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Abstract Background FLNC is one of the few genes associated with all types of cardiomyopathies, but it also underlies neuromuscular phenotype. The combination of concomitant neuromuscular and cardiac involvement is not often observed in filaminopathies and the impact of this on the disease prognosis has hitherto not been analyzed. Results Here we provide a detailed clinical, genetic, and structural prediction analysis of distinct FLNC-associated phenotypes based on twelve pediatric cases. They include early-onset restrictive cardiomyopathy (RCM) in association with congenital myopathy. In all patients the initial diagnosis was established during the first year of life and in five out of twelve (41.7%) patients the first symptoms were observed at birth. RCM was present in all patients, often in combination with septal defects. No ventricular arrhythmias were noted in any of the patients presented here. Myopathy was confirmed by neurological examination, electromyography, and morphological studies. Arthrogryposes was diagnosed in six patients and remained clinically meaningful with increasing age in three of them. One patient underwent successful heart transplantation at the age of 18 years and two patients are currently included in the waiting list for heart transplantation. Two died due to congestive heart failure. One patient had ICD instally as primary prevention of SCD. In ten out of twelve patients the disease was associated with missense variants and only in two cases loss of function variants were detected. In half of the described cases, an amino acid substitution A1186V, altering the structure of IgFLNc10, was found. Conclusions The present description of twelve cases of early-onset restrictive cardiomyopathy with congenital myopathy and FLNC mutation, underlines a distinct unique phenotype that can be suggested as a separate clinical form of filaminopathies. Amino acid substitution A1186V, which was observed in half of the cases, defines a mutational hotspot for the reported combination of myopathy and cardiomyopathy. Several independent molecular mechanisms of FLNC mutations linked to filamin structure and function can explain the broad spectrum of FLNC-associated phenotypes. Early disease presentation and unfavorable prognosis of heart failure demanding heart transplantation make awareness of this clinical form of filaminopathy of great clinical importance.

Myelofibrosis with myeloid metaplasia is chronic mieloproliferative disease with ineffective erythropoiesis, dysplastic-megakaryocyte hyperplasia, and an increase in the ratio of immature granulocytes to total granulocytes. The incidence rate is 3.7–5.7 per 100,000 and the median survival is estimated to be between three and six years. The pathogenesis of myelofibrosis might be explained, in part, by a somatic point mutation on exon 14 (V617F) of the JAK2 kinase gene that is located on chromosome 9p24. However, mechanisms of regulation of microenvironment in bone marrow fibrosis are not clear. Considered that main producents of pro-fibrotic factors are the megakaryocytes and the macrophages. In this study we investigated influence of platelet factors on the cellular characteristics of the macrophages with oncogenic mutation JAK2 V617F. Materials and Methods: THP-1 cell line was modified by lentiviral modification. Two cell lines established: one with expression of JAK2 with oncogenic mutation JAK2 V617F, another wild type JAK2. Cells were cultured in RPMI-1640 containing 0.1% gentamicin, 1% l-glutamine and 10% fetal bovine serum (FBS) or 5%, 10% and 15% platelet lysate (PL). Cell lines were differentiated into the macrophages using 50 ng/ml phorbolmyristate acetate (PMA). Level of expression transforming growth factor β (TGFβ), galectin-3, matrix metalloproteinases (MMP) 2, 9, 12, 13 and tissue inhibitors of matrix metalloproteinase (TIMP) accessed by specific RT-qPCR. Results: We observed increased expression level of galectin-3, MMP-2, MMP-13 and TIMP-3 in JAK2 V617F expressing macrophages cultured with 10% FBS compare to ones with WT JAK2. Also macrophages containing mutation JAK2 V617F has increased level of expression of MMP-2, TIMP-3 and TIMP-4 when cultured with 10% platelet lysate. Also, cell line containing mutation JAK2 V617F has increased levels of expression of MMP-12 for cells cultured with 15% PL. We did not observe any significant difference in expression of TGFβ, MMP-9, TIMP-1 and -2. Conclusion: Increased levels of expression of galectin-3, MMP-12 and -13 suggest that platelet factors induce macrophages with JAK2 V617F mutation to release of profibrotic factors. On the other hand, increase of antifibrotic MMP-2 and TIMP-3 revealing complex nature of melofibrosis development and need to be analyzed further. This study confirms the idea of interaction between macrophages and platelets in pathogenesis of primary myelofibrosis.

Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors.

DNA editing deaminases (APOBECs) are implicated in generation of mutations in somatic cells during tumorigenesis. APOBEC-dependent mutagenesis is thought to occur during transient exposure of unprotected single-stranded DNA. Mutations frequently occur in clusters (kataegis). We investigated mechanisms of mutant generation in growing and resting diploid yeast expressing APOBEC from sea lamprey, PmCDA1, whose kataegistic effect was previously shown to be associated with transcription. We have found that the frequency of canavanine-resistant mutants kept raising after growth cessation, while the profile of transcription remained unchanged. Surprisingly, the overall number of mutations in the genomes did not elevate in resting cells. Thus, mutations were accumulated during vigorous growth stage with both intense replication and transcription. We found that the elevated recovery of can1 mutant clones in non-growing cells is the result of loss of heterozygosity (LOH) leading to clusters of homozygous mutations in the chromosomal regions distal to the reporter gene. We confirmed that recombination frequency in resting cells was elevated by orders of magnitude, suggesting that cells were transiently committed to meiotic levels of recombination, a process referred to in yeast genetics as return-to-growth. In its extreme, on day 6 of starvation, a few mutant clones were haploid, likely resulting from completed meiosis. Distribution of mutations along chromosomes indicated that PmCDA1 was active during ongoing recombination events and sometimes produced characteristic kataegis near initial breakpoints. AID and APOBEC1 behaved similar to PmCDA1. We conclude that replication, transcription, and mitotic recombination contribute to the recovered APOBEC-induced mutations in resting diploids. The mechanism is relevant to the initial stages of oncogenic transformation in terminally differentiated cells, when recombination may lead to the LOH exposing recessive mutations induced by APOBECs in cell’s history and to acquisition of new mutations near original break.

