scholarly journals Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tim Van Den Bossche ◽  
Benoit J. Kunath ◽  
Kay Schallert ◽  
Stephanie S. Schäpe ◽  
Paul E. Abraham ◽  
...  
Keyword(s):  
Bioinformatic Analysis ◽  
Critical Assessment ◽  
Data Sets ◽  
Laboratory Studies ◽  
Human Fecal Sample ◽  
Two Samples ◽  
Peptide Level ◽  
Protein Group ◽  
Functional Profiles ◽  
The Impact

AbstractMetaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

scholarly journals Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows

2021 ◽  
Author(s):  
Tim Van Den Bossche ◽  
Benoit J. Kunath ◽  
Kay Schallert ◽  
Stephanie S. Schäpe ◽  
Paul E. Abraham ◽  
...  
Keyword(s):  
Bioinformatic Analysis ◽  
Critical Assessment ◽  
Data Sets ◽  
Human Fecal Sample ◽  
Two Samples ◽  
Peptide Level ◽  
Protein Group ◽  
Wet Lab ◽  
Functional Profiles ◽  
The Impact

AbstractMetaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear.Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.We observed that variability at the peptide level was predominantly due to wet-lab workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows.CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-lab studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Hydrogen Cyanide Polymers from the Impact of Comet P/Shoemaker-Levy 9 on Jupiter

1997 ◽  
Vol 161 ◽  
pp. 179-187
Author(s):  
Clifford N. Matthews ◽  
Rose A. Pesce-Rodriguez ◽  
Shirley A. Liebman
Keyword(s):  
Amino Acids ◽  
Solar System ◽  
Hydrogen Cyanide ◽  
Nitrogen Heterocycles ◽  
Laboratory Studies ◽  
Heterogeneous Solids ◽  
The Many ◽  
Comet Halley ◽  
The Impact ◽  
By Products

AbstractHydrogen cyanide polymers – heterogeneous solids ranging in color from yellow to orange to brown to black – may be among the organic macromolecules most readily formed within the Solar System. The non-volatile black crust of comet Halley, for example, as well as the extensive orangebrown streaks in the atmosphere of Jupiter, might consist largely of such polymers synthesized from HCN formed by photolysis of methane and ammonia, the color observed depending on the concentration of HCN involved. Laboratory studies of these ubiquitous compounds point to the presence of polyamidine structures synthesized directly from hydrogen cyanide. These would be converted by water to polypeptides which can be further hydrolyzed to α-amino acids. Black polymers and multimers with conjugated ladder structures derived from HCN could also be formed and might well be the source of the many nitrogen heterocycles, adenine included, observed after pyrolysis. The dark brown color arising from the impacts of comet P/Shoemaker-Levy 9 on Jupiter might therefore be mainly caused by the presence of HCN polymers, whether originally present, deposited by the impactor or synthesized directly from HCN. Spectroscopic detection of these predicted macromolecules and their hydrolytic and pyrolytic by-products would strengthen significantly the hypothesis that cyanide polymerization is a preferred pathway for prebiotic and extraterrestrial chemistry.

The impact of acute stress on the neural processing of food cues in bulimia nervosa: Replication in two samples.

2017 ◽  
Vol 126 (5) ◽  
pp. 540-551 ◽  
Author(s):  
Brittany Collins ◽  
Lauren Breithaupt ◽  
Jennifer E. McDowell ◽  
L. Stephen Miller ◽  
James Thompson ◽  
...  
Keyword(s):  
Bulimia Nervosa ◽  
Acute Stress ◽  
Neural Processing ◽  
Food Cues ◽  
Two Samples ◽  
The Impact

scholarly journals Investigating the impact of pre-processing techniques and pre-trained word embeddings in detecting Arabic health information on social media

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yahya Albalawi ◽  
Jim Buckley ◽  
Nikola S. Nikolov
Keyword(s):  
Social Media ◽  
Deep Learning ◽  
Comprehensive Evaluation ◽  
Classification Problem ◽  
Data Sets ◽  
Word Embeddings ◽  
Data Set ◽  
Lower Accuracy ◽  
Health Related ◽  
The Impact

