Microbial Cysteine Degradation Drives Cryptic Sulfide Redox Chemistry in the Gut

Although microbial biochemistry shapes a dynamic environment in the gut, how bacterial metabolites such as hydrogen sulfide (H2S) mechanistically alter the gut chemical landscape is poorly understood. Here we show for the first time that H2S generated during cysteine metabolism drives the reduction of azo (R-N=N-R’) xenobiotics in bacterial cultures, human fecal microbial communities, and in vivo mouse models. Thus, chemical-chemical interactions, derived from microbial community metabolism, are a key missing feature shaping xenobiotic metabolism in the gut. Changing dietary levels of the H2S xenobiotic redox partner Red 40 transiently decreases mouse fecal sulfide, confirming that a xenobiotic can attenuate sulfide concentration in vivo. Cryptic H2S redox thus modulates sulfur homeostasis in the gut and the fate of xenobiotics to which humans are regularly exposed.

Coherence between Decomposed Components of Wrist and Finger PPG Signals by Imputing Missing Features and Resolving Ambiguous Features

Background: Feature extraction from photoplethysmography (PPG) signals is an essential step to analyze vascular and hemodynamic information. Different morphologies of PPG waveforms from different measurement sites appear. Various phenomena of missing or ambiguous features exist, which limit subsequent signal processing. Methods: The reasons that cause missing or ambiguous features of finger and wrist PPG pulses are analyzed based on the concept of component waves from pulse decomposition. Then, a systematic approach for missing-feature imputation and ambiguous-feature resolution is proposed. Results: From the experimental results, with the imputation and ambiguity resolution technique, features from 35,036 (98.7%) of 35,502 finger PPG cycles and 36307 (99.1%) of 36,652 wrist PPG cycles can be successfully identified. The extracted features became more stable and the standard deviations of their distributions were reduced. Furthermore, significant correlations up to 0.92 were shown between the finger and wrist PPG waveforms regarding the positions and widths of the third to fifth component waves. Conclusion: The proposed missing-feature imputation and ambiguous-feature resolution solve the problems encountered during PPG feature extraction and expand the feature availability for further processing. More intrinsic properties of finger and wrist PPG are revealed. The coherence between the finger and wrist PPG waveforms enhances the applicability of the wrist PPG.

Are you really using Yarning research? Mapping Social and Family Yarning to strengthen Yarning research quality

Yarning as a research method has its grounding as an Aboriginal culturally specified process. Significant to the Research Yarn is relationality, however; this is a missing feature of published research findings. This article aims to address this. The research question was, what can an analysis of Social and Family Yarning tell us about relationality that underpins a Research Yarn. Participant recruitment occurred using convenience sampling, and data collection involved Yarning method. Five steps of data analysis occurred featuring Collaborative Yarning and Mapping. Commonality existed between researcher and participants through predominantly experiences of being a part of Aboriginal community, via Aboriginal organisations and Country. This suggests shared explicit and tacit knowledge and generation of thick data. Researchers should report on their experience with Yarning, the types of Yarning they are using, and the relationality generated from the Social, Family and Research Yarn.

Bayesian Specification Curve Analysis

Science suffers from a reproducibility crisis. Specification Curve Analysis (SCA) helps address this crisis by preventing the selective reporting of results and arbitrary data analysis choices. SCA plots the variability (or heterogeneity) of treatment effects against all ‘reasonable specifications’ (ways to conduct analysis). However, SCA has also been used for formal statistical inference on a type of global average (median) treatment effect (ATE), leading a study by Orben & Przybylski to conclude that ‘the association of [adolescent mental] well-being with regularly eating potatoes was nearly as negative as the association with technology use.’ In contrast, we find relevant associations between certain technologies and well-being, and sharp discrepancies between parent and teenager assessments. These heterogeneous effects are masked by taking medians. In layman’s terms, an ATE may appear practically irrelevant due to averaging over apples and oranges. In addition, the SCA median can have large bias and variance, due to over-weighting statistically implausible control variable specifications. With the Bayesian Specification Curve Analysis (BSCA) we extend SCA to estimate both individual and, if desired, average treatment effects, with controls weighted via Bayesian Model Averaging. The strategy allows to test individual effects, a missing feature in SCA, while improving statistical properties and protecting against false positives. We provide R code that implements BSCA and reproduces our analyses.

IonCRAM: a reference-based compression tool for ion torrent sequence files

Background Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. However, the tools for generating the CRAM formats are not designed to handle the flow signals. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving. Results In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%. Conclusions Reducing the space consumption of NGS data reduces the cost of storage and data transfer. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest; as it ultimately contributes to the overall cost reduction of the clinical test. The space saving achieved by our tool is a practical step in this direction. The tool is open source and available at Code Ocean, github, and http://ioncram.saudigenomeproject.com.

Spatial Classification with Limited Observations Based on Physics-Aware Structural Constraint

Spatial classification with limited feature observations has been a challenging problem in machine learning. The problem exists in applications where only a subset of sensors are deployed at certain regions or partial responses are collected in field surveys. Existing research mostly focuses on addressing incomplete or missing data, e.g., data cleaning and imputation, classification models that allow for missing feature values, or modeling missing features as hidden variables and applying the EM algorithm. These methods, however, assume that incomplete feature observations only happen on a small subset of samples, and thus cannot solve problems where the vast majority of samples have missing feature observations. To address this issue, we propose a new approach that incorporates physics-aware structural constraints into the model representation. Our approach assumes that a spatial contextual feature is observed for all sample locations and establishes spatial structural constraint from the spatial contextual feature map. We design efficient algorithms for model parameter learning and class inference. Evaluations on real-world hydrological applications show that our approach significantly outperforms several baseline methods in classification accuracy, and the proposed solution is computationally efficient on a large data volume.

A Hybrid Approach for the Prediction of Relative Permeability Using Machine Learning of Experimental and Numerical Proxy SCAL Data

Summary Accurate estimation of relative permeability is one of the key parameters for decision making in upstream applications from project appraisal to field development and evaluation of various field development options. In this study, we identify Euler number (Arns et al. 2001) (a quantitative measure of fluid connectivity/distribution) and saturation as being the first-order predictors of relative permeability and develop a reliable correlation between them using machine learning of experimental special core analysis (SCAL) data and pore network simulation results. In order to achieve our objective, first, we developed a machine-learning model based on the random forest algorithm (Breiman 2001) to analyze specific SCAL data that indicates a key missing feature in the traditional saturation-based relative permeability prediction. We identified this missing feature and proposed the Euler characteristic as a potential first-order predictor of relative permeability in combination with in-situ fluid saturations. We generated “artificial” relative permeability data using pore network simulation (Valvatne and Blunt 2004) by systematically varying a set of key parameters such as pore geometry, wettability, and saturation history. Subsequently, we used machine learning to rank the importance of each parameter and identify possible correlative responses to those selected variables. At a fixed saturation (zero-dimensional volumetric abundance) and Euler number coordinates, the relative permeability is very consistent and varies insignificantly across different cases, suggesting these two parameters as first-order predictors. Euler number characterizes the fluid connectivity/distribution, while saturation represents the net volumetric fluid quantity. We believe that Euler number could be the missing first-order predictor in traditional saturation-based predictive relative permeability models, especially for connected pathway dominated flow regime. Finally, we identified the quantitative relationship between relative permeability and Euler characteristic, and present a reliable correlation to determine the relative permeability on the basis of Euler number and saturation.