A Markov Multi-State model of lupus nephritis urine biomarker panel dynamics in children: Predicting changes in disease activity.

BACKGROUND: A urine 'biomarker panel' comprising alpha-1-acid-glycoprotein, ceruloplasmin, transferrin and lipocalin-like-prostaglandin-D synthase performs to an 'excellent' level for lupus nephritis identification in children cross-sectionally. The aim of this study was to assess if this biomarker panel predicts lupus nephritis flare/remission longitudinally. METHODS: The novel urinary biomarker panel was quantified by enzyme linked immunoabsorbant assay in participants of the United Kingdom Juvenile Systemic Lupus Erythematosus (UK JSLE) Cohort Study, the Einstein Lupus Cohort, and the South African Paediatric Lupus Cohort. Monocyte chemoattractant protein-1 and vascular cell adhesion molecule-1 were also quantified in view of evidence from other longitudinal studies. Serial urine samples were collected during routine care with detailed clinical and demographic data. A Markov Multi-State model of state transitions was fitted, with predictive clinical/biomarker factors assessed by a corrected Akaike Information Criterion (AICc) score (the better the model, the lower the AICc score). RESULTS: The study included 184 longitudinal observations from 80 patients. The homogeneous multi-state Markov model of lupus nephritis activity AICc score was 147.85. Alpha-1-acid-glycoprotein and ceruloplasmin were identified to be the best predictive factors, reducing the AICc score to 139.81 and 141.40 respectively. Ceruloplasmin was associated with the active-to-inactive transition (hazard ratio 0.60 (95% confidence interval [0.39, 0.93])), and alpha-1-acid-glycoprotein with the inactive-to-active transition (hazard ratio 1.49 (95% confidence interval [1.10, 2.02])). Inputting individual alpha-1-acid-glycoprotein/ceruloplasmin values provides 3, 6 and 12 months probabilities of state transition. CONCLUSIONS: Alpha-1-acid-glycoprotein was predictive of active lupus nephritis flare, whereas ceruloplasmin was predictive of remission. The Markov state-space model warrants testing in a prospective clinical trial of lupus nephritis biomarker led monitoring.

Mangiferin blocks proliferation and induces apoptosis of breast cancer cells via suppression of the mevalonate pathway and by proteasome inhibition.

Mangiferin is a natural xanthone glycoside with therapeutic potential. Herein, its cytotoxic properties were explored in a human cell model of breast adenocarcinoma. The results supported the multi-target nature of mangiferin action, as the inhibition of three enzymatic systems, namely HMG-CoA reductase, the proteasome and plasmin, respectively in charge of regulating cholesterol homeostasis, protein turnover and cell adhesion, was documented for the first time. Globally, mangiferin was able to selectively block breast cancer cell growth by inducing apoptosis and by arresting cell proliferation through a combined action on cholesterol and proteasome pathways, as well as to inhibit plasmin-mediated mechanisms of cell migration.

Heart rate variability at limiting stationarity: evidence of neuro-cardiac control mechanisms operating at ultra-low frequencies.

This study considers the linkage of exogenously stimulated emotional stress with the neurogenic regulation of heart rate operating at very low frequencies. The objectives were three-fold: to consider the present evidence that such a linkage exists as a primary phenomenon; to compare the potential of a frequency-domain method and a time-domain method in revealing this phenomenon by characterizing heart rate variability (HRV) at frequencies of [0.0005...0.4] Hz and to design, implement and report a physiological experiment in which alternating periods of exposure to bland and high valence visual stimuli might reveal this phenomenon. A methodical challenge was to optimize the length of exposure to the stimulus such that subjects did not have time to habituate to stimuli, whilst acquiring sufficient data (heart beats) such that the ultra-low frequency (ULF) components of HRV could be described. With exposure times set to approximately 5 min, during which time the strength of the stimulus and the corresponding evoked response were considered stationary, the lowest HRV frequency component that could be characterized was 0.003 Hz. In trials with parametrically defined test data, the time-domain method based on the Ornstein­Uhlenbeck Gaussian process (OU-GP) was shown to be better than the frequency-domain method in describing the ULF components of the HRV. In an experimental cohort of 16 subjects, analysis using the OU-GP revealed evidence of cardiac regulatory mechanisms influenced by emotional valence operating in the bandwidth (ULF*) [0.002...0.01] Hz.

Pazopanib and sunitinib trigger autophagic and non-autophagic death of bladder tumour cells.

