Conjecturing-Based Computational Discovery of Patterns in Data

Modern machine learning methods are designed to exploit complex patterns in data regardless of their form, while not necessarily revealing them to the investigator. Here we demonstrate situations where modern machine learning methods are ill-equipped to reveal feature interaction effects and other nonlinear relationships. We propose the use of a conjecturing machine that generates feature relationships in the form of bounds for numerical features and boolean expressions for nominal features that are ignored by machine learning algorithms. The proposed framework is demonstrated for a classification problem with an interaction effect and a nonlinear regression problem. In both settings, true underlying relationships are revealed and generalization performance improves. The framework is then applied to patient-level data regarding COVID-19 outcomes to suggest possible risk factors.Comment: 25 pages, 6 figure

Nitrogen Management in a Maize-Groundnut Crop Rotation of Humid Tropics: Effect on N2O Emission

Development of appropriate land management techniques to attain sustainability and increase the N use efficiency of crops in the tropics has been gaining momentum. The nitrous oxides (N2Os) affect global climate change and its contribution from N and C management systems is of great significance. Thus, N transformations and N2O emission during maize-groundnut crop rotation managed with various N sources were studied. Accumulation of nitrate (NO3 –) and its disappearance happened immediately after addition of various N sources, showing liming effect. The mineral N retained for 2–4 weeks depending on the type and amount of N application. The chicken manure showed rapid nitrification in the first week after application during the fallow period, leading to a maximum N2O flux of 9889 μg N2O-N m–2 day– 1. The same plots showed a residual effect by emitting the highest N2O (4053 μg N2O-N m–2 day– 1) during maize cultivation supplied with a halfrate of N fertilizer. Application of N fertilizer only or in combination with crop residues exhibited either lowered fluxes or caused a sink during the groundnut and fallow periods due to small availability of substrates and/or low water-filled pore space (<40%). The annual N2O emission ranged from 1.41 to 3.94 kg N2O-N ha–1; the highest was estimated from the chicken manure plus crop residues and half-rate of inorganic N-amended plots. Results indicates a greater influence of chicken manure on the N transformations and thereby N2O emission

Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO₂

International audienceThe aim of this study was to identify the microbial communities that are actively involved in the assimilation of rhizosphere-C and are most sensitive in their activity to elevated atmospheric CO2 in a temperate semi-natural low-input grassland ecosystem. For this, we analyzed 13C signatures in microbial biomarker phospholipid fatty acids (PLFA) from an in-situ 13CO2 pulse-labeling experiment in the Giessen Free Air Carbon dioxide Enrichment grasslands (GiFACE, Germany) exposed to ambient and elevated (i.e. 50% above ambient) CO2 concentrations. Short-term 13C PLFA measurements at 3 h and 10 h after the pulse-labeling revealed very little to no 13C enrichment after 3 h in biomarker PLFAs and a much greater incorporation of new plant-C into fungal compared to bacterial PLFAs after 10 h. After a period of 11 months following the pulse-labeling experiment, the 13C enrichment of fungal PLFAs was still largely present but had decreased, while bacterial PLFAs were much more enriched in 13C compared to a few hours after the pulse-labeling. These results imply that new rhizodeposit-C is rapidly processed by fungal communities and only much later by the bacterial communities, which we attributed to either a fungal-mediated translocation of rhizosphere-C from the fungal to bacterial biomass or a preferential bacterial use of dead root or fungal necromass materials as C source over the direct utilization of fresh root-exudate C in these N-limited grassland ecosystems. Elevated CO2 caused an increase in the proportional 13C enrichment (relative to the universal biomarker 16:0) of the arbuscular mycorrhizal fungal biomarker PLFA 16:1?5 and one gram-positive bacterial biomarker PLFA i16:0, but a decrease in the proportional 13C enrichment of 18:1?9c, a commonly used though questionable fungal biomarker PLFA. This suggests enhanced fungal rhizodeposit-C assimilation only by arbuscular mycorrhizal fungal species under elevated CO2