AbstractThis paper presents a comprehensive evaluation of data pre-processing and word embedding techniques in the context of Arabic document classification in the domain of health-related communication on social media. We evaluate 26 text pre-processings applied to Arabic tweets within the process of training a classifier to identify health-related tweets. For this task we use the (traditional) machine learning classifiers KNN, SVM, Multinomial NB and Logistic Regression. Furthermore, we report experimental results with the deep learning architectures BLSTM and CNN for the same text classification problem. Since word embeddings are more typically used as the input layer in deep networks, in the deep learning experiments we evaluate several state-of-the-art pre-trained word embeddings with the same text pre-processing applied. To achieve these goals, we use two data sets: one for both training and testing, and another for testing the generality of our models only. Our results point to the conclusion that only four out of the 26 pre-processings improve the classification accuracy significantly. For the first data set of Arabic tweets, we found that Mazajak CBOW pre-trained word embeddings as the input to a BLSTM deep network led to the most accurate classifier with F1 score of 89.7%. For the second data set, Mazajak Skip-Gram pre-trained word embeddings as the input to BLSTM led to the most accurate model with F1 score of 75.2% and accuracy of 90.7% compared to F1 score of 90.8% achieved by Mazajak CBOW for the same architecture but with lower accuracy of 70.89%. Our results also show that the performance of the best of the traditional classifier we trained is comparable to the deep learning methods on the first dataset, but significantly worse on the second dataset.

Survey Data Quality in Analyzing Harmonized Indicators of Protest Behavior: A Survey Data Recycling Approach

2021 ◽  
pp. 000276422110216
Author(s):  
Kazimierz M. Slomczynski ◽  
Irina Tomescu-Dubrow ◽  
Ilona Wysmulek
Keyword(s):  
Data Processing ◽  
Data Quality ◽  
Survey Data ◽  
A Priori ◽  
Data Sets ◽  
New Approach ◽  
Survey Quality ◽  
Survey Error ◽  
Ex Post ◽  
The Impact

This article proposes a new approach to analyze protest participation measured in surveys of uneven quality. Because single international survey projects cover only a fraction of the world’s nations in specific periods, researchers increasingly turn to ex-post harmonization of different survey data sets not a priori designed as comparable. However, very few scholars systematically examine the impact of the survey data quality on substantive results. We argue that the variation in source data, especially deviations from standards of survey documentation, data processing, and computer files—proposed by methodologists of Total Survey Error, Survey Quality Monitoring, and Fitness for Intended Use—is important for analyzing protest behavior. In particular, we apply the Survey Data Recycling framework to investigate the extent to which indicators of attending demonstrations and signing petitions in 1,184 national survey projects are associated with measures of data quality, controlling for variability in the questionnaire items. We demonstrate that the null hypothesis of no impact of measures of survey quality on indicators of protest participation must be rejected. Measures of survey documentation, data processing, and computer records, taken together, explain over 5% of the intersurvey variance in the proportions of the populations attending demonstrations or signing petitions.

scholarly journals A Two-Stage Joint Model for Nonlinear Longitudinal Response and a Time-to-Event with Application in Transplantation Studies

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Magdalena Murawska ◽  
Dimitris Rizopoulos ◽  
Emmanuel Lesaffre
Keyword(s):  
Empirical Bayes ◽  
Cox Model ◽  
Data Sets ◽  
Two Stage ◽  
Nonlinear Mixed Effects Model ◽  
Resistance Evolution ◽  
Longitudinal Response ◽  
Longitudinal Measurements ◽  
Subject Specific ◽  
The Impact

In transplantation studies, often longitudinal measurements are collected for important markers prior to the actual transplantation. Using only the last available measurement as a baseline covariate in a survival model for the time to graft failure discards the whole longitudinal evolution. We propose a two-stage approach to handle this type of data sets using all available information. At the first stage, we summarize the longitudinal information with nonlinear mixed-effects model, and at the second stage, we include the Empirical Bayes estimates of the subject-specific parameters as predictors in the Cox model for the time to allograft failure. To take into account that the estimated subject-specific parameters are included in the model, we use a Monte Carlo approach and sample from the posterior distribution of the random effects given the observed data. Our proposal is exemplified on a study of the impact of renal resistance evolution on the graft survival.

scholarly journals Modeling the impact of climate change on mussel aquaculture in a coastal upwelling system: A critical assessment

2021 ◽  
Vol 775 ◽  
pp. 145020
Author(s):  
Isabel Fuentes-Santos ◽  
Uxío Labarta ◽  
María José Fernández-Reiriz ◽  
Susan Kay ◽  
Solfrid Sætre Hjøllo ◽  
...  
Keyword(s):  
Climate Change ◽  
Coastal Upwelling ◽  
Critical Assessment ◽  
Impact Of Climate Change ◽  
Upwelling System ◽  
System A ◽  
The Impact

scholarly journals Interdependence between L1 and L2: The case of Syrian children with refugee backgrounds in Canada and the Netherlands

