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Submitted
Blanco, F., A. Munoz, D. Almeida, F. Ferreira da Silva, P. Limao-Vieira, A. Verkhovtsev, L. Ellis-Gibbings, K. Krupa, A. Traore, and G. Garcia. "{Modeling secondary particle tracks generated by high-energy protons in water}." {XXIX INTERNATIONAL CONFERENCE ON PHOTONIC, ELECTRONIC, AND ATOMIC COLLISIONS (ICPEAC2015), PTS 1-12}. Eds. C. {Diaz, I. Rabadan, G. Garcia, L. Mendez, and F. } Martin. Vol. {635}. {Journal of Physics Conference Series}, {635}. Submitted. Abstract
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Almeida, D., D. Kinzel, Ferreira F. Da Silva, B. Puschnigg, D. Gschliesser, P. Scheier, S. Denifl, G. Garcia, L. Gonzalez, and P. Limao-Vieira. "{N-site de-methylation in pyrimidine bases as studied by low energy electrons and ab initio calculations}." {PHYSICAL CHEMISTRY CHEMICAL PHYSICS}. {15} (Submitted): {11431-11440}. Abstract
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Almeida, D., F. Ferreira da Silva, G. Garcia, and P. Limao-Vieira. "{Negative ion chemistry of Deoxyribose and THF upon potassium atom collisions}." {XXVIII INTERNATIONAL CONFERENCE ON PHOTONIC, ELECTRONIC AND ATOMIC COLLISIONS (ICPEAC)}. Vol. {488}. {Journal of Physics Conference Series}, {488}. Submitted. Abstract
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Ferreira da Silva, F., D. Almeida, G. Martins, Y. Nunes, G. Garcia, and P. Limao-Vieira. "{Site and bond selective H- formation in methylated pyrimidine bases driven by potassium molecule collisions}." {XXVII INTERNATIONAL CONFERENCE ON PHOTONIC, ELECTRONIC AND ATOMIC COLLISIONS (ICPEAC 2011), PTS 1-15}. Eds. ID {Williams, HW VanDerHart, JF McCann, and DSF} Crothers. Vol. {388}. {Journal of Physics Conference Series}, {388}. Submitted. Abstract
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Ferreira da Silva, F., D. Almeida, G. Garcia, and P. Limao-Vieira. "{Site- and bond-selective H- formation in methylated pyrimidine bases driven by potassium-molecule collisions}." {XXVII INTERNATIONAL CONFERENCE ON PHOTONIC, ELECTRONIC AND ATOMIC COLLISIONS (ICPEAC 2011), PTS 1-15}. Eds. ID {Williams, HW VanDerHart, JF McCann, and DSF} Crothers. Vol. {388}. {Journal of Physics Conference Series}, {388}. Submitted. Abstract
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Da Silva, Ferreira F., M. Nobre, A. Fernandes, R. Antunes, D. Almeida, G. Garcia, N. J. Mason, and P. Limao-Vieira. "{Spectroscopic studies of ketones as a marker for patients with diabetes}." {RADIATION DAMAGE IN BIOMOLECULAR SYSTEMS}. Ed. KG} {McGuigan. Vol. {101}. {Journal of Physics Conference Series}, {101}. Submitted. Abstract
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Da Silva, Ferreira F., D. Almeida, G. Martins, A. R. Milosavljevic, B. P. Marinkovic, S. V. Hoffmann, N. J. Mason, Y. Nunes, G. Garcia, and P. Limao-Vieira. "{The electronic states of pyrimidine studied by VUV photoabsorption and electron energy-loss spectroscopy}." {PHYSICAL CHEMISTRY CHEMICAL PHYSICS}. {12} (Submitted): {6717-6731}. Abstract
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Ferreira da Silva, F., J. Rafael, A. Rebelo, D. Almeida, and P. Limao-Vieira. "{The role of side chains in electron transfer induced fragmentation of amino-acids}." {XXVIII INTERNATIONAL CONFERENCE ON PHOTONIC, ELECTRONIC AND ATOMIC COLLISIONS (ICPEAC)}. Vol. {488}. {Journal of Physics Conference Series}, {488}. Submitted. Abstract
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Nobre, M., A. Fernandes, Ferreira F. Da Silva, R. Antunes, D. Almeida, V. Kokhan, S. V. Hoffmann, N. J. Mason, S. Eden, and P. Limao-Vieira. "{The VUV electronic spectroscopy of acetone studied by synchrotron radiation}." {PHYSICAL CHEMISTRY CHEMICAL PHYSICS}. {10} (Submitted): {550-560}. Abstract
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In Press
Alan J. Cain, António Malheiro, Duarte Ribeiro. "Identities and bases in the sylvester and Baxter monoids." Journal of Algebraic Combinatorics (In Press).
Dias, S., A. Gama, P. Abrantes, M. I. Gomes, M. Fonseca, V. Reigado, D. Simões, E. Carreiras, C. Mora, A. Pinto Ferreira, O. Akpogheneta, and MO Martins. "Patterns of Sexual Risk Behavior, HIV Infection, and Use of Health Services Among Sub-Saharan African Migrants in Portugal." The Journal of Sex Research 19 (In Press).Website
2026
Monge, N., LFV Pinto, E. Ferreira, PL Almeida, J. L. Figueirinhas, AL Carvalho, PJ Sebastião, and M. H. Godinho. "Hierarchical Twist: Chirality Across Scales in Cellulose Cholesterics." Advanced Optical MaterialsAdvanced Optical Materials. 14.4 (2026): e02728. AbstractWebsite

