Most of our work has resulted in scholarly publications. On this page you can review our publications to get an idea about our work.
Learning through work as a data specialis
October, 2026 • Lesson
Karhapää, Anne
Presentation 2.10.2026, Data Steward Training, Tampere University.
This training resource has been developed in a project funded by the Finnish Ministry of Education and Culture and coordinated…
Presentation 2.10.2026, Data Steward Training, Tampere University.
This training resource has been developed in a project funded by the Finnish Ministry of Education and Culture and coordinated by the Tampere University, Data Management Training Development Project.
METHODOLOGY FOR DEVELOPING LEARNERS' LEXICAL SKILLS THROUGH VISUAL AIDS IN ENGLISH LANGUAGE TEACHING
October, 2026 • Dataset • ILM-FAN XABARNOMASI
Shakhzoda Ruzimova
This article examines the methodological foundations of developing learners’ lexical skills through visual aids in English language teaching. The study is based on the premise that vocabulary de…
This article examines the methodological foundations of developing learners’ lexical skills through visual aids in English language teaching. The study is based on the premise that vocabulary development should extend beyond recognition of isolated word meanings and should support the progressive development of form–meaning connections, contextual understanding, retrieval, and communicative use. A theoretical-methodological research design was employed, drawing on contemporary vocabulary-instruction research, multimodal and dual-coding perspectives, studies of digital flashcards and captioned audiovisual input, and established models of vocabulary knowledge. Through literature analysis, comparative analysis, synthesis, systematization, and pedagogical modelling, a six-stage methodological sequence is proposed: selecting target lexical units and visual support; establishing form–meaning connections; contextualizing lexical items; organizing active retrieval; transferring vocabulary into communicative use; and assessing and recycling lexical knowledge. Criteria for selecting visual aids are also specified, including semantic transparency, relevance, age and proficiency appropriateness, cognitive simplicity, contextual value, and pedagogical purpose. The methodology developed in this article treats visual aids not as decorative classroom elements but as structured pedagogical resources that support the transition from initial word recognition to meaningful and productive lexical use. The framework provides a basis for subsequent empirical validation within English language teaching methodology.
English language teaching, vocabulary instruction, lexical skills, visual aids, visual literacy, multimodal learning, retrieval practice, communicative use
Anatomy and physiology of the paediatric immune system: A comprehensive review of immune development, recurrent childhood infections, and homeopathic perspectives
October, 2026 • Journal article • Scienxt Journal of Human Anatomy & Physiology Pharmacy
Dr. R Imran Khan
The paediatric immune system is a dynamic network that develops before birth, changes rapidly during infancy, and continues to acquire functional and immunological experience throughout childhood and …
The paediatric immune system is a dynamic network that develops before birth, changes rapidly during infancy, and continues to acquire functional and immunological experience throughout childhood and adolescence. Its anatomy includes primary lymphoid organs such as the bone marrow and thymus and secondary organs and tissues including lymph nodes, spleen, tonsils, adenoids, Peyer’s patches, and other mucosaassociated lymphoid structures. Its physiology integrates epithelial barriers, innate recognition, complement, phagocytes, natural killer cells, antigen presentation, Tlymphocyte responses, B-cell maturation, antibodies, memory, and mechanisms of immune tolerance. Early-life immunity is not simply a weaker version of adult immunity; it has age-specific features that balance protection with the need to avoid excessive inflammation while the infant encounters food antigens and a newly established microbiota.
Recurrent infection is common in childhood because children encounter many new respiratory and gastrointestinal pathogens, especially after beginning childcare or school. The clinically important task is to distinguish expected infections from patterns suggesting an inborn error of immunity (IEI), anatomical disease, allergy, aspiration, environmental exposure, nutritional compromise, or another underlying condition. Contemporary classification has expanded the concept beyond classical recurrent infection to include autoimmunity, autoinflammation, malignancy, severe viral disease, and other immune dysregulation phenotypes. Warning signs can support recognition but have imperfect sensitivity, so clinical context and appropriate laboratory assessment remain essential.