BACKGROUND: Tyrosine kinase inhibitors (TKI) such as sunitinib and pazopanib display their efficacy in a variety of solid tumours. However, their use in therapy is limited by the lack of evidence about the ability to induce cell death in cancer cells. Our aim was to evaluate cytotoxic effects induced by sunitinib and pazopanib in 5637 and J82 bladder cancer cell lines. METHODS: Cell viability was tested by MTT assay. Autophagy was evaluated by western blot using anti-LC3 and anti-p62 antibodies, acridine orange staining and FACS analysis. Oxygen radical generation and necrosis were determined by FACS analysis using DCFDA and PI staining. Cathepsin B activation was evaluated by western blot and fluorogenic Z-Arg-Arg-AMC peptide. Finally, gene expression was performed using RT-PCR Profiler array. RESULTS: We found that sunitinib treatment for 24 h triggers incomplete autophagy, impairs cathepsin B activation and stimulates a lysosomal-dependent necrosis. By contrast, treatment for 48 h with pazopanib induces cathepsin B activation and autophagic cell death, markedly reversed by CA074-Me and 3-MA, cathepsin B and autophagic inhibitors, respectively. Finally, pazopanib upregulates the α-glucosidase and downregulates the TP73 mRNA expression. CONCLUSION: Our results showing distinct cell death mechanisms activated by different TKIs, provide the biological basis for novel molecularly targeted approaches.

The Ornstein-Uhlenbeck third-order Gaussian process (OUGP) applied directly to the un-resampled heart rate variability (HRV) tachogram for detrending and low-pass filtering.

The heart rate variability signal derived from the ECG is a beat-to-beat record of RR-intervals and is, as a time series, irregularly sampled. It is common engineering practice to resample this record, typically at 4 Hz, onto a regular time axis for conventional analysis using IIR and FIR filters, and power spectral estimators, in the time and frequency domain, respectively. However, such interpolative resampling introduces noise into the signal and the information quality is compromised. Here, the Ornstein-Uhlenbeck third-order band-pass filter is presented which operates on data sampled at arbitrary time and preserves fidelity. The algorithm is available as open source code for MATLAB(®) (MathWorks™ Inc.) and supported by an interactive website at http://clinengnhs.liv.ac.uk/OUGP.htm.

An efficient time-varying filter for detrending and bandwidth limiting the heart rate variability tachogram without resampling: MATLAB open-source code and Internet web-based implementation.

The heart rate variability (HRV) signal derived from the ECG is a beat-to-beat record of RR intervals and is, as a time series, irregularly sampled. It is common engineering practice to resample this record, typically at 4 Hz, onto a regular time axis for analysis in advance of time domain filtering and spectral analysis based on the DFT. However, it is recognised that resampling introduces noise and frequency bias. The present work describes the implementation of a time-varying filter using a smoothing priors approach based on a Gaussian process model, which does not require data to be regular in time. Its output is directly compatible with the Lomb-Scargle algorithm for power density estimation. A web-based demonstration is available over the Internet for exemplar data. The MATLAB (MathWorks Inc.) code can be downloaded as open source.

Targeting proteasomes with natural occurring compounds in cancer treatment.

Aberrant cellular proliferation and compromised apoptotic pathways are hallmarks of cancer aggressiveness, and in this framework, the role of protein degradation machineries has been extensively dissected. Among proteases, the proteasome is unequivocally central in the intracellular regulation of both these processes, thus several proteasome-directed therapies have been investigated, aiming at controlling its activity and possibly restoring normal cell functions. Numerous studies reported proteasome inhibitors (both synthetic and natural occurring) to potently and selectively induce apoptosis in many types of cancer cells. In this review we discuss recent advances in proteasomal modulation by some natural occurring polyphenols, globally providing evidence of the proteasome role as therapeutic target in cancer treatment.

50 Hz extremely low frequency electromagnetic fields enhance protein carbonyl groups content in cancer cells: effects on proteasomal systems.

Electromagnetic fields are an assessed cause of prolonging free radicals lifespan. This study was carried out to investigate the influence of extremely low frequency electromagnetic fields on protein oxidation and on the 20S proteasome functionality, the complex responsible for the degradation of oxidized proteins. Caco 2 cells were exposed, for 24-72 hours, to 1 mT, 50 Hz electromagnetic fields. The treatment induced a time-dependent increase both in cell growth and in protein oxidation, more evident in the presence of TPA, while no changes in cell viability were detected. Exposing the cells to 50 Hz electromagnetic fields caused a global activation of the 20S proteasome catalytic components, particularly evident at 72 hours exposure and in the presence of TPA. The finding that EGCG, a natural antioxidant compound, counteracted the field-related pro-oxidant effects demonstrates that the increased proteasome activity was due to an enhancement in intracellular free radicals.

Aflatoxin B1 misregulates the activity of serine proteases: possible implications in the toxicity of some mycotoxin.

