Multivariate Statistical Analysis Applied to an IL6 Signal Transduction Model in Hepatocytes

This paper introduces the application of linear multivariate statistical techniques, including partial least squares (PLS), canonical correlation analysis (CCA) and reduced rank regression (RRR), into the area of Systems Biology. This new approach aims to extract the important proteins embedded in complex signal transduction pathway models.The analysis is performed on a model of intracellular signalling along the janus-associated kinases/signal transducers and transcription factors (JAK/STAT) and mitogen activated protein kinases (MAPK) signal transduction pathways in interleukin-6 (IL6) stimulated hepatocytes, which produce signal transducer and activator of transcription factor 3 (STAT3).A region of redundancy within the MAPK pathway that does not affect the STAT3 transcription was identified using CCA. This is the core finding of this analysis and cannot be obtained by inspecting the model by eye. In addition, RRR was found to isolate terms that do not significantly contribute to changes in protein concentrations, while the application of PLS does not provide such a detailed picture by virtue of its construction.This analysis has a similar objective to conventional model reduction techniques with the advantage of maintaining the meaning of the states prior to and after the reduction process. A significant model reduction is performed, with a marginal loss in accuracy, offering a more concise model while maintaining the main influencing factors on the STAT3 transcription.The findings offer a deeper understanding of the reaction terms involved, confirm the relevance of several proteins to the production of Acute Phase Proteins and complement existing findings regarding cross-talk between the two signalling pathways.

Extending Zipf’s law to n-grams for large corpora

Experiments show that for a large corpus, Zipf’s law does not hold for all rank of words: the frequencies fall below those predicted by Zipf’s law for ranks greater than about 5,000 word types in the English language and about 30,000 word types in the inflected languages Irish and Latin. It also does not hold for syllables or words in the syllable-based languages, Chinese or Vietnamese. However, when single words are combined together with word n-grams in one list and put in rank order, the frequency of tokens in the combined list extends Zipf’s law with a slope close to -1 on a log-log plot in all five languages. Further experiments have demonstrated the validity of this extension of Zipf’s law to n-grams of letters, phonemes or binary bits in English. It is shown theoretically that probability theory
alone can predict this behavior in randomly created n-grams of binary bits.

Compactness properties of operator multipliers

We continue the study of multidimensional operator multipliers initiated in~cite{jtt}. We introduce the notion of the symbol of an operator multiplier. We characterise completely compact operator multipliers in terms of their symbol as well as in terms of approximation by finite rank multipliers. We give sufficient conditions for the sets of compact and completely compact multipliers to coincide and characterise the cases where an operator multiplier in the minimal tensor product of two C*-algebras is automatically compact. We give a description of multilinear modular completely compact completely bounded maps defined on the direct product of finitely many copies of the C*-algebra of compact operators in terms of tensor products, generalising results of Saar

Jordan isomorphism of purely infinite C*-algebras

We prove that every unital bounded linear mapping from a unital purely infinite C*-algebra of real rank zero into a unital Banach algebra which preserves elements of square zero is a Jordan homomorphism. This entails a description of unital surjective spectral isometries as the Jordan isomorphisms in this setting.

A randomised, controlled trial of conventional versus automated weaning from mechanical ventilation using SmartcareTM/PS

Objective
Preliminary assessment of an automated weaning system (SmartCare™/PS) compared to usual management of weaning from mechanical ventilation performed in the absence of formal protocols.


Design and setting
A randomised, controlled pilot study in one Australian intensive care unit.


Patients
A total of 102 patients were equally divided between SmartCare/PS and Control.

Interventions
The automated system titrated pressure support, conducted a spontaneous breathing trial and provided notification of success (“separation potential”).

Measurements and results
The median time from the first identified point of suitability for weaning commencement to the state of “separation potential” using SmartCare/PS was 20 h (interquartile range, IQR, 2–40) compared to 8 h (IQR 2–43) with Control (log-rank P = 0.3). The median time to successful extubation was 43 h (IQR 6–169) using SmartCare/PS and 40 (14–87) with Control (log-rank P = 0.6). Unadjusted, the estimated probability of reaching “separation potential” was 21% lower (95% CI, 48% lower to 20% greater) with SmartCare/PS compared to Control. Adjusted for other covariates (age, gender, APACHE II, SOFAmax, neuromuscular blockade, corticosteroids, coma and elevated blood glucose), these estimates were 31% lower (95% CI, 56% lower to 9% greater) with SmartCare/PS. The study groups showed comparable rates of reintubation, non-invasive ventilation post-extubation, tracheostomy, sedation, neuromuscular blockade and use of corticosteroids.