The review also examines homeopathy in relation to paediatric immune health. Homeopathy is a historical complementary medical system based on principles such as ‘like cures like’ and serial dilution. It is relevant to this discussion because some families seek homeopathic care for recurrent colds, respiratory symptoms, allergy, or general immune support. However, biological plausibility, clinical evidence, and safety must be considered separately from cultural or personal acceptance. The most recent Cochrane review of oral homeopathic products for acute respiratory tract infections in children found no consistent evidence of benefit, with low or very low certainty for many outcomes (Hawke et al., 2022). Major health-information authorities likewise state that evidence is insufficient for homeopathy as an effective treatment for specific conditions and caution against replacing proven care (NCCIH, 2026). The appropriate paediatric approach is therefore evidence-informed, safety-focused, and respectful of families while protecting children from delayed diagnosis, missed vaccination, and substitution of ineffective treatment for necessary medical care.
PHEMS Bulletin Issue 3: Hospital Benchmarking: Enhancing Quality and Efficiency in Paediatric Care
October, 2026 • Other
PHEMS
Hospital benchmarking is a data-driven approach that enables paediatric hospitals to compare clinical and operational performance, identify best practices, and improve the quality and efficiency of ca…
Hospital benchmarking is a data-driven approach that enables paediatric hospitals to compare clinical and operational performance, identify best practices, and improve the quality and efficiency of care. Within PHEMS, benchmarking is supported through standardised data, automated analysis, and a federated network, enabling secure and meaningful comparisons across institutions while maintaining confidentiality. A structured seven-phase process supports the implementation and continuous monitoring of benchmarking activities, with the paediatric cardiology use case demonstrating how shared data and dashboards can be used to monitor outcomes, identify performance gaps, and drive targeted improvements in patient care.
Minimal Anonymized Dataset for "Topical 5% tetracycline accelerates healing of dermonecrotic lesions in cutaneous loxoscelism: a multicentre randomised placebo-controlled trial"
October, 2026 • Dataset
Tambourgi, Denise Vilarinho, Lopes, Priscila Hess, Tha Marques, Mario Octavio, Weber, Jaqueline Fernanda, Madureira Trufen, Carlos Eduardoet al.
H3K27ac ChIPseq: An IRF1-dependent IFNβ relay propagates IFNγ priming across macrophages
October, 2026 • Dataset
Siebeler, Ricky
Abstract
Macrophages are central regulators of inflammation, and their functional state is shaped by exposure to interferons (IFNs). IFNγ-priming, the pre-exposure of macrophages to IFNγ b…
Abstract
Macrophages are central regulators of inflammation, and their functional state is shaped by exposure to interferons (IFNs). IFNγ-priming, the pre-exposure of macrophages to IFNγ before a secondary stimulus, reinforces subsequent inflammatory and IFN responses, but whether its consequences extend beyond the directly exposed macrophage has remained unclear. Here, we show that IFNγ-priming boosts IFNβ production in response to subsequent Toll-like receptor 4 (TLR4) stimulation. This response is associated with IFNγ-induced interferon regulatory factor 1 (IRF1) expression and chromatin poising at type-I IFN and IFN-stimulated gene loci, accompanied by remodeling of active enhancers and promoters. TLR4 stimulation then converts this poised state into productive IRF1 binding. Using an IFN-stimulated gene factor 3 (ISGF3) reporter system, co-cultures, conditioned-medium transfer and blockade of the type-I IFN receptor, we demonstrate that IFNγ-primed macrophages secrete IRF1-dependent IFNβ capable of priming neighbouring, previously unexposed macrophages. IFNγ-priming therefore does not merely sensitize macrophages to type-I IFNs but drives their production and intercellular spread, reframing the functional unit of IFNγ-priming from the individual macrophage to the population, with implications for chronic inflammatory diseases featuring elevated IFNγ and type-I IFN signatures.
