LazyFox: fast and parallelized overlapping community detection in large graphs

The detection of communities in graph datasets provides insight about a graph's underlying structure and is an important tool for various domains such as social sciences, marketing, traffic forecast, and drug discovery. While most existing algorithms provide fast approaches for community detection, their results usually contain strictly separated communities. However, most datasets would semantically allow for or even require overlapping communities that can only be determined at much higher computational cost. We build on an efficient algorithm, Fox, that detects such overlapping communities. Fox measures the closeness of a node to a community by approximating the count of triangles which that node forms with that community. We propose LazyFox, a multi-threaded adaptation of the Fox algorithm, which provides even faster detection without an impact on community quality. This allows for the analyses of significantly larger and more complex datasets. LazyFox enables overlapping community detection on complex graph datasets with millions of nodes and billions of edges in days instead of weeks. As part of this work, LazyFox's implementation was published and is available as a tool under an MIT licence at https://github.com/TimGarrels/LazyFox.

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks

MOTIVATION

While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem.

RESULTS

We present DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e. molecular differences that are the source of high differential drug scores can be retrieved. We predict differential drug response in breast cancer using transcriptomics, proteomics, phosphosite and metabolomics measurements and contrast estrogen receptor positive and receptor negative patients. DrDimont performs better than drug prediction based on differential protein expression or PageRank when evaluating it on ground truth data from cancer cell lines. We find proteomic and phosphosite layers to carry most information for distinguishing drug response.

AVAILABILITY AND IMPLEMENTATION

DrDimont is available on CRAN: https://cran.r-project.org/package=DrDimont.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

An oscillatory network controlling self-renewal of skeletal muscle stem cells

The balance between proliferation and differentiation of muscle stem cells is tightly controlled, ensuring the maintenance of a cellular pool needed for muscle growth and repair. Muscle stem cells can proliferate, they can generate differentiating cells, or they self-renew to produce new stem cells. Notch signaling plays a crucial role in this process. Recent studies revealed that expression of the Notch effector HES1 oscillates in activated muscle stem cells. The oscillatory expression of HES1 periodically represses transcription from the genes encoding the myogenic transcription factor MYOD and the Notch ligand DLL1, thereby driving MYOD and DLL1 oscillations. This oscillatory network allows muscle progenitor cells and activated muscle stem cells to remain in a proliferative and 'undecided' state, in which they can either differentiate or self-renew. When HES1 is downregulated, MYOD oscillations become unstable and are replaced by sustained expression, which drives the cells into terminal differentiation. During development and regeneration, proliferating stem cells contact each other and the stability of the oscillatory expression depends on regular DLL1 inputs provided by neighboring cells. In such communities of cells that receive and provide Notch signals, the appropriate timing of DLL1 inputs is important, as sustained DLL1 cannot replace oscillatory DLL1. Thus, in cell communities, DLL1 oscillations ensure the appropriate balance between self-renewal and differentiation. In summary, oscillations in myogenic cells are an important example of dynamic gene expression determining cell fate.

Partisan self-interest is an important driver for people's support for the regulation of targeted political advertising

The rapid emergence of online targeted political advertising has raised concerns over data privacy and what the government’s response should be. This paper tested and confirmed the hypothesis that public attitudes toward stricter regulation of online targeted political advertising are partially motivated by partisan self-interest. We conducted an experiment using an online survey of 1549 Americans who identify as either Democrats or Republicans. Our findings show that Democrats and Republicans believe that online targeted political advertising benefits the opposing party. This belief is based on their conviction that their political opponents are more likely to be mobilized by online targeted political advertising than are supporters of their own party. We exogenously manipulated partisan self-interest considerations of a random subset of participants by truthfully informing them that, in the past, online targeted political advertising has benefited Republicans. Our findings show that Republicans informed about this had less favorable attitudes toward regulation than did their uninformed co-partisans. This suggests that Republicans’ attitudes regarding stricter regulation are based not solely on concerns about privacy violations, but also, in part, are caused by beliefs about partisan advantage. The results imply that people are willing to accept violations of their privacy if their preferred party benefits from the use of online targeted political advertising.

