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This study investigates the use of atomic layer deposition (ALD) to mitigate multipacting phenomena inside superconducting radio frequency cavities used in particle accelerators while preserving high quality factors in the 1010 range. The unique ALD capability to control the film thickness down to the atomic level on arbitrary complex shape objects enables the fine-tuning of TiN film resistivity and total electron emission yield (TEEY) from coupons to devices. This level of control allows us to adequately choose a TiN film thickness that provides both high resistivity to prevent Ohmic losses and a low TEEY to mitigate multipacting for the application of interest. The methodology presented in this work can be scaled to other domains and devices subject to RF fields in vacuum and sensitive to multipacting or electron discharge processes with their own requirements in resistivities and TEEY values. [ABSTRACT FROM AUTHOR]

Superconducting qubits have arisen as a leading technology platform for quantum computing, which is on the verge of revolutionizing the world's calculation capacities. Nonetheless, the fabrication of computationally reliable qubit circuits requires increasing the quantum coherence lifetimes, which are predominantly limited by the dissipations of two-level system defects present in the thin superconducting film and the adjacent dielectric regions. In this paper, we demonstrate the reduction of two-level system losses in three-dimensional superconducting radio frequency niobium resonators by atomic layer deposition of a 10 nm aluminum oxide Al2O3 thin films, followed by a high vacuum heat treatment at 650 °C for few hours. By probing the effect of several heat treatments on Al2O3-coated niobium samples by x-ray photoelectron spectroscopy plus scanning and conventional high resolution transmission electron microscopy coupled with electron energy loss spectroscopy and energy dispersive spectroscopy, we witness a dissolution of niobium native oxides and the modification of the Al2O3-Nb interface, which correlates with the enhancement of the quality factor at low fields of two 1.3 GHz niobium cavities coated with 10 nm of Al2O3. [ABSTRACT FROM AUTHOR]

The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, long interspersed nuclear elements and long terminal repeats, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the levels of the repressive histone modification H3K9me3 and a moderate increase in chromatin accessibility. Notably, however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein via transgenic overexpression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes., Competing Interests: Competing interests F.W.M, K.E.M, C.E.M and P.J.M declare no competing or financial interests. B.D. declares that the ABBS technology is protected by an international patent: WO/2021/133999, METHODS AND KITS FOR THE ENRICHMENT AND DETECTION OF DNA AND RNA MODIFICATIONS AND FUNCTIONAL MOTIFS. DELATTE, Benjamin F. ADAMS, Eddie W. FERNANDEZ, Joseph M. (2021)., (© 2023. Published by The Company of Biologists Ltd.)

Background/purpose: Caffeine is the most commonly used psychostimulant worldwide. Although its large intake is suspected to worsen psychotic symptoms because of increasing dopamine neurotransmission, schizophrenic patients are heavier caffeine consumers than the general population. This study aims to assess the impact of a caffeine restriction policy in a psychiatric hospital on patient psychopathology, hospitalization characteristics, and psychotropic prescribing patterns., Methods: It is a retrospective cross-sectional study based on electronic health records of a psychiatric hospital in the French-speaking area of Belgium. Two different periods were compared, the first (n = 142), in 2017, when caffeine was available in the institution and the second (n = 119), between November 2018 and November 2019 after the restriction of access to caffeine was implemented. Adult inpatients with schizophrenia or schizoaffective disorder admitted for an acute hospitalization were included. Antipsychotic exposure, benzodiazepine daily dose, Global Assessment of Functioning scores, length of hospital stay, and some other factors were tested for their potential association with the decaffeinated period., Results: After adjusting for potential confounders, reduced caffeine availability inside the hospital was significantly associated with higher Global Assessment of Functioning scores at discharge (adjusted odds ratio [aOR] = 2.86, 95% confidence interval [CI] = 1.77-4.62) and shorter hospital stays (aOR = 0.68, 95% CI = 0.47-0.99) but was not associated with change in antipsychotic exposure at discharge (aOR = 1.04, 95% CI = 0.64-1.7) or benzodiazepine daily dose (aOR = 0.89, 95% CI = 0.61-1.29)., Conclusions: Limiting access to caffeine in psychiatric hospitals is a simple and inexpensive intervention that should be promoted, especially for patients with schizophrenia., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). ABBS captures accurate DNA methylation information in Escherichia coli and mammals, while requiring up to 10 times fewer sequencing reads than WGBS. ABBS interrogates the entire genome and is not restricted to the CpG islands assayed by methods like Reduced Representation Bisulfite Sequencing (RRBS). The ABBS protocol is simple and can be performed in a single day., (© 2022. The Author(s).)

Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. Here, we show that TET loss of function results in a similar genomic footprint. Both 5hmC in wild-type (WT) genomes and DNA hypermethylation in TET -deficient genomes are largely confined to the active euchromatic compartment, consistent with the known functions of TET proteins in DNA demethylation and the known distribution of 5hmC at transcribed genes and active enhancers. In contrast, an unexpected DNA hypomethylation noted in multiple TET -deficient genomes is primarily observed in the heterochromatin compartment. In a mouse model of T cell lymphoma driven by TET deficiency ( Tet2/3 DKO T cells), genomic analysis of malignant T cells revealed DNA hypomethylation in the heterochromatic genomic compartment, as well as reactivation of repeat elements and enrichment for single-nucleotide alterations, primarily in heterochromatic regions of the genome. Moreover, hematopoietic stem/precursor cells (HSPCs) doubly deficient for Tet2 and Dnmt3a displayed greater losses of DNA methylation than HSPCs singly deficient for Tet2 or Dnmt3a alone, potentially explaining the unexpected synergy between DNMT3A and TET2 mutations in myeloid and lymphoid malignancies. Tet1 -deficient cells showed decreased localization of DNMT3A in the heterochromatin compartment compared with WT cells, pointing to a functional interaction between TET and DNMT proteins and providing a potential explanation for the hypomethylation observed in TET -deficient genomes. Our data suggest that TET loss of function may at least partially underlie the characteristic pattern of global hypomethylation coupled to regional hypermethylation observed in diverse cancer genomes, and highlight the potential contribution of heterochromatin hypomethylation to oncogenesis., Competing Interests: Conflict of interest statement: A.R. is on the scientific advisory board of Cambridge Epigenetix (Cambridge, UK). The other authors declare no competing interests.

The role of YAP (Yes-associated protein 1) and MRTF-A (myocardin-related transcription factor A), two transcriptional co-activators regulated downstream of GPCRs (G protein-coupled receptors) and RhoA, in the growth of glioblastoma cells and in vivo glioblastoma multiforme (GBM) tumor development was explored using human glioblastoma cell lines and tumor-initiating cells derived from patient-derived xenografts (PDX). Knockdown of these co-activators in GSC-23 PDX cells using short hairpin RNA significantly attenuated in vitro self-renewal capability assessed by limiting dilution, oncogene expression, and neurosphere formation. Orthotopic xenografts of the MRTF-A and YAP knockdown PDX cells formed significantly smaller tumors and were of lower morbidity than wild-type cells. In vitro studies used PDX and 1321N1 glioblastoma cells to examine functional responses to sphingosine 1-phosphate (S1P), a GPCR agonist that activates RhoA signaling, demonstrated that YAP signaling was required for cell migration and invasion, whereas MRTF-A was required for cell adhesion; both YAP and MRTF-A were required for proliferation. Gene expression analysis by RNA-sequencing of S1P-treated MRTF-A or YAP knockout cells identified 44 genes that were induced through RhoA and highly dependent on YAP, MRTF-A, or both. Knockdown of F3 (tissue factor (TF)), a target gene regulated selectively through YAP, blocked cell invasion and migration, whereas knockdown of HBEGF (heparin-binding epidermal growth factor-like growth factor), a gene selectively induced through MRTF-A, prevented cell adhesion in response to S1P. Proliferation was sensitive to knockdown of target genes regulated through either or both YAP and MRTF-A. Expression of TF and HBEGF was also selectively decreased in tumors from PDX cells lacking YAP or MRTF-A, indicating that these transcriptional pathways are regulated in preclinical GBM models and suggesting that their activation through GPCRs and RhoA contributes to growth and maintenance of human GBM.

Objective: Repetitive thoughts can be divided in two modes: abstract/analytic (decontextualized and dysfunctional) and concrete/experiential (problem-focused and adaptive). They constitute a transdiagnostic process involved in many psychopathological states but have received little attention in schizophrenia, as earlier studies only indexed increased ruminations (related to dysfunctional repetitive thoughts) without jointly exploring both modes. This study explored the two repetitive thinking modes, beyond ruminations, to determine their imbalance in schizophrenia., Methods: Thirty stabilized patients with schizophrenia and 30 matched controls completed the Repetitive Response Scale and the Mini Cambridge-Exeter Repetitive Thought Scale, both measuring repetitive thinking modes. Complementary measures related to schizophrenic symptomatology, depression and anxiety were also conducted., Results: Compared to controls, patients with schizophrenia presented an imbalance between repetitive thinking modes, with increased abstract/analytic and reduced concrete/experiential thoughts, even after controlling for comorbidities. Schizophrenia is associated with stronger dysfunctional repetitive thoughts (i.e. abstract thinking) and impaired ability to efficiently use repetitive thinking for current problem-solving (i.e. concrete thinking)., Conclusion: This imbalance confirms the double-faced nature of repetitive thinking modes, whose influence on schizophrenia's symptomatology should be further investigated. The present results also claim for evaluating these processes in clinical settings and for rehabilitating the balance between opposite repetitive thinking modes., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Schizophrenia is associated with a strong deficit in the decoding of emotional facial expression (EFE). Nevertheless, it is still unclear whether this deficit is specific for emotions or due to a more general impairment for any type of facial processing. This study was designed to clarify this issue. Thirty patients suffering from schizophrenia and 30 matched healthy controls performed several tasks evaluating the recognition of both changeable (i.e. eyes orientation and emotions) and stable (i.e. gender, age) facial characteristics. Accuracy and reaction times were recorded. Schizophrenic patients presented a performance deficit (accuracy and reaction times) in the perception of both changeable and stable aspects of faces, without any specific deficit for emotional decoding. Our results demonstrate a generalized face recognition deficit in schizophrenic patients, probably caused by a perceptual deficit in basic visual processing. It seems that the deficit in the decoding of emotional facial expression (EFE) is not a specific deficit of emotion processing, but is at least partly related to a generalized perceptual deficit in lower-level perceptual processing, occurring before the stage of emotion processing, and underlying more complex cognitive dysfunctions. These findings should encourage future investigations to explore the neurophysiologic background of these generalized perceptual deficits, and stimulate a clinical approach focusing on more basic visual processing., (Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.)

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Alteration of miRNA levels is common in tumors and contributes to the pathogenesis of human malignancies. In the present study we examined the role played by miR-137 in breast tumorigenesis. We found miR-137 levels to be lower in breast cancer cells than in their non-tumorigenic counterparts and observed reduced proliferation and migration of breast cancer cells overexpressing miR-137. We further identified KDM5B, a histone demethylase known to be involved in breast cancer tumorigenesis, as a target of miR-137. As the involvement of histone demethylases in cancer is still poorly understood and as the role of miRNAs in controlling epigenetic mechanisms in cancer is emerging, we broadened our study to the whole KDM5 histone demethylase family to see if the genes coding for these epigenetic enzymes might be regulated by miRNAs in cancer cells. We discovered that KDM5C is overexpressed in breast cancer cells, providing evidence that miR-138 regulates its expression. We found miR-138 overexpression to affect breast cancer cell proliferation. Altogether, our findings suggest that miRNAs may regulate KDM5 histone demethylase levels in breast cancer and thereby control breast cancer cell proliferation and migration.

Hydroxymethylcytosine, well described in DNA, occurs also in RNA. Here, we show that hydroxymethylcytosine preferentially marks polyadenylated RNAs and is deposited by Tet in Drosophila. We map the transcriptome-wide hydroxymethylation landscape, revealing hydroxymethylcytosine in the transcripts of many genes, notably in coding sequences, and identify consensus sites for hydroxymethylation. We found that RNA hydroxymethylation can favor mRNA translation. Tet and hydroxymethylated RNA are found to be most abundant in the Drosophila brain, and Tet-deficient fruitflies suffer impaired brain development, accompanied by decreased RNA hydroxymethylation. This study highlights the distribution, localization, and function of cytosine hydroxymethylation and identifies central roles for this modification in Drosophila., (Copyright © 2016, American Association for the Advancement of Science.)

Disturbed processing of emotional faces and voices is typically observed in schizophrenia. This deficit leads to impaired social cognition and interactions. In this study, we investigated whether impaired processing of emotions also affects musical stimuli, which are widely present in daily life and known for their emotional impact. Thirty schizophrenic patients and 30 matched healthy controls evaluated the emotional content of musical, vocal and facial stimuli. Schizophrenic patients are less accurate than healthy controls in recognizing emotion in music, voices and faces. Our results confirm impaired recognition of emotion in voice and face stimuli in schizophrenic patients and extend this observation to the recognition of emotion in musical stimuli., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack in vivo models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes GPx1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of in vivo oxidative stress on the global hydroxymethylome.

