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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational methods for the identification of novel targets and to...
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Fabrication of the cross-linked PVA/TiO2/C nanocomposite membrane for alkaline direct methanol fuel cells
PublicationA crosslinked Poly(vinyl alcohol) based composite membrane was developed through a phase inversion process for use in alkaline direct methanol fuel cells (ADMFCs). The titanium dioxide (TiO2) and carbon nanoparticles (NPs) have been incorporated into the PVA polymer matrix to improve the mechanical and thermal properties. The membrane samples were further modified with maleic acid, a carboxylic acid acting as the cross-linker,...
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Regenerative Drug Discovery Using Ear Pinna Punch Wound Model in Mice
PublicationThe ear pinna is a complex tissue consisting of the dermis, cartilage, muscles, vessels, and nerves. Ear pinna healing is a model of regeneration in mammals. In some mammals, including rabbits, punch wounds in the ear pinna close spontaneously; in common-use laboratory mice, they remain for life. Agents inducing ear pinna healing are potential regenerative drugs. We tested the effects of selected bioactive agents on 2 mm ear pinna...
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Thermal Instability of Choline Chloride-Based Deep Eutectic Solvents and Its Influence on Their Toxicity─Important Limitations of DESs as Sustainable Materials
PublicationDeep eutectic solvents (DESs) have become a hot topic in many branches of science due to their remarkable properties. They have been studied in a wide variety of applications. In particular, choline chloride (ChCl)-based DESs are one of the most commonly used representatives of these fluids. Nevertheless, in order to apply DESs in some fields, it is essential to guarantee their stability, reusability, and biocompatibility. In this...
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Thermoplastic starch nanocomposites using cellulose-rich Chrysopogon zizanioides nanofibers
PublicationGreen thermoplastic starch (TPS) nanocomposite films aided by cellulose nanofibers (CNFs) from Chrysopogon zizanioides roots were developed and characterized. When compared to other lignocellulosic fibers, Chrysopogon zizanioides roots revealed exceptionally high cellulose content (~48%). CNFs were separated using an environmentally friendly acid isolation technique that included three stages: (i) alkali treatment; (ii) bleaching;...
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Zastosowanie połączenia mikroekstrakcji do fazy stacjonarnej i chromatografii gazowej do oznaczania lotnych kwasów tłuszczowych w próbkach środowiskowych i pokrewnych=Application of combination of solid phase microextraction and gas chromatography for determination of volatile fatty acids in environmental and related samples
PublicationOznaczanie lotnych kwasów tłuszczowych (LKT) w próbkach środowiskowych wymaga najczęściej izolacji i wzbogacania analitów na etapie przygotowania próbek oraz zastosowania techniki o dużym potencjale separacyjnym i identyfikacyjnym na etapie oznaczeń końcowych. W pracy dokonano krytycznego przeglądu zastosowań wygodnej i często stosowanej techniki mikroekstrakcji do fazy stacjonarnej (SPME) w połączeniu z wysokosprawną techniką...
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Distillation cleanup preceded gc determination of short-chain monocarboxylic acids in aqueous and solid samples of wastewater origin = Oznaczanie krótkołańcuchowych kwasów monokarboksylowych w próbkach wodnych i stałych pochodzących z oczyszczalni ścieków z wykorzystaniem chromatografii gazowej poprzedzonej destylacją
PublicationShort-chain monocarboxylic acids (SCMAs) (C2-C5) formed in the process of aerobic biodegradation of larger organic molecules should often be monitored to optimize wastewater biological treatment and study the processes of converting organic waste matter into methane, etc. Gas chromatography (GC) seems a method of choice for such a task. Majority of samples require clean up before they can be injected into GC system. In this work...
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Novel approach to interference analysis of glucose sensing materials coated with Nafion
PublicationA gold-based sensing platform, TiND | AuNP | Nafion, was prepared as an exemplary electrode material exhibiting a response to glucose in a neutral solution. The change of electrochemical properties after exposure to glucose and interference compounds such as vitamin C, glycine, urea, paracetamol and acetylsalicylic acid was tested.
