Recognition and reconstruction of cell differentiation patterns with deep learning.

Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell communication to replicate common spatial arrangements like checkerboard and engulfing patterns. In this model, the cell-cell communication has been implemented as a signal that disperses throughout the tissue. On the other hand, machine learning models have been developed for pattern recognition and pattern reconstruction tasks. We combined synthetic data generated by the mathematical model with spatial summary statistics and deep learning algorithms to recognize and reconstruct cell fate patterns in organoids of mouse embryonic stem cells. Application of Moran's index and pair correlation functions for in vitro and synthetic data from the model showed local clustering and radial segregation. To assess the patterns as a whole, a graph neural network was developed and trained on synthetic data from the model. Application to in vitro data predicted a low signal dispersion value. To test this result, we implemented a multilayer perceptron for the prediction of a given cell fate based on the fates of the neighboring cells. The results show a 70% accuracy of cell fate imputation based on the nine nearest neighbors of a cell. Overall, our approach combines deep learning with mathematical modeling to link cell fate patterns with potential underlying mechanisms.

Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing.

During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular signaling. We present an analytically tractable mathematical model based on signaling that reliably generates different cell type patterns with specified proportions. Employing statistical mechanics, We derived a cell fate decision model for two cell types. A detailed steady state analysis on the resulting dynamical system yielded necessary conditions to generate spatially heterogeneous patterns. This allows the cell type proportions to be controlled by a single model parameter. Cell-cell communication is realized by local and global signaling mechanisms. These result in different cell type patterns. A nearest neighbor signal yields checkerboard patterns. Increasing the signal dispersion, cell fate clusters and an engulfing pattern can be generated. Altogether, the presented model allows us to reliably generate heterogeneous cell type patterns of different kinds as well as desired proportions.

Ceramic laminate veneers: effect of preparation design and ceramic thickness on fracture resistance and marginal quality in vitro.

OBJECTIVES: The aim of the present study was to investigate the influence of five different preparation designs and two different ceramic thicknesses on margin quality and fracture resistance of ceramic laminate veneers after thermomechanical loading in vitro. MATERIALS AND METHODS: Eighty human central incisors were randomly assigned to 10 groups (n = 8) with five different preparation designs: non-prep (NP), minimally invasive (MI) = exclusively enamel-bonded, semi-invasive (SI) = 50% bonded in dentin, invasive (I) = 100% in dentin, and semi-invasive with two additional class III composite resin restorations (SI-C). IPS InLine veneers were fabricated in two thicknesses (L1 = 0.2-0.5 mm; L2 = 0.5-1.2 mm). After adhesive luting (OptiBond FL, Variolink Veneer) with light curing and polishing, specimens were stored in distilled water at 37 °C for 21 days, then thermocycled (2000 cycles between + 5 and + 55 °C), and finally mechanically loaded at the incisal edge at an angle of 45° for 2,000,000 cycles at 50 N und further 1,000,000 cycles at 100 N. Impressions were taken initially, after thermocycling, and after every 250,000 mechanical cycles in order to evaluate cracks and margin quality under a SEM. The veneers were evaluated in a light microscope (× 20) for cracks, chippings, partial, and catastrophic fractures. RESULTS: Margin quality after three million cycles revealed medians for continuous margin of 82-95% without significant differences among groups, neither at the ceramic/composite (p = 0.943) nor at the tooth/composite interface (p = 0.571). Visual inspection of veneers exhibited 22 cracks, 11 chippings, 4 partial and 4 catastrophic fractures in 38 of 80 veneers. The statistical ranking regarding fracture risk (p ≤ 0.05) was: IL1 = SIL1 = MIL1 = IL2 = CL1 = CL2, MIL2 = NPL1 = NPL2 = SIL2, IL2 = CL1 = CL2 = MIL2 = NPL1 = NPL2 = SIL2. CONCLUSIONS: Even after three million cycles with up to 100 N, all groups showed high survival rates. However, the fracture risk increases with thin veneers and preparations with medium to high dentin portions when compared to thicker veneers with preparations in enamel or partially in dentin (p ≤ 0.05). Preexisting resin composite restorations did not show any significant influence on margin quality and facture risk (p > 0.05). CLINICAL RELEVANCE: Ceramic laminate veneers are extremely durable with thin veneers and substantial enamel loss being main risk factors for fracture.

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering.

