bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implicit–Explicit Multistep Methods for Fast-Wave–Slow-Wave Problems
Authors: Durran Dale R. , Blossey Peter N. 
Published: October 2011

Implicit–explicit (IMEX) linear multistep methods are examined with respect to their suitability for the integration of fast-wave–slow-wave problems in which the fast wave has relatively low amplitude and need not be accurately simulated. The widely used combination of trapezoidal implicit and leapfrog explicit differencing is compared to schemes based on Adams methods or on backward differencing. Two new families of methods are proposed that have good stability properties in fast-wave–slow-wave problems: one family is based on Adams methods and the other on backward schemes. Here the focus is primarily on four specific schemes drawn from these two families: a pair of Adams methods and a pair of backward methods that are either (i) optimized for third-order accuracy in the explicit component of the full IMEX scheme, or (ii) employ particularly good schemes for the implicit component. These new schemes are superior, in many respects, to the linear multistep IMEX schemes currently in use. The behavior of these schemes is compared theoretically in the context of the simple oscillation equation and also for the linearized equations governing stratified compressible flow. Several schemes are also tested in fully nonlinear simulations of gravity waves generated by a localized source in a shear flow.
Support, opinion of support and psychological health among survivors of a natural disaster
Authors: Wahlström Lars , Michélsen Hans , Schulman Abbe , Backheden Magnus 
Published: October 2011

Background: Although formal intervention after disasters is recommended, the evidence base for this is weak. Satisfaction with support after disasters is seldom investigated and the relation to psychological symptoms is unknown. Aims: To investigate whether dissatisfaction with social and formalized support are associated with post-disaster psychological symptoms. Methods: A total of 1,505 Swedish survivors of the 2004 Indian Ocean tsunami responded to a questionnaire 14 months after the disaster, including the General Health Questionnaire-12, the Impact of Events Scale – Revised, the Crisis Support Scale, and questions concerning the reception and appraisal of social and formalized support from health care, psychological services and insurance agencies. Disaster exposure and background factors were controlled for in the analyses. Results: Reception of formalized support, but not social support, was associated with both psychological distress and post-traumatic stress. Dissatisfaction with social but not formalized support, with the exception of support from insurance agencies, was associated with psychological distress. Conclusions: Social support and formalized support should be differentiated in future studies in order to improve preventive intervention efforts after disasters. The reporting of dissatisfaction with social support merits special attention, since this may indicate increased risk for psychological symptoms.
Milrinone, a phosphodiesterase III inhibitor, prevents reduction of jugular bulb saturation during rewarming from hypothermic cardiopulmonary bypass
Authors: Iritakenishi T , Hayashi Y , Yamanaka H , Kamibayashi T , Ueda K , Mashimo T 
Published: October 2011

Introduction: Inadequate cerebral oxygen balance during cardiopulmonary bypass may cause neuropsychological dysfunction. Milrinone, a phosphodiesterase III inhibitor, augments cerebral blood flow by direct vasodilatation. We conducted a prospective, randomized study in patients undergoing cardiac surgery with cardiopulmonary bypass to clarify the clinical efficacy of milrinone in the imbalance of cerebral oxygen supply and demand during the rewarming period of cardiopulmonary bypass. Methods: This is a prospective, randomized and placebo-controlled study. After anesthesia, a 5.5 F fiberoptic oximeter catheter was inserted into the right jugular bulb retrogradely for monitoring the jugular venous oxyhemoglobin saturation (SjO2). Patients were randomly assigned to two groups, one receiving a continuous infusion of milrinone, 0.5 µg/kg/min during hypothermic cardiopulmonary bypass, and the other receiving saline as control. Results: Milrinone significantly prevented the reduction of the jugular venous oxyhemoglobin saturation at 10 minutes from the start of rewarming compared with the control group, but did not do so from 10 to 20 minutes after rewarming. Conclusion: Milrinone suppresses the reduction of SjO2 and improves the balance of cerebral oxygen supply and demand during the early rewarming period of hypothermic cardiopulmonary bypass.
Healthcare tariffs for specialist inpatient neurorehabilitation services: rationale and development of a UK casemix and costing methodology
Authors: Turner-Stokes Lynne , Sutch Stephen , Dredge Robert 
Published: October 2011