Aflatoxins are highly hazardous contaminants of common food and feed. Aflatoxin B1 in particular, the most predominant among aflatoxins, was thoroughly demonstrated to be highly toxic, mutagenic, teratogenic and carcinogenic in many animal species. Besides its established targets and effects, this work investigates on the possible direct interaction between aflatoxin B1 and three major serine proteases, namely elastase, thrombin and trypsin. These proteases belongs to a class of structurally and functionally related proteins pivotal in both direct and indirect regulation of a number of cellular events. Additionally, several pathological processes, including cancer, inflammatory processes and thrombosis, rely upon the subtle equilibrium between these enzymes and their potential modulators: in fact, their misregulation, caused by foreign molecules, could facilitate (or be the cause for) the occurrence of these pathologies. Our results provide the evidence for a reversible binding between AFB1 and these enzymes, likely to have profound implications in the manifestation of aflatoxicosis. Precisely, the toxin behaved as a moderate competitive inhibitor toward the enzymatic activity of the serine proteases in the low micromolar range.

Pomegranate fruit components modulate human thrombin.

Pomegranate (Punica granatum) is an important source of polyphenols with assessed antioxidant properties. The aims of this study were: (i) the characterization of the monomeric phenolic variability on each isolated fruit component (endocarp, mesocarp, aril); (ii) the study on the effect of pomegranate fruit components on human thrombin amidolytic activity. Collectively, our data show that pomegranate components contain bioactive metabolites (mainly ellagic acid) and suggest a potential role for the pomegranate extract in the regulation of a number of physio-pathological processes involving thrombin (or thrombin-like proteinase).

Wheat sprout extract induces changes on 20S proteasomes functionality.

Wheat sprouts contain a very high level of organic phosphates and a powerful cocktail of different molecules such as enzymes, reducing glycosides and polyphenols. The antioxidant properties of wheat sprouts have been widely documented and it has been shown that they are able to protect DNA against free-radicals mediated oxidative damage. Furthermore, we have recently reported on the effects of several polyphenols on 20S proteasomes, underlying the dual role of epigallocatechin-3-gallate as an antioxidant and a proteasome effector in cancer cells. The aim of this study was to investigate the effects of wheat sprout extracts on 20S proteasome functionality. Wheat sprout extracts have been analysed and characterized for their polyphenolic content using the Folin-Ciocalteau reagent and RP-HPLC technique. Comparing our data with a polyphenol standard mixture we identified five different polyphenols: gallic acid, epigallocatechin-3-gallate, epigallocatechin, epicatechin and catechin. The treatment of isolated 20S proteasomes with the extract induced a gradual inhibition of all the tested components, ChT-L, T-L, PGPH and BrAAP, in both the complexes. At low extract concentration a slight activation of the enzyme was evident only for the BrAAP component of the constitutive enzyme and the ChT-L activity of the immunoproteasome. beta-casein degradation rate decreased, particularly with the immunoproteasome. Human Colon adenocarcinoma (Caco) cells, stimulated with 12-O-tetradecanoylphorbol-13-acetate, showed activation of the 20S proteasome activities at short incubation times and an increase in intracellular oxidative proteins. Cells treatment with wheat sprout extract led to proteasome inhibition in unstimulated cells and attenuated the effects mediated by TPA. Finally, exposure to the extract affected the expression levels of pro-apoptotic proteins.

Continuous and discrete time survival analysis: neural network approaches.

In this paper we describe and compare two neural network models aimed at survival analysis modeling, based on formulations in continuous and discrete time. Learning in both models is approached in a Bayesian inference framework. We test the models on a real survival analysis problem, and we show that both models exhibit good discrimination and calibration capabilities. The C index of discrimination varied from 0.8 (SE=0.093) at year 1, to 0.75 (SE=0.034) at year 7 for the continuous time model; from 0.81 (SE=0.07) at year 1, to 0.75 (SE=0.033) at year 7 for the discrete time model. For both models the calibration was good (p<0.05) up to 7 years.

Measurement of the optical parameters of the Virgo interferometer.

The Virgo interferometer, aimed at detecting gravitational waves, is now in a commissioning phase. Measurements of its optical properties are needed for the understanding of the instrument. We present the techniques developed for the measurement of the optical parameters of Virgo. These parameters are compared with the Virgo specifications.

Flavonoids inhibit the amidolytic activity of human thrombin.

The effect of a group of natural flavonoids on human thrombin amidolytic activity was investigated using a spectrophotometric inhibition assay while information on the kinetics and thermodynamics was obtained using optical biosensor techniques. All the flavonoids tested acted as reversible inhibitors, and the quercetin-thrombin complex was found to be most stable at pH=7.5. Docking analysis indicated that quercetin's inhibitory behavior could be related to its planar structure and low steric hindrance, and to its ability to form a critical H-bond with thrombin His57.

