MRzero - Automated discovery of MRI sequences using supervised learning

PURPOSE

A supervised learning framework is proposed to automatically generate MR sequences and corresponding reconstruction based on the target contrast of interest. Combined with a flexible, task-driven cost function this allows for an efficient exploration of novel MR sequence strategies.

METHODS

The scanning and reconstruction process is simulated end-to-end in terms of RF events, gradient moment events in x and y, and delay times, acting on the input model spin system given in terms of proton density, T 1 and T 2 , and Δ B 0 . As a proof of concept, we use both conventional MR images and T 1 maps as targets and optimize from scratch using the loss defined by data fidelity, SAR penalty, and scan time.

RESULTS

In a first attempt, MRzero learns gradient and RF events from zero, and is able to generate a target image produced by a conventional gradient echo sequence. Using a neural network within the reconstruction module allows arbitrary targets to be learned successfully. Experiments could be translated to image acquisition at the real system (3T Siemens, PRISMA) and could be verified in the measurements of phantoms and a human brain in vivo.

CONCLUSIONS

Automated MR sequence generation is possible based on differentiable Bloch equation simulations and a supervised learning approach.

Root exudate composition of grass and forb species in natural grasslands

Plants exude a diverse cocktail of metabolites into the soil as response to exogenous and endogenous factors. So far, root exudates have mainly been studied under artificial conditions due to methodological difficulties. In this study, each five perennial grass and forb species were investigated for polar and semi-polar metabolites in exudates under field conditions. Metabolite collection and untargeted profiling approaches combined with a novel classification method allowed the designation of 182 metabolites. The composition of exuded polar metabolites depended mainly on the local environment, especially soil conditions, whereas the pattern of semi-polar metabolites was primarily affected by the species identity. The profiles of both polar and semi-polar metabolites differed between growth forms, with grass species being generally more similar to each other and more responsive to the abiotic environment than forb species. This study demonstrated the feasibility of investigating exudates under field conditions and to identify the driving factors of exudate composition.

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Mechanism of Olefin Metathesis with Neutral and Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes

A series of neutral molybdenum imido alkylidene N-heterocyclic carbene (NHC) bistriflate and monotriflate monoalkoxide complexes as well as cationic molybdenum imido alkylidene triflate complexes have been subjected to NMR spectroscopic, X-ray crystallographic, and reaction kinetic measurements in order to gain a comprehensive understanding about the underlying mechanism in olefin metathesis of this new type of catalysts. On the basis of experimental evidence and on DFT calculations (BP86/def2-TZVP/D3/cosmo) for the entire mechanism, olefinic substrates coordinate trans to the NHC of neutral 16-electron complexes via an associative mechanism, followed by dissociation of an anionic ligand (e.g., triflate) and formation of an intermediary molybdacyclobutane trans to the NHC. Formation of a cationic complex is crucial in order to become olefin metathesis active. Variations in the NHC, the imido, the alkoxide, and the noncoordinating anion revealed their influence on reactivity. The reaction of neutral 16-electron complexes with 2-methoxystyrene is faster for catalysts bearing one triflate and one fluorinated alkoxide than for catalysts bearing two triflate ligands. This is also reflected by the Gibbs free energy values for the transition states, ΔG^‡₃₀₃, which are significantly lower for catalysts bearing only one triflate than for the corresponding bistriflate complexes. Reaction of a solvent-stabilized cationic molybdenum imido alkylidene N-heterocyclic carbene (NHC) monotriflate complex with 2-methoxystyrene proceeded via an associative mechanism too. Reaction rates of both solvent-free and solvent-stabilized cationic Mo imido alkylidene NHC catalysts with 2-methoxystyrene are controlled by the cross-metathesis step but not by adduct formation.

Semi-polar root exudates in natural grassland communities

In the rhizosphere, plants are exposed to a multitude of different biotic and abiotic factors, to which they respond by exuding a wide range of secondary root metabolites. So far, it has been unknown to which degree root exudate composition is species-specific and is affected by land use, the local impact and local neighborhood under field conditions. In this study, root exudates of 10 common grassland species were analyzed, each five of forbs and grasses, in the German Biodiversity Exploratories using a combined phytometer and untargeted liquid chromatography-mass spectrometry (LC-MS) approach. Redundancy analysis and hierarchical clustering revealed a large set of semi-polar metabolites common to all species in addition to species-specific metabolites. Chemical richness and exudate composition revealed that forbs, such as Plantago lanceolata and Galium species, exuded more species-specific metabolites than grasses. Grasses instead were primarily affected by environmental conditions. In both forbs and grasses, plant functional traits had only a minor impact on plant root exudation patterns. Overall, our results demonstrate the feasibility of obtaining and untargeted profiling of semi-polar metabolites under field condition and allow a deeper view in the exudation of plants in a natural grassland community.

Correction: Linking root exudates to functional plant traits

[This corrects the article DOI: 10.1371/journal.pone.0204128.].

