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- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 4. |
- Asgardoon, MH, et al.
(author)
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Monogenic Primary Immunodeficiency Disorder Associated with Common Variable Immunodeficiency and Autoimmunity
- 2020
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In: International archives of allergy and immunology. - : S. Karger AG. - 1423-0097 .- 1018-2438. ; 181:9, s. 706-714
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Journal article (peer-reviewed)abstract
- <b><i>Background:</i></b> Common variable immunodeficiency (CVID) is the most frequent primary immunodeficiency disorder mainly characterized by recurrent bacterial infections besides other immunological defects including loss of or dysfunction of B cells and decreased immunoglobulin levels. In this study, our aim is to evaluate clinical, immunological, and molecular data of patients with a primary clinical diagnosis of CVID and autoimmune phenotype with a confirmed genetic diagnosis. <b><i>Methods:</i></b> Among 297 patients with CVID, who were registered in the Iranian Primary Immunodeficiency Registry at Children’s Medical Center Hospital in Iran, 83 patients have been genetically examined and 27 patients with autoimmunity and confirmed genetic mutations were selected for analysis. Whole-exome sequencing and confirmatory Sanger sequencing methods were used for the study population. A questionnaire was retrospectively filled for all patients to evaluate demographic, laboratory, clinical, and genetic data. <b><i>Results:</i></b> In the 27 studied patients, 11 different genetic defects were identified, and the most common mutated gene was <i>LRBA</i>, reported in 17 (63.0%) patients. Two patients (7.7%) showed autoimmune complications as the first presentation of immunodeficiency. Eleven patients (40.7%) developed one type of autoimmunity, and 16 patients (59.3%) progressed to poly-autoimmunity. Most of the patients with mono-autoimmunity (<i>n</i> = 9, 90.0%) primarily developed infectious complications, while in patients with poly-autoimmunity, the most common first presentation was enteropathy (<i>n</i> = 6, 37.6%). In 13 patients (61.9%), the diagnosis of autoimmune disorders preceded the diagnosis of primary immunodeficiency. The most frequent autoimmune manifestations were hematologic (40.7%), gastrointestinal (48.1%), rheumatologic (25.9%), and dermatologic (22.2%) disorders. Patients with poly-autoimmunity had lower regulatory T cells than patients with mono-autoimmunity. <b><i>Conclusion:</i></b> In our cohort, the diagnosis of autoimmune disorders preceded the diagnosis of primary immunodeficiency in most patients. This association highlights the fact that patients referring with autoimmune manifestations should be evaluated for humoral immunity.
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- Tavakol, M, et al.
(author)
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Diagnostic Approach to the Patients with Suspected Primary Immunodeficiency
- 2020
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In: Endocrine, metabolic & immune disorders drug targets. - : Bentham Science Publishers Ltd.. - 2212-3873 .- 1871-5303. ; 20:2, s. 157-171
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Journal article (peer-reviewed)abstract
- Primary immunodeficiency diseases (PIDs) are a group of more than 350 disorders affecting distinct components of the innate and adaptive immune systems. In this review, the classic and advanced stepwise approach towards the diagnosis of PIDs are simplified and explained in detail.Results:Susceptibility to recurrent infections is the main hallmark of almost all PIDs. However, noninfectious complications attributable to immune dysregulation presenting with lymphoproliferative and/or autoimmune disorders are not uncommon. Moreover, PIDs could be associated with misleading presentations including allergic manifestations, enteropathies, and malignancies.Conclusion:Timely diagnosis is the most essential element in improving outcome and reducing the morbidity and mortality in PIDs. This wouldn’t be possible unless the physicians keep the diagnosis of PID in mind and be sufficiently aware of the approach to these patients.
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- Sharifinejad, N, et al.
