The Sylvia Lawry Centre for Multiple Sclerosis Research (SLCMSR)--Critical review facing the 20 anniversary.

The SLCMSR was formed as an international Multiple Sclerosis Trials, Research and Resource Center to identify clinical MRI and other predictors of the course of multiple sclerosis (MS) based on a large database of natural history and clinical trial data. Using an elaborate validation concept several key findings were published, challenging established outcome parameters and their assessment in MS such as disability ratings with Expanded Disability Status Scale (EDSS), relapses and MRI endpoints. Sustained increase of EDSS appeared to be an invalid outcome for 2-3 year clinical trials at least in patients with relapsing-remitting MS. The number of gadolinium-enhancing lesions and T2-lesion load on MRI were shown not to have a meaningful additional predictive value for the disease course. These issues risen some 15 years ago had triggered controversial discussions which have also been noticed by regulatory authorities and they all have not been resolved. In addition the SLCMSR contributed to the development of new outcomes such as real-world walking speed as an attractive, ecologically valid tool based on a wearable device. A so-called evidence-based-decision-support tool was constructed to provide individual prognostic estimates based on a matching algorithm to a given database. This paper condensates the findings of 20 years of critical MS research.

Use of fermentation processes for improving the dissolution of phosphorus and its recovery from waste activated sludge.

Recycling phosphorus from waste activated sludge has attracted a lot of interest to tackle the problem of phosphorus stocks depletion and the increase in food demand. In this study, the use of fermentation processes was investigated to enhance phosphorus dissolution from waste activated sludge to improve its recycling. Two fermentation processes, bioacidification and dark fermentation, were used on two different sludges fermented with wheat starch syrup in continuous operating conditions. Hydrogen yield from the co-substrate fermentation with waste activated sludge reached 3.9 mmolH2.gCODcosubstrate-1 yield during dark fermentation process and was negligible during bioacidification. Dissolved phosphorus in the waste activated sludge increased by 68% during bioacidification and by 43% during dark fermentation. In both processes, phosphorus dissolution was accompanied by iron, calcium and magnesium dissolution. Results show that fermentation enhances phosphorus dissolution in waste activated sludge to improve its recovery along with hydrogen and organic acids.

Considerations for development of an evidence dossier to support the use of mobile sensor technology for clinical outcome assessments in clinical trials.

BACKGROUND: Mobile sensors offer enormous potential for the collection of informative clinical endpoints in clinical trials to support regulatory decision making and product labelling. There are currently no specific guidelines on the information needed to enable regulators to review and accept proposed endpoints derived from mobile sensors for use in drug development trials. OBJECTIVE: The purpose of this working group report is to recommend the structure and content of an evidence dossier intended to support whether a clinical endpoint derived from mobile sensor data is fit-for-purpose for use in regulatory submissions for drug approvals. EVIDENCE DOSSIER: The structure and content of a dossier to provide evidence supporting the use of a sensor-derived clinical endpoint is described. Sections include clinical endpoint definition and positioning, the concept of interest, the context of use, clinical validation and interpretation, study implementation, and analytical validity with sensor performance verification in support of the selected sensor. CONCLUSIONS: In the absence of definitive regulatory guidance, this report provides a considered approach to compiling a comprehensive body of evidence to justify acceptance of mobile sensors for support of new drug applications.

Low clinical conversion rate in clinically isolated syndrome patients - diagnostic benefit of McDonald 2010 criteria?

BACKGROUND AND PURPOSE: New diagnostic criteria of multiple sclerosis (MS) increase the number of patients being diagnosed with MS whilst a substantial part might not convert to clinically definite MS (CDMS). The diagnostic accuracy of the McDonald 2005 and 2010 criteria for conversion to CDMS was evaluated in an unselected cohort of patients in whom an MS diagnostic work-up was decided. METHODS: Clinical, magnetic resonance imaging and cerebrospinal fluid data were analysed for all patients who presented with symptoms suspicious for MS at the university based MS outpatient clinic between 2006 and 2010 (n = 165). RESULTS: Follow-up was available for 131 patients. During the mean follow-up period of 2 years, 19% of patients developed CDMS whereas 64% of the patients fulfilling McDonald 2010 criteria did not convert to CDMS. CONCLUSION: The low clinical conversion rate indicates that the new diagnostic criteria may increase the incidence of MS cases with a less active disease course.

