The collection, storage, and analysis of large data sets are relevant in many sectors. Especially in the medical field, the processing of patient data promises great progress in personalized health ...care. However, it is strictly regulated, such as by the General Data Protection Regulation (GDPR). These regulations mandate strict data security and data protection and, thus, create major challenges for collecting and using large data sets. Technologies such as federated learning (FL), especially paired with differential privacy (DP) and secure multiparty computation (SMPC), aim to solve these challenges.
This scoping review aimed to summarize the current discussion on the legal questions and concerns related to FL systems in medical research. We were particularly interested in whether and to what extent FL applications and training processes are compliant with the GDPR data protection law and whether the use of the aforementioned privacy-enhancing technologies (DP and SMPC) affects this legal compliance. We placed special emphasis on the consequences for medical research and development.
We performed a scoping review according to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews). We reviewed articles on Beck-Online, SSRN, ScienceDirect, arXiv, and Google Scholar published in German or English between 2016 and 2022. We examined 4 questions: whether local and global models are "personal data" as per the GDPR; what the "roles" as defined by the GDPR of various parties in FL are; who controls the data at various stages of the training process; and how, if at all, the use of privacy-enhancing technologies affects these findings.
We identified and summarized the findings of 56 relevant publications on FL. Local and likely also global models constitute personal data according to the GDPR. FL strengthens data protection but is still vulnerable to a number of attacks and the possibility of data leakage. These concerns can be successfully addressed through the privacy-enhancing technologies SMPC and DP.
Combining FL with SMPC and DP is necessary to fulfill the legal data protection requirements (GDPR) in medical research dealing with personal data. Even though some technical and legal challenges remain, for example, the possibility of successful attacks on the system, combining FL with SMPC and DP creates enough security to satisfy the legal requirements of the GDPR. This combination thereby provides an attractive technical solution for health institutions willing to collaborate without exposing their data to risk. From a legal perspective, the combination provides enough built-in security measures to satisfy data protection requirements, and from a technical perspective, the combination provides secure systems with comparable performance with centralized machine learning applications.
The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens
. Its main components are haematopoietic immune cells, including myeloid cells that control ...innate immunity, and lymphoid cells that constitute adaptive immunity
. However, immune functions are not unique to haematopoietic cells, and many other cell types display basic mechanisms of pathogen defence
. To advance our understanding of immunology outside the haematopoietic system, here we systematically investigate the regulation of immune genes in the three major types of structural cells: epithelium, endothelium and fibroblasts. We characterize these cell types across twelve organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling and epigenome mapping. This comprehensive dataset revealed complex immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and seem to modulate the extensive interactions between structural cells and haematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights the prevalence and organ-specific complexity of immune gene activity in non-haematopoietic structural cells, and it provides a high-resolution, multi-omics atlas of the epigenetic and transcriptional networks that regulate structural cells in the mouse.
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been ...fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.
Implantation in humans is a complex process that is temporally and spatially restricted. Over the past decade, using a one-by-one approach, several genes and gene products that may participate in ...this process have been identified in secretory phase endometrium. Herein, we have investigated global gene expression during the window of implantation (peak E2 and progesterone levels) in well characterized human endometrial biopsies timed to the LH surge, compared with the late proliferative phase (peak E2 level) of the menstrual cycle. Tissues were processed for poly(A(+)) RNA and hybridization of chemically fragmented, biotinylated cRNAs on high density oligonucleotide microarrays, screening for 12,686 genes and expressed sequence tags. After data normalization, mean values were obtained for gene readouts and fold ratios were derived comparing genes up- and down-regulated in the window of implantation vs. the late proliferative phase. Nonparametric testing revealed 156 significantly (P < 0.05) up-regulated genes and 377 significantly down-regulated genes in the implantation window. Up-regulated genes included those for cholesterol trafficking and transport apolipoprotein (Apo)E being the most induced gene, 100-fold, prostaglandin (PG) biosynthesis (PLA2) and action (PGE2 receptor), proteoglycan synthesis (glucuronyltransferase), secretory proteins glycodelin, mammaglobin, Dickkopf-1 (Dkk-1, a Wnt inhibitor), IGF binding protein (IGFBP), and TGF-beta superfamilies, signal transduction, extracellular matrix components (osteopontin, laminin), neurotransmitter synthesis (monoamine oxidase) and receptors (gamma aminobutyric acid A receptor pi subunit), numerous immune modulators, detoxification genes (metallothioneins), and genes involved in water and ion transport e.g. Clostridia Perfringens Enterotoxin (CPE) 1 receptor (CPE1-R) and K(+) ion channel, among others. Down-regulated genes included intestinal trefoil factor (ITF) the most repressed gene (50-fold), matrilysin, members of the G protein-coupled receptor signaling pathway, frizzled-related protein (FrpHE, a Wnt antagonist), transcription factors, TGF-beta signaling pathway members, immune modulators (major histocompatibility complex class II subunits), and other cellular functions. Validation of select genes was conducted by Northern analysis and RT-PCR using RNA from endometrial biopsies obtained in the proliferative phase and the implantation window and by RT-PCR using RNA from cultured endometrial epithelial and stromal cells. These approaches confirmed up-regulation of genes corresponding to IGFBP-1, glycodelin, CPE1-R, Dkk-1, mammaglobin, and ApoD and down-regulation for PR membrane component 1, FrpHE, matrilysin, and ITF, as with the microarray data. Cultured endometrial epithelial cells were found to express mRNAs for glycodelin, CPE-1R, Dkk-1, the gamma aminobutyric acid A receptor pi subunit, mammaglobin, matrilysin, ITF and PR membrane component 1. The expression of IGFBP-1, CPE1-R, Dkk-1, and ApoD mRNAs increased upon decidualization of stromal cells in vitro with progesterone after E2 priming, whereas FrpHE decreased, consistent with the microarray results. Overall, the data demonstrate numerous genes and gene families not heretofore recognized in human endometrium or associated with the implantation process. Reassuringly, several gene products, known to be differentially expressed in the implantation window or in secretory endometrium, were verified, and the striking regulation of select secretory proteins, water and ion channels, signaling molecules, and immune modulators underscores the important roles of these systems in endometrial development and endometrial-embryonic interactions. In addition, the current study validates using high density oligonucleotide microarray technology to investigate global changes in gene expression in human endometrium.
Onion (Allium cepa) is regarded as a nonclimacteric vegetable. In onions, however, ethylene can suppress sprouting while the ethylene-binding inhibitor l-methylcyclopropene (1-MCP) can also suppress ...sprout growth; yet, it is unknown how ethylene and 1-MCP elicit the same response. In this study, onions were treated with 10 μL L⁻¹ ethylene or 1 μAL L⁻¹ 1-MCP individually or in combination for 24 h at 20°C before or after curing (6 weeks) at 20°C or 28°C and then stored at 1°C. Following curing, a subset of these same onions was stored separately under continuous air or ethylene (10 μL L⁻¹) at 1°C. Onions treated with ethylene and 1-MCP in combination after curing for 24 h had reduced sprout growth as compared with the control 25 weeks after harvest. Sprout growth following storage beyond 25 weeks was only reduced through continuous ethylene treatment.This observation was supported by a higher proportion of down-regulated genes characterized as being involved in photosynthesis, measured using a newly developed onion microarray. Physiological and biochemical data suggested that ethylene was being perceived in the presence of 1-MCP, since sprout growth was reduced in onions treated with 1-MCP and ethylene applied in combination but not when applied individually. A cluster of probes representing transcripts up-regulated by 1-MCP alone but down-regulated by ethylene alone or in the presence of 1-MCP support this suggestion. Ethylene and 1-MCP both down-regulated a probe tentatively annotated as an ethylene receptor as well as ethylene-insensitive 3, suggesting that both treatments down-regulate the perception and signaling events of ethylene.