Oscillations of Delta-like1 regulate the balance between differentiation and maintenance of muscle stem cells

Cell-cell interactions mediated by Notch are critical for the maintenance of skeletal muscle stem cells. However, dynamics, cellular source and identity of functional Notch ligands during expansion of the stem cell pool in muscle growth and regeneration remain poorly characterized. Here we demonstrate that oscillating Delta-like 1 (Dll1) produced by myogenic cells is an indispensable Notch ligand for self-renewal of muscle stem cells in mice. Dll1 expression is controlled by the Notch target Hes1 and the muscle regulatory factor MyoD. Consistent with our mathematical model, our experimental analyses show that Hes1 acts as the oscillatory pacemaker, whereas MyoD regulates robust Dll1 expression. Interfering with Dll1 oscillations without changing its overall expression level impairs self-renewal, resulting in premature differentiation of muscle stem cells during muscle growth and regeneration. We conclude that the oscillatory Dll1 input into Notch signaling ensures the equilibrium between self-renewal and differentiation in myogenic cell communities.

Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN-amplified neuroblastoma

Here we sought metabolic alterations specifically associated with MYCN amplification as nodes to indirectly target the MYCN oncogene. Liquid chromatography-mass spectrometry-based proteomics identified seven proteins consistently correlated with MYCN in proteomes from 49 neuroblastoma biopsies and 13 cell lines. Among these was phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in de novo serine synthesis. MYCN associated with two regions in the PHGDH promoter, supporting transcriptional PHGDH regulation by MYCN. Pulsed stable isotope-resolved metabolomics utilizing ¹³ C-glucose labeling demonstrated higher de novo serine synthesis in MYCN-amplified cells compared to cells with diploid MYCN. An independence of MYCN-amplified cells from exogenous serine and glycine was demonstrated by serine and glycine starvation, which attenuated nucleotide pools and proliferation only in cells with diploid MYCN but did not diminish these endpoints in MYCN-amplified cells. Proliferation was attenuated in MYCN-amplified cells by CRISPR/Cas9-mediated PHGDH knockout or treatment with PHGDH small molecule inhibitors without affecting cell viability. PHGDH inhibitors administered as single-agent therapy to NOG mice harboring patient-derived MYCN-amplified neuroblastoma xenografts slowed tumor growth. However, combining a PHGDH inhibitor with the standard-of-care chemotherapy drug, cisplatin, revealed antagonism of chemotherapy efficacy in vivo. Emergence of chemotherapy resistance was confirmed in the genetic PHGDH knockout model in vitro. Altogether, PHGDH knockout or inhibition by small molecules consistently slows proliferation, but stops short of killing the cells, which then establish resistance to classical chemotherapy. Although PHGDH inhibition with small molecules has produced encouraging results in other preclinical cancer models, this approach has limited attractiveness for patients with neuroblastoma.

Of Gene Expression and Cell Division Time: A Mathematical Framework for Advanced Differential Gene Expression and Data Analysis

Estimating fold changes of average mRNA and protein molecule counts per cell is the most common way to perform differential expression analysis. However, these gene expression data may be affected by cell division, an often-neglected phenomenon. Here, we develop a quantitative framework that links population-based mRNA and protein measurements to rates of gene expression in single cells undergoing cell division. The equations we derive are easy-to-use and widely robust against biological variability. They integrate multiple "omics" data into a coherent, quantitative description of single-cell gene expression and improve analysis when comparing systems or states with different cell division times. We explore these ideas in the context of resting versus activated B cells. Analyzing differences in protein synthesis rates enables to account for differences in cell division times. We demonstrate that this improves the resolution and hit rate of differential gene expression analysis when compared to analyzing population protein abundances alone.

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models

Background: Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context. Modules, i.e., groups of nodes with similar topological properties in these networks characterize important biological functions of the underlying biomolecular system. Edges in such molecular networks represent regulatory and physical interactions, and comparing them between conditions provides valuable information on differential molecular mechanisms. However, biological data is inherently noisy and network reduction techniques can propagate errors particularly to the level of edges. We aim to improve the analysis of networks of biological molecules by deriving modules together with edge relevance estimations that are based on global network characteristics. Methods: The key challenge we address here is investigating the capability of stochastic block models (SBMs) for representing and analyzing different types of biomolecular networks. Fitting them to SBMs both delivers modules of the networks and enables the derivation of edge confidence scores, and it has not yet been investigated for analyzing biomolecular networks. We apply SBM-based analysis independently to three correlation-based networks of breast cancer data originating from high-throughput measurements of different molecular layers: either transcriptomics, proteomics, or metabolomics. The networks were reduced by thresholding for correlation significance or by requirements on scale-freeness.  Results and discussion: We find that the networks are best represented by the hierarchical version of the SBM, and many of the predicted blocks have a biologically and phenotypically relevant functional annotation. The edge confidence scores are overall in concordance with the biological evidence given by the measurements. We conclude that biomolecular networks can be appropriately represented and analyzed by fitting SBMs. As the SBM-derived edge confidence scores are based on global network connectivity characteristics and potential hierarchies within the biomolecular networks are considered, they could be used as additional, integrated features in network-based data comparisons.