The relationship of age with the clinical phenotype in multiple sclerosis.

BACKGROUND: The multiple sclerosis (MS) clinical course and relapses frequency before progression vary widely. OBJECTIVE: To investigate the influence of age on the MS phenotype. METHODS: Among 751 primary progressive (PP = 217) and secondary progressive (SP = 534) MS patients from the London Ontario database, we assessed the relationship of age on the relapse frequency and on the progressive phase evolution, and the impact of relapses on the age at onset of progression. RESULTS: Age at onset did not influence the early attacks frequency, but patients younger at onset had larger number of total attacks before progression (age = 27.4, 31.0 and 32.8 mean years; ⩾4, 2-3 and 1 relapses, respectively) and longer latency to SP. Although frequent early relapses predicted younger age at SP onset, patients with no attacks (primary progressive multiple sclerosis (PPMS)), or 1, 2-3 and ⩾4 relapses during the relapsing-remitting phase started progressing at similar age (38.6, 41.3, 41.4 and 39.2 mean years, respectively). The age at onset of progressive phase did not affect its evolution. CONCLUSIONS: Age strongly influences the phenotype before progression. Relapsing-remitting patients younger at onset are more likely to display a predominantly inflammatory course, yet relapses number does not affect the age at onset of progression.

Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants.

Plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs) increase the risk of virological failure to first-line non-nucleoside reverse transcriptase inhibitor antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3G/F (APOBEC3G/F) activity. Out of 236 ART-naive subjects evaluated, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I or V108I, were significantly associated with APOBEC3G/F activity (Fisher's P < 0.005), defined as the presence of > 0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a re-analysis of the parent case control study, the presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of non-nucleoside reverse transcriptase inhibitor ART.

Ecological validity of walking capacity tests in multiple sclerosis.

BACKGROUND: Ecological validity implicates in how far clinical assessments refer to real life. Short clinical gait tests up to ten meters and 2- or 6-Minutes Walking Tests (2MWT/6MWT) are used as performance-based outcomes in Multiple Sclerosis (MS) studies and considered as moderately associated with real life mobility. OBJECTIVE: To investigate the ecological validity of 10 Meter Walking Test (10mWT), 2MWT and 6MWT. METHODS: Persons with MS performed 10mWT, 6MWT including 2MWT and 7 recorded days by accelerometry. Ecological validity was assumed if walking tests represented a typical walking sequence in real-life and correlations with accelerometry parameters were strong. RESULTS: In this cohort (n=28, medians: age=45, EDSS=3.2, disease duration=9 years), uninterrupted walking of 2 or 6 minutes occurred not frequent in real life (2.61 and 0.35 sequences/day). 10mWT correlated only with slow walking speed quantiles in real life. 2MWT and 6MWT correlated moderately with most real life walking parameters. CONCLUSION: Clinical gait tests over a few meters have a poor ecological validity while validity is moderate for 2MWT and 6MWT. Mobile accelerometry offers the opportunity to control and improve the ecological validity of MS mobility outcomes.

Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B.

Human APOBEC3 (A3) cytosine deaminases are antiviral restriction factors capable of editing the genome the hepatitis B virus (HBV). Despite the importance of the human A3 protein family for the innate immune response little is known about the clinical relevance for hepatitis B. The aim of this study was to utilize ultra-deep pyrosequencing (UDPS) data to analyse the phenomenon of G-to-A hypermutation of the complete HBV genome and to relate it to fundamental characteristics of patients with chronic hepatitis B. By analysing the viral population of 80 treatment naïve patients (47 HBeAg-positive and 33 HBeAg-negative), we identified an unequal distribution of G-to-A hypermutations across the genome. Our data indicate that G-to-A hypermutation occurs predominantly in a region between nucleotide positions 600 and 1800 a region which is usually single stranded in matured HBV particles. This implies that A3 likely edits HBV in the virion. Hypermutation rates for HBeAg-negative patients were more than 10-fold higher than those of HBeAg-positive patients. For HBeAg-negative patients higher hypermutation rates were significantly associated with the degree of fibrosis. Additionally, we found that for HBeAg-positive chronic hepatitis G-to-A hypermutation rates were significantly associated with the relative prevalence of the G1764A mutation, which is related to HBeAg seroconversion. In total, our data imply an important association of hypermutation mediated by A3 deaminases with the natural progression of chronic hepatitis B infections both in terms of HBeAg seroconversion and disease progression towards cirrhosis.