I survey the nature of costs and benefits of financial regulation, both macroregulation designed to stop crises and microregulation of products, markets, and institutions. The nature of financial ...regulatory costs and benefits poses a great challenge for formalized analysis. Health-and-safety or environmental regulation focuses on simple actions, like releasing a pollutant. The costs and benefits of financial regulation focus on the behavioral, market, general equilibrium, and political reactions. I offer some suggestions on the structure of a cost-benefit process that recognizes the nature of financial regulation costs and benefits, lying between pure conceptual cost-benefit analysis and the rigid legal structure currently envisioned.
Bromodomain and extra terminal domain (BET) proteins function as epigenetic signaling factors that associate with acetylated histones and facilitate transcription of target genes. Inhibitors ...targeting the activity of BET proteins have shown potent antiproliferative effects in hematological cancers through the suppression of c-MYC and downstream target genes. However, as the epigenetic landscape of a cell varies drastically depending on lineage, transcriptional coactivators such as BETs would be expected to have different targets in cancers derived from different cells of origin, and this may influence the activity and mechanism of action of BET inhibitors. To test this hypothesis, we treated a panel of lung adenocarcinoma (LAC) cell lines with the BET inhibitor JQ1 and found that a subset is acutely susceptible to BET inhibition. In contrast to blood tumors, we show that LAC cells are inhibited by JQ1 through a mechanism independent of c-MYC down-regulation. Through gene expression profiling, we discovered that the oncogenic transcription factor FOSL1 and its targets are suppressed by JQ1 in a dose-dependant manner. Knockdown of BRD4 also decreased FOSL1 levels, and inhibition of FOSL1 phenocopied the effects of JQ1 treatment suggesting that loss of this transcription factor may be partly responsible for the cytotoxic effects of BET inhibition in LAC cells, although ectopic expression of FOSL1 alone did not rescue the phenotype. Together, these findings suggest that BET inhibitors may be useful in solid tumors and that cell-lineage-specific differences in transcriptional targets of BETs may influence the activity of inhibitors of these proteins in different cancer types.
Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes. Cis-acting lncRNAs, which constitute a substantial fraction of lncRNAs with an ...attributed function, regulate gene expression in a manner dependent on the location of their own sites of transcription, at varying distances from their targets in the linear genome. Through various mechanisms, cis-acting lncRNAs have been demonstrated to activate, repress or otherwise modulate the expression of target genes. We discuss the activities that have been ascribed to cis-acting lncRNAs, the evidence and hypotheses regarding their modes of action, and the methodological advances that enable their identification and characterization. The emerging principles highlight lncRNAs as transcriptional units highly adept at contributing to gene regulatory networks and to the generation of fine-tuned spatial and temporal gene expression programmes.
Maintaining steady economic growth while considering environmental protection and achieving high-efficiency energy utilization is a challenge that China is' increasingly facing in the new normal. ...This study employs the super-efficiency data envelopment analysis and spatial econometric model to analyze energy utilization efficiency against the backdrop of environmental constraints. It uses China's inter-provincial panel data from 2007 to 2017 to examine the impact of green finance on high-efficiency utilization of energy. China's energy efficiency utilization shows an upward trend overall, but the utilization level is low. Energy efficiency utilization levels in the east, middle, and west show a declining gradient change. Green credit, credit scale, environmental regulation, technological progress, and industrial structure have a significant role in promoting high-efficiency utilization of energy. China's regional high-efficiency utilization of energy has an apparent spatial effect. Green credit, environmental regulation, technological progress, and industrial structure have a certain influence on the regional high-efficiency utilization of energy, but the influence of the credit scale is not apparent. Therefore, from the perspective of environmental constraints, green credit has a positive impact on high-efficiency utilization of energy in China.
•Super-efficiency data envelopment analysis and spatial econometric model are used.•Green credit is an important tool for green finance.•China's energy efficiency utilization is low, but on the rise.•Green credit has a significant role in promoting high-efficiency utilization of energy.•China's regional high-efficiency utilization of energy has an apparent spatial effect.
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