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models

Background: Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context. Modules, i.e., groups of nodes with similar topological properties in these networks characterize important biological functions of the underlying biomolecular system. Edges in such molecular networks represent regulatory and physical interactions, and comparing them between conditions provides valuable information on differential molecular mechanisms. However, biological data is inherently noisy and network reduction techniques can propagate errors particularly to the level of edges. We aim to improve the analysis of networks of biological molecules by deriving modules together with edge relevance estimations that are based on global network characteristics.  Methods: We propose to fit the networks to stochastic block models (SBM), a method that has not yet been investigated for the analysis of biomolecular networks. This procedure both delivers modules of the networks and enables the derivation of edge confidence scores. We apply it to correlation-based networks of breast cancer data originating from high-throughput measurements of diverse molecular layers such as transcriptomics, proteomics, and metabolomics. The networks were reduced by thresholding for correlation significance or by requirements on scale-freeness.  Results and discussion: We find that the networks are best represented by the hierarchical version of the SBM, and many of the predicted blocks have a biological meaning according to functional annotation. The edge confidence scores are overall in concordance with the biological evidence given by the measurements. As they are based on global network connectivity characteristics and potential hierarchies within the biomolecular networks are taken into account, they could be used as additional, integrated features in network-based data comparisons. Their tight relationship to edge existence probabilities can be exploited to predict missing or spurious edges in order to improve the network representation of the underlying biological system.

PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ

CCAAT enhancer-binding protein beta (C/EBPβ) is a pioneer transcription factor that specifies cell differentiation. C/EBPβ is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPβ differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPβ alters protein interactions and cell differentiation, suggesting that a C/EBPβ PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPβ using an array technique based on spot-synthesized C/EBPβ-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions. We identified interaction footprints of ∼1,300 proteins in nuclear extracts, many with chromatin modifying, chromatin remodeling, and RNA processing functions. The results suggest that C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.

Self-assembly of Mutant Huntingtin Exon-1 Fragments into Large Complex Fibrillar Structures Involves Nucleated Branching

Huntingtin (HTT) fragments with extended polyglutamine tracts self-assemble into amyloid-like fibrillar aggregates. Elucidating the fibril formation mechanism is critical for understanding Huntington's disease pathology and for developing novel therapeutic strategies. Here, we performed systematic experimental and theoretical studies to examine the self-assembly of an aggregation-prone N-terminal HTT exon-1 fragment with 49 glutamines (Ex1Q49). Using high-resolution imaging techniques such as electron microscopy and atomic force microscopy, we show that Ex1Q49 fragments in cell-free assays spontaneously convert into large, highly complex bundles of amyloid fibrils with multiple ends and fibril branching points. Furthermore, we present experimental evidence that two nucleation mechanisms control spontaneous Ex1Q49 fibrillogenesis: (1) a relatively slow primary fibril-independent nucleation process, which involves the spontaneous formation of aggregation-competent fibrillary structures, and (2) a fast secondary fibril-dependent nucleation process, which involves nucleated branching and promotes the rapid assembly of highly complex fibril bundles with multiple ends. The proposed aggregation mechanism is supported by studies with the small molecule O4, which perturbs early events in the aggregation cascade and delays Ex1Q49 fibril assembly, comprehensive mathematical and computational modeling studies, and seeding experiments with small, preformed fibrillar Ex1Q49 aggregates that promote the assembly of amyloid fibrils. Together, our results suggest that nucleated branching in vitro plays a critical role in the formation of complex fibrillar HTT exon-1 aggregates with multiple ends.

[Impact of a Senso-Motoric Intervention in COPD-Patients Participating in an Outpatient Pulmonary Rehabilitation Program: A Randomized Controlled Trial]