Conclusions
Substantial reductions in weaning duration previously demonstrated were not confirmed when the SmartCare/PS system was compared to weaning managed by experienced critical care specialty nurses, using a 1:1 nurse-to-patient ratio. The effect of SmartCare/PS may be influenced by the local clinical organisational context.

Balanced Weights and Three-Sided Coalition Formation

We consider three-sided coalition formation problems when each agent is concerned about his local status as measured by his relative rank position within the group of his own type and about his global status as measured by the weighted sum of the average rankings of the other types of groups. We show that a core stable coalition structure always exists, provided that the corresponding weights are balanced and each agent perceives the two types of status as being substitutable.

Efficacy of sod removal in regenerating fen vegetation for the conservation of the marsh fritillary butterfly Euphydryas aurinia, Montiaghs Moss Nature Reserve, County Antrim, Northern Ireland.

The efficacy of ‘sod removal’ as a fenland restoration technique was tested using an experimental approach at Montiaghs Moss Nature Reserve, Northern Ireland, from 2006 to 2008. The site suffered from rank growth of purple moor-grass Molinia caerulea which was out-competing herbaceous species. Soil was removed up to a depth of 15 cm completely denuding vegetation in the experimental plot exposing bare peat. By July 2007, 15.2% of sod-removal areas were revegetated; by October 2008 cover had risen to 64.6%. Of this cover, purple moor-grass accounted for only 9-11% compared to 78- 79% on control plots. Cover of other rank-forming grass species was also significantly reduced. Sod removal significantly increased the cover of species characteristic of fenlands including sedges Carex spp., rushes Juncus spp., marsh pennywort Hydrocotyle vulgaris and lesser spearwort Ranunculus flammula. It seems likely that sod removal, which lowered the surface of the peat, restored minerotrophic conditions and exposed the historical seed bank stimulating regeneration of some fenland specialists and pioneer species; this resulted in significantly higher species richness on sod removal plots than control plots two years after treatment. There was no demonstrable effect of sod removal on abundance of devil’s-bit scabious Succisa pratensis, the larval food plant of the Annex II listed marsh fritillary butterfly Euphydryas aurinia. We recommend that consideration should be given to artificially seeding devil’s-bit scabious soon after sod removal treatment to promote early recolonisation and to increase plant abundance on the site.

Identification of high-affinity binding sites for the insulin sensitizer rosiglitazone (BRL-49653) in rodent and human adipocytes using a radioiodinated ligand for peroxisomal proliferator-activated receptor gamma.

A radioiodinated ligand, [125I]SB-236636 [(S)-(-)3-[4-[2-[N-(2-benzoxazolyl)-N-methylamino]ethoxy]3-[125I]iodophenyl]2-ethoxy propanoic acid], which is specific for the ? isoform of the peroxisomal proliferator activated receptor (PPAR?), was developed. [125I]SB-236636 binds with high affinity to full-length human recombinant PPAR?1 and to a GST (glutathione S-transferase) fusion protein contg. the ligand binding domain of human PPAR?1 (KD = 70 nM). Using this ligand, the authors characterized binding sites in adipose-derived cells from rat, mouse and humans. In competition expts., rosiglitazone (BRL-49653), a potent antihyperglycemic agent, binds with high affinity to sites in intact adipocytes (IC50 = 12, 4 and 9 nM for rat, 3T3-L1 and human adipocytes, resp.). Binding affinities (IC50) of other thiazolidinediones for the ligand binding domain of PPAR?1 were comparable with those detd. in adipocytes and reflected the rank order of potencies of these agents as stimulants of glucose transport in 3T3-L1 adipocytes and antihyperglycemic agents in vivo: rosiglitazone > pioglitazone > troglitazone. Competition of [125I]SB-236636 binding was stereoselective in that the IC50 value of SB-219994, the (S)-enantiomer of an ?-trifluoroethoxy propanoic acid insulin sensitizer, was 770-fold lower than that of SB-219993 [(R)-enantiomer] at recombinant human PPAR?1. The higher binding affinity of SB-219994 also was evident in intact adipocytes and reflected its 100-fold greater potency as an antidiabetic agent. The results strongly suggest that the high-affinity binding site for [125I]SB-236636 in intact adipocytes is PPAR? and that the pharmacol. of insulin-sensitizer binding in rodent and human adipocytes is very similar and, moreover, predictive of antihyperglycemic activity in vivo.