Description
This repository contains raw H3K27ac CHIPseq data generated to characterize transcriptional differences between naive and IFNγ-primed BLaER1 macrophages, for both wild-type and IRF1-/- macrophages
Culture
Human B cell Leukemia C/EBPα Estrogen Receptor clone 1 (BLaER1) eGFP-/- cells were a gift from the lab of Holger Heine (Research Center Borstel) and cultured in RPMI 1640 (Thermo Fisher) supplemented with 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Thermo Fisher) and 10% fetal calf serum (FCS) (Gibco). Cells were cultured at 37°C, 5% CO2. To induce macrophage trans-differentiation, BLaER1 cells were cultured for six days in trans-differentiation medium, consisting of complete RPMI 1640 with 10 ng/mL IL-3 (PeproTech), 10 ng/mL M-CSF (Miltenyi) and 200 nM β-estradiol (Sigma Aldrich), as previously described(9). Fresh trans-differentiation medium was added on day three of the trans-differentiation. On day five, cells were lifted from the culture flask using TrypLE Express (Thermo Fisher), density normalized, and replated for experiment specific purposes on day six and onwards. Stimulations were done with 10 ng/mL LPS (InvivoGen). For IFNγ priming, trans-differentiating BLaER1s were treated with 25ng/mL of recombinant IFNγ from day three until day five. Subsequently, IFNγ-primed BLaER1 macrophages were lifted from the culture flask using TrypLE Express (Thermo Fisher), washed, density normalized, and replated for experiment specific purposes on day six and onwards.
Content
paired-end sequencing fastq.gz
.bam files
Metadata
Beyond the Eight-Week Convention: A Rapid Review of Assigned Program Architecture and Temporal Change in Mindfulness-Based Programs — Screening, Coding and Protocol Materials
October, 2026 • Dataset
Tse, Barry
This record contains the two primary research files supporting the rapid review Beyond the Eight-Week Convention: A Rapid Review of Assigned Program Architecture and Temporal Change in Mindfulness-Bas…
This record contains the two primary research files supporting the rapid review Beyond the Eight-Week Convention: A Rapid Review of Assigned Program Architecture and Temporal Change in Mindfulness-Based Programs.
The Excel workbook contains the complete research record for the review, including search metadata, the PsycINFO export, deduplication audit, title-and-abstract screening, full-text eligibility assessment, decision log, codebook, included-study extraction, quality-control recheck, flow counts, risk-of-bias appraisal, GRADE assessment and related classifications and analyses.
The accompanying DOCX contains the review protocol and methodological process record, including the final PsycINFO search strategy, search-development and sensitivity-testing decisions, eligibility criteria, screening procedures, extraction rules, quality-control procedures, reporting requirements and documented methodological decisions.
The review used APA PsycINFO via Ovid, searched to 3 September 2026. The final retrieval contained 301 records. The completed screening record contains 52 included reports representing 47 distinct studies. Screening, appraisal and analysis were conducted by one reviewer. AI-generated provisional title-and-abstract suggestions are retained transparently in the workbook and were subsequently reviewed and confirmed or amended by the reviewer.
The Excel workbook is the authoritative record for final screening counts, eligibility decisions, study linkage, extraction, appraisal and classifications. The DOCX preserves the protocol and methodological process record, including decisions made during search development, screening and analysis.