Objective Exercise training provides a cornerstone of pulmonary rehabilitation (PR) in COPD-patients. However, the components of the training are not yet fully investigated. We conducted a randomized controlled trial to investigate the effectiveness of a sensory-motoric training (SMT) in comparison to a conventional strength training (KT) according to the physical performance. Patients and Methods: 43 COPD patients were randomized and participated either in the intervention group (SMT = 30 minutes SMT per day) or in the control group (KT = 30 minutes KT per day). The SMT was performed as circuit training with five stations. The primary endpoint was the difference between T1 (start of the PR) and T2 (end of the PR) in 5-Times Sit-to-stand test (5-STST) in the intergroup comparison. Secondary endpoints were the intra- and intergroup comparisons of T1 and T2 in the 6-Minute Walk Test (6-MWT), COPD Assessment Test (CAT), St. George Respiratory Questionnaire (SGRQ), Hospital Anxiety- and Depression Scale (HADS) and in lung function. Results No significant differences were seen in the results of the 5-STST between the groups. Likewise, in the 6-MWT, SGRQ, CAT, HADS and lung function. The intragroup comparison between T1 and T2 showed significant differences in 5-STST, 6-MWT, SGRQ, CAT and HADS in both groups. The differences in lung function were not significantly, neither in the inter- nor in the intragroup comparison. Conclusion Similarly to a conventional strength training improvements in exercise capacity could be achieved with a SMT during PR in COPD patients. Further studies are necessary to define the role of the SMT in regards to postural control.

Cardiorespiratory Kinetics Determined by Pseudo-Random Binary Sequences - Comparisons between Walking and Cycling

This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O₂) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O₂ of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O₂ kinetics were estimated from heart rate and pulmonary V̇O₂ using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O₂ kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O₂ showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O₂ during walking, the assessment of muscular V̇O₂ kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry.

Recommendations for resistance exercise in cardiac rehabilitation. Recommendations of the German Federation for Cardiovascular Prevention and Rehabilitation

Aerobic endurance training has been an integral component of the international recommendations for cardiac rehabilitation for more than 30 years. Notwithstanding, only in recent years have recommendations for a dynamic resistance-training program been cautiously put forward. The perceived increased risk of cardiovascular complications related to blood pressure elevations are the primary concern with resistance training in cardiac patients; recent studies however have demonstrated that this need not be a contraindication in all cardiac patients. While blood pressure certainly may rise excessively during resistance training, the actual rise depends on a variety of controllable factors including magnitude of the isometric component, the load intensity, the amount of muscle mass involved as well as the number of repetitions and/or the load duration. Intra-arterial blood pressure measurements in cardiac patients have demonstrated that that during low-intensity resistance training [40-60% maximum voluntary contraction (MVC)] with 15-20 repetitions, only modest elevations in blood pressure are revealed, similar to those seen during moderate endurance training. When properly implemented by an experienced exercise therapist, in specific patient groups an individually tailored, medically supervised dynamic resistance training program carries no inherent higher risk for the patient than aerobic endurance training. As an adjunct to endurance training, in selected patients, resistance training can increase muscle strength and endurance, as well as positively influence cardiovascular risk factors, metabolism, cardiovascular function, psychosocial well-being and quality of life. According to present data, resistance training is however not recommended for all patient groups. The appropriate training method and correct performance are highly dependent on each patient's clinical status, cardiac stress tolerance and possible comorbidities. Most studies have used middle-aged men of average normal aerobic performance capacity and with good left-ventricular (LV) function. Data are lacking for high-risk groups, women and older patients. With the current knowledge it is reasonable to include resistance training without any restraints as part of cardiac rehabilitation programs for coronary artery disease (CAD) patients with good cardiac performance capacity (i.e., revascularised and with good myocardial function). As patients with myocardial ischaemia and/or poor left ventricular function may develop wall motion disturbances and/or severe ventricular arrhythmias during resistance exercise, the following criteria are suggested for resistance training: moderate-to-good LV function, good cardiac performance capacity [>5-6 metabolic equivalents of oxygen consumption (METS)=1.4 watt/kg body weight], no symptoms of angina pectoris or ST segment depression under continued maintenance of the medical therapy. Based on available data, this article presents recommendations for risk stratification in cardiac rehabilitation programs with respect to the implementation of dynamic resistance training. Additional recommendations for specific patient groups and detailed directions showing how to structure and implement such therapy programs are presented as well.

Safety and Tolerability of a ‘Refrigeration-free’ Formulation of Interferon Beta-1b - Results of a Double-blind, Multicentre, Comparative Study in Patients with Relapsing-Remitting or Secondary Progressive Multiple Sclerosis