Automated conjecturing II : chomp and reasoned game play

We demonstrate the use of a program that generates conjectures about positions of the combinatorial game Chomp—explanations of why certain moves are bad. These could be used in the design of a Chomp-playing program that gives reasons for its moves. We prove one of these Chomp conjectures—demonstrating that our conjecturing program can produce genuine Chomp knowledge. The conjectures are generated by a general purpose conjecturing program that was previously and successfully used to generate mathematical conjectures. Our program is initialized with Chomp invariants and example game boards—the conjectures take the form of invariant-relation statements interpreted to be true for all board positions of a certain kind. The conjectures describe a theory of Chomp positions. The program uses limited, natural input and suggests how theories generated on-the-fly might be used in a variety of situations where decisions—based on reasons—are required

Breath analysis by gas chromatography-mass spectrometry and electronic nose to screen for pleural mesothelioma : a cross-sectional case-control study

Rationale: Malignant pleural mesothelioma (MPM) is mainly caused by previous exposure to asbestos fibers and has a poor prognosis. Due to a long latency period between exposure and diagnosis, MPM incidence is expected to peak between 2020-2025. Screening of asbestos-exposed individuals is believed to improve early detection and hence, MPM management. Recent developments focus on breath analysis for screening since breath contains volatile organic compounds (VOCs) which reflect the cell’s metabolism. Objectives: The goal of this cross-sectional, case-control study is to identify VOCs in exhaled breath of MPM patients with gas chromatography-mass spectrometry (GC-MS) and to assess breath analysis to screen for MPM using an electronic nose (eNose). Methods: Breath and background samples were taken from 64 subjects: 16 healthy controls (HC), 19 asymptomatic former asbestos-exposed (AEx) individuals, 15 patients with benign asbestos-related diseases (ARD) and 14 MPM patients. Samples were analyzed with both GC-MS and eNose. Results: Using GC-MS, AEx individuals were discriminated from MPM patients with 97% accuracy, with diethyl ether, limonene, nonanal, methylcyclopentane and cyclohexane as important VOCs. This was validated by eNose analysis. MPM patients were discriminated from AEx+ARD participants by GC-MS and eNose with 94% and 74% accuracy, respectively. The sensitivity, specificity, positive and negative predictive values were 100%, 91%, 82%, 100% for GC-MS and 82%, 55%, 82%, 55% for eNose, respectively. Conclusion: This study shows accurate discrimination of patients with MPM from asymptomatic asbestos-exposed persons at risk by GC-MS and eNose analysis of exhaled VOCs and provides proof-of-principle of breath analysis for MPM screening

Impact of critical illness and withholding of early parenteral nutrition in the pediatric intensive care unit on long-term physical performance of children:a 4-year follow-up of the PEPaNIC randomized controlled trial

Background: Many critically ill children face long-term developmental impairments. The PEPaNIC trial attributed part of the problems at the level of neurocognitive and emotional/behavioral development to early use of parenteral nutrition (early-PN) in the PICU, as compared with withholding it for 1 week (late-PN). Insight in long-term daily life physical functional capacity after critical illness is limited. Also, whether timing of initiating PN affects long-term physical function of these children remained unknown. Methods: This preplanned follow-up study of the multicenter PEPaNIC randomized controlled trial subjected 521 former critically ill children (253 early-PN, 268 late-PN) to quantitative physical function tests 4 years after PICU admission in Leuven or Rotterdam, in comparison with 346 age- and sex-matched healthy children. Tests included handgrip strength measurement, timed up-and-go test, 6-min walk test, and evaluation of everyday overall physical activity with an accelerometer. We compared these functional measures for the former critically ill and healthy children and for former critically ill children randomized to late-PN versus early-PN, with multivariable linear or logistic regression analyses adjusting for risk factors. Results: As compared with healthy children, former critically ill children showed less handgrip strength (p &lt; 0.0001), completed the timed up-and-go test more slowly (p &lt; 0.0001), walked a shorter distance in 6 min (p &lt; 0.0001) during which they experienced a larger drop in peripheral oxygen saturation (p ≤ 0.026), showed a lower energy expenditure (p ≤ 0.024), performed more light and less moderate physical activity (p ≤ 0.047), and walked fewer steps per day (p = 0.0074). Late-PN as compared with early-PN did not significantly affect these outcomes. Conclusions: Four years after PICU admission, former critically ill children showed worse physical performance as compared with healthy children, without impact of timing of supplemental PN in the PICU. This study provides further support for de-implementing the early use of PN in the PICU. Trial registration ClinicalTrials.gov, NCT01536275; registered on February 22, 2012.</p

Adult-Onset ANCA-Associated Vasculitis in SAVI: Extension of the Phenotypic Spectrum, Case Report and Review of the Literature.

STING-associated vasculopathy with onset in infancy (SAVI) is an autosomal dominant disorder due to gain-of-function mutations in STING1, also known as TMEM173, encoding for STING. It was reported as a vasculopathy of infancy. However, since its description a wider spectrum of associated manifestations and disease-onset has been observed. We report a kindred with a heterozygous STING mutation (p.V155M) in which the 19-year-old proband suffered from isolated adult-onset ANCA-associated vasculitis. His father suffered from childhood-onset pulmonary fibrosis and renal failure attributed to ANCA-associated vasculitis, and died at the age of 30 years due to respiratory failure. In addition, an overview of the phenotypic spectrum of SAVI is provided highlighting (a) a high phenotypic variability with in some cases isolated manifestations, (b) the potential of adult-onset disease, and (c) a novel manifestation with ANCA-associated vasculitis

Healthcare providers' views on the acceptability of financial incentives for breastfeeding:a qualitative study

BACKGROUND: Despite a gradual increase in breastfeeding rates, overall in the UK there are wide variations, with a trend towards breastfeeding rates at 6–8 weeks remaining below 40% in less affluent areas. While financial incentives have been used with varying success to encourage positive health related behaviour change, there is little research on their use in encouraging breastfeeding. In this paper, we report on healthcare providers’ views around whether using financial incentives in areas with low breastfeeding rates would be acceptable in principle. This research was part of a larger project looking at the development and feasibility testing of a financial incentive scheme for breastfeeding in preparation for a cluster randomised controlled trial. METHODS: Fifty–three healthcare providers were interviewed about their views on financial incentives for breastfeeding. Participants were purposively sampled to include a wide range of experience and roles associated with supporting mothers with infant feeding. Semi-structured individual and group interviews were conducted. Data were analysed thematically drawing on the principles of Framework Analysis. RESULTS: The key theme emerging from healthcare providers’ views on the acceptability of financial incentives for breastfeeding was their possible impact on ‘facilitating or impeding relationships’. Within this theme several additional aspects were discussed: the mother’s relationship with her healthcare provider and services, with her baby and her family, and with the wider community. In addition, a key priority for healthcare providers was that an incentive scheme should not impact negatively on their professional integrity and responsibility towards women. CONCLUSION: Healthcare providers believe that financial incentives could have both positive and negative impacts on a mother’s relationship with her family, baby and healthcare provider. When designing a financial incentive scheme we must take care to minimise the potential negative impacts that have been highlighted, while at the same time recognising the potential positive impacts for women in areas where breastfeeding rates are low

Factors and Situations Affecting the Value of Patient Preference Studies: Semi-Structured Interviews in Europe and the US

Objectives: Patient preference information (PPI) is gaining recognition among the pharmaceutical industry, regulatory authorities, and health technology assessment (HTA) bodies/payers for use in assessments and decision-making along the medical product lifecycle (MPLC). This study aimed to identify factors and situations that influence the value of patient preference studies (PPS) in decision-making along the MPLC according to different stakeholders. Methods: Semi-structured interviews (n = 143) were conducted with six different stakeholder groups (physicians, academics, industry representa