RANG: Reconstructing reproducible R computational environments

A complete declarative description of the computational environment is often missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational reproducibility in the future, even when data and computer code are available. The R package rang is a complete solution for generating the declarative description for other researchers to automatically reconstruct the computational environment at a specific time point. The reconstruction process, based on Docker, has been tested for R code as old as 2001. The declarative description generated by rang satisfies the definition of a reproducible research compendium and can be shared as such. In this contribution, we show how rang can be used to make otherwise unexecutable code, spanning from fields such as computational social science and bioinformatics, executable again. We also provide instructions on how to use rang to construct reproducible and shareable research compendia of current research. The package is currently available from CRAN (https://cran.r-project.org/web/packages/rang/index.html) and GitHub (https://github.com/chainsawriot/rang)

Biodegradation of methyl ethyl ketone and methyl isopropyl ketone in a composite bead biofilter

[Abstract] Biodegradation of methyl ethyl ketone (MEK) and methyl isopropyl ketone (MIPK) in a composite bead biofilter was investigated. Both microbial growth rate kg and biochemical reaction rate kd would be inhibited at higher inlet concentration. The kg and kd values of MEK were greater than those of MIPK in the average inlet concentration of 100-300 ppm. For the microbial growth process, the degree of inhibitive effect was almost the same sensitivity for two ketone compounds. Zeroorder kinetic with the diffusion rate limitation could be regarded as the most adequate biochemical reaction model. For the biochemical reaction process, the inhibitive effect was more pronounced for MEK in the average inlet concentration of 100-150 ppm and it was more pronounced for MIPK in the average inlet concentration of 150-300 ppm. The maximum elimination capacity of MEK and MIPK were 0.127 and 0.101 g-C h-1 kg-1 packed material

The influence of nonionic surfactant Brij 30 on biodegradation of toluene in a biofilter

The influence of nonionic surfactant Brij 30 on toluene dissolved in the water phase and biodegradation kinetic behaviors of toluene in a polyvinyl alcohol (PVA)/peat/KNO3/ (granular activated carbon) GAC composite bead biofilter were investigated. The toluene dissolved in the water phase was enhanced by the addition of surfactant into the aqueous solution and the maximum amount of toluene dissolved in the water phase occurred at the surfactant concentration of 34.92 mgl-1. Zero-order kinetics with diffusion limitation was regarded as the most adequate biochemical reaction kinetic model. The microbial growth rate and biochemical reaction rate were inhibited at higher surfactant content and toluene inlet concentration. The degree of inhibitive effect was more pronounced at lower toluene inlet concentration. The maximum elimination capacity decreased with increasing surfactant content. The addition of nonionic surfactant Brij 30 into filter material was unfavorable for toluene degraded by the microbial.Keywords: Nonionic surfactant Brij30, toluene, dissolution capacity, biodegradation, composite bead biofilterAfrican Journal of Biotechnology Vol. 9(36), pp. 5914-5921, 6 September, 201

Misclassification in Automated Content Analysis Causes Bias in Regression. Can We Fix It? Yes We Can!

Automated classifiers (ACs), often built via supervised machine learning (SML), can categorize large, statistically powerful samples of data ranging from text to images and video, and have become widely popular measurement devices in communication science and related fields. Despite this popularity, even highly accurate classifiers make errors that cause misclassification bias and misleading results in downstream analyses-unless such analyses account for these errors. As we show in a systematic literature review of SML applications, communication scholars largely ignore misclassification bias. In principle, existing statistical methods can use "gold standard" validation data, such as that created by human annotators, to correct misclassification bias and produce consistent estimates. We introduce and test such methods, including a new method we design and implement in the R package misclassificationmodels, via Monte Carlo simulations designed to reveal each method's limitations, which we also release. Based on our results, we recommend our new error correction method as it is versatile and efficient. In sum, automated classifiers, even those below common accuracy standards or making systematic misclassifications, can be useful for measurement with careful study design and appropriate error correction methods.Comment: 41 page, 21 Figures, Top Paper Award from the 2023 Annual Meeting of The International Communication Association Computational Methods Divisio

Contested Chinese dreams of AI? Public discourse about artificial intelligence on WeChat and people’s daily online