(author)
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Autoimmunity in monogenic combined immune deficiencies with associated or syndromic features
- 2022
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In: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 13, s. 1023127-
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Journal article (peer-reviewed)abstract
- Combined immune deficiencies (CIDs) with associated or syndromic features are a highly heterogeneous subgroup of inherited immune disorders. These patients represent specific clinical complications with an increased risk of autoimmune conditions.MethodsWe analyzed data of monogenic patients with syndromic CIDs adopted from the Iranian inborn errors of immunity registry up to January 2022. A comprehensive comparison in terms of demographic, clinical, and immunological features was performed between patients with and without autoimmunity and also among four mutation groups with the most registered cases including ATM, STAT3 (AD-LOF), DNMT3B/ZBTB24, and WAS mutations.ResultsA total of 137 patients with monogenic syndromic CIDs were included. Most commonly mutated genes were the ATM [80 (58.4%)] and STAT3 (AD-LOF) [19 (13.9%)], followed by DNMT3B [11 (8%)], and WAS [11 (8%)]. More than 18% of all patients with syndromic CIDs, including most DNMT3B/ZBTB24 mutations patients, were clinically diagnosed with antibody deficiencies before genetic evaluation. Patients with ATM and WAS mutations had the latest age of onset and the lowest age of diagnosis, respectively. Autoimmune disorders were diagnosed in 24 patients at a median age of 3.5 (2.6-6.0) years, 70.6% of which were diagnosed prior to the diagnosis of immunodeficiency. Lymphoproliferation, particularly hepatosplenomegaly, was significantly higher in patients with autoimmunity (p=0.004). Syndromic CID patients with autoimmunity had significantly lower IgG levels. Hematologic autoimmunity mainly immune thrombocytopenic purpura was the most frequent autoimmunity among major groups of ATM, STAT3 (AD-LOF), DNMT3B/ZBTB24, and WAS mutations, however ATM-mutated patients present more diversified involved organs including rheumatologic, gastrointestinal and dermatologic autoimmunity.ConclusionAbout 18% of patients with monogenic syndromic CIDs developed autoimmunity, mainly in the form of hematological immune diseases. Autoimmunity could be an early-onset involvement with a potential diagnostic impact on suspicious cases of syndromic CIDs.
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- Tavakol, M, et al.
(author)
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Diversity of malignancies in patients with different types of inborn errors of immunity
- 2022
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In: Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology. - : Springer Science and Business Media LLC. - 1710-1484. ; 18:1, s. 106-
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Journal article (peer-reviewed)abstract
- Genetic defects in the development, maturation, and/or function of the immune cells can lead to Inborn errors of immunity (IEI) which may predispose patients to malignancies. The overall risk for cancer in children with IEI ranges from 4 to 25% and the type of malignancy is highly dependent on the specific mutant gene underlying IEI. We investigated 3056 IEI patients registered in the Iranian national registry between the years 1999 and 2020 in this retrospective cohort study. The frequency of malignancy and its association with the type of IEI in these patients were evaluated. A total of 82 IEI patients with malignancy were enrolled in this study. Among them, predominantly lymphoma was the most common type of malignancy (67.1%), followed by leukemia (11%), and cancers of the head and neck (7.3%). Among identified lymphoma cancers, non-Hodgkin’s lymphomas were the most frequent type (43.9%) followed by different subtypes of Hodgkin’s lymphoma (23.2%). Solid tumors (18.3%) appeared to be very heterogeneous by type and localization. The correlation between the type of malignancy and survival status and the association between the type of malignancy and IEI entities were unremarkable. The awareness of the association between the presence of IEI and cancer highlights the importance of a synergistic effort by oncologists and immunologists in the early diagnosis of malignancy and personalized therapeutic strategies in IEI patients.
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| 22. |
- Seidel, M., et al.