RNAseq_IRF1: An IRF1-dependent IFNβ relay propagates IFNγ priming across macrophages
October, 2026 • Dataset
Siebeler, Ricky
Abstract
Macrophages are central regulators of inflammation, and their functional state is shaped by exposure to interferons (IFNs). IFNγ-priming, the pre-exposure of macrophages to IFNγ b…
Abstract
Macrophages are central regulators of inflammation, and their functional state is shaped by exposure to interferons (IFNs). IFNγ-priming, the pre-exposure of macrophages to IFNγ before a secondary stimulus, reinforces subsequent inflammatory and IFN responses, but whether its consequences extend beyond the directly exposed macrophage has remained unclear. Here, we show that IFNγ-priming boosts IFNβ production in response to subsequent Toll-like receptor 4 (TLR4) stimulation. This response is associated with IFNγ-induced interferon regulatory factor 1 (IRF1) expression and chromatin poising at type-I IFN and IFN-stimulated gene loci, accompanied by remodeling of active enhancers and promoters. TLR4 stimulation then converts this poised state into productive IRF1 binding. Using an IFN-stimulated gene factor 3 (ISGF3) reporter system, co-cultures, conditioned-medium transfer and blockade of the type-I IFN receptor, we demonstrate that IFNγ-primed macrophages secrete IRF1-dependent IFNβ capable of priming neighbouring, previously unexposed macrophages. IFNγ-priming therefore does not merely sensitize macrophages to type-I IFNs but drives their production and intercellular spread, reframing the functional unit of IFNγ-priming from the individual macrophage to the population, with implications for chronic inflammatory diseases featuring elevated IFNγ and type-I IFN signatures.
Description
This repository contains raw and processed RNAseq data generated to characterize transcriptional differences IFNγ-primed BLaER1 macrophages in presence of lipopolysaccharid, for wild-type and IRF1-/-.
Culture
Human B cell Leukemia C/EBPα Estrogen Receptor clone 1 (BLaER1) eGFP-/- cells were a gift from the lab of Holger Heine (Research Center Borstel) and cultured in RPMI 1640 (Thermo Fisher) supplemented with 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Thermo Fisher) and 10% fetal calf serum (FCS) (Gibco). Cells were cultured at 37°C, 5% CO2. To induce macrophage trans-differentiation, BLaER1 cells were cultured for six days in trans-differentiation medium, consisting of complete RPMI 1640 with 10 ng/mL IL-3 (PeproTech), 10 ng/mL M-CSF (Miltenyi) and 200 nM β-estradiol (Sigma Aldrich), as previously described(9). Fresh trans-differentiation medium was added on day three of the trans-differentiation. On day five, cells were lifted from the culture flask using TrypLE Express (Thermo Fisher), density normalized, and replated for experiment specific purposes on day six and onwards. Stimulations were done with 10 ng/mL LPS (InvivoGen). For IFNγ priming, trans-differentiating BLaER1s were treated with 25ng/mL of recombinant IFNγ from day three until day five. Subsequently, IFNγ-primed BLaER1 macrophages were lifted from the culture flask using TrypLE Express (Thermo Fisher), washed, density normalized, and replated for experiment specific purposes on day six and onwards. Stimulations were done with 10 ng/mL LPS (InvivoGen).
Content
paired-end sequencing fastq.gz
.bam files
Metadata
The data for Forecasting Fundamental-Plane Tests of Intermediate-mass Black Holes in Radio-selected Dwarf Galaxies
October, 2026 • Dataset
Santra, Ramananda, MITRA, SAMIK, Abbassi, Shahram
Machine-readable source catalogue, forecast products, and Python analysis code supporting manuscript AAS79479, “Forecasting Fundamental-Plane Tests of Intermediate-mass Black Holes in Radio-sele…
Machine-readable source catalogue, forecast products, and Python analysis code supporting manuscript AAS79479, “Forecasting Fundamental-Plane Tests of Intermediate-mass Black Holes in Radio-selected Dwarf Galaxies.” The package reproduces the four analysis figures and source-specific Fundamental-Plane detection forecasts. It contains derived quantities rather than the raw HST or Chandra observations. HST data are available from MAST at DOI 10.17909/h9mh-tg88.
intermediate-mass black holesdwarf galaxiesFundamenta PlaneVLBIX-ray
There is an increasing interest in upgrading the EModel, a parametric tool for speech quality estimation, to the wideband and super-wideband contexts. The
Contemporary models of Unmanned Aerial Vehicles (UAVs) are largely developed using simulators. In a typical scheme, a flight simulator is dovetailed with a
Undertaking engineering research can be compounding for beginning graduate students and thwarting even for seasoned researchers. With a wealth of academic
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