Abstract. The article identifies the impact of sources of funding for innovation in the country on economic growth through economic and mathematical modeling and construction of regression equations between GDP and funding for innovation and research costs with the construction of a multifactor regression equation. As a result of regression analysis, it was found that the most significant impact on the resulting indicator have such variables as capital investment from state and local budgets and research and development costs. Using the method of extrapolation, GDP growth was forecast for 4 years, and it was found that capital investment from own funds of enterprises and organizations will grow by 24,08%, capital investment from state and local budgets by 28,42%, research costs and development by 22,76% for the analyzed period.Subject to compliance with the projected values of the financial determinants of the innovative component of increasing the country’s competitiveness, the volume of estimated GDP in actual prices for the forecast period will increase by 936039,011 million UAH or 23,26%. The reasons for the low level of the state of the innovation sphere in the domestic economy are outlined: underdevelopment of the market of innovative products due to low indicators of development of integration processes in it; weakness of relations that determine the innovative nature of economic development; low motivation of the industrial sector in innovative development; the supply of technological innovations created by national industrial companies and research institutions in the domestic market is limited; high cost of development and implementation, high interest rates on the investment portfolio, a long payback period, the focus of financial institutions on the issuance of «short loans», usually consumer loans for technological renewal of industrial sectors. To resolve such contradictions, the system-forming factors of a set of measures to intensify integration processes in the innovation sphere of Ukraine were proposed. Systematized foreign experience in scientific, technical and innovation policy, as well as commercialization of innovations, taking into account which proposed conceptual guidelines for organizational and financial support of the effectiveness of the innovative component of competitiveness: economic mechanisms (direct budget investments; preferential lending; integration with foreign institutions; financial activities; increase the share of GDP aimed at financing innovation processes, development of an effective set of measures to attract international grants and household savings as investments to implement the concept of innovative development of the country’s economy, etc.); organizational mechanisms (formation of integration clusters using the potential of education, business, government, public; state assistance in the development of innovation infrastructure, etc.). Keywords:innovations, financial support of innovative development, country competitiveness, innovation system, cluster, regression, correlation, integration processes. JEL Classification O11, O19, O16, O33, E62, F20 Formulas: 1; fig.: 5; tabl.: 3; bibl.: 12.

Oxadiamondoids representing a new class of carbon nanoparticles were prepared from the respective diamondoid ketones via an effective two-step procedure involving addition of methyl magnesium iodide and oxidation with trifluoroperacetic acid in trifluoroacetic acid. The reactivities of the oxacages are determined by the position of the dopant and are in good agreement with computational predictions. [ABSTRACT FROM AUTHOR]

The setae in Eriophyoidea are filiform, slightly bent and thickened near the base. Confocal microscopy indicates that their proximal and distal parts differ in light reflection and autofluorescence. Approximately 50 genera have atypically shaped setae: bifurcated, angled or swollen. These modifications are known in the basal part of prosomal setae u′, ft′, ft″, d, v, bv, ve, sc and caudal setae h2. We assessed the distribution of atypically shaped setae in Eriophyoidea and showed that they are scattered in different phylogenetic lineages. We hypothesized that the ancestral setae of eriophyoid mites were bifurcated before later simplifying into filiform setae. We also proposed that hypo-furcating setae are a synapomorphy that unites Eriophyoidea with Nematalycidae. We analyzed four new mitochondrial genomes of Leipothrix, the largest genus with bifurcated d, and showed that it is monophyletic and has a unique mitochondrial gene order with translocated trnK. We exclude Cereusacarus juniperensis n. comb. Xue and Yin, 2020 from Leipothrix and transfer five Epitrimerus spp. to Leipothrix: L. aegopodii (Liro 1941) n. comb., L. femoralis (Liro 1941) n. comb., L. geranii (Liro 1941) n. comb., L. ranunculi (Liro 1941) n. comb., and L. triquetra (Meyer 1990) n. comb.