Induction and rejoining of DNA double-strand breaks in bladder tumor cells

The induction and rejoining of radiation-induced double-strand breaks (DSBs) in cells of six bladder tumor cell lines (T24, UM-UC3, TCC-SUP, RT112, J82, HT1376) were measured using the neutral comet assay. Radiation dose-response curves (0-60 Gy) showed damage (measured as mean tail moment) for five of the cell lines in the same rank order as cell survival (measured over 0-10 Gy), with the least damage in the most radioresistant cell line. Damage induction correlated well with clonogenic survival at high doses (SF10) for all six cell lines. At the clinically relevant dose of 2 Gy, correlation was good for four cell lines but poor for two (TCC-SUP and T24), The rejoining process had a fast and slow component for all cell lines. The rate of these two components of DNA repair did not correlate with cell survival. However, the time taken to reduce the amount of DNA damage to preirradiated control levels correlated positively with cell survival at 10 Gy but not 2 Gy; radioresistant cells rejoined the induced DSBs to preirradiation control levels more quickly than the radiosensitive cells. Although the results show good correlation between SF10 and DSBs for all six cell lines, the lack of correlation with SF2 for TCC-SUP and T24 cells would suggest that a predictive test should be carried out at the clinically relevant dose. At present the neutral comet assay cannot achieve this. (C) 2000 by Radiation Research Society.

Men, Women and an Integrated History of the Russian Revolutionary Movement

Since its emergence as a discipline in the 1960s, women’s history has had a profound effect on the study of the past. Scholarship on women’s experiences of and contributions to the Russian revolutionary movement has increased exponentially since the publication of a number of biographies of Aleksandra Kollontai in the 1970s and 1980s and a comprehensive picture has emerged of women’s involvement in all the major revolutionary parties, as leading figures as well as rank and file activists. Despite this wealth of historical discovery, remarkably little has found its way into so-called ‘general’ histories of the revolution. An integrated history, which is the ultimate aim of women’s history, has yet to be produced for the Russian revolutionary movement, even though recent prosopographical studies of revolutionary women have made clear the numerous ways in which men and women cooperated and interacted on a daily basis in the underground. This article explores the nature of and reasons for this failure, makes a case for why incorporating women’s experiences into the grand narrative of the Russian revolution is important and discusses how this might be achieved.

Norm attaining operators and pseudospectrum

It is shown that if $11$, the operator $I+T$ attains its norm. A reflexive Banach space $X$ and a bounded rank one operator $T$ on $X$ are constructed such that $\|I+T\|>1$ and $I+T$ does not attain its norm.

Meta-analysis of 32 genome-wide linkage studies of schizophrenia

A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (P-SR) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for 'aggregate' genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies. Molecular Psychiatry (2009) 14, 774-785; doi:10.1038/mp.2008.135; published online 30 December 2008