Patients at risk for peritoneal surface malignancy of colorectal cancer origin: the role of second look laparotomy.

Peritoneal surface malignancy (PSM) is a frequent occurrence in the natural history of colorectal cancer (CRC). Although significant advances have been made in screening of CRC, similar progress has yet to be made in the early detection of PSM of colorectal cancer origin. The fact that advanced CRC can be confined to the peritoneal surface without distant dissemination forms the basis for aggressive multi-modality therapy consisting of cytoreductive surgery (CRS) plus hyperthermic intra-peritoneal chemotherapy (HIPEC), and neoadjuvant and/or adjuvant systemic therapy. Reported overall survival with complete CRS+HIPEC exceeds that of systemic therapy alone for the treatment of PSM from CRC, underscoring the advantage of this multi-modality therapeutic approach. Patients with limited peritoneal disease from CRC can undergo complete cytoreduction, which is associated with the best reported outcomes. As early or limited peritoneal carcinomatosis is undetectable by conventional imaging modalities, second look laparotomy is an important means to identify disease in high-risk patients at a stage most amenable to complete cytoreduction. This review focuses on the identification of patients at risk for PSM from CRC and discusses the role of second look laparotomy.

A web-based tool for personalized prediction of long-term disease course in patients with multiple sclerosis.

BACKGROUND AND PURPOSE: The Evidence-Based Decision Support Tool in Multiple Sclerosis (EBDiMS) is the first web-based prognostic calculator in multiple sclerosis (MS) capable of delivering individualized estimates of disease progression. It has recently been extended to provide long-term predictions based on the data from a large natural history cohort. METHODS: We compared the predictive accuracy and consistency of EBDiMS with that of 17 neurologists highly specialized in MS. RESULTS: We show that whilst the predictive accuracy was similar, neurologists showed a significant intra-rater and inter-rater variability. CONCLUSIONS: Because EBDiMS was consistent, it is of superior utility in a specialist setting. Further field testing of EBDiMS in non-specialist settings, and investigation of its usefulness for counselling patients in treatment decisions, is warranted.

Age and disability accumulation in multiple sclerosis.

OBJECTIVES: We tested the hypothesis that age is a prognostic factor with respect to long-term accumulation of disability in multiple sclerosis (MS). METHODS: Kaplan-Meier analysis and binary logistic regression models determined the effect of age at disease onset, age at onset of progression, and current age on attainment of severe disability levels (Disability Status Scale [DSS] 6-8-10) from the London, Ontario, database (n = 1,023). RESULTS: Older age at relapsing-remitting (RR) phase onset was associated with higher risk of reaching advanced DSS scores. This was independent of disease duration and early relapse frequency but secondary to increased risk of conversion to secondary progressive (SP) MS. Onset at age 40 (odds ratio [OR] = 4.22) and at age 50 (OR = 6.04) doubled and tripled risks of developing SP, compared to age 20 (OR = 2.05). Younger age at conversion to SPMS was associated with shorter times to high DSS scores from disease onset. The progressive course, unaffected by age at RR onset, was only modestly affected by age at SP onset. Among primary progressive and RR/SP patients, median ages at attainment of DSS scores were strikingly similar: DSS = 6, 49 vs 48 years; DSS = 8, 58 vs 58 years; and DSS = 10, 78 years for both (p = NS for all comparisons). CONCLUSIONS: Development of SP is the dominant determinant of long-term prognosis, independent of disease duration and early relapse frequency. Age independently affects disability development primarily by changing probability and latency of SP onset, with little effect on the progressive course.

HAGIL (Hamburg Vigil Study): a randomized placebo-controlled double-blind study with modafinil for treatment of fatigue in patients with multiple sclerosis.