Objective: To describe the rationale and development of a casemix model and costing methodology for tariff development for specialist neurorehabilitation services in the UK. Rationale for development of a new methodology: Patients with complex needs incur higher treatment costs. Fair payment should be weighted in proportion to costs of providing treatment, and should allow for variation over time Casemix model and band-weighting: Case complexity is measured by the Rehabilitation Complexity Scale (RCS). Cases are divided into five bands of complexity, based on the total RCS score. The principal determinant of costs in rehabilitation is staff time. Total staff hours/week (estimated from the Northwick Park Nursing and Therapy Dependency Scales) are analysed within each complexity band, through cross-sectional analysis of parallel ratings. A ‘band-weighting’ factor is derived from the relative proportions of staff time within each of the five bands. Costing methodology: Total unit treatment costs are obtained from retrospective analysis of provider hospitals’ budget and accounting statements. Mean bed-day costs (total unit cost/occupied bed days) are divided broadly into ‘variable’ and ‘non-variable’ components. In the weighted costing model, the band-weighting factor is applied to the variable portion of the bed-day cost to derive a banded cost, and thence a set of cost-multipliers. Preliminary data from one unit are presented to illustrate how this weighted costing model will be applied to derive a multilevel banded payment model, based on serial complexity ratings, to allow for change over time.
Protein phosphatase 2a (PP2A) binds within the oligomerization domain of striatin and regulates the phosphorylation and activation of the mammalian Ste20-Like kinase Mst3
Authors: Gordon Johnthan , Hwang Juyeon , Carrier Karma J , Jones Candace A , Kern Quiana L , Moreno Carlos S , Karas Richard H , Pallas David C 
Published: October 2011

Abstract

Background
Striatin, a putative protein phosphatase 2A (PP2A) B-type regulatory subunit, is a multi-domain scaffolding protein that has recently been linked to several diseases including cerebral cavernous malformation (CCM), which causes symptoms ranging from headaches to stroke. Striatin association with the PP2A A/C (structural subunit/catalytic subunit) heterodimer alters PP2A substrate specificity, but targets and roles of striatin-associated PP2A are not known. In addition to binding the PP2A A/C heterodimer to form a PP2A holoenzyme, striatin associates with cerebral cavernous malformation 3 (CCM3) protein, the mammalian Mps one binder (MOB) homolog, Mob3/phocein, the mammalian sterile 20-like (Mst) kinases, Mst3, Mst4 and STK25, and several other proteins to form a large signaling complex. Little is known about the molecular architecture of the striatin complex and the regulation of these sterile 20-like kinases.

Results
To help define the molecular organization of striatin complexes and to determine whether Mst3 might be negatively regulated by striatin-associated PP2A, a structure-function analysis of striatin was performed. Two distinct regions of striatin are capable of stably binding directly or indirectly to Mob3--one N-terminal, including the coiled-coil domain, and another more C-terminal, including the WD-repeat domain. In addition, striatin residues 191-344 contain determinants necessary for efficient association of Mst3, Mst4, and CCM3. PP2A associates with the coiled-coil domain of striatin, but unlike Mob3 and Mst3, its binding appears to require striatin oligomerization. Deletion of the caveolin-binding domain on striatin abolishes striatin family oligomerization and PP2A binding. Point mutations in striatin that disrupt PP2A association cause hyperphosphorylation and activation of striatin-associated Mst3.

Conclusions
Striatin orchestrates the regulation of Mst3 by PP2A. It binds Mst3 likely as a dimer with CCM3 via residues lying between striatin's calmodulin-binding and WD-domains and recruits the PP2A A/C heterodimer to its coiled-coil/oligomerization domain. Residues outside the previously reported coiled-coil domain of striatin are necessary for its oligomerization. Striatin-associated PP2A is critical for Mst3 dephosphorylation and inactivation. Upon inhibition of PP2A, Mst3 activation appears to involve autophosphorylation of multiple activation loop phosphorylation sites. Mob3 can associate with striatin sequences C-terminal to the Mst3 binding site but also with sequences proximal to striatin-associated PP2A, consistent with a possible role for Mob 3 in the regulation of Mst3 by PP2A.
An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry
Authors: Jeong Jaesik , Shi Xue , Zhang Xiang , Kim Seongho , Shen Changyu 
Published: October 2011

Abstract

Background
Mass spectrometry (MS) based metabolite profiling has been increasingly popular for scientific and biomedical studies, primarily due to recent technological development such as comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS). Nevertheless, the identifications of metabolites from complex samples are subject to errors. Statistical/computational approaches to improve the accuracy of the identifications and false positive estimate are in great need. We propose an empirical Bayes model which accounts for a competing score in addition to the similarity score to tackle this problem. The competition score characterizes the propensity of a candidate metabolite of being matched to some spectrum based on the metabolite's similarity score with other spectra in the library searched against. The competition score allows the model to properly assess the evidence on the presence/absence status of a metabolite based on whether or not the metabolite is matched to some sample spectrum.