Methods to increase response to postal and electronic questionnaires

Background: Postal and electronic questionnaires are widely used for data collection in epidemiological studies but non-response reduces the effective sample size and can introduce bias. Finding ways to increase response to postal and electronic questionnaires would improve the quality of health research. Objectives: To identify effective strategies to increase response to postal and electronic questionnaires. Search strategy: We searched 14 electronic databases to February 2008 and manually searched the reference lists of relevant trials and reviews, and all issues of two journals. We contacted the authors of all trials or reviews to ask about unpublished trials. Where necessary, we also contacted authors to confirm methods of allocation used and to clarify results presented. We assessed the eligibility of each trial using pre-defined criteria. Selection criteria: Randomised controlled trials of methods to increase response to postal or electronic questionnaires. Data collection and analysis: We extracted data on the trial participants, the intervention, the number randomised to intervention and comparison groups and allocation concealment. For each strategy, we estimated pooled odds ratios (OR) and 95% confidence intervals (CI) in a random-effects model. We assessed evidence for selection bias using Egger's weighted regression method and Begg's rank correlation test and funnel plot. We assessed heterogeneity among trial odds ratios using a Chi 2 test and the degree of inconsistency between trial results was quantified using the I 2 statistic. Main results: Postal We found 481 eligible trials.The trials evaluated 110 different ways of increasing response to postal questionnaires.We found substantial heterogeneity among trial results in half of the strategies. The odds of response were at least doubled using monetary incentives (odds ratio 1.87; 95% CI 1.73 to 2.04; heterogeneity P < 0.00001, I 2 = 84%), recorded delivery (1.76; 95% CI 1.43 to 2.18; P = 0.0001, I 2 = 71%), a teaser on the envelope - e.g. a comment suggesting to participants that they may benefit if they open it (3.08; 95% CI 1.27 to 7.44) and a more interesting questionnaire topic (2.00; 95% CI 1.32 to 3.04; P = 0.06, I 2 = 80%). The odds of response were substantially higher with pre-notification (1.45; 95% CI 1.29 to 1.63; P < 0.00001, I 2 = 89%), follow-up contact (1.35; 95% CI 1.18 to 1.55; P < 0.00001, I 2 = 76%), unconditional incentives (1.61; 1.36 to 1.89; P < 0.00001, I 2 = 88%), shorter questionnaires (1.64; 95%CI 1.43 to 1.87; P < 0.00001, I 2 = 91%), providing a second copy of the questionnaire at follow up (1.46; 95% CI 1.13 to 1.90; P < 0.00001, I 2 = 82%), mentioning an obligation to respond (1.61; 95% CI 1.16 to 2.22; P = 0.98, I 2 = 0%) and university sponsorship (1.32; 95% CI 1.13 to 1.54; P < 0.00001, I 2 = 83%). The odds of response were also increased with non-monetary incentives (1.15; 95% CI 1.08 to 1.22; P < 0.00001, I 2 = 79%), personalised questionnaires (1.14; 95% CI 1.07 to 1.22; P < 0.00001, I 2 = 63%), use of hand-written addresses (1.25; 95% CI 1.08 to 1.45; P = 0.32, I 2 = 14%), use of stamped return envelopes as opposed to franked return envelopes (1.24; 95% CI 1.14 to 1.35; P < 0.00001, I 2 = 69%), an assurance of confidentiality (1.33; 95% CI 1.24 to 1.42) and first class outward mailing (1.11; 95% CI 1.02 to 1.21; P = 0.78, I 2 = 0%). The odds of response were reduced when the questionnaire included questions of a sensitive nature (0.94; 95% CI 0.88 to 1.00; P = 0.51, I 2 = 0%). Electronic: We found 32 eligible trials. The trials evaluated 27 different ways of increasing response to electronic questionnaires. We found substantial heterogeneity among trial results in half of the strategies. The odds of response were increased by more than a half using non-monetary incentives (1.72; 95% CI 1.09 to 2.72; heterogeneity P < 0.00001, I 2 = 95%), shorter e-questionnaires (1.73; 1.40 to 2.13; P = 0.08, I 2 = 68%), including a statement that others had responded (1.52; 95% CI 1.36 to 1.70), and a more interesting topic (1.85; 95% CI 1.52 to 2.26). The odds of response increased by a third using a lottery with immediate notification of results (1.37; 95% CI 1.13 to 1.65), an offer of survey results (1.36; 95% CI 1.15 to 1.61), and using a white background (1.31; 95% CI 1.10 to 1.56). The odds of response were also increased with personalised e-questionnaires (1.24; 95% CI 1.17 to 1.32; P = 0.07, I 2 = 41%), using a simple header (1.23; 95% CI 1.03 to 1.48), using textual representation of response categories (1.19; 95% CI 1.05 to 1.36), and giving a deadline (1.18; 95% CI 1.03 to 1.34). The odds of response tripled when a picture was included in an e-mail (3.05; 95% CI 1.84 to 5.06; P = 0.27, I 2 = 19%). The odds of response were reduced when "Survey" was mentioned in the e-mail subject line (0.81; 95% CI 0.67 to 0.97; P = 0.33, I 2 = 0%), and when the e-mail included a male signature (0.55; 95% CI 0.38 to 0.80; P = 0.96, I 2 = 0%). Authors' conclusions: Health researchers using postal and electronic questionnaires can increase response using the strategies shown to be effective in this systematic review. Copyright © 2009 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.