(author)
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Multi-pass Cell Based Nonlinear Pulse Compression of Yb : YAG Pump-Probe Lasers at FLASH
- 2023
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In: X-Ray Free-Electron Lasers : Advances in Source Development and Instrumentation VI - Advances in Source Development and Instrumentation VI. - 0277-786X .- 1996-756X. - 9781510662827 ; 12581
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Conference paper (peer-reviewed)abstract
- The majority of user experiments at the high repetition-rate free electron laser (FEL) facility FLASH are of pump-probe type, combining the extreme ultraviolet (XUV) or soft x-ray radiation from the FEL with ultrashort pulses generated by optical lasers. In this contribution, we demonstrate the advantages of using high-power Yb:YAG lasers with subsequent nonlinear pulse compression stages based on multi-pass cells (MPC). The approach enables the combination of hundreds of kHz to MHz repetition-rates, hundreds of watts of average powers and excellent intensity stabilities. We present the characteristics of the MPC-based pump-probe laser at the FLASH plane-grating beamlines. Furthermore, we report pulse compression to 8.2 fs pulse duration and the seeding of an optical parametric amplifier generating mid-IR radiation tunable from 1.4 µm to 16 µm.
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| 30. |
- Balla, Prannay, et al.
(author)
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Post-compression of picosecond pulses to four optical cycles
- 2020
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In: High Intensity Lasers and High Field Phenomena, HILAS 2020. - 9781557528209
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Conference paper (peer-reviewed)abstract
- We report post-compression of 1.2 ps pulses into the few-cycle regime via multi-pass spectral broadening. We achieve compression factors of 40 in single and 93 in a dual stage scheme using a compact setup.
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| 31. |
- Balla, Prannay, et al.
(author)
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Postcompression of picosecond pulses into the few-cycle regime
- 2020
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In: Optics Letters. - 0146-9592. ; 45:9, s. 2572-2575
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Journal article (peer-reviewed)abstract
- In this work,we demonstrate postcompression of 1.2 ps laser pulses to 13 fs via gas-based multipass spectral broadening. Our results yield a single-stage compression factor of about 40 at 200 W in-burst average power and a total compression factor >90 at reduced power. The employed scheme represents a route toward compact few-cycle sources driven by industrial-grade Yb:YAG lasers at high average power.
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| 33. |
- Käpylä, P. J., et al.
(author)
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Convective dynamos in spherical wedge geometry
- 2010
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In: Astronomical Notes - Astronomische Nachrichten. - : Wiley. - 0004-6337 .- 1521-3994. ; 331:1, s. 73-81
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Journal article (peer-reviewed)abstract
- Self-consistent convective dynamo simulations in wedge-shaped spherical shells are presented. Differential rotation is generated by the interaction of convection with rotation. Equatorward acceleration and dynamo action are obtained only for sufficiently rapid rotation. The angular velocity tends to be constant along cylinders. Oscillatory large-scale fields are found to migrate in the poleward direction. Comparison with earlier simulations in full spherical shells and Cartesian domains is made.
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| 35. |
- Pakizeh, Tavakol, 1977, et al.
(author)
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Structural asymmetry and induced optical magnetism in plasmonic nanosandwiches
- 2008
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In: J. Opt. Soc. Am. B. ; 25, s. 659-
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Journal article (peer-reviewed)abstract
- A number of recent studies have shown that hybridized antiphase dipolar plasmons, qualitatively similar tomagnetic dipole resonances, can be excited in metal–dielectric–metal structures over a wide frequency range.Here, we study how structural asymmetry in plasmonic nanosandwiches, composed of two Au disks separatedby a thin SiO2 layer, affects their near- and far-field optical properties using point-dipole analysis, electrodynamicssimulations, and optical spectroscopy. We find that the strength of the antiphase resonant mode can beincreased significantly compared to a symmetrical sandwich if the diameters or thicknesses of the nanodisks inthe sandwich are made to differ. Such asymmetrical nanosandwiches also exhibit a generally stronger magneticresponse, as characterized by the magnetic near-field enhancement in the region between the disks. However,symmetry breaking also leads to pronounced directionality effects in the magnetic near-field, i.e., the enhancementdepends on which side of the sandwich that is first illuminated.
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