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A new B-D-galactosidase with a low temperature optimum isolated from the Antarctic Arthrobacter sp. 20B: gene cloning, purification and characterization.
PublicationA psychrotrophic bacterium producing a coldadaptedB-galactosidase upon growth at low temperatureswas classiWed as Arthrobacter sp. 20B. A genomic DNAlibrary of strain 20B introduced into Escherichia coliTOP10F' and screening on X-Gal (5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside)-containing agar plates ledto the isolation of B-galactosidase gene. The B-galactosidasegene (bgaS) encoding a protein of 1,053 amino acids,with a...
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Scarabaeidae as human food – A comprehensive review
PublicationRising global population and sustainable protein demand have sparked interest in unique food sources. Entomophagy, or insect consumption, presents a solution and Scarab beetles, part of the Scarabaeidae family, offer a novel food option. The comprehensive review underscores their potential as human food, with strong nutrition, low environmental impact, and the ability to ease strain on conventional agriculture. Nutritional analysis...
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Green monoterpenes based deep eutectic solvents for effective BTEX absorption from biogas
PublicationThe combustion of biogas which contains significant amounts of monoaromatic hydrocarbons, i.e. benzene, ethylbenzene, toluene, and xylene (BTEX) can cause many technological, environmental, and health problems. Therefore, in these studies, a new physical absorption method based on deep eutectic solvents (DES) consisting of monoterpenes and carboxylic acids was developed for BTEX removal. A total of 39 DES were synthesized, of which...
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STOMACH, Body of stomach - Male, 44 - Tissue image [12060630017624261]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Hyalinizing trabecular tumor - Female, 46 - Tissue image [11010630088571531]
Open Research DataThis is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Other mycoses, not elsewhere classified - Female, 40 - Tissue image [6290730011493361]
Open Research DataThis is the histopathological image of ACCESSORY SINUSES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mucoepidermoid carcinoma - Female, 63 - Tissue image [6010730010702581]
Open Research DataThis is the histopathological image of BASE OF TONGUE tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Other specified mycoses - Female, 41 - Tissue image [6290730011482201]
Open Research DataThis is the histopathological image of ACCESSORY SINUSES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Infiltrating duct and lobular carcinoma - Female, 72 - Tissue image [7240729592878081]
Open Research DataThis is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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New 3D printable filaments with nanodiamonds, physicochemical additives characteristics and electrochemical activity
Open Research DataThis dataset contains the physicochemical analyses (XRD, Raman spectroscopy, BET analyses) and electrochemical analyses (CV, EIS) for a new 3D-printable composite has been developed dedicated to electroanalytical applications. Two types of diamondised nanocarbons - detonation nanodiamonds (DNDs) and boron-doped carbon nanowalls (BCNWs) - were added...
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Liniowe i nieliniowe modele wielowymiarowej kalibracji do predykcji stężenia substancji z pomiarów woltamperometrycznych
PublicationPomiary woltamperometryczne znajdują zastosowanie w wielu dziedzinach nauki i techniki, np. w przemyśle farmaceutycznym. Dane uzyskane w wyniku takich pomiarów zawierają informację odnośnie rodzaju i stężenia badanej substancji, jednakże są one często kłopotliwe w bezpośredniej interpretacji. Z tego powodu, istnieje konieczność wykorzystania odpowiednich metod matematycznych, które umożliwiają uzyskanie bezpośredniej i precyzyjnej...
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Hydrogels Based on Natural Polymers for Cardiac Applications
PublicationIn this work agar- and borax-based hydrogels with and without the addition of poly(vinyl alcohol) (PVA) at different concentrations were synthesized. Hydrogels were modified by the same amount of acetylsalicylic acid (ASA) which exhibits antithrombotic properties. The effect of modification by ASA on the properties of hydrogels was analyzed.