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A probabilistic modelling scheme for analysis of long-term failure of cemented femoral joint replacements

Reliable prediction of long-term medical device performance using computer simulation requires consideration of variability in surgical procedure, as well as patient-specific factors. However, even deterministic simulation of long-term failure processes for such devices is time and resource consuming so that including variability can lead to excessive time to achieve useful predictions. This study investigates the use of an accelerated probabilistic framework for predicting the likely performance envelope of a device and applies it to femoral prosthesis loosening in cemented hip arthroplasty.
A creep and fatigue damage failure model for bone cement, in conjunction with an interfacial fatigue model for the implant–cement interface, was used to simulate loosening of a prosthesis within a cement mantle. A deterministic set of trial simulations was used to account for variability of a set of surgical and patient factors, and a response surface method was used to perform and accelerate a Monte Carlo simulation to achieve an estimate of the likely range of prosthesis loosening. The proposed framework was used to conceptually investigate the influence of prosthesis selection and surgical placement on prosthesis migration.
Results demonstrate that the response surface method is capable of dramatically reducing the time to achieve convergence in mean and variance of predicted response variables. A critical requirement for realistic predictions is the size and quality of the initial training dataset used to generate the response surface and further work is required to determine the recommendations for a minimum number of initial trials. Results of this conceptual application predicted that loosening was sensitive to the implant size and femoral width. Furthermore, different rankings of implant performance were predicted when only individual simulations (e.g. an average condition) were used to rank implants, compared with when stochastic simulations were used. In conclusion, the proposed framework provides a viable approach to predicting realistic ranges of loosening behaviour for orthopaedic implants in reduced timeframes compared with conventional Monte Carlo simulations.

Comparisons between different polychemotherapy regimens for early breast cancer: meta-analyses of long-term outcome among 100,000 women in 123 randomised trials

Background Moderate di?erences in e?cacy between adjuvant chemotherapy regimens for breast cancer are plausible, and could a? ect treatment choices. We sought any such di?erences.

Methods We undertook individual-patient-data meta-analyses of the randomised trials comparing: any taxane-plusanthracycline-based regimen versus the same, or more, non-taxane chemotherapy (n=44 000); one anthracyclinebased regimen versus another (n=7000) or versus cyclo phosphamide, methotrexate, and ?uorouracil (CMF; n=18 000); and polychemotherapy versus no chemotherapy (n=32 000). The scheduled dosages of these three drugs and of the anthracyclines doxorubicin (A) and epirubicin (E) were used to de? ne standard CMF, standard 4AC, and CAF and CEF. Log-rank breast cancer mortality rate ratios (RRs) are reported.

Findings In trials adding four separate cycles of a taxane to a ?xed anthracycline-based control regimen, extending treatment duration, breast cancer mortality was reduced (RR 0·86, SE 0·04, two-sided signi?cance [2p]=0·0005). In trials with four such extra cycles of a taxane counterbalanced in controls by extra cycles of other cytotoxic drugs, roughly doubling non-taxane dosage, there was no signi?cant di?erence (RR 0·94, SE 0·06, 2p=0·33). Trials with CMF-treated controls showed that standard 4AC and standard CMF were equivalent (RR 0·98, SE 0·05, 2p=0·67), but that anthracycline-based regimens with substantially higher cumulative dosage than standard 4AC (eg, CAF or CEF) were superior to standard CMF (RR 0·78, SE 0·06, 2p=0·0004). Trials versus no chemotherapy also suggested greater mortality reductions with CAF (RR 0·64, SE 0·09, 2p<0·0001) than with standard 4AC (RR 0·78, SE 0·09, 2p=0·01) or
standard CMF (RR 0·76, SE 0·05, 2p<0·0001). In all meta-analyses involving taxane-based or anthracycline-based regimens, proportional risk reductions were little a? ected by age, nodal status, tumour diameter or di?erentiation (moderate or poor; few were well di?erentiated), oestrogen receptor status, or tamoxifen use. Hence, largely independently of age (up to at least 70 years) or the tumour characteristics currently available to us for the patients selected to be in these trials, some taxane-plus-anthracycline-based or higher-cumulative-dosage anthracycline-based regimens (not requiring stem cells) reduced breast cancer mortality by, on average, about one-third. 10-year overall mortality di?erences paralleled breast cancer mortality di?erences, despite taxane, anthracycline, and other toxicities.

Interpretation 10-year gains from a one-third breast cancer mortality reduction depend on absolute risks without chemotherapy (which, for oestrogen-receptor-positive disease, are the risks remaining with appropriate endocrine therapy). Low absolute risk implies low absolute bene?t, but information was lacking about tumour gene expression markers or quantitative immunohistochemistry that might help to predict risk, chemosensitivity, or both.