The original glucose-based formulation of Betaferon®/Betaseron® (interferon beta-1b) requires refrigerated storage. A refrigeration-free formulation of interferon beta-1b, based on mannitol, is stable at room temperature for up to 2 years, and offers a greater degree of flexibility for patients with multiple sclerosis (MS). We compared the safety and tolerability of the two formulations in a 24-week, randomized, double-blind, parallel group, Phase IV clinical study conducted in 303 patients with MS. Patients received the glucose formulation (IFNβ-1b-G) for 8 weeks, and were then randomized to receive either IFNβ-1b-G or the refrigeration-free formulation (IFNβ-1b-M) for a further 8 weeks. On completion of the double-blind phase, all patients received IFNβ-1b-M for an 8-week follow-up period. The primary outcome measure was the proportion of injection sites that developed reactions per patient during the double-blind period. In addition, a range of secondary outcomes relating to these reactions was also assessed. The difference in the proportion of injection-site reactions between the two groups was not statistically significant (59% IFNβ-1b-G versus 60% IFNβ-1b-M). There were no statistically significant differences observed between the two treatment groups in any of the secondary tolerability endpoints. The results from this study demonstrate that the tolerability and safety profiles of both formulations are extremely good, and that the refrigeration-free formulation of interferon beta-1b is comparable with that of the original glucose formulation.

A 10-year follow-up of the European multicenter trial of interferon β-1b in secondary-progressive multiple sclerosis

OBJECTIVES

To explore long-term effects of treatment and prognostic relevance of variables assessed at baseline and during the European secondary progressive multiple sclerosis (SPMS) trial of interferon beta 1b (IFNB-1b).

METHODS

We assessed 362 patients (60% female; median age 41 years; Expanded Disability Status Scale (EDSS): 5.5; 51% randomized to IFNB-1b) for their EDSS and treatment history after 10 years. Non-parametric analysis of covariance (ANCOVA) and multivariate linear regression models were applied.

RESULTS

Median EDSS was 6.0 at the end of the randomized controlled trial (RCT), in the IFNB-1b and placebo groups, and 7.0 in long-term follow-up patients (those receiving IFNB-1b in the RCT were 6.5 and those receiving placebo in the RCT were 7.0; p = 0.086). 24 patients (6.6%) were deceased. The EDSS at baseline and the EDSS change during the RCT were the most important predictors of the EDSS 10 years later (partial R(2): 0.47). The ability to predict changes in EDSS 10 years after the RCT was limited (R(2): 0.12). Magnetic resonance imaging (MRI) measures remained in the predictive models, but explained < 5% of the variability.

CONCLUSIONS

The results from this analysis did not provide convincing evidence to support a favorable long-term outcome in those patients allocated IFNB-1b during the RCT, in our SPMS cohort. The progressive stage of the disease remains largely unpredictable by clinical and conventional MRI measures, so better prognostic markers are needed.

[Efficacy of epidural steroid injections for chronic lumbar pain syndromes without neurological deficits. A randomized, double blind study as part of a multimodal treatment concept]

BACKGROUND

Chronic lumbar pain syndromes without neurological deficits are generated by a multitude of causes. Functional, morphological and psychosocial factors are discussed. In many cases a diseased intervertebral disc is found on radiological examination but the clinical relevance of these findings is not clear. For this study it was postulated that a diseased disc results in a local inflammatory reaction therefore causing pain and impairing treatability of patients. An epidural injection of steroids can reduce inflammation and therefore improve treatability and ultimately treatment outcome.

METHODS

A double blind randomized prospective trial was carried out. Patients treated in hospital for a chronic lumbar pain syndrome without neurological deficits within a multimodal treatment program were screened for indications for an epidural steroid injection (e.g. diseased lumbar disc and intention to treat). Patients eligible for the study were randomized into two groups. The treatment group received an epidural injection of 80 mg triamcinolone and 8 ml bupivacaine 0.25 %. The control group received only an epidural injection of 8 ml bupivacaine 0.25 %.

RESULTS

In both groups pain intensity and treatability showed a statistically significant improvement after the epidural injection. The differences between the control and treatment groups were small and not clinically relevant. A small subgroup might profit from the steroid injection. In addition the treatability was dependent on psychometric values and the long-term outcome from a reduction of muscular skeletal dysfunctions.

DISCUSSION

After the epidural injection the decrease in pain and increase in treatability was statistically significant. The mechanism of the improvement is not clear and should be examined further. The epidural injection of a steroid in this subgroup of patients did not lead to a clinical improvement in the outcome.

Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis

The mechanisms that govern proteolytic maturation or complete destruction of the precursor proteins p100 and p105 are fundamental to homeostasis and activation of NF-κB; however, they remain poorly understood. Using mass-spectrometry-based quantitative analysis of noncanonical LTβR-induced signaling, we demonstrate that stimulation induces simultaneous processing of both p100 and p105. The precursors not only form hetero-oligomers but also interact with the ATPase VCP/p97, and their induced proteolysis strictly depends on the signal response domain (SRD) of p100, suggesting that the SRD-targeting proteolytic machinery acts in cis and in trans. Separation of cellular pools by isotope labeling revealed synchronous dynamics of p105 and p100 proteolysis. The generation of p50 and p52 from their precursors depends on functional VCP/p97. We have developed quantitative mathematical models that describe the dynamics of the system and predict that p100-p105 complexes are signal responsive.