Spontaneous or induced DNA lesions can result in stable gene mutations and chromosomal aberrations due to their inaccurate repair, ultimately resulting in phenotype changes. Some DNA lesions per se may interfere with transcription, leading to temporary phenocopies of mutations. The direct impact of primary DNA lesions on phenotype before their removal by repair is not well understood. To address this question, we used the alpha-test, which allows for detecting various genetic events leading to temporary or hereditary changes in mating type α→a in heterothallic strains of yeast Saccharomyces cerevisiae. Here, we compared yeast strains carrying mutations in DNA repair genes, mismatch repair (pms1), base excision repair (ogg1), and homologous recombination repair (rad52), as well as mutagens causing specific DNA lesions (UV light and camptothecin). We found that double-strand breaks and UV-induced lesions have a stronger effect on the phenotype than mismatches and 8-oxoguanine. Moreover, the loss of the entire chromosome III leads to an immediate mating type switch α→a and does not prevent hybridization. We also evaluated the ability of primary DNA lesions to persist through the cell cycle by assessing the frequency of UV-induced inherited and non-inherited genetic changes in asynchronous cultures of a wild-type (wt) strain and in a cdc28-4 mutant arrested in the G1 phase. Our findings suggest that the phenotypic manifestation of primary DNA lesions depends on their type and the stage of the cell cycle in which it occurred.

Eriophyoidea is a group of phytoparasitic mites with poorly resolved phylogeny. Previous studies inferred Eriophyidae s.l. as the largest molecular clade of Eriophyoidea, and Nothopodinae as the basal divergence of Eriophyidae s.l. We investigate the morphology and molecular phylogeny of Nothopoda todeica n. sp. (Nothopodinae, Nothopodini), associated with a disjunct Afro-Australasian fern Todea barbara (Osmundaceae) from South Africa. Our analyses (1) determine new erroneous sequences (KF782375, KF782475, KF782586) wrongly assigned to Nothopodinae instead of Phyllocoptinae, (2) confirm the basal position of Nothopodinae in Eriophyoidea s.l., (3) question the monophyly of the Colopodacini and Nothopodini tribes, and (4) show the nested position of African fern-associated Nothopoda within a clade dominated by Asian nothopodines from angiosperms, which implies (a) a secondary association of nothopodines with ferns and (b) no relation between geography (continents) and the phylogenetic relationships of Nothopodinae species. Finally, we obtained a first complete mitochondrial genome for Nothopodinae and revealed a new gene order in the mitogenome of N. todeica n. sp., notably deviating from those in other investigated eriophyoids. Our results contribute to resolving the phylogeny of Eriophyoidea and provide an example of an integrative study of a new taxon belonging to an economically important group of acariform mites.

Baker’s yeast, S. cerevisiae, is an excellent model organism exploited for molecular genetic studies of the mechanisms of genome stability in eukaryotes. Genetic peculiarities of commonly used yeast strains impact the processes of DNA replication, repair, and recombination (RRR). We compared the genomic DNA sequence variation of the five strains that are intensively used for RRR studies. We used yeast next-generation sequencing data to detect the extent and significance of variation in 183 RRR genes. We present a detailed analysis of the differences that were found even in closely related strains. Polymorphisms of common yeast strains should be considered when interpreting the outcomes of genome stability studies, especially in cases of discrepancies between laboratories describing the same phenomena.

The detection and identification of plant diseases is a fundamental task for sustainable crop production. Septoria tritici and Stagonospora nodorum blotch (STB and SNB) are two of the most common diseases of cereal crops that cause significant economic damage. Both pathogens are difficult to identify at early stages of infection. Determining the degree of the disease at a late infection stage is useful for assessing cereal crops before harvesting, as it allows the assessment of potential yield losses. Hyperspectral sensing could allow for automatic recognition of Septoria harmfulness on wheat in field conditions. In this research, we aimed to collect information on the hyperspectral data on wheat plants with different lesion degrees of STB&SNB and to create and train a neural network for the detection of lesions on leaves and ears caused by STB&SNB infection at the late stage of disease development. Spring wheat was artificially infected twice with Septoria pathogens in the stem elongation stage and in the heading stage. Hyperspectral reflections and brightness measurements were collected in the field on wheat leaves and ears on the 37th day after STB and the 30th day after SNB pathogen inoculation using an Ocean Insight “Flame” VIS-NIR hyperspectrometer. Obtained non-imaging data were pre-treated, and the perceptron model neural network (PNN) was created and trained based on a pairwise comparison of datasets for healthy and diseased plants. Both statistical and neural network approaches showed the high quality of the differentiation between healthy and damaged wheat plants by the hyperspectral signature. A comparison of the results of visual recognition and automatic STB&SNB estimation showed that the neural network was equally effective in the quality of the disease definition. The PNN, based on a neuron model of hyperspectral signature with a spectral step of 6 nm and 2000–4000 value datasets, showed a high quality of detection of the STB&SNB severity. There were 0.99 accuracy, 0.94 precision, 0.89 recall and 0.91 F-score metrics of the PNN model after 10,000 learning epochs. The estimation accuracy of diseased/healthy leaves ranged from 88.1 to 97.7% for different datasets. The accuracy of detection of a light and medium degree of disease was lower (38–66%). This method of non-imaging hyperspectral signature classification could be useful for the identification of the STB and SNB lesion degree identification in field conditions for pre-harvesting crop estimation.

