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Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them. In this study, we evaluated the performance of five popular quantitative label-free proteomics software workflows using four different spike-in data sets. Our extensive testing included the number of proteins quantified and the number of missing values produced by each workflow, the accuracy of detecting differential expression and logarithmic fold change and the effect of different imputation and filtering methods on the differential expression results. We found that the Progenesis software performed consistently well in the differential expression analysis and produced few missing values. The missing values produced by the other software decreased their performance, but this difference could be mitigated using proper data filtering or imputation methods. Among the imputation methods, we found that the local least squares (lls) regression imputation consistently increased the performance of the software in the differential expression analysis, and a combination of both data filtering and local least squares imputation increased performance the most in the tested data sets.

Prospective, community-based surveillance systems for measuring birth, death, and population movement rates may have advantages over the 'gold-standard' retrospective household survey in humanitarian contexts. A community-based, monthly surveillance system was established in South Kivu, Democratic Republic of the Congo, in partnership with a local implementing partner and the national ministry of health. Data were collected on the occurrence of births, deaths, arrivals, and departures over the course of one year, and a retrospective survey was conducted at the end of the period to validate the information. Discrepancies between the two approaches were resolved by a third visit to the households with discordant records. The study found that the surveillance system was superior in terms of its specificity and sensitivity in measuring crude mortality and birth rates as compared to the survey, demonstrating the method's potential to measure accurately important population-level health metrics in an insecure setting in a timely, community-acceptable manner.

One of the main challenges in food contact materials research is to prove that the presence of non-intentionally added substances (NIAS) is not a safety issue. Migration extracts may contain many unknown substances present at low concentrations. It is difficult and time-consuming to identify all these potential NIAS and concurrently to assess their health risk upon exposure, whereas the health relevance at low exposure levels might not even be an issue. This paper describes a scientifically based, but pragmatic safety assessment approach for unknown substances present at low exposure levels in food contact matrices. This complex mixture safety assessment strategy (CoMSAS) enables one to distinguish toxicologically relevant from toxicologically less relevant substances, when related to their respective levels of exposure, and allows one to focus on the substances of potential health concern. In particular, substances for which exposure will be below certain thresholds may be considered not of health relevance in case specific classes of substances are excluded. This can reduce the amount of work needed for identification, characterisation and evaluation of unknown substances at low concentration. The CoMSAS approach is presented in this paper using a safety assessment of unknown NIAS that may migrate from three carton samples. © 2014 Taylor & Francis. Chemicals/CAS: aflatoxin, 1402-68-2; aflatoxin B1, 1162-65-8; aflatoxin B2, 7220-81-7; aflatoxin G1, 1165-39-5; aflatoxin G2, 7241-98-7; aflatoxin M1, 6795-23-9; ergocornine, 564-36-3; ergocristine, 511-08-0; ergocryptine, 511-09-1; ergometrine, 60-79-7; ergotamine, 113-15-5, 52949-35-6; ether, 60-29-7; fumonisin B1, 116355-83-0; HT 2 toxin, 26934-87-2; nivalenol, 23282-20-4; ochratoxin, 303-47-9, 37203-43-3; T 2 toxin, 21259-20-1; vomitoxin, 51481-10-8; zearalenone, 17924-92-4

Control of human African trypanosomiasis (HAT) in the Democratic Republic of Congo is based on mass population screening by mobile teams; a costly and labor-intensive approach. We hypothesized that blood samples collected on filter paper by village health workers and processed in a central laboratory might be a cost-effective alternative. We estimated sensitivity and specificity of micro-card agglutination test for trypanosomiasis (micro-CATT) and enzyme-linked immunosorbent assay (ELISA)/T.b. gambiense on filter paper samples compared with parasitology-based case classification and used the results in a Monte Carlo simulation of a lot quality assurance sampling (LQAS) approach. Micro-CATT and ELISA/T.b. gambiense showed acceptable sensitivity (92.7% [95% CI 87.4-98.0%] and 82.2% [95% CI 75.3-90.4%]) and very high specificity (99.4% [95% CI 99.0-99.9%] and 99.8% [95% CI 99.5-100%]), respectively. Conditional on high sample size per lot (> or = 60%), both tests could reliably distinguish a 2% from a zero prevalence at village level. Alternatively, these tests could be used to identify individual HAT suspects for subsequent confirmation.