During mammalian preimplantation, cells of the inner cell mass (ICM) adopt either an embryonic or an extraembryonic fate. This process is tightly regulated in space and time and has been studied previously in mouse embryos and embryonic stem cell models. Current research suggests that cell fates are arranged in a salt-and-pepper pattern of random cell positioning or a spatially alternating pattern. However, the details of the three-dimensional patterns of cell fate specification have not been investigated in the embryo nor in in vitro systems. We developed ICM organoids as a, to our knowledge, novel three-dimensional in vitro stem cell system to model mechanisms of fate decisions that occur in the ICM. ICM organoids show similarities to the in vivo system that arise regardless of the differences in geometry and total cell number. Inspecting ICM organoids and mouse embryos, we describe a so far unknown local clustering of cells with identical fates in both systems. These findings are based on the three-dimensional quantitative analysis of spatiotemporal patterns of NANOG and GATA6 expression in combination with computational rule-based modeling. The pattern identified by our analysis is distinct from the current view of a salt-and-pepper pattern. Our investigation of the spatial distributions both in vivo and in vitro dissects the contributions of the different parts of the embryo to cell fate specifications. In perspective, our combination of quantitative in vivo and in vitro analyses can be extended to other mammalian organisms and thus creates a powerful approach to study embryogenesis.

Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters.

Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project µAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health. Monitoring for organisms with molecular tools is rapid, more accurate and more reliable than traditional methods. Rapid detection means that mitigation strategies come into play faster with less harm to the community and to humans. Samples were collected from several waters in France, Germany, Ireland, Italy and Turkey over 2 years. We present microarray results for the presence of freshwater pathogens from brackish and freshwater sites in Northern Germany, and cyanobacterial cell numbers inferred from these sites. In a companion study from the same samples, cyanobacterial toxins were analyzed using two methods and those sites with highest toxin values also had highest cell numbers as inferred from this microarray study.

Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey.

Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project µAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives. Molecular tools are more rapid, accurate and reliable than traditional methods, which means faster mitigation strategies with less harm to humans and the community. We present microarray results for the presence of freshwater pathogens from a Turkish lake used drinking water and inferred cyanobacterial cell equivalents from samples concentrated from 40 into 1 L in 45 min using hollow fibre filters. In two companion studies from the same samples, cyanobacterial toxins were analysed using chemical methods and those dates with highest toxin values also had highest cell equivalents as inferred from this microarray study.

An ancestral allele of grapevine transcription factor MYB14 promotes plant defence.

Stilbene synthase is a key enzyme for the production of the phytoalexin resveratrol. Some clones of Vitis sylvestris, a wild European grapevine species which is almost extinct, have been shown to accumulate more resveratrol in response to different forms of stress. In the current study, we asked whether the induction of stilbene synthase transcripts in Hoe29, one of the V. sylvestris clones with elevated stilbene inducibility, might result from the elevated induction of the transcription factor MYB14. The MYB14 promoter of Hoe29 and of Ke83 (a second stilbene-inducible genotype) harboured distinct regions and were applied to a promoter-reporter system. We show that stilbene synthase inducibility correlates with differences in the induction of MYB14 transcripts for these two genotypes. Both alleles were induced by UV in a promoter-reporter assay, but only the MYB14 promoter from Hoe29 was induced by flg22, consistent with the stilbene synthase expression of the donor genotypes, where both respond to UV but only Hoe29 is responsive to Plasmopara viticola during defence. We mapped upstream signals and found that a RboH-dependent oxidative burst, calcium influx, a MAPK cascade, and jasmonate activated the MYB14 promoter, whereas salicylic acid was ineffective. Our data suggest that the Hoe29 allele of the MYB14 promoter has potential as a candidate target for resistance breeding.

One precursor, three apolipoproteins: the relationship between two crustacean lipoproteins, the large discoidal lipoprotein and the high density lipoprotein/ß-glucan binding protein.

