our main effort was to provide a robust integrated research environment, giving a particular emphasis to the integration process and facing different challenges, consecutively listed: biospecimen samples privacy and anonymization; synchronization of the biobank database with the i2b2 data warehouse through a series of Extract, Transform, Load (ETL) operations; development and integration of a Natural Language Processing (NLP) module, to retrieve coded information, such as SNOMED terms and malignant tumors (TNM) classifications, and clinical tests results from unstructured medical records. Furthermore, we have developed an internal SNOMED ontology rested on the NCBO BioPortal web services.

Results
Onco-i2b2 manages data of more than 6,500 patients with breast cancer diagnosis collected between 2001 and 2011 (over 390 of them have at least one biological sample in the cancer biobank), more than 47,000 visits and 96,000 observations over 960 medical concepts.

Conclusions
Onco-i2b2 is a concrete example of how integrated Information and Communication Technology architecture can be implemented to support translational research. The next steps of our project will involve the extension of its capabilities by implementing new plug-in devoted to bioinformatics data analysis as well as a temporal query module.
Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS
Authors: Lista Florigio , Reubsaet Frans AG , De Santis Riccardo , Parchen Rene R , de Jong Ad L , Kieboom Jasper , van der Laaken Anton L , Voskamp-Visser Ingrid AI , Fillo Silvia , Jansen Hugo-Jan , Van der Plas Jan , Paauw Armand 
Published: March 2012

Abstract

Background
The genus Brucella contains highly infectious species that are classified as biological threat agents. The timely detection and identification of the microorganism involved is essential for an effective response not only to biological warfare attacks but also to natural outbreaks. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is a rapid method for the analysis of biological samples. The advantages of this method, compared to conventional techniques, are rapidity, cost-effectiveness, accuracy and suitability for the high-throughput identification of bacteria. Discrepancies between taxonomy and genetic relatedness on the species and biovar level complicate the development of detection and identification assays.

Results
In this study, the accurate identification of Brucella species using MALDI-TOF-MS was achieved by constructing a Brucella reference library based on multilocus variable-number tandem repeat analysis (MLVA) data. By comparing MS-spectra from Brucella species against a custom-made MALDI-TOF-MS reference library, MALDI-TOF-MS could be used as a rapid identification method for Brucella species. In this way, 99.3% of the 152 isolates tested were identified at the species level, and B. suis biovar 1 and 2 were identified at the level of their biovar. This result demonstrates that for Brucella, even minimal genomic differences between these serovars translate to specific proteomic differences.

Conclusions
MALDI-TOF-MS can be developed into a fast and reliable identification method for genetically highly related species when potential taxonomic and genetic inconsistencies are taken into consideration during the generation of the reference library.
Pharmacist provision of primary health care: a modified Delphi validation of pharmacists' competencies
Authors: Kennie-Kaulbach Natalie , Farrell Barbara , Ward Natalie , Johnston Sharon , Gubbels Ashley , Eguale Tewodros , Dolovich Lisa , Jorgenson Derek , Waite Nancy , Winslade Nancy 
Published: March 2012

AbstractBackgroundPharmacists have expanded their roles and responsibilities as a result of primary health care reform. There is currently no consensus on the core competencies for pharmacists working in these evolving practices. The aim of this study was to develop and validate competencies for pharmacists' effective performance in these roles, and in so doing, document the perceived contribution of pharmacists providing collaborative primary health care services.MethodsUsing a modified Delphi process including assessing perception of the frequency and criticality of performing tasks, we validated competencies important to primary health care pharmacists practising across Canada.ResultsTen key informants contributed to competency drafting; thirty-three expert pharmacists replied to a second round survey. The final primary health care pharmacist competencies consisted of 34 elements and 153 sub-elements organized in seven CanMeds-based domains. Highest importance rankings were allocated to the domains of care provider and professional, followed by communicator and collaborator, with the lower importance rankings relatively equally distributed across the manager, advocate and scholar domains.ConclusionsExpert pharmacists working in primary health care estimated their most important responsibilities to be related to direct patient care. Competencies that underlie and are required for successful fulfillment of these patient care responsibilities, such as those related to communication, collaboration and professionalism were also highly ranked. These ranked competencies can be used to help pharmacists understand their potential roles in these evolving practices, to help other health care professionals learn about pharmacists' contributions to primary health care, to establish standards and performance indicators, and to prioritize supports and education to maximize effectiveness in this role.
Intravenous non-high-dose pantoprazole is equally effective as high-dose pantoprazole in preventing rebleeding among low risk patients with a bleeding peptic ulcer after initial endoscopic hemostasis
Authors: Liang Chih-Ming , Lee Jyong-Hong , Kuo Yuan-Hung , Wu Keng-Liang , Chiu Yi-Chun , Chou Yeh-Pin , Hu Ming-Luen , Tai Wei-Chen , Chiu King-Wah , Hu Tsung-Hui , Chuah Seng-Kee 
Published: March 2012

