Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples.

BACKGROUND: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinical research study, from human biological sample collection and storage, sample preparation, spectral data acquisition, to peptide and protein quantification. In order to remove such diverse and unwanted variability, normalization of the protein data is performed. There have been already several published reviews comparing normalization methods in the -omics field, but reports focusing on proteomic data generated with mass spectrometry (MS) are much fewer. Additionally, most of these reports have only dealt with small datasets. RESULTS: As a case study, here we focused on the normalization of a large MS-based proteomic dataset obtained from an overweight and obese pan-European cohort, where different normalization methods were evaluated, namely: center standardize, quantile protein, quantile sample, global standardization, ComBat, median centering, mean centering, single standard and removal of unwanted variation (RUV); some of these are generic normalization methods while others have been specifically created to deal with genomic or metabolomic data. We checked how relationships between proteins and clinical variables (e.g., gender, levels of triglycerides or cholesterol) were improved after normalizing the data with the different methods. CONCLUSIONS: Some normalization methods were better adapted for this particular large-scale shotgun proteomic dataset of human plasma samples labeled with isobaric tags and analyzed with liquid chromatography-tandem MS. In particular, quantile sample normalization, RUV, mean and median centering showed very good performances, while quantile protein normalization provided worse results than those obtained with unnormalized data.

Trophic dynamics of a simple model ecosystem.

We have constructed a model of community dynamics that is simple enough to enumerate all possible food webs, yet complex enough to represent a wide range of ecological processes. We use the transition matrix to predict the outcome of succession and then investigate how the transition probabilities are governed by resource supply and immigration. Low-input regimes lead to simple communities whereas trophically complex communities develop when there is an adequate supply of both resources and immigrants. Our interpretation of trophic dynamics in complex communities hinges on a new principle of mutual replenishment, defined as the reciprocal alternation of state in a pair of communities linked by the invasion and extinction of a shared species. Such neutral couples are the outcome of succession under local dispersal and imply that food webs will often be made up of suites of trophically equivalent species. When immigrants arrive from an external pool of fixed composition a similar principle predicts a dynamic core of webs constituting a neutral interchange network, although communities may express an extensive range of other webs whose membership is only in part predictable. The food web is not in general predictable from whole-community properties such as productivity or stability, although it may profoundly influence these properties.

Death wishes and explicit requests for euthanasia in a palliative care hospital: an analysis of patients files.

BACKGROUND: In the current public debate in France about end-of-life and legalization of euthanasia, palliative care is considered as a suitable answer or an alternative or even a supplement to euthanasia. The debate is based on opinion surveys, partly because there is a lack of objective data about the incidence of euthanasia requests (ER) in palliative care settings. The aim of this study was to collect, classify and quantify the expressions of wishes to die (WD), based on computerized files for patients admitted to an 81-bed palliative care hospital (PCH) in Paris during 2010-2011. METHODS: Two researchers analyzed the carers' notes extracted on the basis of containing the words "wish to die", "euthanasia" or any expressions relating to death. Notes related to WD and the corresponding patients were then classified in the order: ER, suicidal thought (ST) and other wish to die (OWD). Repeated ER were qualitatively analyzed according to a grid. RESULTS: We found that 195 of the 2157 patients (9%) expressed a WD: 61 (3%) expressed an ER; 15 (1%) described ST and 119 (6%) expressed an OWD without requiring acting. The WD group was predominantly female, stayed longer in the hospital (median 24 vs. 13 days), and consumed more anxiolytics and antidepressants. None of age, disease or marital status was associated with ER. More women and widows expressed an OWD. Twenty-six ER patients also expressed an OWD and two a ST. Six patients repeated their ER: all had poorly controlled symptoms with repercussions for their mental state. CONCLUSION: Our data show the existence of various expressions of WD with a low incidence of ER in a French PCH. The observation of WD including ER is suggestive of good communication between the patients and the care teams. Independent of the changeability of expressions of WD, their very existence should lead to a consideration of the dynamic changes in these WD, and to care staff paying additional attention to the individual, their suffering and the context.