Abstract One of the unresolved aspects of cellulose-based liquid crystalline phases is their chirality. Although cellulose is intrinsically chiral, both left-handed (LH) and right-handed (RH) chiral nematic phases are reported in cellulose derivatives under different conditions. The origin of these discrepancies?and whether LH and RH twisted structures coexist within a single material?has remained unclear. Here, the first direct evidence of hierarchical LH and RH twisted structures coexisting in a solvent-free, thermotropic cellulose derivative at room temperature is provided. Free-standing cholesteric films exhibit distinct LH and RH twisted domains, whose pitches respond oppositely to uniaxial mechanical strain: the LH pitch increases, while the RH pitch decreases with increasing strain. This contrasting response results from the coexistence of intertwined LH and RH twisted structures, whose optical axes are oriented differently relative to the strain direction. Notably, after stretching beyond their elastic limit, the films spontaneously recover their original shape within minutes. During this recovery, circular dichroism (CD) measurements reveal an increase in RH pitch and a decrease in LH pitch, evidencing reversible, strain-responsive behavior. Multiscale structural characterization confirms the hierarchical chiral organization and its mechanoresponsive nature, providing new insights into the origin of chirality in cellulose-based liquid crystalline materials.

Simões, Rita S. M., João S. Teodoro, Victor D. Alves, Ana Luísa Carvalho, Carlos M. G. A. Fontes, and Pedro Bule. "Noncatalytic surface electrostatic networks tune thermolability in uracil-DNA glycosylase." 302.7 (2026): 113212. AbstractWebsite

Uracil-DNA glycosylases (UDGs) are widely used to prevent carryover contamination in nucleic acid amplification–based diagnostics; however, existing thermolabile UDGs exhibit limited thermal inactivation windows for emerging applications. Here, we combine evolutionary mining, structural analysis, and structure-guided saturation mutagenesis to define non-catalytic determinants that tune UDG thermolability without compromising catalytic function. From 8482 bacterial UDG sequences, we assembled a 24-member diversity panel and identified UDG_7 as a naturally thermolabile scaffold coupling robust low-temperature activity with sharp inactivation near 45 °C. The crystal structure of UDG_7 reveals a canonical family-I α/β fold with a fully conserved active site, closely resembling both mesophilic human and Escherichia coli UDGs and thermolabile cod UDG. These structural insights guided the design of a single-site variant library targeting 48 non-catalytic positions involved in packing and electrostatic networks. Pooled thermal shift assays distinguished a rigid structural core from 16 surface thermolability hotspots. A high-throughput functional screening of 480 single mutants yielded 114 clones with a desirable “on–off–off” profile and, after sequence consolidation, identified 54 unique variants that retained activity at 25 °C but lost activity at 30 to 37.5 °C. Biochemical characterization revealed nine single substitutions, Q51I, T112Y, V144M, D167F, R201F, R201Y, D219M, R221P, and R221D, that markedly lower the melting temperature while preserving near-native activity. Together, these results indicate that UDG_7 thermolability is encoded by a distributed, surface-biased electrostatic network that can be selectively disrupted without perturbing the conserved catalytic core, shifting the functional inactivation boundary downward and supporting robust carryover control under low-temperature amplification constraints.