OBJECTIVE: To reassess the effect of modafinil, a wakefulness-promoting artificial psychostimulant, on fatigue and neuropsychological measures in patients with multiple sclerosis. METHODS: Multiple sclerosis (MS) patients with a baseline score of ≥4 on the Fatigue Severity Scale (FSS) and an Expanded Disability Status Scale score <7 were eligible for the 8-week randomized, double-blind, placebo-controlled study. Modafinil was dosed up to 200 mg/day within 1 week. Assessments were performed at baseline and after 4 and 8 weeks. The primary outcome parameter was the mean change of the FSS mean score. Secondary outcome variables were other questionnaires covering fatigue, daytime sleepiness and sleep quality. Cognitive impairment was assessed by the oral version of the Symbol Digit Modalities Test (SDMT) and the Paced Auditory Serial Addition Test (PASAT). RESULTS: The study included 121 MS patients. Dropout rate was 9%. Both treatment groups showed improvements through time. While mean FSS at 8 weeks showed a trend difference between groups in the intention-to-treat analysis, the primary endpoint was not met. Assessment of cognitive impairment by SDMT and PASAT showed contradictory results. All other secondary endpoints were not met. There was no major safety concern. CONCLUSIONS: In general, the study does not support modafinil as an effective treatment for MS fatigue. However, the study shows the need for new study designs and endpoints in MS fatigue studies.

Technical and economical assessment of formic acid to recycle phosphorus from pig slurry by a combined acidification-precipitation process.

Dissolution by acidification followed by a liquid/solid separation and precipitation of phosphorus from the liquid phase is one possibility to recycle phosphorus from livestock effluents. To avoid increase of effluent salinity by using mineral acids in the recycling process, the efficiency of two organic acids, formic and acetic acid, in dissolving the mineral phosphorus from piggery wastewater was compared. The amount of formic acid needed to dissolve the phosphorus was reduced three fold, compared to acetic acid. The amount of magnesium oxide needed for further precipitation was decreased by two with formic acid. Neither the carbon load nor the effluent salinity was significantly increased by using formic acid. An economical comparison was performed for the chemical recycling process (mineral fertilizer) vs. centrifugation (organic fertilizer) considering the centrifugation and the mineral fertilizers sold in the market. After optimisation of the process, the product could be economically competitive with mineral fertilizer as superphosphate in less than 10 years.

MRI as an outcome in multiple sclerosis clinical trials.

INTRODUCTION: T2-weighted and gadolinium enhanced T1-weighted MRI scans measure plaque burden and breakdown of the blood-brain barrier, respectively, in multiple sclerosis (MS) lesions. These have become widely used outcome measures for monitoring disease activity in clinical trials and clinical practice. However, their use as surrogates or biomarkers for disability and relapses, key clinical outcome measures, has remained incompletely validated. METHODS: In a clinical trial database comprised of 31 relapsing-remitting and secondary progressive MS trial placebo groups, we assessed relationships between 1) T2 lesion load (TLL) change and disability change and 2) gadolinium enhancement of MS lesions and on-study relapses with univariate and multivariate analyses. RESULTS: In relapsing-remitting MS, TLL change (n = 223) made no independent contribution to predicting change in disability from baseline to trials' end. Similarly, inclusion of gadolinium enhancing lesions (n = 170) into multivariate models did not independently contribute to the predictive value for on-trial relapses. In secondary progressive MS, a small effect of TLL was found for disability change (n = 355) but in multivariate analysis this accounted for less than 5% of the variance in end-of-trial disability. Results were replicated in independent datasets, more than doubling effective sample sizes. CONCLUSIONS: MRI measures widely used in trials of relapsing-remitting and progressive multiple sclerosis add little if anything independently to the clinically relevant relapse and disability outcomes. These results reemphasize the importance of validating potential surrogate markers against clinical measures and highlight the need for better MRI markers of disease activity and progression.

CMA: a comprehensive Bioconductor package for supervised classification with high dimensional data.

BACKGROUND: For the last eight years, microarray-based classification has been a major topic in statistics, bioinformatics and biomedicine research. Traditional methods often yield unsatisfactory results or may even be inapplicable in the so-called "p >> n" setting where the number of predictors p by far exceeds the number of observations n, hence the term "ill-posed-problem". Careful model selection and evaluation satisfying accepted good-practice standards is a very complex task for statisticians without experience in this area or for scientists with limited statistical background. The multiplicity of available methods for class prediction based on high-dimensional data is an additional practical challenge for inexperienced researchers. RESULTS: In this article, we introduce a new Bioconductor package called CMA (standing for "Classification for MicroArrays") for automatically performing variable selection, parameter tuning, classifier construction, and unbiased evaluation of the constructed classifiers using a large number of usual methods. Without much time and effort, users are provided with an overview of the unbiased accuracy of most top-performing classifiers. Furthermore, the standardized evaluation framework underlying CMA can also be beneficial in statistical research for comparison purposes, for instance if a new classifier has to be compared to existing approaches. CONCLUSION: CMA is a user-friendly comprehensive package for classifier construction and evaluation implementing most usual approaches. It is freely available from the Bioconductor website at (http://bioconductor.org/packages/2.3/bioc/html/CMA.html).