Aim. To perform a combined experimental and computational study on the luminescent properties of practically important class of organic dyes – 4-aminophthalimides. Results and discussion. The absorption and fluorescence spectra of 4-aminophthalimide derivatives in polar protic and aprotic solvents were computed and matched vs. the experimental data. The changes in emission spectra are mainly related to the NH2-group derivatization. The methyl substitution of amide hydrogen causes a batochromic shift of about 7 nm in the absorption peak and a negligible hypsochromic shift in the fluorescence peak, while introducing alkyl substituents to the amine moiety causes bathochromic shifts in absorption and emission peaks of 30 – 40 nm and 10 – 60 nm, respectively. Experimental part. Absorption and emission wavelengths were computed by the standard algorithm based on the ground state geometry optimization (equilibrium solvation), vertical excitation with nonequilibrium solvation, and the TD-DFT geometry optimization of the excited state structures. A reliable hybrid B3LYP functional was used in combination with DZ and TZ-quality basis sets. Conclusions. The computed absorption wavelengths are in excellent agreement with the experimental data and are only slightly solvent-dependent. At the same time, the discrepancy with the experiment for Stokes shifts reaches about 20 % at IEF-PCM-TD-B3LYP/6-31G(d). However, the general tendency for both absorption and fluorescence wavelengths is identical for all solvents within one molecule.

Aim. To study the effect of electronic (α- and β-hyperconjugations) and steric (noncovalent interactions) factors on the structures of olefinic radical cations. Results and discussion. The effect of intramolecular dispersion interactions on the structures of crowded alkenes in the neutral and ionized forms has been studied at the density functional theory (DFT) level with and without dispersion corrections included, as well as at the MP2 theory level with medium size basis sets. The results obtained are compared to the available experimental data. An excellent agreement has been found between the experimental and MP2/DFT-computed geometries of sesquihomoadamantene, adamantylidene adamantane, bis-2,2,5,5-tetramethylcyclopentylidene, bis-D3-homocub-4-ylidene, and bis-CS-homocub-8-ylidene in the neutral and ionized forms. The experimental ionization potentials are better reproduced with the DFT-methods. Experimental part. The structure and composition of compounds were proved by the methods of 1H and 13C NMR-spectroscopy, and GC-MS-analysis. Elemental analysis was performed for the compounds obtained. Conclusions. The twisting of the olefinic moieties in the sesquihomoadamantene and adamantylidene adamantane radical cations is determined by the balance between the σ-π-hyperconjugation and residual one-electron π-bonding and is close to that of the prototypical ethylene radical cation (29°). The twisting reaches 55° for the bis-2,2,5,5-tetramethylcyclopentylidene radical cation due to substantial steric repulsions between methyl groups. At the same time, the ionized states of bis-D3-homocub-4-ylidene and bis-CS-homocub-8-ylidene retain their planarity due to β-CC-hyperconjugation and intramolecular dispersion attractions.

Arthropods include a high diversity of lineages adapted for silk production. Several species of microscopic phytophagous mites of the hyperdiverse superfamily Eriophyoidea spin web; however, the origin of their silk is unknown. We described a new web-spinning mite, Aberoptus schotiae n. sp., collected from leaves of Schotia brachypetala (Fabaceae) in South Africa and showed that it has a complex life cycle, including two morphotypes of adults and nymphs. Molecular phylogenetic analyses and 28S sequence comparison showed conspecificity of heteromorphic females and rejected synonymy of Aberoptus and Aceria proposed by previous authors. For the first time, we provided SEM images of the web nests and, using a set of different microscopic techniques, described the silk-producing anal secretory apparatus (ASA) of Aberoptus. It comprises two pairs of anal glands (hypertrophied in web-spinning females), three cuticular sacs and a rectal tube leading to the anal opening. This is a unique case (analogy) of anal silk secretion in Chelicerata previously reported only in Serianus (Pseudoscorpiones). Recent findings of rudimentary ASA in distant eriophyoid lineages and the results of this study transform the current paradigm of exoticism of web-spinning eriophyoid taxa into the concept of synapomorphic specialization of the hindgut for excreting the anal gland secretions in Eriophyoidea.

Background: Primary ciliary dyskinesia (PCD) is a group of rare genetically heterogeneous disorders caused by defective cilia and flagella motility. The clinical phenotype of PCD patients commonly includes chronic oto-sino-pulmonary disease, infertility, and, in about half of cases, laterality defects due to randomization of left-right body asymmetry. To date, pathogenic variants in more than 50 genes responsible for motile cilia structure and assembly have been reported in such patients. While multiple population-specific mutations have been described in PCD cohorts from different countries, the data on genetic spectrum of PCD in Russian population are still extremely limited., Results: The present study provides a comprehensive clinical and genetic characterization of 21 Russian families with PCD living in various country regions. Anomalies of ciliary beating in patients` respiratory epithelial cells were confirmed by high-speed video microscopy. In the most cases, custom-designed panel sequencing allowed to uncover causative variants in well-known or rarely mentioned PCD-related genes, including DNAH5, DNAH11, CFAP300, LRRC6, ZMYND10, CCDC103, HYDIN, ODAD4, DNAL1, and OFD1. The variations comprised common mutations, as well as novel genetic variants, some of which probably specific for Russian patients. Additional targeted analysis of mRNA transcripts from ciliated cells enabled us to specify functional effects of newly identified genetic variants in DNAH5 (c.2052+3G>T, c.3599-2A>G), HYDIN (c.10949-2A>G, c.1797C>G), and ZMYND10 (c.510+1G>C) on splicing process. In particular, the splice site variant c.2052+3G>T, detected in four unrelated families, resulted in skipping of exon 14 in DNAH5 transcripts and, according to haplotype analysis of affected probands, was proposed as an ancestral founder mutation in Udmurt population., Conclusions: The reported data provide a vital insight into genetic background of primary ciliary dyskinesia in the Russian population. The findings clearly illustrate the utility of gene panel sequencing coupled with transcriptional analysis in identification and clinical interpretation of novel genetic variants., (© 2024. The Author(s).)