Ruciński, Maciej, Lope Ezquerro Ruiz, Hugo Campos, Octávio Mateus, Paulo Fernandes, Margarida Vilas-Boas, Haytham El Atfy, and Ingmar Werneburg. "Palaeoenvironments, stratigraphy and taphonomy of an Upper Triassic vertebrate-bearing unit, Silves Group, central Algarve, southern Portugal." Lethaia. 59.3 (2026): 1-31. Abstractruciskietal.2026-lethaia-palaeoenvironmentsalgavre.pdfWebsite

Triassic to Lower Jurassic deposits known as the Silves Group in the Algarve, southern Portugal, have been studied for over 150 years. However, many of this unit’s sedimentological, stratigraphical, and palaeontological aspects remain poorly documented. Here, we present novel observations on sedimentology, stratigraphy, taphonomy, and fauna at the Rocha da Pena site, located in the central part of the Algarve Basin. The investigated sequence is established to correspond to the upper part of the Silves Group. The mudstone, calcrete, and palustrine carbonate facies comprise most of the sequence thickness and are interpreted as having been deposited within coastal alluvial mudflats to palustrine settings under semi-arid and seasonal climates. The overlying siltstone and sandstone facies indicate an environmental shift towards tidally influenced environments, subsequently covered by the latest Triassic to earliest Jurassic volcaniclastics and basaltic lava flows. Furthermore, novel faunal elements, including actinopterygian and unionoid bivalves, are described from mudstone layers. New fossiliferous beds are identified within palustrine facies that yield numerous but poorly preserved materials assigned to cyamodontoid placodonts, hybodont sharks, and actinopterygians. The poor preservation of the remains is attributed to the pedogenetic processes prevalent in the palustrine depositional setting. A distinct faunal composition between the mudstone and palustrine facies is observed. It is preliminarily hypothesized to be likely linked with salinity fluctuations, but sampling bias cannot currently be excluded. The recovered vertebrate fauna aligns most closely with the Carnian and, to a lesser extent, the Norian fossil record. Nonetheless, the precise age of the fossil-bearing levels remains uncertain and can currently be reliably constrained to the upper Carnian–Rhaetian interval. Consequently, this work provides new insights into the palaeoenvironmental evolution of the western Tethys margin during the Late Triassic and highlights the relevance of the Silves Group in reconstructing coastal-continental ecosystem dynamics in southwestern Iberia.Triassic to Lower Jurassic deposits known as the Silves Group in the Algarve, southern Portugal, have been studied for over 150 years. However, many of this unit’s sedimentological, stratigraphical, and palaeontological aspects remain poorly documented. Here, we present novel observations on sedimentology, stratigraphy, taphonomy, and fauna at the Rocha da Pena site, located in the central part of the Algarve Basin. The investigated sequence is established to correspond to the upper part of the Silves Group. The mudstone, calcrete, and palustrine carbonate facies comprise most of the sequence thickness and are interpreted as having been deposited within coastal alluvial mudflats to palustrine settings under semi-arid and seasonal climates. The overlying siltstone and sandstone facies indicate an environmental shift towards tidally influenced environments, subsequently covered by the latest Triassic to earliest Jurassic volcaniclastics and basaltic lava flows. Furthermore, novel faunal elements, including actinopterygian and unionoid bivalves, are described from mudstone layers. New fossiliferous beds are identified within palustrine facies that yield numerous but poorly preserved materials assigned to cyamodontoid placodonts, hybodont sharks, and actinopterygians. The poor preservation of the remains is attributed to the pedogenetic processes prevalent in the palustrine depositional setting. A distinct faunal composition between the mudstone and palustrine facies is observed. It is preliminarily hypothesized to be likely linked with salinity fluctuations, but sampling bias cannot currently be excluded. The recovered vertebrate fauna aligns most closely with the Carnian and, to a lesser extent, the Norian fossil record. Nonetheless, the precise age of the fossil-bearing levels remains uncertain and can currently be reliably constrained to the upper Carnian–Rhaetian interval. Consequently, this work provides new insights into the palaeoenvironmental evolution of the western Tethys margin during the Late Triassic and highlights the relevance of the Silves Group in reconstructing coastal-continental ecosystem dynamics in southwestern Iberia.