The definitive version is available at www3.interscience.wiley.com, Most Human African Trypanosomiasis (HAT) control programmes in areas endemic for Trypanosoma brucei gambiense rely on a strategy of active mass screening with the Card Agglutination Test for Trypanosomiasis (CATT)/T. b. gambiense. We evaluated the performance, stability and reproducibility of the CATT/T. b. gambiense on blood-impregnated filter papers (CATT-FP) in Kajo-Keji County, South-Sudan, where some areas are inaccessible to mobile teams. The CATT-FP was performed with a group of 100 people with a positive CATT on whole blood including 17 confirmed HAT patients and the results were compared with the CATT on plasma (CATT-P). The CATT-FP was repeated on impregnated filter papers stored at ambient and refrigerated temperature for 1, 3, 7 and 14 days. Another 82 patients with HAT, including 78 with a positive parasitology, were tested with the CATT-FP and duplicate filter paper samples were sent to a reference laboratory to assess reproducibility. The CATT-FP was positive in 90 of 99 patients with HAT (sensitivity: 91%). It was less sensitive than the CATT-P (mean dilution difference: −2.5). There was no significant loss of sensitivity after storage for up to 14 days both at ambient and cool temperature. Reproducibility of the CATT-FP was found to be excellent (kappa: 0.84). The CATT-FP can therefore be recommended as a screening test for HAT in areas where the use of CATT-P is not possible. Further studies on larger population samples in different endemic foci are still needed before the CATT-FP can be recommended for universal use.

BackgroundResearch in quality of life traditionally relies on paper-and-pencil questionnaires. Easy access to the Internet has inspired a number of studies that use the Internet to collect questionnaire data. However, Internet-based data collection may differ from traditional methods with respect to response rate and data quality as well as the validity and reliability of the involved scales. Objective We used a randomized design to compare a paper-and-pencil questionnaire with an Internet version of the same questionnaire with respect to differences in response rate and completeness of data. Methods Women referred for mammography at a Danish public hospital from September 2004 to April 2005, aged less than 67 years and without a history of breast cancer, were eligible for the study. The women received the invitation to participate along with the usual letter from the Department of Radiology. A total of 533 women were invited to participate. They were randomized to receive either a paper questionnaire, with a prepaid return envelope, or a guideline on how to fill in the Internet-based version online. The questionnaire consisted of 17 pages with a total of 119 items, including the Short Form-36, Multidimensional Fatigue Inventory-20, Hospital Anxiety and Depression Scale, and questions regarding social status, education level, occupation, and access to the Internet. Nonrespondents received a postal reminder giving them the option of filling out the other version of the questionnaire. Results The response rate before the reminder was 17.9% for the Internet group compared to 73.2% for the paper-and-pencil group (risk difference 55.3%, P < .001). After the reminder, when the participant could chose between versions of the questionnaire, the total response rate for the Internet and paper-and-pencil group was 64.2% and 76.5%, respectively (risk difference 12.2%, P = .002). For the Internet version, 97.8% filled in a complete questionnaire without missing data, while 63.4% filled in a complete questionnaire for the paper-and-pencil version (risk difference 34.5%, P < .001). Conclusions The Internet version of the questionnaire was superior with respect to completeness of data, but the response rate in this population of unselected patients was low. The general population has yet to become more familiar with the Internet before an online survey can be the first choice of researchers, although it is worthwhile considering within selected populations of patients as it saves resources and provides more complete answers. An Internet version may be combined with the traditional version of a questionnaire, and in follow-up studies of patients it may be more feasible to offer Internet versions.

The filter paper method for measuring soil water potential was evaluated. The method was calibrated using salt solutions (-1.4 bars to -22.4 bars), sample chamber psychrometer (-1 to -50 bars), pressure plate (-0.1 to - 15 bars) and soil column at equilibrium (0 to -0.2 bars). It was found that the absolute temperature had little effect on the predicted soil water potential, but a temperature variation had a large effect. It was found that the temperature fluctuation must be small. The predicted water potential was influenced by the type of contact of the soil with the filter paper. It is suggested that one filter paper be placed beneath the soil (good contact for liquid or vapour flow) and one filter paper be placed above the soil not in physical contact (allowing vapour flow only). The equilibrium between the filter paper and soil mass was essential completed by the end of two days and certainly by the end of five days.