Reduced magnetisation transfer ratio in cognitively impaired patients at the very early stage of multiple sclerosis: a prospective, multicenter, cross-sectional study

OBJECTIVES

Cognitive impairment belongs to the core symptoms in multiple sclerosis (MS) and can already be present at the very early stages of the disease. The present study evaluated cognitive functioning after the first clinical presentation suggestive of MS and brain tissue damage in a non-lesion focused MRI approach by using magnetisation transfer imaging (MTI).

SETTING AND PARTICIPANTS

47 patients (15 men and 32 women; mean age: 31.17 years) after the first clinical event suggestive of MS were recruited in six different MS centres in Germany and underwent a neuropsychological test battery including tests for attention, memory and executive function as well as depression and fatigue. MTI and conventional MRI measures (T1/T2 lesion load) were assessed. In addition, Magnetisation Transfer Ratio (MTR) maps were calculated. Primary outcome measure was the investigation of cognitive dysfunction in very early MS in correlation to MRI data.

RESULTS

55.3% of patients with MS failed at least one test parameter. Specifically, 6% were reduced in working memory, 14.9% in focused attention, 25.5% in figural learning and up to 14.9% in executive function. When the sample was subdivided into cognitively impaired and preserved, MTR scores within the cognitively impaired subgroup were significantly lower compared with the preserved group (t(43)=2.346, p=0.02*). No significant differences between the two groups were found in T2-weighted and T1-weighted lesion volume.

CONCLUSIONS

After the first MS-related clinical event, 55.3% of patients showed distinct cognitive deficits. Cognitively impaired patients had significantly lower whole brain MTR, but no differences in focal brain lesion volumes supporting the idea that early cognitive deficits may be related to diffuse loss of brain tissue integrity.

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease

The extent of proteolytic processing of the amyloid precursor protein (APP) into neurotoxic amyloid-β (Aβ) peptides is central to the pathology of Alzheimer's disease (AD). Accordingly, modifiers that increase Aβ production rates are risk factors in the sporadic form of AD. In a novel systems biology approach, we combined quantitative biochemical studies with mathematical modelling to establish a kinetic model of amyloidogenic processing, and to evaluate the influence by SORLA/SORL1, an inhibitor of APP processing and important genetic risk factor. Contrary to previous hypotheses, our studies demonstrate that secretases represent allosteric enzymes that require cooperativity by APP oligomerization for efficient processing. Cooperativity enables swift adaptive changes in secretase activity with even small alterations in APP concentration. We also show that SORLA prevents APP oligomerization both in cultured cells and in the brain in vivo, eliminating the preferred form of the substrate and causing secretases to switch to a less efficient non-allosteric mode of action. These data represent the first mathematical description of the contribution of genetic risk factors to AD substantiating the relevance of subtle changes in SORLA levels for amyloidogenic processing as proposed for patients carrying SORL1 risk alleles.

Long term administration of LMWH - pharmacodynamic parameters under therapeutic or prophylactic regimen of enoxaparin or tinzaparin in neurological rehabilitation patients

We investigated anti-FXa- and anti-FIIa-activity, thrombin generation (ETP), tissue factor pathway inhibitor (TFPI) - and D-dimer in patients exhibiting high bleeding risk in early neurological rehabilitation over 2 months in an observational study. Blood of 64 patients under LMWH administration due to therapeutic (cohort 1 [tinzaparin 90 IE/kg BID, N = 18] and 2 [enoxaparin 100 IE/kg BID; N = 15]) or prophylactic (cohort 3 [tinzaparin 4500 IE; N = 16] and 4 [enoxaparin 4000 IE; N = 15]) indication was drawn before and 4h after injection on day 7 (V1) and 2 months (follow up [V2]). Although the dose in cohort 1 and 2 was similar (median 7000 IE BID), a-FXa-activity was significantly larger under enoxaparin than under tinzaparin (e.g. median at V2: 0.70 IU/ml vs. 0.33 IU/ml). Also, prophylactic enoxaparin exhibited larger a-FXa-activity than tinzaparin (e.g. median at V2: 0.37 IU/ml vs. 0.22 IU/ml). The a-FXa/a-FIIa-ratio in plasma samples at 4h p.a. was about 4 (tinzaparin) and 8 (enoxaparin), respectively. No differences were seen for TFPI and ETP between cohort 1 and 2 or between cohort 3 and 4. D-dimer levels decreased significantly between V1 (e.g. cohort 4 median 1940 ng/ml) and V2 (median 652 ng/ml). Minimal bleeding events occurred in 6 patients (2 under tinzaparin, 4 under enoxaparin) and were associated with significantly higher anti-FXa-activity. In conclusion, although marked differences between tinzaparin and enoxaparin based on anti-FXa-activity were seen, markers of in vivo biological activity such as TFPI and D-dimer were not different. Furthermore, BID tinzaparin is a feasible option for therapeutic anticoagulation in patients with high bleeding risk.