The novel discoidal lipoprotein (dLp) recently detected in the crayfish, differs from other crustacean lipoproteins in its large size, apoprotein composition and high lipid binding capacity, We identified the dLp sequence by transcriptome analyses of the hepatopancreas and mass spectrometry. Further de novo assembly of the NGS data followed by BLAST searches using the sequence of the high density lipoprotein/1-glucan binding protein (HDL-BGBP) of Astacus leptodactylus as query revealed a putative precursor molecule with an open reading frame of 14.7 kb and a deduced primary structure of 4889 amino acids. The presence of an N-terminal lipid bind- ing domain and a DUF 1943 domain suggests the relationship with the large lipid transfer proteins. Two-putative dibasic furin cleavage sites were identified bordering the sequence of the HDL-BGBP. When subjected to mass spectroscopic analyses, tryptic peptides of the large apoprotein of dLp matched the N-terminal part of the precursor, while the peptides obtained for its small apoprotein matched the C-terminal part. Repeating the analysis in the prawn Macrobrachium rosenbergii revealed a similar protein with identical domain architecture suggesting that our findings do not represent an isolated instance. Our results indicate that the above three apolipoproteins (i.e HDL-BGBP and both the large and the small subunit of dLp) are translated as a large precursor. Cleavage at the furin type sites releases two subunits forming a heterodimeric dLP particle, while the remaining part forms an HDL-BGBP whose relationship with other lipoproteins as well as specific functions are yet to be elucidated.

Clinical presentation and outcome in a series of 88 patients with the cblC defect.

UNLABELLED: The cblC defect is the most common inborn error of vitamin B12 metabolism. Despite therapeutic measures, the long-term outcome is often unsatisfactory. This retrospective multicentre study evaluates clinical, biochemical and genetic findings in 88 cblC patients. The questionnaire designed for the study evaluates clinical and biochemical features at both initial presentation and during follow up. Also the development of severity scores allows investigation of individual disease load, statistical evaluation of parameters between the different age of presentation groups, as well as a search for correlations between clinical endpoints and potential modifying factors. RESULTS: No major differences were found between neonatal and early onset patients so that these groups were combined as an infantile-onset group representing 88 % of all cases. Hypotonia, lethargy, feeding problems and developmental delay were predominant in this group, while late-onset patients frequently presented with psychiatric/behaviour problems and myelopathy. Plasma total homocysteine was higher and methionine lower in infantile-onset patients. Plasma methionine levels correlated with "overall impression" as judged by treating physicians. Physician's impression of patient's well-being correlated with assessed disease load. We confirmed the association between homozygosity for the c.271dupA mutation and infantile-onset but not between homozygosity for c.394C>T and late-onset. Patients were treated with parenteral hydroxocobalamin, betaine, folate/folinic acid and carnitine resulting in improvement of biochemical abnormalities, non-neurological signs and mortality. However the long-term neurological and ophthalmological outcome is not significantly influenced. In summary the survey points to the need for prospective studies in a large cohort using agreed treatment modalities and monitoring criteria.

Popeye domain containing proteins modulate the voltage-gated cardiac sodium channel Nav1.5.

Popeye domain containing (POPDC) proteins are predominantly expressed in the heart and skeletal muscle, modulating the K2P potassium channel TREK-1 in a cAMP-dependent manner. POPDC1 and POPDC2 variants cause cardiac conduction disorders with or without muscular dystrophy. Searching for POPDC2-modulated ion channels using a functional co-expression screen in Xenopus oocytes, we found POPDC proteins to modulate the cardiac sodium channel Nav1.5. POPDC proteins downregulate Nav1.5 currents in a cAMP-dependent manner by reducing the surface expression of the channel. POPDC2 and Nav1.5 are both expressed in different regions of the murine heart and consistently POPDC2 co-immunoprecipitates with Nav1.5 from native cardiac tissue. Strikingly, the knock-down of popdc2 in embryonic zebrafish caused an increased upstroke velocity and overshoot of cardiac action potentials. The POPDC modulation of Nav1.5 provides a new mechanism to regulate cardiac sodium channel densities under sympathetic stimulation, which is likely to have a functional impact on cardiac physiology and inherited arrhythmias.

Tissues as networks of cells: towards generative rules of complex organ development.

Network analysis is a well-known and powerful tool in molecular biology. More recently, it has been introduced in developmental biology. Tissues can be readily translated into spatial networks such that cells are represented by nodes and intercellular connections by edges. This discretization of cellular organization enables mathematical approaches rooted in network science to be applied towards the understanding of tissue structure and function. Here, we describe how such tissue abstractions can enable the principles that underpin tissue formation and function to be uncovered. We provide an introduction into biologically relevant network measures, then present an overview of different areas of developmental biology where these approaches have been applied. We then summarize the general developmental rules underpinning tissue topology generation. Finally, we discuss how generative models can help to link the developmental rule back to the tissue topologies. Our collection of results points at general mechanisms as to how local developmental rules can give rise to observed topological properties in multicellular systems.

The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors.