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities

The rhizosphere encompasses the soil surrounding the surface of plants’ fine roots. Accordingly, the microbiome present is influenced by both soil type and plant species. Furthermore, soil microbial communities respond to land-use intensity due to the effects on soil conditions and plant performance. However, there is limited knowledge about the impact of grassland management practices under field conditions on the composition of both bacteria and fungi in the rhizosphere of different plant functional groups. In spring 2014 we planted four phytometer species, two forbs (Plantago lanceolata, Achillea millefolium) and two grasses (Dactylis glomerata, Arrhenatherum elatius) into 13 permanent experimental grassland plots, differing in management. After 6 months, rhizosphere and bulk soil associated with the phytometer plants were sampled, microbial genomic DNA was extracted and bacterial 16S and fungal ITS rDNA were sequenced using Illumina MiSeq. Our study revealed that the rhizosphere microbial community was more diverse than the bulk soil community. There were no differences in microbial community composition between the two plant functional groups, but a clear impact of root traits and edaphic conditions. Land-use intensity strongly affected plant productivity, neighboring plant richness and edaphic conditions, especially soil C/N ratio, which in turn had a strong influence on root traits and thereby explained to large extent microbial community composition. Rhizosphere microbes were mainly affected by abiotic factors, in particular by land-use intensity, while plant functional type had only subordinate effects. Our study provides novel insights into the assembly of rhizosphere bacterial and fungal communities in response to land-use intensity and plant functional groups in managed grassland ecosystems.

Linking root exudates to functional plant traits

Primary and secondary metabolites exuded by plant roots have mainly been studied under laboratory conditions, while knowledge of root exudate patterns of plants growing in natural communities is very limited. Focusing on ten common European grassland plant species, we asked to which degree exuded metabolite compositions are specific to species or growth forms (forbs and grasses), depend on environments and local neighbourhoods, and reflect traditional plant functional traits. Root exudates were collected under field conditions and analysed using a non-targeted gas chromatography coupled mass spectrometry (GC-MS) approach. In total, we annotated 153 compounds of which 36 were identified by structure and name as metabolites mainly derived from the primary metabolism. Here we show by using variance partitioning, that the composition of exuded polar metabolites was mostly explained by plot identity, followed by plant species identity while plant species composition of the local neighbourhood played no role. Total and root dry biomass explained the largest proportion of variance in exudate composition, with additional variance explained by traditional plant traits. Although the exudate composition was quite similar between the two growth forms, we found some metabolites that occurred only in one of the two growth forms. Our study demonstrated the feasibility of measuring polar exudates under non-sterile field conditions by mass spectrometry, which opens new avenues of research for functional plant ecology.

Predicting individual plant performance in grasslands

Plant functional traits are widely used to predict community productivity. However, they are rarely used to predict individual plant performance in grasslands. To assess the relative importance of traits compared to environment, we planted seedlings of 20 common grassland species as phytometers into existing grassland communities varying in land‐use intensity. After 1 year, we dug out the plants and assessed root, leaf, and aboveground biomass, to measure plant performance. Furthermore, we determined the functional traits of the phytometers and of all plants growing in their local neighborhood. Neighborhood impacts were analyzed by calculating community‐weighted means (CWM) and functional diversity (FD) of every measured trait. We used model selection to identify the most important predictors of individual plant performance, which included phytometer traits, environmental conditions (climate, soil conditions, and land‐use intensity), as well as CWM and FD of the local neighborhood. Using variance partitioning, we found that most variation in individual plant performance was explained by the traits of the individual phytometer plant, ranging between 19.30% and 44.73% for leaf and aboveground dry mass, respectively. Similarly, in a linear mixed effects model across all species, performance was best predicted by phytometer traits. Among all environmental variables, only including land‐use intensity improved model quality. The models were also improved by functional characteristics of the local neighborhood, such as CWM of leaf dry matter content, root calcium concentration, and root mass per volume as well as FD of leaf potassium and root magnesium concentration and shoot dry matter content. However, their relative effect sizes were much lower than those of the phytometer traits. Our study clearly showed that under realistic field conditions, the performance of an individual plant can be predicted satisfyingly by its functional traits, presumably because traits also capture most of environmental and neighborhood conditions.

Performance and responses to competition in two congeneric annual species: does seed heteromorphism matter?

Variations in seed characteristics observed in heteromorphic species may affect various stages of their life cycles, e.g. seed dormancy, germination characteristics or even adult plant performance. Highly specialised seed morphs - described as colonisers and maintainers - exhibit a trade-off between colonisation capacity and competitive traits. The performance of distinct seed morph progeny under competitive conditions, and especially in multi-species arrangements, had previously not been given much attention. In this study, we compared performance and response to competition among distinct seed morph progenies in two congeneric, co-occurring species: the invasive Bidens frondosa and the non-invasive Bidens tripartita. We hypothesised that maintainer seed morphs of both species would perform better under increased plant densities and within inter-morphic mixtures, while coloniser morphs would show stronger responses to increased densities and perform relatively poorly in inter-morphic mixtures. We conducted a growth trial and a greenhouse experiment, which revealed that seed morph progeny differed significantly in plant height when grown without competition, while under competitive conditions such differences became less apparent. The observed pattern was more strongly pronounced in B. frondosa, which showed a general predominance in stature and biomass over its non-invasive congener. Although seed morphs performed equally well under competitive conditions, increased plant height and more rapid germination can favour the maintainer seed morph on sites where vegetation is already present.