Comparison of skeletal muscle strength between cardiac patients and age-matched healthy controls

The purpose of the present study was to compare muscular strength of knee extensors and arm flexor muscles of cardiac patients (n = 638) and healthy controls (n = 961) in different age groups. Isometric torques were measured in a sitting position with the elbow, hip, and knee flexed to 90(0). For statistical analysis, age groups were pooled in decades from the age of 30 to 90 years. Additionally, the influence of physical lifestyle prior to disease on muscular strength was obtained in the patients. For statistical analysis three-way ANOVA (factors age, gender, and physical activity level) was used.Both in patients and in controls a significant age-dependent decline in maximal torque could be observed for arm flexors and knee extensors. Maximal leg extensor muscle showed statistically significant differences between healthy controls and cardiac patients as well as between subgroups of patients: Physically inactive patients showed lowest torques (male: 148 +/- 18 Nm; female: 82 +/- 25 Nm) while highest values were measured in control subjects (male: 167 +/- 16 Nm; female: 93 +/- 17 Nm). In contrast, arm flexor muscles did not show any significant influence of health status or sports history.This qualitative difference between weight-bearing leg muscles and the muscle group of the upper extremity suggest that lower skeletal muscle strength in heart patients is mainly a consequence of selective disuse of leg muscles rather than any pathological skeletal muscle metabolism. Since a certain level of skeletal muscle strength is a prerequisite to cope with everyday activities, strength training is recommended as an important part of cardiac rehabilitation.

Age-related changes in marathon and half-marathon performances

We examined age-related changes in endurance performance of marathon and half-marathon finishers. A total of 405 515 running times were separated into groups based on age, sex, and distance. After exclusion of repetitive running times, 300 757 runners were analyzed by ANOVA (factors: age, sex). For each age group (six decades, 20-79 years), mean running times for all finishers, as well as top-ten performers, were assessed. As expected, age and sex had significant influence on running times. Female running times were about 10 % (marathon) and 13 % (half-marathon) above the corresponding times of their age-matched peers. The main finding is that in our sample of trained subjects significant age-related losses in endurance performance did not occur before the age of 50 years. Mean marathon and half-marathon times were virtually identical for the age groups from 20-49 years. Moreover, age-related performance decreases (p < 0.01) of the 50 - 69-year-old subjects were only in the range of 2.6 - 4.4 % per decade. These results suggest that the majority of older athletes are able to maintain a high degree of physical plasticity. The hypothesis that lifestyle factors have considerably stronger influences on functional capacity than the factor age is also supported by these findings from physically active and fit elderly.

Comparison of injection site pain and injection site reactions in relapsing-remitting multiple sclerosis patients treated with interferon beta-1a or 1b

This prospective, multicentre, international, observational, cohort study compared injection site pain (ISP) and injection site reactions (ISRS) between interferon beta-1b (IFNB-1b; Betaferon ®) 250 μg subcutaneously every other day and interferon beta-1a (IFNB-1a; Rebif®) 44 μg subcutaneously three times weekly in patients with relapsing-remitting MS. Patients started treatment within 3 months before recruitment and were on full dose of therapy at inclusion. Patients self-injected IFNB and self-assessed ISP for 15 consecutive injections immediately, 30 and 60 min after injection, using a visual analogue scale diary. Study staff assessed ISRS. Of 445 patients (valid cases), ~90% used autoinjectors. More patients were pain-free at all timepoints with IFNB-1b than with IFNB-1a (eg, 30 min: 42.6% versus 19.7%; P< 0.0001). The mean proportion of pain-free injections was greater for IFNB-1b (eg, 30 min: 79.0%) than for IFNB-1a (53.3%; P < 0.0001). The proportion of patients without ISRS was greater for IFNB-1b (second visit 51.8% versus 33.8%; P < 0.0001). Compared with IFNB-1a, more IFNB-1b patients either had no pain or their ISP had no influence on treatment satisfaction (76.9% versus 64.1%; P = 0.006). The impact on tolerability and patient acceptability of any new IFNB product formulations would, however, have to be evaluated in comparative studies. Multiple Sclerosis 2007; 13 : 1153—1160. http://msj.sagepub.com