A novel information geometric approach to variable selection in MLP networks.

In this paper, a novel information geometric-based variable selection criterion for multi-layer perceptron networks is described. It is based on projections of the Riemannian manifold defined by a multi-layer perceptron network on submanifolds defined by multi-layer perceptron networks with reduced input dimension. We show how the divergence between models can be used as a criterion for an efficient search in the space of networks with different inputs. Then, we show how the posterior probabilities of the models can be evaluated to rank the projected models. Finally, we test our algorithm on synthetic and real data, and compare its performances with other methods reported in literature.

Aspirin modulates LPS-induced nitric oxide release in rat glial cells.

Nitric oxide and prostaglandins are among the numerous substances released by activated glial cells. The aim of this study was to evaluate the effect of high-level aspirin on iNOS expression in cultured rat glial cells treated with lipopolysaccharide (LPS) as pathological stimulator. Using Western Blotting, we verified that aspirin enhanced LPS-induced iNOS expression and the presence of 15-deoxy-Delta(12,14)-prostaglandin (15d-PGJ2) suppressed this aspirin effect. However, the exposure of LPS-treated glial cells to aspirin resulted in a decrease of NO production. These results suggest that aspirin interferes with the cross-talk of prostaglandins and NO, blocking the endogenous negative control exerted by COX products on iNOS expression. On the other side, aspirin seems to act directly on iNOS reducing its activity, even if it does not completely block NO release by LPS-stimulated glial cells. Then aspirin could maintain homeostatic functions of NO, while it prevents toxic effects, corresponding to high NO concentrations.

Effect of neurotoxic metal ions on the proteolytic activities of the 20S proteasome from bovine brain.

The effect of oxidative stress induced by neurotoxic metal ions on the properties of the brain 20S proteasome or multicatalytic proteinase complex (MPC) has been studied. Exposure of the 20S proteasome to increasing amounts of Fe(III), Fe(II), Cu(II) or Zn(II) affects its main hydrolytic activities: trypsin-like (T-L), chymotrypsin-like (ChT-L), peptidylglutamyl-peptide hydrolase (PGPH), branched-chain amino acid preferring (BrAAP) and caseinolytic activities, although in different ways. T-L activity showed gradual activation by both iron ions but inhibition by Cu(II) and Zn(II). ChT-L and PGPH activities were inhibited whereas BrAAP activity was widely activated by all the tested metal salts except for zinc ions. Moreover, the exposure to ferrous salt increased the degradation rate of casein. The functional effects appear to be linked to oxidation-induced modifications, as demonstrated by an increase of carbonyl groups following the exposure to metal ions. In addition, modifications induced by ferrous salt on the catalytic subunits were also supported by western blot analyses performed using anti-X, anti-Y and anti-Z antibodies. The results obtained clearly indicate that metal-catalyzed oxidation strongly affects the functions of the brain 20S proteasome, even though the catalytic subunits seem to be differently influenced by oxidative phenomena.

Interaction of Hsp90 with 20S proteasome: thermodynamic and kinetic characterization.

The proteasome and heat shock proteins have been found in the centrosome. The evidence of their copurification reported by several studies suggests that they form stable complex. In addition, Hsp90 is involved in the loading of proteasome-generated antigenic peptides to the class I major histocompatibility complex. In this article, we report a detailed thermodynamic and kinetic characterization of the Hsp90-20S proteasome interaction, using a surface plasmon resonance technique. The modulation exerted by protons in solution has been investigated, and the results have been discussed, taking into account structural motifs characterizing the binding interface between the two macromolecules.

Structure--function relationships in bovine thymus 20S proteasome: a fluorimetric study.

The structure--function relationships occurring on the bovine thymus 20S proteasome, which exhibits the features of an immunoproteasome, have been studied. The investigation has been performed, essentially, using a fluorimetric approach, taking advantage either of the sensitivity of the complex to sodium dodecil sulfate and chaotropic agents (urea and guanidine hydrochloride) or of the presence, on the molecule, of a high number of tryptophan residues. The results obtained indicate that the perturbation or the oxidation of these residues affect the catalytic events taking place on the thymus proteasome and that the functional effects determined by SDS and chaotropic agents most likely occur through a series of progressive structural modifications leading to an inactive molecule. The presence of structural intermediates in the proteasome inactivation process suggests that thymus proteasome is a molecule characterized, at the same time, by structural flexibility (modulation of active sites) and structural stability (maintaining of the quaternary structure) in agreement with its crucial role in the cell life cycle.