Embryos develop in a concerted sequence of spatiotemporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analyzed so far. We investigate the spatiotemporal distribution of NANOG- and GATA6-expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single-cell-based neighborhood analyses. A combination of spatial statistics and agent-based modeling reveals that the cell fate distribution follows a local clustering pattern. Using ordinary differential equations modeling, we show that this pattern can be established by a distance-based signaling mechanism enabling cells to integrate information from the whole inner cell mass into their cell fate decision. Our work highlights the importance of longer-range signaling to ensure coordinated decisions in groups of cells to successfully build embryos.

Neuropathy in paediatric type 1 diabetes mellitus - clinical characterization and analysis of risk factors in the diabetes prospective follow-up registry DPV (Diabetes-Patienten-Verlaufsdokumentation)-registry.

OBJECTIVES: Data on the prevalence, clinical features and risk factors associated with paediatric diabetic neuropathy (DN) are scarce. METHODS: We retrospectively analysed data from the DPV registry, including patients under 20 years of age, treated for type 1 diabetes mellitus (T1D) between 2005 and 2021. Patients with non-diabetic neuropathy were excluded. Data came from centres in Austria, Germany, Luxembourg and Switzerland. RESULTS: 1,121 of the 84,390 patients included had been diagnosed with DN. Univariate analysis showed patients with DN to be older and predominantly female, with a longer duration of T1D, higher insulin dosages per kg and day, lower rates of insulin pump therapy, higher postprandial glucose-, higher HbA1c-and higher cholesterol levels, and higher diastolic and systolic blood pressure values. There was also a larger proportion of smokers and higher prevalence of diabetic retinopathy. Median duration of diabetes at diagnosis of DN was 8.3 years. Multivariable analysis, adjusted for demographics revealed an increased risk for DN among female patients and those who were older, underweight (BMI-SDS), smoked cigarettes or had a longer duration of T1D or higher levels of HbA1c and postprandial blood glucose. The presence of retinopathy and higher cholesterol levels were also linked to increased risk while not-using insulin pump therapy was not. CONCLUSIONS: DN can develop after just a short duration of T1D. Prevention may be achieved by a lowering of HbA1c-and postprandial glucose levels through improved glycaemic control. This warrants further investigation. The slight female predominance suggests further hormonal and genetic etiological factors.

The development of lipoprotein apheresis in Saxony in the last years.

METHODS: Three hundred thirty-nine patients (230 men, 109 women) treated with lipoprotein apheresis in Saxony, Germany, in 2018 are described in terms of age, lipid pattern, risk factors, cardiovascular events, medication, and number of new admissions since 2014, and the data are compared with figures from 2010 to 2013. RESULTS: Patients were treated by 45.5 physicians in 16 lipoprotein apheresis centers. With about 10 patients per 100 000 inhabitants, the number of patients treated with lipoprotein apheresis in Saxony is twice as high as in Germany as a whole. The median treatment time was 3 years. Almost all patients had hypertension; type 2 diabetes mellitus was seen significantly more often in patients with low Lipoprotein(a). Cardiovascular events occurred in almost all patients before initiation of lipoprotein apheresis, under apheresis therapy the cardiovascular events rate was very low in this high-risk group. For some cardiovascular regions even no events could be observed. CONCLUSIONS: The importance of lipoprotein apheresis in Saxony had been increasing from 2010 to 2018.

Sex chromosome DSD individuals with mosaic 45,X0 and aberrant Y chromosomes in 46,XY cells: distinct gender phenotypes and germ cell tumour risks§.

"Differences of Sexual Development (DSD)," individuals with rearranged Y chromosome breaks in their 46,XY cells are reported with male and female gender phenotypes and differences in germ cell tumour (GCT) risk. This raised the question of whether male or female gender and GCT risk depends on the site of the break and/or rearrangement of the individual´s Y chromosome. In this paper, we report molecular mapping of the breakpoint on the aberrant Y chromosome of 22 DSD individuals with a 45,X/46,XY karyotype reared with a different gender. Their Y chromosome breaks are found at different sites on the long and short Y arms. Our data indicate that gender rearing is, neither dependent on the site of Y breakage, nor on the amount of 45,X0 cells in the individuals' leukocytes. Most prominent are secondary rearrangements of the Y chromosome breaks forming di-centric Y-structures ("dic-Y"). Duplications of the short Y arm and the proximal part of the long Y arm are the results. A putative GCT risk has been analysed with immunohistochemical experiments on some dysgenetic gonadal tissue sections. With specific antibodies for OCT3/4 expression, we marked the pluripotent germ cell fraction being potential tumour precursor cells. With specific antibodies for DDX3Y, TSPY, and UTY we analyzed their putative Gonadoblastoma Y (GBY) tumour susceptibility function in the same specimen. We conclude GBY expression is only diagnostic for GCT development in the aberrant germ cells of these DSD individuals when strong OCT3/4 expression has marked their pluripotency.