Results
With a mixture of metabolite standards, we demonstrated that our method has better identification accuracy than other four existing methods. Moreover, our method has reliable false discovery rate estimate. We also applied our method to the data collected from the plasma of a rat and identified some metabolites from the plasma under the control of false discovery rate.

Conclusions
We developed an empirical Bayes model for metabolite identification and validated the method through a mixture of metabolite standards and rat plasma. The results show that our hierarchical model improves identification accuracy as compared with methods that do not structurally model the involved variables. The improvement in identification accuracy is likely to facilitate downstream analysis such as peak alignment and biomarker identification. Raw data and result matrices can be found at http://www.biostat.iupui.edu/~ChangyuShen/index.htm

Trial Registration
2123938128573429
Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences
Authors: Ruegger Paul M , Della Vedova Gianluca , Jiang Tao , Borneman James 
Published: October 2011

Abstract

Background
Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups.

Results
Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups.

Conclusions
Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes
Authors: Lv Jie , Havlak Paul , Putnam Nicholas H 
Published: October 2011

Abstract

Background
Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny”) from the common ancestor of multicellular animal life [1–4], but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis [5], but as we show here, it is not sufficent to explain long-term macro-synteny conservation.

Results
We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”), and is available as open source software from http://github.com/putnamlab/dcj-c.

Conclusions
A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
Development of an indirect competitive enzyme-linked immunosorbent assay applied to the Botrytis cinerea quantification in tissues of postharvest fruits
Authors: Fernández-Baldo Martín A , Fernández Jorge G , Pereira Sirley V , Messina Germán A , Salinas Eloy , Raba Julio , Sanz Ferramola María I 
Published: October 2011

AbstractBackgroundBotrytis cinereais a phytopathogenic fungus responsible for the disease known as gray mold, which causes substantial losses of fruits at postharvest. This fungus is present often as latent infection and an apparently healthy fruit can deteriorate suddenly due to the development of this infection. For this reason, rapid and sensitive methods are necessary for its detection and quantification. This article describes the development of an indirect competitive enzyme-linked immunosorbent assay (ELISA) for quantification ofB. cinereain apple (Red Delicious), table grape (pink Moscatel), and pear (William's) tissues.ResultsThe method was based in the competition for the binding site of monoclonal antibodies betweenB. cinereaantigens present in fruit tissues andB. cinereapurified antigens immobilized by a crosslinking agent onto the surface of the microtiter plates. The method was validated considering parameters such as selectivity, linearity, precision, accuracy and sensibility. The calculated detection limit was 0.97 μg mL-1B. cinereaantigens. The immobilized antigen was perfectly stable for at least 4 months assuring the reproducibility of the assay. The fungus was detected and quantified in any of the fruits tested when the rot was not visible yet. Results were compared with a DNA quantification method and these studies showed good correlation.ConclusionsThe developed method allowed detects the presence ofB. cinereain asymptomatic fruits and provides the advantages of low cost, easy operation, and short analysis time determination for its possible application in the phytosanitary programs of the fruit industry worldwide.
A novel bacteriophage Tail-Associated Muralytic Enzyme (TAME) from Phage K and its development into a potent antistaphylococcal protein
Authors: Paul Vivek Daniel , Rajagopalan Sanjeev Saravanan , Sundarrajan Sudarson , George Shilpa E , Asrani Jiya Y , Pillai Renjith , Chikkamadaiah Ravisha , Durgaiah Murali , Sriram Bharathi , Padmanabhan Sriram 
Published: October 2011

Abstract

Background

Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. However, the rapid emergence of antibiotic resistance limits the choice of therapeutic options for treating infections caused by this organism. Muralytic enzymes from bacteriophages have recently gained attention for their potential as antibacterial agents against antibiotic-resistant gram-positive organisms. Phage K is a polyvalent virulent phage of the Myoviridae family that is active against many Staphylococcus species.