Conditional and specific NF-kappaB blockade protects pancreatic beta cells from diabetogenic agents

Type 1 diabetes is characterized by the infiltration of inflammatory cells into pancreatic islets of Langerhans, followed by the selective and progressive destruction of insulin-secreting beta cells. Islet-infiltrating leukocytes secrete cytokines such as IL-1beta and IFN-gamma, which contribute to beta cell death. In vitro evidence suggests that cytokine-induced activation of the transcription factor NF-kappaB is an important component of the signal triggering beta cell apoptosis. To study the in vivo role of NF-kappaB in beta cell death, we generated a transgenic mouse line expressing a degradation-resistant NF-kappaB protein inhibitor (DeltaNIkappaBalpha), acting specifically in beta cells, in an inducible and reversible manner, by using the tet-on regulation system. In vitro, islets expressing the DeltaNIkappaBalpha protein were resistant to the deleterious effects of IL-1beta and IFN-gamma, as assessed by reduced NO production and beta-cell apoptosis. This effect was even more striking in vivo, where nearly complete protection against multiple low-dose streptozocin-induced diabetes was observed, with reduced intraislet lymphocytic infiltration. Our results show in vivo that beta cell-specific activation of NF-kappaB is a key event in the progressive loss of beta cells in diabetes. Inhibition of this process could be a potential effective strategy for beta-cell protection.

Escalating immunotherapy of multiple sclerosis--new aspects and practical application

Recent clinical studies in multiple sclerosis (MS) provide new data on the treatment of clinically isolated syndromes, on secondary progression, on direct comparison of immunomodulatory treatments and on dosing issues. All these studies have important implications for the optimized care of MS patients. The multiple sclerosis therapy consensus group (MSTCG) critically evaluated the available data and provides recommendations for the application of immunoprophylactic therapies. Initiation of treatment after the first relapse may be indicated if there is clear evidence on MRI for subclinical dissemination of disease. Recent trials show that the efficacy of interferon beta treatment is more likely if patients in the secondary progressive phase of the disease still have superimposed bouts or other indicators of inflammatory disease activity than without having them. There are now data available, which suggest a possible dose-effect relation for recombinant beta-interferons. These studies have to be interpreted with caution, as some potentially important issues in the design of these studies (e. g. maintenance of blinding in the clinical part of the study) were not adequately addressed. A meta-analysis of selected interferon trials has been published challenging the value of recombinant IFN beta in MS. The pitfalls of that report are discussed in the present review as are other issues relevant to treatment including the new definition of MS, the problem of treatment failure and the impact of cost-effectiveness analyses. The MSTCG panel recommends that the new diagnostic criteria proposed by McDonald et al. should be applied if immunoprophylactic treatment is being considered. The use of standardized clinical documentation is now generally proposed to facilitate the systematic evaluation of individual patients over time and to allow retrospective evaluations in different patient cohorts. This in turn may help in formulating recommendations for the application of innovative products to patients and to health care providers. Moreover, in long-term treated patients, secondary treatment failure should be identified by pre-planned follow-up examinations, and other treatment options should then be considered.

Normierung der Brief Repeatable Battery of Neuropsychological Tests (BRB-N) f�r den deutschsprachigen Raum

The Brief Repeatable Battery of Neuropsychological Tests (BRB-N) is a neuropsychological screening battery, often applied in multiple sclerosis (MS) patients. It is almost exclusively administered in trials and not in the daily practice routine because of the lack of normative values. Using a stepwise linear regression analysis, the dependence of test results on age, gender, and education of 241 healthy control subjects was investigated. Z-values of -1.68 or less were considered pathological. Based on the normative values, the proportions of cognitively impaired patients with relapsing-remitting MS (RRMS, n=43) and secondary progressive MS patients (SPMS, n=60) were calculated. The regression model explained 2.7-25.0% of the variance of test performances. Cognitive impairment occurred in 38% and in 47% of the RRMS and the SPMS groups, respectively. In both groups attention and concentration impairment was prominent, while in the SPMS group memory was also frequently affected. The proportion of cognitively impaired MS patients reflected the figures that could be found in the literature.