Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users.

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multidimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardised group-specific naming convention, metadata curation with tagging and Key-Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

Using Health IT Standards to Facilitate Metadata Exchange Between Research Data Management Systems.

The National Research Data Infrastructure for Personal Health Data (NFDI4Health) uses Local Data Hubs (LDHs) to manage locally research studies, documents and sensitive personal data to support controlled data sharing. While research data management (RDM) systems facilitate the storage and preparation of data and metadata as well as organizational access, they often lack support for interoperability standards of the application domain. To support the exchange with external registries of research studies, we chose 17 attributes to characterize the most relevant aspects of clinical trials (in the following named "metadata profile"). We implemented the metadata profile in the RDM system FAIRDOM SEEK using core attributes and SEEK's extended metadata feature and created a mapping conforming to the Health Level 7 Fast Healthcare Interoperability Resources (FHIR) standard version R4. Finally, we implemented a prototype application interface for exports in FHIR-JSON format. We plan to extend the interface to serve central registries and support specific FHIR Implementation Guides from various use cases.

Dissociable roles of the mPFC-to-VTA Pathway in the control of Impulsive Action and Risk-Related Decision-Making in Roman High- And Low-Avoidance Rats.

BACKGROUND: Impulsive action and risk-related decision-making (RDM) are associated with various psychiatric disorders including drug abuse. Both behavioral traits have also been linked to reduced frontocortical activity and alterations in dopamine function in the ventral tegmental area (VTA). However, despite direct projections from the medial prefrontal cortex (mPFC) to the VTA, the specific role of the mPFC-to-VTA pathway in controlling impulsive action and RDM remains unexplored. METHODS: We used Positron Emission Tomography with [18F]-Fluorodeoxyglucose to evaluate brain metabolic activity in Roman High- (RHA) and Low-avoidance (RLA) rats, which exhibit innate differences in impulsive action and RDM. Notably, we used a viral-based double dissociation chemogenetic strategy to isolate, for the first time, the role of the mPFC-to-VTA pathway in controlling these behaviors. We selectively activated the mPFC-to-VTA pathway in RHA rats and inhibited it in RLA rats, assessing the effects on impulsive action and RDM in the rat gambling task. RESULTS: Our results showed that RHA rats displayed higher impulsive action, less optimal decision-making, and lower cortical activity than RLA rats at baseline. Chemogenetic activation of the mPFC-to-VTA pathway reduced impulsive action in RHA rats, whereas chemogenetic inhibition had the opposite effect in RLA rats. However, these manipulations did not affect RDM. Thus, by specifically targeting the mPFC-to-VTA pathway in a phenotype-dependent way, we were reverted innate patterns of impulsive action, but not RDM. CONCLUSION: Our findings suggest a dissociable role of the mPFC-to-VTA pathway in impulsive action and RDM, highlighting its potential as a target for investigating impulsivity-related disorders.

Multidimensional solution of fuzzy linear programming.

There are several approaches to address fuzzy linear programming problems (FLPP). However, due to using standard interval arithmetic (SIA), these methods have some limitations and are not complete solutions. This article establishes a new approach to fuzzy linear programming via the theory of horizontal membership functions and the multidimensional relative-distance-measure fuzzy interval arithmetic. Furthermore, we propose a multidimensional solution based on the primal Simplex approach that satisfies any equivalent form of FLPP. The new solutions of FLPP are also compared with the results of existing methods. Some numerical examples have been illustrated to show the efficiency of the proposed method.

Trends in Research Data Management and Academic Health Sciences Libraries.

Spurred by the National Institute of Health mandating a data management and sharing plan as a requirement of grant funding, research data management has exploded in importance for librarians supporting researchers and research institutions. This editorial examines the role and direction of libraries in this process from several viewpoints. Key markers of success include collaboration, establishing new relationships, leveraging existing relationships, accessing multiple avenues of communication, and building niche expertise and cachè as a valued and trustworthy partner.

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices.

Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.

Open science and Big Data in South Africa.

With the Square Kilometer Array (SKA) project and the new Multi-Purpose Reactor (MPR) soon coming on-line, South Africa and other collaborating countries in Africa will need to make the management, analysis, publication, and curation of "Big Scientific Data" a priority. In addition, the recent draft Open Science policy from the South African Department of Science and Innovation (DSI) requires both Open Access to scholarly publications and research outputs, and an Open Data policy that facilitates equal opportunity of access to research data. The policy also endorses the deposit, discovery and dissemination of data and metadata in a manner consistent with the FAIR principles - making data Findable, Accessible, Interoperable and Re-usable (FAIR). The challenge to achieve Open Science in Africa starts with open access for research publications and the provision of persistent links to the supporting data. With the deluge of research data expected from the new experimental facilities in South Africa, the problem of how to make such data FAIR takes center stage. One promising approach to make such scientific datasets more "Findable" and "Interoperable" is to rely on the Dataset representation of the Schema.org vocabulary which has been endorsed by all the major search engines. The approach adds some semantic markup to Web pages and makes scientific datasets more "Findable" by search engines. This paper does not address all aspects of the Open Science agenda but instead is focused on the management and analysis challenges of the "Big Scientific Data" that will be produced by the SKA project. The paper summarizes the role of the SKA Regional Centers (SRCs) and then discusses the goal of ensuring reproducibility for the SKA data products. Experiments at the new MPR neutron source will also have to conform to the DSI's Open Science policy. The Open Science and FAIR data practices used at the ISIS Neutron source at the Rutherford Appleton Laboratory in the UK are then briefly described. The paper concludes with some remarks about the important role of interdisciplinary teams of research software engineers, data engineers and research librarians in research data management.

Feasibility of a national open data policy in Zimbabwe.

A study on the feasibility of a national open data policy in Zimbabwe was done to document open government data globally and in Zimbabwe. The study showcases the benefits of open government data and the opportunities and challenges toward the development of a national open data policy. Web content analysis and document analysis were used to collect data concerning the readiness of the country in implementing open data activities. The open data barometer was used to gather qualitative data which is essential in assessing the preparedness of the country in opening up government and research data. Content analysis was used to analyse the data which was presented thematically based on the objectives of the study. The findings indicated that the Government of Zimbabwe has endorsed a couple of open data frameworks though some projects are done by non-governmental organizations. The major challenge is implementation of these conventions and commitment to make the data accessible. The results indicated that open data must be made available and accessible within Zimbabwe as a matter of national policy. The author recommends the need for advocacy and continuous awareness creation among the stakeholders so that a national open data policy can be crafted and enacted. The enactment of a national open data policy would guide the use of and access to government data and research data which is valuable in research.

Association of RDM1 with osteosarcoma progression via cell cycle and MEK/ERK signalling pathway regulation.

RAD52 motif-containing 1 (RDM1), a key regulator of DNA double-strand break repair and recombination, has been reported to play an important role in the development of various human cancers, such as papillary thyroid carcinoma, neuroblastoma and lung cancer. However, the effect of RDM1 on osteosarcoma (OS) progression remains unclear. Here, this study mainly explored the connection between RDM1 and OS progression, as well as the underlying mechanism. It was found that RDM1 was highly expressed in OS cells compared with human osteoblast cells. Knockdown of RDM1 caused OS cell proliferation inhibition, cell apoptosis promotion and cell cycle arrest at G1 stage, whereas RDM1 overexpression resulted in the opposite phenotypes. Furthermore, RDM1 silencing leads to a significant decrease in tumour growth in xenograft mouse model. RDM1 also increased the protein levels of MEK 1/2 and ERK 1/2. All these findings suggest that RDM1 plays an oncogenic role in OS via stimulating cell cycle transition from G1 to S stage, and regulating MEK/ERK signalling pathway, providing a promising therapeutic factor for the treatment of OS.

Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis.

RNA silencing pathways control eukaryotic gene expression transcriptionally or posttranscriptionally in a sequence-specific manner. In RNA silencing, the production of double-stranded RNA (dsRNA) gives rise to various classes of 20-24 nucleotide (nt) small RNAs (smRNAs). In Arabidopsis thaliana, smRNAs are often derived from long dsRNA molecules synthesized by one of the six genomically encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding cofactors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their cofactors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDRγ clade proteins (RDR3-5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general cofactor for the RDR family of proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses, including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have a higher survival rate under salt treatment in comparison to wild-type plants. In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.

The pre-mRNA splicing factor RDM16 regulates root stem cell maintenance in Arabidopsis.

Pre-mRNA (messenger RNA) splicing participates in the regulation of numerous biological processes in plants. For example, alternative splicing shapes transcriptomic responses to abiotic and biotic stress, and controls developmental programs. However, no study has revealed a role for splicing in maintaining the root stem cell niche. Here, a screen for defects in root growth in Arabidopsis thaliana identified an ethyl methane sulfonate mutant defective in pre-mRNA splicing (rdm16-4). The rdm16-4 mutant displays a short-root phenotype resulting from fewer cells in the root apical meristem. The PLETHORA1 (PLT1) and PLT2 transcription factor genes are important for root development and were alternatively spliced in rdm16-4 mutants, resulting in a disordered root stem cell niche and retarded root growth. The root cap of rdm16-4 contained reduced levels of cytokinins, which promote differentiation in the developing root. This reduction was associated with the alternative splicing of genes encoding cytokinin signaling factors, such as ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN5 and ARABIDOPSIS RESPONSE REGULATORS (ARR1, ARR2, and ARR11). Furthermore, expression of the full-length coding sequence of ARR1 or exogenous cytokinin application partially rescued the short-root phenotype of rdm16-4. This reveals that the RDM16-mediated alternative splicing of cytokinin signaling components contributes to root growth.

Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth.

Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.

RDM1 plays an oncogenic role in human ovarian carcinoma cells.

Ovarian cancer is one of the deadliest gynecological cancer, with a low overall 5-year survival rate. RDM1, RAD52 motif-containing protein 1, is sensitive to cisplatin, a common chemotherapy drug and it has an important role inDNA damage repair pathway. Until now, the effect of RDM1 in ovarian cancer is undiscovered. Here, clinical data shows that the tumour tissues of ovarian carcinoma patients with higher mRNA and protein expression of RDM1. Knockdown of RDM1 in ovarian carcinoma cells reduces cell proliferation and promotes apoptosis, consistent with the role RDM1 in the overexpression experiments. The research of xenograft mouse model shows stable knockdown of RDM1 significantly inhibits ovarian cancer tumour growth. These in vitro and in vivo results conclude that RDM1 plays an oncogenic role in human ovarian carcinoma. Interestingly, p53/RAD51/RAD52 signalling pathway can be regulated by RDM1, and the negative regulation of p53 by RDM1 may be one of major mechanisms for RDM1 to accomplish its oncogenic functions in ovarian carcinoma. Therefore, RDM1 may be a new target for the treatment of ovarian carcinoma.

Loss of RDM1 enhances hepatocellular carcinoma progression via p53 and Ras/Raf/ERK pathways.

Hepatocellular carcinoma (HCC), with its ineffective therapeutic options and poor prognosis, represents a global threat. In the present study, we show that RAD52 motif 1 (RDM1), a key regulator of DNA double-strand break repair and recombination, is downregulated in HCC tissues and suppresses tumor growth. In clinical HCC samples, low expression of RDM1 correlates with larger tumor size, poor tumor differentiation, and unfavorable survival. In vitro and in vivo data demonstrate that knockdown of RDM1 increases HCC cell proliferation, colony formation, and cell population at G2/M phase, whereas RDM1 overexpression results in the opposite phenotypes. Mechanistically, RDM1 binds to the tumor suppressor p53 and enhances its protein stability. In the presence of p53, RDM1 suppresses the phosphorylation of Raf and ERK. Overexpression of p53 or treatment with ERK inhibitor significantly abolishes cell proliferation induced by the depletion of RDM1. In addition, overexpression of methyltransferase-like 3 markedly induces N6-methyladenosine modification of RDM1 mRNA and represses its expression. Taken together, our study indicates that RDM1 functions as a tumor suppressor and may be a potential prognostic and therapeutic factor for HCC.

Fuzzy tracking control of fuzzy linear dynamical systems.