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Liniowe i nieliniowe układy elektroniczne (podstawy) - 2023/24(lato)
e-Learning CoursesWydział ETI / I stopień studiów EiT/IBM/ACiR: "Układy elektroniczne" oraz "Analogowe układy elektroniczne"
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Isolation and some properties of collagen from the backbone of Baltic cod(Gadus morhua)
PublicationOssein from Baltic cod backbone was obtained after extraction of non-collagenous protein with 0.1 M NaOH solution and demineralization with 1.0 M HCl solution. The extractions were performed at 4 C for24, 48 and 72 h using a solid/solution ratio from 1:4 to 1:8 (w/v). After 48 h of extraction in 0.5 M acetic acid only about 25% of collagen was dissolved. After 48 h of extraction at optimal concentration of pepsin(4 mg/g ossein)...
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Introduction of Pro and Its Analogues in the Conserved P1 Position of Trypsin Inhibitor SFTI-1 Retains Its Inhibitory Activity
PublicationA number of monocyclic SFTI-1 analogues modified in the conserved inhibitor P1 position by Pro, its L-hydroxyproline (Hyp) derivative as well as mimetics with different ring size were synthesized by the solid-phase method. Replacement of Ser6 by Pro, Hyp, and a four-member ring, L-azetidine-2-carboxylic acid (Aze), retained trypsin or chymotrypsin inhibitory activity. The determined association equilibrium constants of these analogues...
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Morphology and local chain structure of polyamide 6 modified in the solid state with a semi-aromatic nylon salt
PublicationStructural and conformational differences between the polyamide 6 (PA6) homopolymer and two copolymers of PA6 modified in the solid state with 20 and 30 wt% of the semi-aromatic nylon salt of 1,5-diamino-2-methylpentane (Dytek A) and isophthalic acid (IPA) in the feed were investigated. Room temperature wide-angle X-ray diffraction (WAXD) analysis together with 13C{1H} cross-polarization/magic-angle spinning solid-state (CP/MAS)...
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Bis(ammonium) Zoledronate Dihydrate
PublicationNeutralization of 2-(1-imidazole)-1-hydroxyl-1,1`-ethylidenediphosphonic acid (zoledronic acid) by an excess of ammonia yielded bis(ammonium) zoledronate dihydrate, {C5H8N2O7P2 2−, 2(H4N+), 2(H2O)}. The product is readily soluble in water and forms monocrystals for which the X-ray structural analysis was carried out. The zoledronic anion is of double negative charge due to deprotonation of three P–OH groups and protonation of the...
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A novel method of creating thermoplastic chitosan blends to produce cell scaffolds by FDM additive manufacturing
PublicationDue to its remarkable and promising biological and structural properties, chitosan has been widely studied in several potential applications in the biomedical sector. Attempts are being made to use this polymer and its properties in thermoplastics dedicated to 3D printing in FDM technology. However, chitosan can be processed only from acid solution, which limits its applications. The paper presents a new path for the production...
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Modification of structured bio‑carbon derived from spongin-based scaffolds with nickel compounds to produce a functional catalyst for reduction and oxidation reactions: Potential for use in environmental protection
PublicationThree different 3D fibrous-like NiO/Ni(OH)2/Ni‑carbonized spongin-based materials were prepared via a simple sorption–reduction method. Depending on the support used, the catalysts were composed of carbon, nickel oxide, nickel hydroxide and zero-valent nickel, with the surface content of the nickel-containing phase in the range 15.2–26.0 wt%. Catalytic studies showed promising activity in the oxidation of phenolic compounds in water...
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ZASTOSOWANIE APLIKACJI INTERNETOWEJ W OCENIE JAKOŚCI DOPASOWANIA APARATÓW SŁUCHOWYCH
PublicationW pracy opisano zastosowanie aplikacji internetowej do oceny jakości dopasowania aparatów słuchowych. Metoda oceny polega na badaniu ankietowym, uzupełnionym testem rozumienia słów jednosylabowych w polu swobodnym. Opisywana aplikacja internetowa pozwala na przeprowadzenie badania z dowolnego komputera z dostępem do sieci. Dzięki implementacji metody w postaci aplikacji internetowej, można w systematyczny i uporządkowany sposób...