Artificial intelligence (AI) has become a prominent public issue, particularly in China, where the government has announced plans to turn the country into a global AI power. This study analyses public discourse about AI in China through the conceptual lens of public spheres theory and counter-public spheres. It compares the official AI narrative on People’s Daily Online with public discussion about AI on the social medium WeChat, where we assumed that official views would be challenged. Using a combination of qualitative and computational methods, 140,000 AI-related articles published between 2015 and 2018 were studied. Findings reveal that AI-related discourse on WeChat is surprisingly similar to that on People’s Daily Online. That is, it is dominated by industry and political actors, such as government agencies and technology companies, and is mostly characterized by discussions about the economic potential of the technology, with strongly positive evaluations, and little critical debate

oolong: An R package for validating automated content analysis tools

Intended to create standard human-in-the-loop validity tests for typical automated content analysis such as topic modeling and dictionary-based methods. This package offers a standard workflow with functions to prepare, administer and evaluate a human-in-the-loop validity test. This package provides functions for validating topic models using word intrusion and Topic intrusion tests, as described in Chang et al. (2009) . This package also provides functions for generating gold-standard data which are useful for validating dictionary-based methods. The default settings of all generated tests match those suggested in Chang et al. (2009) and Song et al. (2020)

Simulation of Low-density Nozzle Plumes in Non-zero Ambient Pressures

The direct simulation Monte-Carlo (DSMC) method was applied to the analysis of low-density nitrogen plumes exhausting from a small converging-diverging nozzle into finite ambient pressures. Two cases were considered that simulated actual test conditions in a vacuum facility. The numerical simulations readily captured the complicated flow structure of the overexpanded plumes adjusting to the finite ambient pressures, including Mach disks and barrel shaped shocks. The numerical simulations compared well to experimental data of Rothe

Cytokine Profile in Plasma Extracellular Vesicles of Parkinson's Disease and the Association with Cognitive Function

Plasma extracellular vesicles (EVs) containing various molecules, including cytokines, can reflect the intracellular condition and participate in cell-to-cell signaling, thus emerging as biomarkers for Parkinson’s disease (PD). Inflammation may be a crucial risk factor for PD development and progression. The present study investigated the role of plasma EV cytokines as the biomarkers of PD. This cross-sectional study recruited 113 patients with PD, with mild to moderate stage disease, and 48 controls. Plasma EVs were isolated, and the levels of cytokines, including pro-interleukin (IL)-1β, IL-6, IL-10, tumor necrosis factor (TNF)-α, and transforming growth factor (TGF)-β1, were evaluated. Patients with PD had significantly increased plasma EV pro-IL-1β and TNF-α levels compared with controls after adjustment for age and sex. Despite the lack of a significant association between plasma EV cytokines and motor symptom severity in patients with PD, cognitive dysfunction severity, assessed using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment, was significantly associated with plasma EV pro-IL-1β, IL-6, IL-10, and TNF-α levels. This association was PD specific and not found in controls. Furthermore, patients with PD cognitive deficit (MMSE < 26) exhibited a distinguished EV cytokine profile compared to those without cognitive deficit. The findings support the concept of inflammatory pathogenesis in the development and progression of PD and indicate that plasma EV cytokines may serve as PD biomarkers in future

Parental use of the term "Hot Qi" to describe symptoms in their children in Hong Kong: a cross sectional survey "Hot Qi" in children

BACKGROUND: The Chinese term "Hot Qi" is often used by parents to describe symptoms in their children. The current study was carried out to estimate the prevalence of using the Chinese term "Hot Qi" to describe symptoms in children by their parents and the symptomatology of "Hot Qi". METHOD: A cross sectional survey by face-to-face interview with a semi-structured questionnaire was carried out in a public hospital and a private clinic in Hong Kong. The parental use of the term "Hot Qi", the symptoms of "Hot Qi" and the remedies used for "Hot Qi" were asked. RESULTS: 1060 pairs of children and parents were interviewed. 903 (85.1%) of parents claimed that they had employed the term "Hot Qi" to describe their children's symptoms. Age of children and place of birth of parents were the predictors of parents using the term "Hot Qi". Eye discharge (37.2%), sore throat (33.9%), halitosis(32.8%), constipation(31.0%), and irritable (21.2%) were the top five symptoms of "Hot Qi" in children. The top five remedies for "Hot Qi" were the increased consumption of water (86.8%), fruit (72.5%), soup (70.5%), and the use of herbal beverages "five-flower- tea" (a combination of several flowers such as Chrysanthemum morifolii, Lonicera japonica, Bombax malabaricum, Sophora japonica, and Plumeria rubra) (57.6%) or selfheal fruit spike (Prunella vulgaris) (42.4%). CONCLUSION: "Hot Qi" is often used by Chinese parents to describe symptoms in their children in Hong Kong. Place of birth of parents and age of the children are main factors for parents to apply the term "Hot Qi" to describe symptoms of their children. The common symptoms of "Hot Qi" suggest infections or allergy