Results
We identified a phage K gene, designated orf56, as encoding the phage tail-associated muralytic enzyme (TAME). The gene product (ORF56) contains a C-terminal domain corresponding to cysteine, histidine-dependent amidohydrolase/peptidase (CHAP), which demonstrated muralytic activity on a staphylococcal cell wall substrate and was lethal to S. aureus cells. We constructed N-terminal truncated forms of ORF56 and arrived at a 16-kDa protein (Lys16) that retained antistaphylococcal activity. We then generated a chimeric gene construct encoding Lys16 and a staphylococcal cell wall-binding SH3b domain. This chimeric protein (P128) showed potent antistaphylococcal activity on global clinical isolates of S. aureus including methicillin-resistant strains. In addition, P128 was effective in decolonizing rat nares of S. aureus USA300 in an experimental model.

Conclusions
We identified a phage K gene that encodes a protein associated with the phage tail structure. The muralytic activity of the phage K TAME was localized to the C-terminal CHAP domain. This potent antistaphylococcal TAME was combined with an efficient Staphylococcus-specific cell-wall targeting domain SH3b, resulting in the chimeric protein P128. This protein shows bactericidal activity against globally prevalent antibiotic resistant clinical isolates of S. aureus and against the genus Staphylococcus in general. In vivo, P128 was efficacious against methicillin-resistant S. aureus in a rat nasal colonization model.
MiR-125b promotes proliferation and migration of type II endometrial carcinoma cells through targeting TP53INP1 tumor suppressor in vitro and in vivo
Authors: Jiang Feizhou , Liu Te , He Yinyan , Yan Qin , Chen Xiaoyue , Wang Hui , Wan Xiaoping 
Published: October 2011

Abstract

Background
Our previous studies have identified that miR-125b was overexpressed in type II endometrial carcinoma (EC) cells compared with type I using microRNAs microarray. Although recent studies have shown the important role of miR-125b in several tumors and overexpression of miR-125b in advanced EC, its function in this disease has not yet been defined. In the present study, we tried to confirm the result of microRNAs microarray and further investigated the functions of miR-125b in EC, and tried to find new downstream targets of miR-125b.

Methods
Differential expression of miR-125b was detected between type II EC cells (KLE, AN3CA) with ER negative and type I EC cells (ishikawa, RL95-2) with ER positive by qRT-PCR and northern blotting. The effects of miR-125b of on proliferation, migration, and target protein expression were evaluated by CCK8 assay, wound healing assay, transwell migration assay, western blotting, and Tumorigenicity assays in nude mice. In addition, luciferase reporter plasmid was constructed to demonstrate the direct target of miR-125b.

Results
MiR-125b was overexpressed in type II EC cells compared with type I. Exogenous miR-125b expression increased proliferation and migration of ishikawa cells and abrogating expression of miR-125b suppressed proliferation, and migration of AN3CA cells in vitro. In addition, in vivo tumor formation assay confirmed that forced miR-125b expression promoted proliferation potential of ishikawa cells, and tumor suppressor gene Tumor Protein 53-Induced Nuclear Protein 1 (TP53INP1) was identified to be the direct target of miR-125b.

Conclusions
TP53INP1 was newly identified to be the direct downstream target of miR-125b. MiR-125b, which was overexpressed in type II EC cells compared with type I, contributes to malignancy of type II EC possibly through down-regulating TP53INP1.
Nitric oxide involvement in the acrosome reaction triggered by leptin in pig sperm
Authors: Aquila Saveria , Giordano Francesca , Guido Carmela , Rago Vittoria , Carpino Amalia 
Published: October 2011

AbstractBackgroundNitric oxide (NO) is a signaling molecule produced by intracellular nitric oxide synthase (NOS) enzymes. This free radical appears to affect sperm capacitation, a maturation step preceding acrosome reaction. Recent studies have reported leptin ability to promote capacitation and acrosome reaction in pig male gametes.MethodsThis study has investigated nitric oxide production in leptin-treated pig spermatozoa by fluorescence-activated cell sorting, while the intracellular NOS isoforms were assessed by Western blot analysis. In addition, acrosome status of treated-spermatozoa was evaluated by FITC-PNA staining.ResultsSignificant increases of nitric oxide levels and acrosome reaction extent were detected in leptin-treated spermatozoa, but both the effects were reversed in presence ofL-NAME. Furthermore, the immunoblots of sperm extracts have evidenced three bands of ~160 Kd(bNOS), ~130 Kd (iNOS) and ~135 Kd (eNOS).ConclusionsThe identification of the three intracellular NOS isoforms suggests that pig spermatozoa could produce NO, while the augmented nitric oxide levels in leptin-treated male gametes indicates the capacity of the hormone to induce nitric oxide production. Furthermore, the inhibitory effect ofL-NAME and of Ab-ObR on the promotion of acrosome reaction triggered by leptin suggests a possible involvement of NO in the hormone action.