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Isolation and identification of the restriction endonuclease Ptal fromPhormidium tadzschicicum, an isoschizomer of BspMII
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Targeted DNA oxidation by LSD1–SMAD2/3 primes TGF-β1/ EMT genes for activation or repression
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Endogenous oxidative DNA base modifications analysed with repair enzymes and GC/MS technique
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublicationDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp.,recognizes novel asymmetric sequence 5´-ACGGA(N11/9)-3
PublicationA novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5′-ACGGA-3′ and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found...
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A new Thermus sp. class-IIS enzyme subfamily: isolation of a ''twin'' endo nuclease TspDTI with a novel specificity 5´-ATGAA(N11/9)-3´, related to TspGWI, Taqll and Tth111II. 5´-ATGAA(N11/9)-3´, spokrewnionej z TspGWI, TaqII i Tth111II.
PublicationOdkryto i scharakteryzowano nową subrodzinę enzymów klasy IIS z Thermus sp.
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Application of Artificial Intelligence by Poland’s Public Administration
PublicationThis chapter presents an overview and analysis of artificial intelligence-driven solutions created and implemented by or with the support of Poland’s central public administration (PA). After discussing governance of AI-related issues, we analyze a set of examples of AI innovation to map the actors and their relations within the ecosystem, describe the field where innovation in AI for PA occurs, and highlight the potentialities...
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Conceptualizing Digital Government for Social Solidarity
PublicationThis paper motivates the study of the impact of digital government on social solidarity; builds a conceptual foundation with four types of solidarity – group-based, compassionate, instrumental and emphatic; relates digital government to the type and moment – pre-technological, technological and post-technological of solidarity; and puts forward the type-moment frame to study how digital government is supporting social solidarity...
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Trust and Distrust in e-Democracy
PublicationIn the digital government research literature, the concept of trust is typically used as a precondition for the adoption of digital technology in the public sector or an outcome of a roadmap leading up to such adoption. The concept plays a central role in many decisions linked to the planning, adoption and management of the public sector technology. In contrast, the concept of...
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New methodology for calculating cost-efficiency of different ways of voting: is internet voting cheaper?
PublicationNew ways of voting in elections are being sought by electoral administrations worldwide who want to reverse declining voter turnouts without increasing electoral budgets. This paper presents a novel approach to cost accounting for multi-channel elections based on local elections in Estonia. By doing so, it addresses an important gap in the academic literature in this field. The authors confirm that internet voting was most cost-efficient...
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Trust and Distrust in e-Democracy
PublicationIn the digital government research literature, the concept of trust is typically used as a precondition for the adoption of digital technology in the public sector or an outcome of a roadmap leading up to such adoption. The concept plays a central role in many decisions linked to the planning, adoption and management of the public sector technology. In contrast, the concept of distrust is almost neglected in such literature but,...
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Safeguarding democracy during pandemics. Social distancing, postal, or internet voting—the good, the bad, or the ugly?
PublicationDuring a pandemic, many countries and organizations must decide whether to postpone upcoming elections or to hold them (Krimmer et al., 2020a). If the decision is made to hold the election, three main scenarios come to mind: continue using the existing system but include measures to ensure the health of participants; or look for alternatives among remote voting channels which could ensure social distancing is guaranteed either...
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Technology and democracy: the who and how in decision-making. The cases of Estonia and Catalonia
PublicationThis paper focuses on the use of technology to improve democracy, comparing the cases of Estonia and Catalonia. Both examples are closely related in their use of technology to further democratize the decision-making processes but have opposite starting points. Estonia’s internet voting system is an offshoot of the comprehensive e-governance system developed by the Estonian government. It is meant to make it more convenient for...