Sox9 is a transcription factor expressed in most solid tumors. However, the molecular mechanisms underlying Sox9 function during tumorigenesis remain unclear. Here, using a genetic mouse model of basal cell carcinoma (BCC), the most frequent cancer in humans, we show that Sox9 is expressed from the earliest step of tumor formation in a Wnt/β-catenin-dependent manner. Deletion of Sox9 together with the constitutive activation of Hedgehog signaling completely prevents BCC formation and leads to a progressive loss of oncogene-expressing cells. Transcriptional profiling of oncogene-expressing cells with Sox9 deletion, combined with in vivo ChIP sequencing, uncovers a cancer-specific gene network regulated by Sox9 that promotes stemness, extracellular matrix deposition, and cytoskeleton remodeling while repressing epidermal differentiation. Our study identifies the molecular mechanisms regulated by Sox9 that link tumor initiation and invasion., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Background: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which tumours can arise., Results: Here, we show that colorectal tumours and cancer cells express Ten-Eleven-Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells., Conclusions: Together our results indicate that promoters that acquire 5hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5hmC in tumours. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.

Cancer stem cells (CSCs) have been reported in various cancers, including in skin squamous-cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here we find that Sox2, a transcription factor expressed in various types of embryonic and adult stem cells, was the most upregulated transcription factor in the CSCs of squamous skin tumours in mice. SOX2 is absent in normal epidermis but begins to be expressed in the vast majority of mouse and human pre-neoplastic skin tumours, and continues to be expressed in a heterogeneous manner in invasive mouse and human SCCs. In contrast to other SCCs, in which SOX2 is frequently genetically amplified, the expression of SOX2 in mouse and human skin SCCs is transcriptionally regulated. Conditional deletion of Sox2 in the mouse epidermis markedly decreases skin tumour formation after chemical-induced carcinogenesis. Using green fluorescent protein (GFP) as a reporter of Sox2 transcriptional expression (SOX2-GFP knock-in mice), we showed that SOX2-expressing cells in invasive SCC are greatly enriched in tumour-propagating cells, which further increase upon serial transplantations. Lineage ablation of SOX2-expressing cells within primary benign and malignant SCCs leads to tumour regression, consistent with the critical role of SOX2-expressing cells in tumour maintenance. Conditional Sox2 deletion in pre-existing skin papilloma and SCC leads to tumour regression and decreases the ability of cancer cells to be propagated upon transplantation into immunodeficient mice, supporting the essential role of SOX2 in regulating CSC functions. Transcriptional profiling of SOX2-GFP-expressing CSCs and of tumour epithelial cells upon Sox2 deletion uncovered a gene network regulated by SOX2 in primary tumour cells in vivo. Chromatin immunoprecipitation identified several direct SOX2 target genes controlling tumour stemness, survival, proliferation, adhesion, invasion and paraneoplastic syndrome. We demonstrate that SOX2, by marking and regulating the functions of skin tumour-initiating cells and CSCs, establishes a continuum between tumour initiation and progression in primary skin tumours.

Methylation of the fifth carbon of cytosine was the first epigenetic modification to be discovered in DNA. Recently, three new DNA modifications have come to light: hydroxymethylcytosine, formylcytosine, and carboxylcytosine, all generated by oxidation of methylcytosine by Ten Eleven Translocation (TET) enzymes. These modifications can initiate full DNA demethylation, but they are also likely to participate, like methylcytosine, in epigenetic signalling per se. A scenario is emerging in which coordinated regulation at multiple levels governs the participation of TETs in a wide range of physiological functions, sometimes via a mechanism unrelated to their enzymatic activity. Although still under construction, a sophisticated picture is rapidly forming where, according to the function to be performed, TETs ensure epigenetic marking to create specific landscapes, and whose improper build-up can lead to diseases such as cancer and neurodegenerative disorders., (© 2014 The Authors.)

TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O-GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3-OGT co-localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3-OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step-wise model, involving TET-OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation.

The nature of the impairment in the processing of emotional information in schizophrenia is still being debated. Some authors reported that schizophrenia patients would show deficits in the treatment processing of negative emotional information without a negative bias, as observed in controls, when in a combined emotional situation including positive/negative information. Eighteen subjects with paranoid schizophrenia in remission with a low level of negative symptoms and 18 control subjects were exposed to 108 pairs of pictures (International Affective Picture System) depicting different emotions (N = negative, P = positive, n = neutral) from six different combinations: N/N, P/P, n/n, P/N, P/n, and N/n. The subjects responded by clicking on a right or left button in response to a negative or positive feeling toward the stimuli (forced choice task). They were also asked to classify each of the individual pictures as positive, negative, or neutral (emotion-recognition task). In this well-defined group of paranoid schizophrenia patients in remission, we observed the persistence of a negative bias when an ambiguous situation is displayed (P/N) with the absence of an impairment in negative emotional information recognition and the presence of a positive bias in the recognition of neutral stimuli, reflecting a tendency to keep arousal-provoking perceptual cues from entering into subjective awareness., (Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.)