Delta like canonical notch ligand 4 (Dll4) expression levels in tumors are known to affect the efficacy of cancer therapies. This study aimed to develop a model to predict Dll4 expression levels in tumors using dynamic enhanced near-infrared (NIR) imaging with indocyanine green (ICG). Two rat-based consomic xenograft (CXM) strains of breast cancer with different Dll4 expression levels and eight congenic xenograft strains were studied. Principal component analysis (PCA) was used to visualize and segment tumors, and modified PCA techniques identified and analyzed tumor and normal regions of interest (ROIs). The average NIR intensity for each ROI was calculated from pixel brightness at each time interval, yielding easily interpretable features including the slope of initial ICG uptake, time to peak perfusion, and rate of ICG intensity change after reaching half-maximum intensity. Machine learning algorithms were applied to select discriminative features for classification, and model performance was evaluated with a confusion matrix, receiver operating characteristic curve, and area under the curve. The selected machine learning methods accurately identified host Dll4 expression alterations with sensitivity and specificity above 90%. This may enable stratification of patients for Dll4 targeted therapies. NIR imaging with ICG can noninvasively assess Dll4 expression levels in tumors and aid in effective decision making for cancer therapy.

A series of mono- and bis-polyethylene glycol (PEG)-substituted BF 2 -azadipyrromethene fluorophores have been synthesized with emissions in the near-infrared region (700-800 nm) for the purpose of fluorescence guided intraoperative imaging; chiefly ureter imaging. The Bis-PEGylation of fluorophores resulted in higher aqueous fluorescence quantum yields, with PEG chain lengths of 2.9 to 4.6 kDa being optimal. Fluorescence ureter identification was possible in a rodent model with the preference for renal excretion notable through comparative fluorescence intensities from the ureters, kidneys and liver. Ureteral identification was also successfully performed in a larger animal porcine model under abdominal surgical conditions. Three tested doses of 0.5, 0.25 and 0.1 mg/kg all successfully identified fluorescent ureters within 20 min of administration which was sustained up to 120 min. 3-D emission heat map imaging allowed the spatial and temporal changes in intensity due to the distinctive peristaltic waves of urine being transferred from the kidneys to the bladder to be identified. As the emission of these fluorophores could be spectrally distinguished from the clinically-used perfusion dye indocyanine green, it is envisaged that their combined use could be a step towards intraoperative colour coding of different tissues.

The HUSH (human silencing hub) complex contains the H3K9me3 binding protein M-phase phosphoprotein 8 (MPP8) and recruits the histone methyltransferase SETDB1 as well as Microrchidia CW-type zinc finger protein 2 (MORC2). Functional and mechanistic studies of the HUSH complex have hitherto been centered around SETDB1 while the in vivo functions of MPP8 and MORC2 remain elusive. Here, we show that genetic inactivation of Mphosph8 or Morc2a in the nervous system of mice leads to increased brain size, altered brain architecture, and behavioral changes. Mechanistically, in both mouse brains and human cerebral organoids, MPP8 and MORC2 suppress the repetitive-like protocadherin gene cluster in an H3K9me3-dependent manner. Our data identify MPP8 and MORC2, previously linked to silencing of repetitive elements via the HUSH complex, as key epigenetic regulators of protocadherin expression in the nervous system and thereby brain development and neuronal individuality in mice and humans.

Background: FLNC is one of the few genes associated with all types of cardiomyopathies, but it also underlies neuromuscular phenotype. The combination of concomitant neuromuscular and cardiac involvement is not often observed in filaminopathies and the impact of this on the disease prognosis has hitherto not been analyzed., Results: Here we provide a detailed clinical, genetic, and structural prediction analysis of distinct FLNC-associated phenotypes based on twelve pediatric cases. They include early-onset restrictive cardiomyopathy (RCM) in association with congenital myopathy. In all patients the initial diagnosis was established during the first year of life and in five out of twelve (41.7%) patients the first symptoms were observed at birth. RCM was present in all patients, often in combination with septal defects. No ventricular arrhythmias were noted in any of the patients presented here. Myopathy was confirmed by neurological examination, electromyography, and morphological studies. Arthrogryposes was diagnosed in six patients and remained clinically meaningful with increasing age in three of them. One patient underwent successful heart transplantation at the age of 18 years and two patients are currently included in the waiting list for heart transplantation. Two died due to congestive heart failure. One patient had ICD instally as primary prevention of SCD. In ten out of twelve patients the disease was associated with missense variants and only in two cases loss of function variants were detected. In half of the described cases, an amino acid substitution A1186V, altering the structure of IgFLNc10, was found., Conclusions: The present description of twelve cases of early-onset restrictive cardiomyopathy with congenital myopathy and FLNC mutation, underlines a distinct unique phenotype that can be suggested as a separate clinical form of filaminopathies. Amino acid substitution A1186V, which was observed in half of the cases, defines a mutational hotspot for the reported combination of myopathy and cardiomyopathy. Several independent molecular mechanisms of FLNC mutations linked to filamin structure and function can explain the broad spectrum of FLNC-associated phenotypes. Early disease presentation and unfavorable prognosis of heart failure demanding heart transplantation make awareness of this clinical form of filaminopathy of great clinical importance., (© 2022. The Author(s).)

The wide availability of near infrared light sources in interventional medical imaging stacks enables non-invasive quantification of perfusion by using fluorescent dyes, typically Indocyanine Green (ICG). Due to their often leaky and chaotic vasculatures, intravenously administered ICG perfuses through cancerous tissues differently. We investigate here how a few characteristic values derived from the time series of fluorescence can be used in simple machine learning algorithms to distinguish benign lesions from cancers. These features capture the initial uptake of ICG in the colon, its peak fluorescence, and its early wash-out. By using simple, explainable algorithms we demonstrate, in clinical cases, that sensitivity (specificity) rates of over 95% (95%) for cancer classification can be achieved., (©2021 AMIA - All rights reserved.)

We demonstrate how a linear factor model with latent variables can be used to estimate correlations between the outcomes of clinical trials. These correlations are needed for many policy questions of drug/vaccine development (such as calculating the optimal size of financial incentives) and the literature so far has relied on expert opinions. We apply our methodology to the case of vaccines and show that the estimated correlations are highly significant. We also illustrate how the estimated correlations can be used to find the probability of obtaining a successful vaccine out of a certain number of candidates and to determine optimal investment in vaccine development., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 Informa UK Limited, trading as Taylor & Francis Group.)

Dual emissions at ~700 and 800 nm have been achieved from a single NIR-AZA fluorophore 1 by establishing parameters in which it can exist in either its isolated molecular or aggregated states. Dual near infrared (NIR) fluorescence color lymph node (LN) mapping with 1 was achieved in a large-animal porcine model, with injection site, channels and nodes all detectable at both 700 and 800 nm using a preclinical open camera system. The fluorophore was also compatible with imaging using two clinical instruments for fluorescence guided surgery. Methods: An NIR-AZA fluorophore with hydrophilic and phobic features was synthesised in a straightforward manner and its aggregation properties characterised spectroscopically and by TEM imaging. Toxicity was assessed in a rodent model and dual color fluorescence imaging evaluated by lymph node mapping in a large animal porcine models and in ex-vivo human tissue specimen. Results: Dual color fluorescence imaging has been achieved in the highly complex biomedical scenario of lymph node mapping. Emissions at 700 and 800 nm can be achieved from a single fluorophore by establishing molecular and aggregate forms. Fluorophore was compatible with clinical systems for fluorescence guided surgery and no toxicity was observed in high dosage testing. Conclusion: A new, biomedical compatible form of NIR-dual emission wavelength imaging has been established using a readily accessible fluorophore with significant scope for clinical translation., Competing Interests: Competing Interests: DFOS has a financial interest in patents filed and granted relating to NIR-fluorophores and processes for visual determination of tissue biology. RC is named on a patent filed in relation to processes for visual determination of tissue biology and receives speaker fees from Stryker Corp, consultancy fees from Distal Motion and holds research funding from Intuitive Corp and with IBM Corp and Deciphex. PMA, SZ are full-time employees of IBM Research, a division of IBM Corporation. IBM Corporation provides technical products and services world-wide to government, healthcare and life-sciences companies. PMA, SZ hold and have filed patents concerning technologies related to the subject matter of this paper. MD is member of the Advisory Board of Diagnostic Green and is the recipient of the ELIOS grant from the ARC Foundation. JM is the President of the IRCAD Institute, which is partly funded by KARL STORZ and Medtronic., (© The author(s).)

Virtual fractional flow reserve (vFFR) is an emerging technology employing patient-specific computational fluid dynamics (CFD) simulations to infer the hemodynamic significance of a coronary stenosis. Patient-specific boundary conditions are an important aspect of this approach and while most efforts make use of lumped parameter models to capture key phenomena, they lack the ability to specify the associated parameters on a patient-specific basis. When applying vFFR in a catheter laboratory setting using X-ray angiograms as the basis for creating the simulations, there is some indirect functional information available through the observation of the radio-opaque contrast agent motion. In this work, we present a novel method for tuning the lumped parameter arterial resistances (commonly incorporated in such simulations), based on simulating the physics of the contrast motion and comparing the observed and simulated arrival times of the contrast front at key points within a coronary tree. We present proof of principle results on a synthetically generated coronary tree comprised of multiple segments, demonstrating that the method can successfully optimize the arterial resistances to reconstruct the underlying velocity and pressure fields, providing a potential new means to improve the patient specificity of simulation-based technologies in this area., (Copyright © 2020 by ASME.)

Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.

The ability to directly uncover the contributions of genes to a given phenotype is fundamental for biology research. However, ostensibly homogeneous cell populations exhibit large clonal variance that can confound analyses and undermine reproducibility. Here we used genome-saturated mutagenesis to create a biobank of over 100,000 individual haploid mouse embryonic stem (mES) cell lines targeting 16,970 genes with genetically barcoded, conditional and reversible mutations. This Haplobank is, to our knowledge, the largest resource of hemi/homozygous mutant mES cells to date and is available to all researchers. Reversible mutagenesis overcomes clonal variance by permitting functional annotation of the genome directly in sister cells. We use the Haplobank in reverse genetic screens to investigate the temporal resolution of essential genes in mES cells, and to identify novel genes that control sprouting angiogenesis and lineage specification of blood vessels. Furthermore, a genome-wide forward screen with Haplobank identified PLA2G16 as a host factor that is required for cytotoxicity by rhinoviruses, which cause the common cold. Therefore, clones from the Haplobank combined with the use of reversible technologies enable high-throughput, reproducible, functional annotation of the genome.

We have investigated the impact of Cu 2 ZnSnS 4 -Molybdenum (Mo) interface quality on the performance of sputter-grown Cu 2 ZnSnS 4 (CZTS) solar cell. Thin film CZTS was deposited by sputter deposition technique using stoichiometry quaternary CZTS target. Formation of molybdenum sulphide (MoS x ) interfacial layer is observed in sputter grown CZTS films after sulphurization. Thickness of MoS x layer is found ~142 nm when CZTS layer (550 nm thick) is sulphurized at 600 °C. Thickness of MoS x layer significantly increased to ~240 nm in case of thicker CZTS layer (650 nm) under similar sulphurization condition. We also observe that high temperature (600 °C) annealing suppress the elemental impurities (Cu, Zn, Sn) at interfacial layer. The amount of out-diffused Mo significantly varies with the change in sulphurization temperature. The out-diffused Mo into CZTS layer and reconstructed interfacial layer remarkably decreases series resistance and increases shunt resistance of the solar cell. The overall efficiency of the solar cell is improved by nearly five times when 600 °C sulphurized CZTS layer is applied in place of 500 °C sulphurized layer. Molybdenum and sulphur diffusion reconstruct the interface layer during heat treatment and play the major role in charge carrier dynamics of a photovoltaic device.

The current state of thin film heterojunction solar cells based on cuprous oxide (Cu₂O), cupric oxide (CuO) and copper (III) oxide (Cu₄O₃) is reviewed. These p-type semiconducting oxides prepared by Cu oxidation, sputtering or electrochemical deposition are non-toxic, sustainable photovoltaic materials with application potential for solar electricity. However, defects at the copper oxide heterojunction and film quality are still major constraining factors for achieving high power conversion efficiency, η. Amongst the Cu₂O heterojunction devices, a maximum η of 6.1% has been obtained by using pulsed laser deposition (PLD) of Al x Ga 1- x O onto thermal Cu₂O doped with Na. The performance of CuO/n-Si heterojunction solar cells formed by magnetron sputtering of CuO is presently limited by both native oxide and Cu rich copper oxide layers at the heterointerface. These interfacial layers can be reduced by using a two-step sputtering process. A high η of 2.88% for CuO heterojunction solar cells has been achieved by incorporation of mixed phase CuO/Cu₂O nanopowder. CuO/Cu₂O heterojunction solar cells fabricated by electrodeposition and electrochemical doping has a maximum efficiency of 0.64% after surface defect passivation and annealing. Finally, early stage study of Cu₄O₃/GaN deposited on sapphire substrate has shown a photovoltaic effect and an η of ~10 -2 %.

Bicuspid aortic valve is the most common congenital heart malformation and the reasons for the aortopathies associated with bicuspid aortic valve remain unclear. NOTCH1 mutations are associated with bicuspid aortic valve and have been found in individuals with various left ventricular outflow tract abnormalities. Notch is a key signaling during cardiac valve formation that promotes the endothelial-to-mesenchymal transition. We address the role of Notch signaling in human aortic endothelial cells from patients with bicuspid aortic valve and aortic aneurysm. Aortic endothelial cells were isolated from tissue fragments of bicuspid aortic valve-associated thoracic aortic aneurysm patients and from healthy donors. Endothelial-to-mesenchymal transition was induced by activation of Notch signaling. Effectiveness of the transition was estimated by loss of endothelial and gain of mesenchymal markers by immunocytochemistry and qPCR. We show that aortic endothelial cells from the patients with aortic aneurysm and bicuspid aortic valve have down regulated Notch signaling and fail to activate Notch-dependent endothelial-to-mesenchymal transition in response to its stimulation by different Notch ligands. Our findings support the idea that bicuspid aortic valve and associated aortic aneurysm is associated with dysregulation of the entire Notch signaling pathway independently on the specific gene mutation., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Obesity, type 2 diabetes and associated metabolic diseases are characterized by low-grade systemic inflammation which involves interplay of nutrition and monocyte/macrophage functions. We suggested that some factors such as nutrient components, neuropeptides involved in the control of gastrointestinal functions, and gastrointestinal hormones might influence immune cell functions and in this way contribute to the disease pathogenesis. The aim of this study was to investigate the mRNA expression of twelve nutrition-associated receptors in peripheral blood mononuclear cells (PBMC), isolated monocytes and monocyte-derived macrophages and their regulation under the switching from the high-carbohydrate low-fat diet to the low-carbohydrate high-fat (LC/HFD) isocaloric diet in healthy humans. The mRNA expression of receptors for short chain fatty acids (GPR41, GPR43), bile acids (TGR5), incretins (GIPR, GLP1R), cholecystokinin (CCKAR), neuropeptides VIP and PACAP (VIPR1, VIPR2), and neurotensin (NTSR1) was detected in PBMC and monocytes, while GPR41, GPR43, GIPR, TGR5, and VIPR1 were found in macrophages. Correlations of the receptor expression in monocytes with a range of metabolic and inflammatory markers were found. In non-obese subjects, the dietary switch to LC/HFD induced the increase of GPR43 and VIPR1 expression in monocytes. No significant differences of receptor expression between normal weight and moderately obese subjects were found. Our study characterized for the first time the expression pattern of nutrition-associated receptors in human blood monocytes and its dietary-induced changes linking metabolic responses to nutrition with immune functions in health and metabolic diseases., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Diabetes mellitus type 2 (T2DM), insulin therapy, and hyperinsulinemia are independent risk factors of liver cancer. Recently, the use of a novel inhibitor of insulin degrading enzyme (IDE) was proposed as a new therapeutic strategy in T2DM. However, IDE inhibition might stimulate liver cell proliferation via increased intracellular insulin concentration. The aim of this study was to characterize effects of inhibition of IDE activity in HepG2 hepatoma cells and to analyze liver specific expression of IDE in subjects with T2DM. HepG2 cells were treated with 10 nM insulin for 24 h with or without inhibition of IDE activity using IDE RNAi, and cell transcriptome and proliferation rate were analyzed. Human liver samples (n = 22) were used for the gene expression profiling by microarrays. In HepG2 cells, IDE knockdown changed expression of genes involved in cell cycle and apoptosis pathways. Proliferation rate was lower in IDE knockdown cells than in controls. Microarray analysis revealed the decrease of hepatic IDE expression in subjects with T2DM accompanied by the downregulation of the p53-dependent genes FAS and CCNG2, but not by the upregulation of proliferation markers MKI67, MCM2 and PCNA. Similar results were found in the liver microarray dataset from GEO Profiles database. In conclusion, IDE expression is decreased in liver of subjects with T2DM which is accompanied by the dysregulation of p53 pathway. Prolonged use of IDE inhibitors for T2DM treatment should be carefully tested in animal studies regarding its potential effect on hepatic tumorigenesis.

Background and Objective: Malformations of the left ventricular outflow tract are one of the most common forms of congenital heart disorders. Recently, it has been shown that mutations in the NOTCH1 gene can lead to bicuspid aortic valve, aortic aneurysm, and hypoplastic left heart syndrome. The aim of our study was to estimate the frequency of NOTCH1 gene mutations/substitutions in patients with aortic coarctation, isolated or combined with bicuspid aortic valve., Design and Patients: The study included 51 children with coarctation. Detailed family history was obtained for every study subject, and echocardiographic data were obtained for the relatives when available. We applied a strategy of targeted mutation screening for 10 out of 34 exons of the NOTCH1 gene by direct sequencing. Control DNA was obtained from 200 healthy donors., Results: In more than half of the cases, coarctation was combined with bicuspid aortic valve, and in approximately half of the cases, it was combined with hypoplasia of the aortic arch or descending aorta. Familial history of congenital heart disease was observed in 34.3% of the cases. In total, 29 variants of the NOTCH1 gene were identified in the patient group and in the control subjects. Four of those variants led to amino acid exchange, of which only one, R1279H, was identified in both the patient group and in the controls. This variant was significantly overrepresented in the patients with aortic coarctation compared with those in the control group (P < .05). We conclude that the R1279H substitution in the NOTCH1 gene is significantly overrepresented in patients with aortic coarctation and, therefore, may represent a disease-susceptibility allele., (© 2014 Wiley Periodicals, Inc.)

Background: Abortion services are legally available in Ukraine although there are issues in quality and access. Two studies were conducted in Ukraine to expand options for women, and to determine the efficacy and acceptability of medical abortion., Study Design: Two open-label clinical trials were conducted at six clinics in Ukraine. Women were given 200 mg mifepristone followed after 48 hours by 400 μg oral misoprostol (Study One) and mifepristone followed after 24 hours by 400 μg sublingual misoprostol (Study Two). Follow-up visits were scheduled for two weeks after mifepristone administration to assess whether complete uterine evacuation had occurred., Results: Success rates were 97% in the first study and 98% in the second one. The vast majority of participants were satisfied or very satisfied with their abortion method (Study One: 94%; Study Two: 98%)., Conclusions: The two studies demonstrate high rates of success and acceptability of early medical abortion in Ukraine.

A 56-year-old woman with a history of trabeculectomy in both eyes sustained blunt trauma to the right eye at home. She initially presented with pain, loss of vision, total hyphema, and hypotony with no evidence of rupture or tissue prolapse. Prompt anterior chamber wash out revealed a partially subluxated crystalline lens behind the pupil, but the globe was intact. At 1 month postoperatively, subconjunctival displacement of the crystalline lens was detected. The patient gave a history of severe bouts of coughing and sneezing a few days earlier. During removal of phacocele, the trabeculectomy wound was intact with no evidence of leakage. A shallow concentric furrow was noticed across the flap approximately 3 mm from the limbus. It is believed that repeat trauma pushed the crystalline lens through the weakened trabeculectomy scleral flap. The wound later self-sealed., (Copyright 2012, SLACK Incorporated.)