Abstract

Background
Many studies have shown that high-dose proton-pumps inhibitors (PPI) do not further reduce the rate of rebleeding compared to non-high-dose PPIs but we do not know whether intravenous non-high-dose PPIs reduce rebleeding rates among patients at low risk (Rockall score < 6) or among those at high risk, both compared to high-dose PPIs. This retrospective case-controlled study aimed to identify the subgroups of these patients that might benefit from treatment with non-high-dose PPIs.

Methods
Subjects who received high dose and non-high-dose pantoprazole for confirmed acute PU bleeding at a tertiary referral hospital were enrolled (n = 413). They were divided into sustained hemostasis (n = 324) and rebleeding groups (n = 89). The greedy method was applied to allow treatment-control random matching (1:1). Patients were randomly selected from the non-high-dose and high-dose PPI groups who had a high risk peptic ulcer bleeding (n = 104 in each group), and these were then subdivided to two subgroups (Rockall score ≥ 6 vs. < 6, n = 77 vs. 27).

Results
An initial low hemoglobin level, serum creatinine level, and Rockall score were independent factors associated with rebleeding. After case-control matching, the significant variables between the non-high-dose and high-dose PPI groups for a Rockall score ≥ 6 were the rebleeding rate, and the amount of blood transfused. Case-controlled matching for the subgroup with a Rockall score < 6 showed that the rebleeding rate was similar for both groups (11.1% in each group).

Conclusion
Intravenous non-high-dose pantoprazole is equally effective as high-dose pantoprazole when treating low risk patients with a Rockall sore were < 6 who have bleeding ulcers and high-risk stigmata after endoscopic hemostasis.
[11C]Flumazenil brain uptake is influenced by the blood-brain barrier efflux transporter P-glycoprotein
Authors: Froklage Femke E , Syvänen Stina , Hendrikse N Harry , Huisman Marc C , Molthoff Carla FM , Tagawa Yoshihiko , Reijneveld Jaap C , Heimans Jan J , Lammertsma Adriaan A , Eriksson Jonas , de Lange Elizabeth CM , Voskuyl Rob A 
Published: March 2012

Abstract

Background
[11C]Flumazenil and positron emission tomography (PET) are used clinically to assess gamma-aminobutyric acid (GABA)-ergic function and to localize epileptic foci prior to resective surgery. Enhanced P-glycoprotein (P-gp) activity has been reported in epilepsy and this may confound interpretation of clinical scans if [11C]flumazenil is a P-gp substrate. The purpose of this study was to investigate whether [11C]flumazenil is a P-gp substrate.

Methods
[11C]Flumazenil PET scans were performed in wild type (WT) (n = 9) and Mdr1a/1b, (the genes that encode for P-gp) double knockout (dKO) (n = 10) mice, and in naive rats (n = 10). In parallel to PET scanning, [11C]flumazenil plasma concentrations were measured in rats. For 6 of the WT and 6 of the dKO mice a second, [11C]flumazenil scan was acquired after administration of the P-gp inhibitor tariquidar. Cerebral [11C]flumazenil concentrations in WT and Mdr1a/1b dKO mice were compared (genetic disruption model). Furthermore, pre and post P-gp-blocking cerebral [11C]flumazenil concentrations were compared in all animals (pharmacological inhibition model).

Results

Mdr1a/1b dKO mice had approximately 70% higher [11C]flumazenil uptake in the brain than WT mice. After administration of tariquidar, cerebral [11C]flumazenil uptake in WT mice increased by about 80% in WT mice, while it remained the same in Mdr1a/1b dKO mice. In rats, cerebral [11C]flumazenil uptake increased by about 60% after tariquidar administration. Tariquidar had only a small effect on plasma clearance of flumazenil.

Conclusions
The present study showed that [11C]flumazenil is a P-gp substrate in rodents. Consequently, altered cerebral [11C]flumazenil uptake, as observed in epilepsy, may not reflect solely GABAA receptor density changes but also changes in P-gp activity.