Sensitivity and specificity of intrapartum computerised FIGO criteria for cardiotocography and fetal scalp pH during labour: multicentre, observational study.

OBJECTIVE: To identify sensitivity and specificity of computerised cardiotocography (CTG) analysis for fetal acidosis during delivery. DESIGN: Retrospective observational study. SETTING: Tertiary referral labour ward, Technical University München (TUM) and University Witten/Herdecke (UWH). POPULATION: All deliveries, which had at least one fetal scalp pH measurement and electronically saved CTG traces, between 2000 and 2002 (TUM) and between 2004 and 2005 (UWH). METHOD: Correlation analysis of fetal scalp pH values and computerised International Federation of Obstetrics and Gynecology (FIGO) classification using 'CTG Online' program of digitally saved CTG traces. MAIN OUTCOME MEASURES: Fetal scalp pH values, FIGO parameter (baseline, variability, acceleration and deceleration) using computerised analysis. RESULTS: Both collectives showed a high sensitivity (95.0%) for computerised FIGO classification 'suspect' and 'pathological', together with a low specificity (21.8%) for fetal acidosis. The most sensitive single FIGO parameter was deceleration. Very low sensitivity (<50%) was shown for the parameters variability and acceleration. CONCLUSIONS: Computerised CTG analysis is highly sensitive for fetal acidosis and can be used as an objective adjunctive criterion during delivery. Further CTG data are needed to adjust and optimise each FIGO parameter and increase sensitivity and specificity.

The efficiency of biological aerobic treatment of piggery wastewater to control nitrogen, phosphorus, pathogen and gas emissions.

Due to the water pollution and in order to reduce the nitrogen load applied on soils, biological nitrogen removal treatment of piggery wastewaters was developed in Brittany (France), with 250-300 units running. Four types of treatment processes were built including a biological reactor allowing to remove about 60-70% of the nitrogen content as gas by nitrification/denitrification. The addition of different mechanical separators (screw-press, centrifuge decanter ...) led to concentration of phosphorus in an exportable solid phase, allowing a reduction up to 80% of the phosphorus applied locally on soils. Moreover, a reduction of the gaseous emissions was observed using this management process as compared to conventional management (storage + land spreading) including ammonia (up to 68%) and greenhouse gases (55%). Finally, the level of enteric and pathogenic bacteria was also decreased with the treatment process as compared to conventional management systems. However, in spite of these results, the significant cost of the treatment must be underlined and alternative systems including anaerobic digestion will have to be studied.

Disability as an outcome in MS clinical trials.

BACKGROUND: Inferences about long-term effects of therapies in multiple sclerosis (MS) have been based on surrogate markers studied in short-term trials. Preventing progressive disability is the key therapeutic goal but there remains no validated definition for its measurement in a trial context. Meanwhile, MS trials continue to shorten and to depend on unvalidated surrogates. Since there have been no treatment claims for improving unremitting disability, worsening of disability in the placebo/control arm must occur for effectiveness on this outcome to be shown. METHODS: We examined widely-used clinical surrogates of long-term disability progression in individual patients with MS within a unique database from the placebo arms of 31 randomized clinical trials. RESULTS: Detection of treatment effects in secondary progressive MS trials is undermined by noise in disability measurement. Whereas existing measures can be partially validated in secondary progressive MS, this is not the case in relapsing-remitting MS. Here, examination of widely used definitions of treatment failure demonstrated that disability progression was no more likely than similarly defined improvement. Existing definitions of disease progression in short-term intervention trials in relapsing-remitting patients reflect random variation, measurement error, and remitting relapses. CONCLUSION: Clinical surrogates of unremitting disability used in trials of relapsing-remitting multiple sclerosis cannot be validated. Trials have been too short or degrees of disability change too small to measure the key outcomes. These analyses highlight the difficulty in determining effectiveness of therapy in chronic diseases.

Evaluating microarray-based classifiers: an overview.

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy.