A causal inference and Bayesian optimisation framework for modelling multi-trait relationships—Proof-of-concept using Brassica napus seed yield under controlled conditions

The improvement of crop yield is a major breeding target and there is a long history of research that has focussed on unravelling the mechanisms and processes that contribute to yield. Quantitative prediction of the interplay between morphological traits, and the effects of these trait-trait relationships on seed production remains, however, a challenge. Consequently, the extent to which crop varieties optimise their morphology for a given environment is largely unknown. This work presents a new combination of existing methodologies by framing crop breeding as an optimisation problem and evaluates the extent to which existing varieties exhibit optimal morphologies under the test conditions. In this proof-of-concept study using spring and winter oilseed rape plants grown under greenhouse conditions, we employ causal inference to model the hierarchically structured effects of 27 morphological yield traits on each other. We perform Bayesian optimisation of seed yield, to identify and quantify the morphologies of ideotype plants, which are expected to be higher yielding than the varieties in the studied panels. Under the tested growth conditions, we find that existing spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant winter varieties. The same approach can be used to evaluate trait (morphology) space for any environment

Influence of water content on the basic friction angle of porous limestones—experimental study using an automated tilting table

An accurate evaluation of the shear strength of discontinuities is frequently a key aspect for determining the safety of mining and civil engineering works and for solving instability issues at rock mass scale. This is usually done by using empirical shear strength criteria in which the basic friction angle (φb) is a relevant input parameter. Tilt testing is probably the most widespread method to obtain the φb due to its simplicity and low cost, but previous research has demonstrated that the results are strongly affected by several factors (e.g. surface finishing, cutting speed, specimen geometry, wear, time and rock type). In this connection, despite it is well known that water significantly reduces the mechanical properties of sedimentary rocks, very scarce research has focused on assessing the impact of the variations in water content on tilt test results. With the aim to fill this gap, saw-cut slabs of three limestone lithotypes were tilt tested in dry state, wet condition (fully water saturated, non-submerged samples) and under exposure to an environmental relative humidity (RH) of 90%. The results revealed that full water saturation caused moderate φb reductions in two lithotypes and a φb increase in one lithotype. This can be explained by their different microstructure and mineralogy, which makes that lubrication effect prevails over suction effect or vice versa. However, the exposure to a high RH environment did not cause significant φb variations. In addition, some important considerations related to tilt testing are provided and discussed, such as the intrinsic variability of the sliding angle (β) and the impact of multiple sliding on the same rock surfaces on β.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was partially supported by the Vicerrectorado de Investigación y Transferencia del Conocimiento of the University of Alicante through the projects UAUSTI18-21, UAUSTI20-20 and UAUSTI19-25

Impact of using an evidence-based clinical guideline for the management of primary vesicoureteral reflux in children

Objective: To analyze changes in the therapeutic approach at a tertiary care hospital following the implementation of a clinical guideline for the treatment of primary vesicoureteral reflux (VUR) in children. Population and methods: Retrospective study conducted in a cohort of patients with primary VUR (1989-2015) aged 0-15 years at a tertiary care hospital. The therapeutic approach before and after the development of the clinical guideline (2008) was compared. Results: A total of 297 patients (49.8% boys, 50.2% girls) were included; their mean age at the time of diagnosis was 21.71 months. VUR grading was: VUR I-III 45.1%, VUR IV-V 54, 9%; 124 were treated after the implementation of the clinical guideline (group 1), and 173, before (group 2). The mean follow-up period was 124.32 months. A conservative approach was the initial treatment in 70.3% of group 1 patients and 67.9% of group 2 patients. The number of surgeries remains constant (31.45% versus 31.79%), with an increase in the number of endoscopic surgeries (p< 0.005). The profile of patients has changed based on the application of the algorithm proposed by the guideline. Fewer surgeries were done in patients with VUR IV-V (82.32% versus 59.9%, p= 0.000) and there were fewer cases of kidney damage at diagnosis (49.4% versus 9.8%, p= 0.000). Conclusions: The implementation of the clinical guideline has favored an initially conservative approach in patients with severe grade VUR and nephropathy, for whom surgery was traditionally indicated initially. Using clinical guidelines favors a unanimous, evidence-based approach that reduces the performance of unnecessary invasive procedures