2021 ◽  
pp. 1-36
Author(s):  
Elma Blom ◽  
Adriana Soto-Corominas ◽  
Zahraa Attar ◽  
Evangelia Daskalaki ◽  
Johanne Paradis
Keyword(s):  
The Netherlands ◽  
Maternal Education ◽  
First Language ◽  
Refugee Camp ◽  
Syntactic Skills ◽  
Two Samples ◽  
Bilingual Language Development ◽  
Dutch Sample ◽  
L1 And L2 ◽  
The Impact

Abstract Children who are refugees become bilingual in circumstances that are often challenging and that can vary across national contexts. We investigated the second language (L2) syntactic skills of Syrian children aged 6-12 living in Canada (n = 56) and the Netherlands (n = 47). Our goal was to establish the impact of the first language (L1 = Syrian Arabic) skills on L2 (English, Dutch) outcomes and whether L1–L2 interdependence is influenced by the length of L2 exposure. To measure L1 and L2 syntactic skills, cross-linguistic Litmus Sentence Repetition Tasks (Litmus-SRTs) were used. Results showed evidence of L1–L2 interdependence, but interdependence may only surface after sufficient L2 exposure. Maternal education level and refugee camp experiences differed between the two samples. Both variables impacted L2 outcomes in the Canadian but not in the Dutch sample, demonstrating the importance to examine refugee children’s bilingual language development in different national contexts.

scholarly journals Clinical, Genetics, and Bioinformatic Characterization of Mutations Affecting an Essential Region of PLS3 in Patients with BMND18

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Ting Chen ◽  
Haiying Wu ◽  
Chenxi Zhang ◽  
Jiarong Feng ◽  
Linqi Chen ◽  
...  
Keyword(s):  
Novel Mutation ◽  
Homology Modelling ◽  
Gene Sequencing ◽  
Bioinformatic Analysis ◽  
Actin Binding ◽  
Clinical Genetics ◽  
Loss Of Function ◽  
Mineral Density ◽  
Trait Locus ◽  
The Impact

Background. Bone mineral density quantitative trait locus 18 (BMND18, OMIM #300910) is a type of early-onset osteogenesis imperfecta (OI) caused by loss-of-function mutations in the PLS3 gene, which encodes plastin-3, a key protein in the formation of actin bundles throughout the cytoskeleton. Here, we report a patient with PLS3 mutation caused BMND18 and evaluated all the reported disease-causing mutations by bioinformatic analysis. Methods. Targeted gene sequencing was performed to find the disease-causing mutation in our patient. Bioinformatic analyses mainly including homology modelling and molecular dynamics stimulation were conducted to explore the impact of the previously reported mutations on plastin-3. Results. Gene sequencing showed a novel nonsense mutation (c.745G > T, p.E249X), which locates at a highly conserved region containing residues p.240–266 (LOOP-1) in the PLS3 gene. Further bioinformatic analyses of the previously reported mutations revealed that LOOP-1 is predicted to physically connect the calponin-homology 1 (CH1) and CH2 domains of the ABD1 fragment and spatially locates within the interface of ABD1 and ABD2. It is crucial to the conformation transition and actin-binding function of plastin-3. Conclusions. This report identified a novel mutation that truncates the PLS3 gene. Moreover, bioinformatic analyses of the previous reported mutations in PLS3 gene lead us to find a critical LOOP-1 region of plastin-3 mutations at which may be detrimental to the integral conformation of plastin-3 and thus affect its binding to actin filament.

Human Performance Evaluation of a Metaphor Graphic Display for Respiratory Data

1994 ◽  
Vol 33 (04) ◽  
pp. 390-396 ◽  
Author(s):  
J. G. Stewart ◽  
W. G. Cole
Keyword(s):  
Performance Evaluation ◽  
Human Performance ◽  
Pattern Detection ◽  
Data Sets ◽  
Complex Task ◽  
Graphic Display ◽  
Literal Sense ◽  
Single Number ◽  
The Impact ◽  
Human Problem

Abstract:Metaphor graphics are data displays designed to look like corresponding variables in the real world, but in a non-literal sense of “look like”. Evaluation of the impact of these graphics on human problem solving has twice been carried out, but with conflicting results. The present experiment attempted to clarify the discrepancies between these findings by using a complex task in which expert subjects interpreted respiratory data. The metaphor graphic display led to interpretations twice as fast as a tabular (flowsheet) format, suggesting that conflict between earlier studies is due either to differences in training or to differences in goodness of metaphor, Findings to date indicate that metaphor graphics work with complex as well as simple data sets, pattern detection as well as single number reporting tasks, and with expert as well as novice subjects.

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