[Megacystis-microcolon intestinal hypoperistalsis syndrome (MMIHS) as a rare differential diagnosis of foetal megacystis on ultrasonography]

INTRODUCTION

Foetal megacystis (incidence 1:1 500) occurring in the first trimester may already be a sign of congenital malformation. Often, urethral valves are causally responsible in male foetuses far more frequently than urethral atresia. As a further differential diagnosis, the "prune-belly syndrome" needs to be distinguished. Far more difficult to classify prenatally is the rare MMIHS which, in contrast to the diagnosis of urethral valves, is associated with an unfavourable prognosis.

CASE REPORT

This is a report on a 28-year-old IG/0P, whose foetus of 26+4 gestational weeks was found on ultrasonography for the first time to have a megacystis of 48 mm diameter and bilateral hydronephrosis. The female foetus was surrounded by a normal amount of amniotic fluid which, during the further course of the pregnancy, developed into polyhydramnios. The serial puncture of the urinary bladder showed a normal karyotype and no impairment of the renal concentrating capacity or of protein loss. By reason of an immense enlargement of the abdomen due to the 100 mm large urinary bladder, a Caesarean section was conducted at 36+0 gestational weeks. A catheter could be inserted into the urinary bladder postpartum easily. However, nourishment was not possible and after radiological examination, MMIHS was diagnosed.

CONCLUSION

In the case of a foetal megacystis detected by ultrasonography, especially associated with polyhydramnios and female gender, the rare MMIHS, which is infaust, should be taken into consideration.

[Late preterms: the influence of foetal gender on neonatal outcome]

BACKGROUND

The group of the so-called late preterms (infants born at 34 0/7-36 6/7 weeks gestational age) has been underestimated with respect to their neonatal outcome. Among infants born before the 29th week of pregnancy, a gender-specific difference in favour of females regarding morbidity became evident. The aim of this study is to investigate whether these findings are transferable to the group of late preterms.

METHODS

The neonatal outcome of 528 consecutive singletons, born at 34 0/7-36 6/7 weeks gestational age and requiring intensive care, was examined.

RESULTS

Neonatal complications have been particularly analysed with regard to gender-specific differences. Boys (n=292) were significantly more frequently affected by sepsis (3.8 vs. 0.9%; p=0,0314, x²-test). Girls had significantly longer stays in the neonatal intensive care unit (median 12 (Q1:8; Q3:17) vs. 11 (6;16) days; p=0.0149, t-test). In a multiple logistic regression model, male gender and premature rupture of membranes were borderline significant with respect to the occurrence of sepsis - boys had a 4.4-fold risk (OR=0.228 [95% CI: 0.050-1.041]; p=0.0564) and premature rupture of membranes had a 3.5-fold risk (OR=3.462 [0.938-12.779]; p=0.0623). Strong cause variables for the length of stay in the neonatal intensive care unit were birth weight, gestational age and premature rupture of membranes after adjustment.

CONCLUSION

The influence of foetal gender on the neonatal outcome in the late preterm group (34 0/7-36 6/7 gestational age) has been relativised.

Flexible and monolithically integrated CIGS-Modules

Monolithically integrated Cu(In,Ga)Se2-mini-modules (CIGS) have been fabricated on polymer as well as on metal foils. Preferred foils with view on costs and physical properties were ferritic steel, titanium, Fe/Ni-alloys (e.g. Kovar®) and polyimide as the only appropriate low temperature candidate. The metal substrates were isolated by multiple layers of SiOx and Al2O3 which served both as diffusion barrier against substrate elements and dielectric barrier. Small area cell efficiencies of 13.8% on ferritic steel foils and 10.6% on polymer foils (both without antireflective coating) were obtained. First monolithically integrated submodules of up to 10×10cm2 substrate area were fabricated both on ferritic steel and polyimide substrates. Different patterning methods have been applied and matched to the respective substrate materials.

NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+antiporter

Na(+)/H(+) antiporters are ubiquitous membrane proteins that are involved in homeostasis of H(+) and Na(+) throughout the biological kingdom. Corroborating their role in pH homeostasis, many of the Na(+)/H(+) antiporter proteins are regulated directly by pH. The pH regulation of NhaA, the Escherichia coli Na(+)/H(+) antiporter (EcNhaA), as of other, both eukaryotic and prokaryotic Na(+)/H(+) antiporters, involves a pH sensor and conformational changes in different parts of the protein that transduce the pH signal into a change in activity. Thus, residues that affect the pH response, the translocation or both activities cluster in separate domains along the antiporter molecules. Importantly, in the NhaA family, these domains are conserved. Helix-packing model of EcNhaA based on cross-linking data suggests, that in the three dimensional structure of NhaA, residues that affect the pH response may be in close proximity, forming a single pH sensitive domain. Therefore, it is suggested that, despite considerable differences in the primary structure of the antiporters from the bacterial NhaA to the mammalian NHEs, their three-dimensional architectures are conserved. Test of this possibility awaits the atomic resolution of the 3D structure of the antiporters.