Zebrafish Ext2 is necessary for Fgf and Wnt signaling, but not for Hh signaling.

BACKGROUND: Heparan sulfate (HS) biosynthesis is tightly regulated during vertebrate embryo development. However, potential roles for HS biosynthesis in regulating the function of paracrine signaling molecules that bind to HS are incompletely understood. RESULTS: In this report we have studied Fgf, Wnt and Hedgehog (Hh) signaling in ext2 mutants, where heparan sulfate content is low. We found that Fgf targeted gene expression is reduced in ext2 mutants and that the remaining expression is readily inhibited by SU5402, an FGF receptor inhibitor. In the ext2 mutants, Fgf signaling is shown to be affected during nervous system development and reduction of Fgf ligands in the mutants affects tail development. Also, Wnt signaling is affected in the ext2 mutants, as shown by a stronger phenotype in ext2 mutants injected with morpholinos that partially block translation of Wnt11 or Wnt5b, compared to injected wild type embryos. In contrast, Hh dependent signaling is apparently unaffected in the ext2 mutants; Hh targeted gene expression is not reduced, the Hh inhibitor cyclopamine is not more affective in the mutants and Hh dependent cell differentiation in the retina and in the myotome are normal in ext2 mutants. In addition, no genetic interaction between ext2 and shha during development could be detected. CONCLUSION: We conclude that ext2 is involved in Fgf and Wnt signaling but not in Hh signaling, revealing an unexpected specificity for ext2 in signaling pathways during embryonic development. Thus, our results support the hypothesis that regulation of heparan sulfate biosynthesis has distinct instructive functions for different signaling factors.

Type 2 diabetes in octogenarians is associated with decreased low molecular weight adiponectin.

BACKGROUND: Adiponectin circulates in the blood in three different multimer isoforms, of which the high molecular weight form (HMW) is presumed to mediate insulin sensitivity. We examined whether adiponectin oligomer distribution is associated with aging and type 2 diabetes (T2D) in octogenarians without characteristic features of metabolic syndrome. METHODS: The study included 154 octogenarians (58 men, 96 women), 24 normoglycemic middle-aged controls (11 men, 13 women; mean age 44 years), and 33 middle-aged individuals (14 men, 19 women; mean age 55 years) with T2D. Based on oral glucose tolerance test 62 octogenarians had normal, 63 impaired glucose tolerance, and 29 octogenarians had newly detected T2D. Serum adiponectin multimer isoforms were measured after overnight fast by enzyme-linked immunosorbent assays. RESULTS: Compared to the normoglycemic middle-aged control group, male normoglycemic octogenarians revealed significantly higher total adiponectin and all adiponectin isoforms. The same was true for females with the exception of low molecular weight (LMW) adiponectin, which was not statistically higher in octogenarians. Male and female octogenarians with T2D had significantly higher levels of total, HMW, and middle molecular weight (MMW) adiponectin, but not LMW adiponectin, than middle-aged individuals with T2D. Female, but not male, octogenarians revealed significantly lower total adiponectin than normoglycemic octogenarians. Compared with normoglycemic octogenarians, male and female octogenarians with T2D were characterized by significantly lower LMW adiponectin. In male and female octogenarians, total adiponectin and all multimer isoforms were directly correlated with HDL cholesterol. LMW adiponectin in octogenarians of both sexes was inversely correlated with glucose level at 2-hour oral glucose tolerance test. CONCLUSIONS: Serum levels of total adiponectin as well as its HMW and MMW isoforms were significantly higher in octogenarians with normoglycemia or T2D than in corresponding middle-aged control groups. In male and female octogenarians without metabolic syndrome, T2D was associated with lower LMW adiponectin, while the HMW and MMW isoforms were not statistically different.

Nanoassembled plasmonic-photonic hybrid cavity for tailored light-matter coupling.

We propose and demonstrate a hybrid cavity system in which metal nanoparticles are evanescently coupled to a dielectric photonic crystal cavity using a nanoassembly method. While the metal constituents lead to strongly localized fields, optical feedback is provided by the surrounding photonic crystal structure. The combined effect of plasmonic field enhancement and high quality factor (Q approximately 900) opens new routes for the control of light-matter interaction at the nanoscale.