Multiple terahertz beams based on a Fourier grating and a quantum cascade laser

Large heterodyne receiver arrays (~100 pixel) allow astronomical instrumentations mapping more area within limited space mission lifetime. One challenge is to generate multiple local oscillator (LO) beams. Here, We succeeded in generating 81 beams at 3.86 THz by combining a reflective, metallic Fourier grating with an unidirectional antenna coupled 3rd-order distributed feedback (DFB) quantum cascade laser (QCL). We have measured the diffracted 81 beams by scanning a single pyroelectric detector at a plane, which is in the far field for the diffraction beams. The measured output beam pattern agrees well with a simulated result from COMSOL Multiphysics with respect to the angular distribution and power distribution among the 81 beams. We also derived the diffraction efficiency to be 94\pm 3\%, which is very close to what was simulated for a manufactured Fourier grating (97%). For an array of equal superconducting hot electron bolometer mixers, 64 out of 81 beams can pump the HEB mixers with similar power, resulting in receiver sensitivities within 10%. Such a combination of a Fourier grating and a QCL can create an LO with 100 beams or more, enabling a new generation of large heterodyne arrays for astronomical instrumentation. This paper is essentially a copy of our paper in Optics Express

Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meat

The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).info:eu-repo/publishedVersio

Boundary-layer water vapor profiling using differential absorption radar

Remote sensing of water vapor in the presence of clouds and precipitation constitutes an important observational gap in the global observing system. We present ground-based measurements using a new radar instrument operating near the 183&thinsp;GHz H2O line for profiling water vapor inside of planetary-boundary-layer clouds, and develop an error model and inversion algorithm for the profile retrieval. The measurement technique exploits the strong frequency dependence of the radar beam attenuation, or differential absorption, on the low-frequency flank of the water line in conjunction with the radar's ranging capability to acquire range-resolved humidity information. By comparing the measured differential absorption coefficient with a millimeter-wave propagation model, we retrieve humidity profiles with 200&thinsp;m resolution and typical statistical uncertainty of 0.6&thinsp;g&thinsp;m−3 out to around 2&thinsp;km. This value for humidity uncertainty corresponds to measurements in the high-SNR (signal-to-noise ratio) limit, and is specific to the frequency band used. The measured spectral variation of the differential absorption coefficient shows good agreement with the model, supporting both the measurement method assumptions and the measurement error model. By performing the retrieval analysis on statistically independent data sets corresponding to the same observed scene, we demonstrate the reproducibility of the measurement. An important trade-off inherent to the measurement method between retrieved humidity precision and profile resolution is discussed.</p

Assessment of Chemical Inhibitor Addition to Improve the Gas Production from Biowaste

The coexistence of sulphate-reducing bacteria and methanogenic archaea in the reactors during the anaerobic digestion from sulphate-containing waste could favor the accumulation of sulfide on the biogas, and therefore reduce its quality. In this study, the effect of sulphate-reducing bacteria inhibitor (MoO−2 4 ) addition in a two phase system from sulphate-containing municipal solid waste to improve the quality of the biogas has been investigated. The results showed that although SRB and sulphide production decreased, the use of inhibitor was not effective to improve the anaerobic digestion in a two phase system from sulphate-containing waste, since a significant decrease on biogas and organic matter removal were observed. Before MoO−2 4 addition the average values of volatile solid were around 12 g/kg, after 5 days of inhibitor use, those values did exceed to 28 g/kg. Molybdate caused acidification in the reactor and it was according to decrease in the pH values. In relation to microbial consortia, the effect of inhibitor was a decrease in Bacteria (44%; 60% in sulphate-reducing bacteria) and Archaea (38%) population

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases