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Bojič Burgos J, Pustišek M. Decentralized IoT Data Authentication with Signature Aggregation. Sensors (Basel) 2024; 24:1037. [PMID: 38339754 PMCID: PMC10857348 DOI: 10.3390/s24031037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The rapid expansion of the Internet of Things (IoT) has introduced significant challenges in data authentication, necessitating a balance between scalability and security. Traditional approaches often rely on third parties, while blockchain-based solutions face computational and storage bottlenecks. Our novel framework employs edge aggregating servers and Ethereum Layer 2 rollups, offering a scalable and secure IoT data authentication solution that reduces the need for continuous, direct interaction between IoT devices and the blockchain. We utilize and compare the Nova and Risc0 proving systems for authenticating batches of IoT data by verifying signatures, ensuring data integrity and privacy. Notably, the Nova prover significantly outperforms Risc0 in proving and verification times; for instance, with 10 signatures, Nova takes 3.62 s compared to Risc0's 369 s, with this performance gap widening as the number of signatures in a batch increases. Our framework further enhances data verifiability and trust by recording essential information on L2 rollups, creating an immutable and transparent record of authentication. The use of Layer 2 rollups atop a permissionless blockchain like Ethereum effectively reduces on-chain storage costs by approximately 48 to 57 times compared to direct Ethereum use, addressing cost bottlenecks efficiently.
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Affiliation(s)
- Jay Bojič Burgos
- Faculty of Electrical Engineering, University of Ljubljana, 1000 Ljubljana, Slovenia;
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Kurnik Mesarič K, Damjanac Ž, Debeljak T, Kodrič J. Effectiveness of psychoeducation for children, adolescents and caregivers in the treatment of eating disorders: A systematic review. Eur Eat Disord Rev 2024; 32:99-115. [PMID: 37656835 DOI: 10.1002/erv.3028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/31/2023] [Accepted: 08/19/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Eating disorders in childhood and adolescence negatively affect many areas of development and functioning of children, adolescents, and their families. Psychoeducation has an important role in management and treatment of eating disorders. METHODS A systematic literature review was performed using multiple databases (PsycInfo, PubMed, and Web of Science). The inclusion criteria comprised empirical studies of psychoeducation for patients with eating disorders or their caregivers. The study reporting quality was assessed with the revised Cochrane Collaboration's risk of bias tool and the Standard Quality Assessment Criteria for Evaluating Primary Research Papers from a Variety of Fields for non-randomized studies. RESULTS Ten studies met the inclusion criteria, in three of which the interventions were patient-centred and in seven of which the interventions were caregiver-centred. The studies differed in terms of methodology, outcome measures, and quality. The results suggest that psychoeducation is an effective intervention for children, adolescents and caregivers in the treatment of eating disorders. It may lead to weight gain, a decrease in eating disorder symptoms, and a reduction in caregiver burden. CONCLUSIONS There is a need for more randomized controlled trials to determine the effectiveness of psychoeducation for children, adolescents and caregivers in treatment of eating disorders.
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Affiliation(s)
- Katja Kurnik Mesarič
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Psychology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Damjanac
- Unit of Child Psychiatry, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tjaš Debeljak
- Unit of Child Psychiatry, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jana Kodrič
- Unit of Child Psychiatry, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Banović P, Mijatović D, Bogdan I, Simin V, Meletis E, Kostoulas P, Resman Rus K, Knap N, Korva M, Avšič-Županc T, Cabezas-Cruz A. Evidence of tick-borne encephalitis virus neutralizing antibodies in Serbian individuals exposed to tick bites. Front Microbiol 2023; 14:1314538. [PMID: 38156013 PMCID: PMC10754514 DOI: 10.3389/fmicb.2023.1314538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
Introduction Tick-borne encephalitis (TBE) is an emerging vector-borne and food-borne disease caused by the tick-borne encephalitis virus (TBEV; Orthoflavivirus encephalitidis), with a distribution spanning the Eurasian continent. Despite its significant public health impact in various European regions, TBE remains largely underdiagnosed in Serbia due to limited awareness and diagnostic challenges. In response to this, our study aimed to comprehensively assess TBEV exposure in individuals infested with ticks and to identify potential TBEV foci within Serbia. Materials and methods From 2019 to 2021, we conducted an observational study involving 450 patients who reported tick infestations. Results Our demographic analysis revealed a median age of 38 years, with a slight male predominance among the participants. We documented tick infestations in 38 municipalities across 14 districts of Serbia, with a notable concentration in proximity to Fruška Gora Mountain. The ticks most frequently removed were Ixodes ricinus, with nymphs and adult females being the predominant stages. On average, nymphs were removed after about 27.1 hours of feeding, while adult females remained attached for approximately 44.4 hours. Notably, we found age as a significant predictor of infestation time for both nymphs and adult females. Furthermore, we detected TBEV-neutralizing antibodies in 0.66% of the serum samples, shedding light on potential TBEV foci, particularly in Fruška Gora Mountain and other regions of Serbia. Conclusion Our study emphasizes the urgent need for active TBE surveillance programs, especially in areas suspected of hosting TBEV foci, in order to assess the true TBE burden, identify at-risk populations, and implement effective preventive measures.
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Affiliation(s)
- Pavle Banović
- Clinic for Lyme Borreliosis and Other Tick-Borne Diseases, Pasteur Institute Novi Sad, Novi Sad, Serbia
- Department of Microbiology with Parasitology and Immunology, Faculty of Medicine in Novi Sad, University of Novi Sad, Novi Sad, Serbia
| | - Dragana Mijatović
- Department for Research and Monitoring of Rabies and Other Zoonoses, Pasteur Institute Novi Sad, Novi Sad, Serbia
| | - Ivana Bogdan
- Department of Microbiology, Pasteur Institute Novi Sad, Novi Sad, Serbia
| | - Verica Simin
- Department of Microbiology, Pasteur Institute Novi Sad, Novi Sad, Serbia
| | - Eleftherios Meletis
- Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Polychronis Kostoulas
- Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Katarina Resman Rus
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
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Antić A, Pavčnik M, Lukanović A, Matjašič M, Lukanović D. Magnetic stimulation in the treatment of female urgency urinary incontinence: a systematic review. Int Urogynecol J 2023; 34:1669-1676. [PMID: 36877276 PMCID: PMC10415412 DOI: 10.1007/s00192-023-05492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023]
Abstract
INTRODUCTION AND HYPOTHESIS This systematic review analyzes published studies about magnetic stimulation (MS) treatment for UUI and determines whether this treatment is effective and non-invasive. METHODS A systematic literature search was conducted using PubMed, the Cochrane Library, and Embase. The international standard for reporting results of systematic reviews and meta-analyses (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) was used to guide the methodology of this systematic review. The key search terms were as follows: "magnetic stimulation" and "urinary incontinence." We limited the time frame to articles published from 1998, when the FDA approved MS as a conservative treatment option for UI. The last search was performed on 5 August 2022. RESULTS Two authors independently reviewed 234 article titles and abstracts, of which only 5 fitted the inclusion criteria. All 5 studies included women with UUI, but every study had different diagnostic and entry criteria for patients. They also differed in their treatment regimens and methodological approaches to assessing the efficacy of treating UUI with MS, which made it impossible to compare the results. Nonetheless, all five studies established that MS is an effective and non-invasive way of treating UUI. CONCLUSIONS The systematic literature review led to the conclusion that MS is an effective and conservative way of treating UUI. Despite this, literature in this area is lacking. Further randomized controlled trials are needed, with standardized entry criteria, UUI diagnostics, MS programs, and standardized protocols to measure the efficacy of MS in UUI treatment, with a longer follow-up period for post-treatment patients.
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Affiliation(s)
- Anja Antić
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Pavčnik
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Adolf Lukanović
- Division of Gynecology and Obstetrics, Ljubljana University Medical Center, Ljubljana, Slovenia
- Department of Gynecology and Obstetrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Matjašič
- Department of Education Studies, Faculty of Education, University of Ljubljana, Ljubljana, Slovenia
| | - David Lukanović
- Division of Gynecology and Obstetrics, Ljubljana University Medical Center, Ljubljana, Slovenia
- Department of Gynecology and Obstetrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Zupan A, Salapura V, Šekoranja D, Pižem J. Subcutaneous chondromyxoid fibroma with a novel PNISR::GRM1 fusion-report of a primary soft tissue tumour without connection to an underlying bone. Virchows Arch 2023; 482:917-921. [PMID: 36810795 PMCID: PMC10156755 DOI: 10.1007/s00428-023-03519-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 02/23/2023]
Abstract
Chondromyxoid fibroma (CMF) is a rare benign bone tumour. While CMF located entirely on the surface of a bone (i.e. juxtacortical CMF) has been well characterised, CMF has not so far been convincingly documented to arise in soft tissues without connection to an underlying bone.We report a subcutaneous CMF in a 34-year-old male, located on the distal medial aspect of the right thigh without any connection with the femur. The tumour measured 15 mm, it was well-circumscribed and displayed typical morphological features of a CMF. At the periphery, there was a small area of metaplastic bone. Immunohistochemically, the tumour cells were diffusely positive for smooth muscle actin and GRM1, and negative for S100 protein, desmin and cytokeratin AE1AE3. Whole transcriptome sequencing revealed a novel PNISR::GRM1 gene fusion.Our case indicates that CMF should be included in the differential diagnosis of soft tissue (including subcutaneous) tumours composed of spindle/ovoid cells, with a lobular architecture and chondromyxoid matrix. The diagnosis of CMF arising in soft tissues can be confirmed by identifying a GRM1 gene fusion or GRM1 expression by immunohistochemistry.
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Affiliation(s)
- Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Vladka Salapura
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, 1000, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Daja Šekoranja
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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Kučič AC, Gašperšič R. Minimally invasive non-surgical therapy (MINST) in stage III periodontitis patients: 6-month results of a split-mouth, randomised controlled clinical trial. Clin Oral Investig 2023; 27:2075-2087. [PMID: 37014505 PMCID: PMC10071470 DOI: 10.1007/s00784-023-04994-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
OBJECTIVES To determine if minimally invasive non-surgical therapy (MINST) outperforms classical non-surgical periodontal therapy for stage III periodontitis with primarily suprabony (horizontal) type defects. MATERIALS AND METHODS In a split-mouth randomised controlled trial, 20 patients' dental quadrants were randomly assigned to MINST or classical non-surgical treatment. The primary outcome variable was the number of sites with probing pocket depth ≥ 5 mm and BOP. Treatment method, tooth type, smoking status, and gender were evaluated using a multivariate multilevel logistic regression model. RESULTS After 6 months, the percentage of sites with PD ≥ 5 mm and BOP that healed (MINST = 75.5%; control group = 74.1%; p = 0.98), and the median number of persisting sites (MINST: 6.5, control group: 7.0; p = 0.925) were similar in both groups. In the test and control groups, respectively, median probing pocket depths (2.0 mm vs. 2.1 mm) and clinical attachment level (1.7 mm vs. 2.0 mm) changed significantly (p < 0.05) but similarly. Significantly less gingival recession occurred in the MINST group's deep molar pockets compared to the control group (p = 0.037). Men (OR = 0.52, p = 0.014) and non-molars (OR = 3.84, p 0.001) had altered odds for healing of sites with PD ≥ 5 mm and BOP. CONCLUSIONS MINST reduces gingival recession associated with molar teeth, although it performs similarly to traditional non-surgical therapy in treating stage III periodontitis with predominately horizontal-type defects. CLINICAL RELEVANCE MINST performs similarly to non-surgical periodontal therapy in stage III periodontitis with predominantly suprabony defects. TRIAL REGISTRATION Clinicaltrials.gov (NCT04036513) on June 29, 2019.
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Affiliation(s)
- Alja Cmok Kučič
- Public Health Centre Celje, Gregorčičeva 5, 3000, Celje, Slovenia
| | - Rok Gašperšič
- Department of Oral Medicine and Periodontology, Faculty of Medicine, University of Ljubljana, Hrvatski Trg 6, 1000, Ljubljana, Slovenia.
- Department of Oral Medicine and Periodontology, Dental Clinic, University Clinical Centre, Hrvatski Trg 6, 1000, LjubljanaLjubljana, Slovenia.
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Krajcar D, Grabnar I, Jereb R, Legen I, Opara J. Predictive Potential of BCS and Pharmacokinetic Parameters on Study Outcome: Analysis of 198 In Vivo Bioequivalence Studies. Eur J Drug Metab Pharmacokinet 2023; 48:241-255. [PMID: 36872388 PMCID: PMC10175306 DOI: 10.1007/s13318-023-00821-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND AND OBJECTIVES Understanding predictive potential of parameters to perform early bioequivalence (BE) risk assessment is crucial for good planning and risk mitigation during product development. The objective of the present study was to evaluate predictive potential of various biopharmaceutical and pharmacokinetic parameters on the outcome of BE study. METHODS Retrospective analysis was performed on 198 Sandoz (Lek Pharmaceuticals d.d., A Sandoz Company, Verovskova 57, 1526 Ljubljana, Slovenia) sponsored BE studies [52 active pharmaceutical ingredients (API)] where characteristics of BE study and APIs were collected for immediate-release products and their predictive potential on the study outcome was assessed using univariate statistical analysis. RESULTS Biopharmaceutics Classification System (BCS) was confirmed to be highly predictive of BE success. BE studies with poorly soluble APIs were riskier (23% non-BE) than with highly soluble APIs (0.1% non-BE). APIs with either lower bioavailability (BA), presence of first-pass metabolism, and/or being substrate for P-glycoprotein substrate (P-gP) were associated with higher non-BE occurrence. In silico permeability and time at peak plasma concentrations (Tmax) were shown as potentially relevant features for predicting BE outcome. In addition, our analysis showed significantly higher occurrence of non-BE results for poorly soluble APIs with disposition described by multicompartment model. The conclusions for poorly soluble APIs were the same on a subset of fasting BE studies; for a subset of fed studies there were no significant differences between factors in BE and non-BE groups. CONCLUSION Understanding the association of parameters and BE outcome is important for further development of early BE risk assessment tools where focus should be first in finding additional parameters to differentiate BE risk within a group of poorly soluble APIs.
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Affiliation(s)
- Dejan Krajcar
- Lek Pharmaceuticals d.d., A Sandoz Company, Verovskova 57, 1526, Ljubljana, Slovenia.
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Iztok Grabnar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Rebeka Jereb
- Lek Pharmaceuticals d.d., A Sandoz Company, Verovskova 57, 1526, Ljubljana, Slovenia
| | - Igor Legen
- Lek Pharmaceuticals d.d., A Sandoz Company, Verovskova 57, 1526, Ljubljana, Slovenia
| | - Jerneja Opara
- Lek Pharmaceuticals d.d., A Sandoz Company, Verovskova 57, 1526, Ljubljana, Slovenia
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Lovšin N. Copy Number Variation and Osteoporosis. Curr Osteoporos Rep 2023; 21:167-172. [PMID: 36795294 PMCID: PMC10105686 DOI: 10.1007/s11914-023-00773-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent findings on copy number variations and susceptibility to osteoporosis. RECENT FINDINGS Osteoporosis is highly influenced by genetic factors, including copy number variations (CNVs). The development and accessibility of whole genome sequencing methods has accelerated the study of CNVs and osteoporosis. Recent findings include mutations in novel genes and validation of previously known pathogenic CNVs in monogenic skeletal diseases. Identification of CNVs in genes previously associated with osteoporosis (e.g. RUNX2, COL1A2, and PLS3) has confirmed their importance in bone remodelling. This process has been associated also with the ETV1-DGKB, AGBL2, ATM, and GPR68 genes, identified by comparative genomic hybridisation microarray studies. Importantly, studies in patients with bone pathologies have associated bone disease with the long non-coding RNA LINC01260 and enhancer sequences residing in the HDAC9 gene. Further functional investigation of genetic loci harbouring CNVs associated with skeletal phenotypes will reveal their role as molecular drivers of osteoporosis.
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Affiliation(s)
- Nika Lovšin
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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Horvatinovic T, Mikic M, Dabić M. Dissecting entrepreneurial team research: a bibliometric analysis. Rev Manag Sci 2023. [PMCID: PMC10037398 DOI: 10.1007/s11846-023-00652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Despite the massive volume of published articles, the pool of knowledge on entrepreneurial teams needs to be algorithmically classified and meticulously scrutinised. It is crucial for the field to be historically positioned under relevant themes, internally connected in terms of conceptual foundations, and systematically categorised in consonance with previously utilised frameworks of analysis. These concerns are resolved in this study by conducting a bibliometric analysis of 672 relevant articles. This form of analysis has not been previously employed on the topic of entrepreneurial teams. First, this study identifies eight main thematic clusters in the entrepreneurial teams field and their sub-themes. The eight main thematic clusters are: (i) Intellectual Capital, (ii) Cognition and Behaviour, (iii) Science and Technology, (iv) Finance, (v) Transformation, (vi) Internationalisation, (vii) Family, and (viii) Community and Surroundings. Second, the study reveals the clusters most needing restoration, relations between clusters, and input-mediator-output variables by their respective cluster. In addition, an implied scholarly depiction of entrepreneurial teams is articulated, which can serve as a basis for developing an entrepreneurial teams theory. Finally, promising avenues for future research are suggested for the entire field and every cluster specifically.
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Affiliation(s)
- Tin Horvatinovic
- grid.4808.40000 0001 0657 4636Faculty of Business and Economics, University of Zagreb, Trg J. F. Kennedyja 6, Zagreb, 10 000 Croatia
| | - Mihaela Mikic
- grid.4808.40000 0001 0657 4636Faculty of Business and Economics, University of Zagreb, Trg J. F. Kennedyja 6, Zagreb, 10 000 Croatia
| | - Marina Dabić
- grid.4808.40000 0001 0657 4636Faculty of Business and Economics, University of Zagreb, Trg J. F. Kennedyja 6, Zagreb, 10 000 Croatia
- grid.445423.0University of Dubrovnik, Dubrovnik, 20 000 Croatia
- grid.8954.00000 0001 0721 6013School of Economics and Business, University of Ljubljana, Kardeljeva ploščad 17, Ljubljana, 1 000 Slovenia
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Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, da Rocha ST, Eckersley-Maslin M. IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Res 2020; 48:e92. [PMID: 32621604 PMCID: PMC7498334 DOI: 10.1093/nar/gkaa567] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/16/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We adapted amplicon bisulfite-sequencing protocols to design IMPLICON for ICRs in adult tissues of inbred mice, validating it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
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Affiliation(s)
- Tajda Klobučar
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Elisa Kreibich
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Maria Arez
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Duarte Pólvora-Brandão
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Simão Teixeira da Rocha
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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