This paper deals with the fuzzy tracking control problem of a class of uncertain linear dynamical systems. In the uncertain linear dynamical system the uncertainty is considered as fuzzy numbers. This kind of uncertain linear dynamic systems is called fuzzy linear dynamic systems which are expressed in the form of a fuzzy differential equations system. The Mazandarani's approach and the powerful concept of granular differentiability are utilized to deal with the fuzzy differential equations system. Fuzzy tracking control of fuzzy linear dynamic systems looks for a law for the fuzzy control signal by which the output of the system tracks the reference input. In this regard, two fuzzy control laws are proposed under two theorems. First, it is proved that the fuzzy control law is in the form of a fuzzy state feedback with fuzzy gains and an additional term which is a pre-compensator as a fuzzy number. Since in the presence of disturbances this fuzzy control law fails to tackle the problem then other fuzzy control law is proposed under the second theory. Thus, in the second theory, it is proved that the proposed fuzzy controller desirably leads to the output of the fuzzy linear dynamic system tracks the input and the fuzzy disturbance is rejected. In addition, two lemmas regarding the theories are also proved. Moreover, fuzzy tracking control of output of a two tanks in series system and landing jet aircraft are given showing the effectiveness of the proposed approaches.

RDM1 promotes critical processes in breast cancer tumorigenesis.

Breast cancer is currently among the most common cancers in women, with almost 200,000 new cases diagnosed annually. Dysregulation of DNA repair pathways allows cells to accumulate damage and eventually mutations, with a subsequent reduction in DNA repair capacity in breast tissue, leading to tumorigenesis. One component of the DNA damage repair pathway is RAD52 motif-containing 1 (RDM1), but the specific role of RDM1 in breast cancer and the underlying mechanism remain unclear. Here, we examined the role played by RDM1 in breast cancer cell culture using the HBL100 and MCF-7 breast cancer cell lines. Disruption of RDM1 reduced in vitro cell proliferation and promoted apoptosis. Knockdown of RDM1 also induced up-regulation of p53 levels, whereas RAD51 and RAD52, both involved in DNA repair, were down-regulated. In addition, the in vivo growth of RDM1-deficient cells was significantly repressed, suggesting that RDM1 is a novel oncogenic protein in human breast cancer cells. This study reveals a link between the DNA damage response pathway and oncogenic functionality in breast cancer. Accordingly, therapeutic targeting of RDM1 is a potential treatment strategy for breast cancer and overcoming drug resistance.

RDM1 promotes neuroblastoma growth through the RAS-Raf-MEK-ERK pathway.

Neuroblastoma (NB) is an aggressive cancer that originates in the sympathetic nervous system and primarily affects children. Here, we show that high levels of RAD52 motif containing 1 (RDM1; a protein with similarities to RAD52, which is important for double-strand DNA repair) are associated with poor clinical outcomes for NB. In addition, RDM1-/- cells exhibited increased sensitivity to cisplatin, a common chemotherapy drug, and disruption of RDM1 suppressed NB cell proliferation. We also report that loss of RDM1 augmented cell apoptosis and induced cell cycle arrest, and that stable knockdown of RDM1 significantly inhibited NB tumor growth in a xenograft mouse model. Importantly, we identified that RDM1 promoted cell proliferation via the RAS-Raf-mitogen-activated protein kinase kinase (MEK)-extracellular signal-regulated kinase (ERK) signaling pathway. In conclusion, the current study demonstrates a correlation between DNA damage regulator RDM1 and the oncogenic RAS-Raf-MEK-ERK pathway in NB.

Sub-optimal control of fuzzy linear dynamical systems under granular differentiability concept.

This paper deals with sub-optimal control of a fuzzy linear dynamical system. The aim is to keep the state variables of the fuzzy linear dynamical system close to zero in an optimal manner. In the fuzzy dynamical system, the fuzzy derivative is considered as the granular derivative; and all the coefficients and initial conditions can be uncertain. The criterion for assessing the optimality is regarded as a granular integral whose integrand is a quadratic function of the state variables and control inputs. Using the relative-distance-measure (RDM) fuzzy interval arithmetic and calculus of variations, the optimal control law is presented as the fuzzy state variables feedback. Since the optimal feedback gains are obtained as fuzzy functions, they need to be defuzzified. This will result in the sub-optimal control law. This paper also sheds light on the restrictions imposed by the approaches which are based on fuzzy standard interval arithmetic (FSIA), and use strongly generalized Hukuhara and generalized Hukuhara differentiability concepts for obtaining the optimal control law. The granular eigenvalues notion is also defined. Using an RLC circuit mathematical model, it is shown that, due to their unnatural behavior in the modeling phenomenon, the FSIA-based approaches may obtain some eigenvalues sets that might be different from the inherent eigenvalues set of the fuzzy dynamical system. This is, however, not the case with the approach proposed in this study. The notions of granular controllability and granular stabilizability of the fuzzy linear dynamical system are also presented in this paper. Moreover, a sub-optimal control for regulating a Boeing 747 in longitudinal direction with uncertain initial conditions and parameters is gained. In addition, an uncertain suspension system of one of the four wheels of a bus is regulated using the sub-optimal control introduced in this paper.

RDM1 gene overexpression represents a therapeutic target in papillary thyroid carcinoma.

RAD52 motif containing 1 (RDM1) encodes the RAD52 protein involved in DNA double-strand break repair and recombination events. However, the importance of RDM1 in papillary thyroid carcinoma (PTC) is largely unknown. In the present study, we examined the role of RDM1 in thyroid cancer. The RDM1 expression in PTC patients was examined using immunohistochemistry. The expression levels of RDM1 mRNA in thyroid cancer cells were measured by quantitative real-time PCR (qRT-PCR). Lentivirus-mediated small interfering RNAs (siRNAs) were used to knock down the RDM1 expression in the K1 and TPC1 cells. Then, changes in the RDM1 target gene expression were determined by qRT-PCR and Western blot. Cell proliferation was examined by a high content screening assay. Cell cycle distribution and apoptosis were detected by flow cytometric analysis and MTT analysis. We showed that the RDM1 expression was higher in PTC tissue compared to pericarcinous tissue. RDM1 mRNA was found to be expressed by qRT-PCR. Using a lentivirus-based RNA interference (RNAi) approach, the RDM1 expression was significantly inhibited. The inhibition of RDM1 expression by RNAi significantly impaired cell proliferation, increased apoptosis and arrested cells in the G2/M phase. These data showed that RDM1 was highly expressed in PTC tissue and thyroid cancer cell lines. Moreover, RDM1 may play an important role in cell proliferation, cell cycle distribution and apoptosis of human PTC cells.

Design, rationale and feasibility of a multidimensional experimental protocol to study early life stress.

There is a rapidly accumulating body of evidence regarding the influential role of early life stress (ELS) upon medical and psychiatric conditions. While self-report instruments, with their intrinsic limitations of recall, remain the primary means of detecting ELS in humans, biological measures are generally limited to a single biological system. This paper describes the design, rationale and feasibility of a study to simultaneously measure neuroendocrine, immune and autonomic nervous system (ANS) responses to psychological and physiological stressors in relation to ELS. Five healthy university students were recruited by advertisement. Exclusion criteria included chronic medical conditions, psychotic disorders, needle phobia, inability to tolerate pain, and those using anti-inflammatory medications. They were clinically interviewed and physiological recordings made over a two-hour period pre, during and post two acute stressors: the cold pressor test and recalling a distressing memory. The Childhood Trauma Questionnaire and the Parental Bonding Index were utilised to measure ELS. Other psychological measures of mood and personality were also administered. Measurements of heart rate, blood pressure, respiratory rate, skin conductance, skin blood flow and temporal plasma samples were successfully obtained before, during and after acute stress. Participants reported the extensive psychological and multisystem physiological data collection and stress provocations were tolerable. Most (4/5) participants indicated a willingness to return to repeat the protocol, indicating acceptability. Our protocol is viable and safe in young physically healthy adults and allows us to assess simultaneously neuroendocrine, immune and autonomic nervous system responses to stressors in persons assessed for ELS.