Cardoso, F., E. Costa-Camilo, I. Duarte, MGP Carvalho, RG Sobral, JMF Almeida, and C. Pinheiro. "Mediterranean diet impact on plasma proteins: biomarker networks linking nutrition to the modulation of inflammation and oxidative stress." Frontiers in Nutrition. in press (2026).
Ayık, H., Vítor H. Fernandes, and E. Korkmaz. "On the monoid of partial order-preserving transformations of a finite chain whose domains and ranges are intervals (DOI 10.55730/1300-0098.3774)." Turkish Journal of Mathematics. 50.5 (2026): 913-932. AbstractWebsite

In this paper, we consider the monoid PIO_n, of all partial order-preserving transformations on a chain with n elements whose domains and ranges are intervals, along with its submonoid PIO_n^- of order-decreasing transformations. Our main aim is to give presentations for PIO_n^- and PIO_n. Moreover, for both monoids, we describe regular elements and determine their ranks, cardinalities and the numbers of idempotents and nilpotents.

Fanton, Andreia Romero, Orlando Matheus de Lima Almeida, Luiz Carlos de Almeida, Leandro Mouta Trautwein, and António Pinho Ramos. "Analytical Assessment of Punching Shear Reliability in Flat Slabs Exposed to Fire." fib Symposium. 2026. 495-504. Abstract
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Pereira, Maria Elias, Jonas Deuermeier, Tomás Mingates, Patrícia Almeida Carvalho, Tomás Calmeiro, Elvira Fortunato, Rodrigo Martins, Pedro Barquinha, and Asal Kiazadeh. "Influence of fabrication parameters on the Schottky barrier modulation of Mo/MoO x /IGZO/Ti/Mo memristor." Journal of Physics: Materials. 9 (2026): 015015. AbstractWebsite
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Marchão, Carla, Rui Marreiros, António Pinho Ramos, Francisco Martins, and Magnela Agostinho. "Punching behavior of slab-column connections with recycled coarse aggregates concrete under horizontal cyclic loads." fib Symposium. 2026. 421-431. Abstract
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2025
de Almeida, João M. G. C. F., Cândido Pinto Ricardo, and Carla Pinheiro. "Unveiling DIR proteins involved in cork formation: insights from transcriptome analysis and cis-element co-occurrence." Theoretical and Experimental Plant Physiology. 37 (2025). AbstractWebsite
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Araújo, A., J. O. Cerdeira, N. Lopes, and A. Moura. "Minimizing costs in signal provision by communication antennas along a railway line." 4OR-Q J Oper Res. 23 (2025): 435-454. AbstractWebsite

In this paper we address a wireless network design problem on a railway line. Given a finite set of locations along a railway line and different types of communication antennas that can be installed at each of these locations, which locations and which type of antenna should be selected to ensure a certain level of signal coverage along the railway line while minimizing construction costs? We formulate the problem as a 0/1 linear optimization model, prove that the problem is NP-hard, and report computational experiments using real and simulated data. The computational tests showed that the model is capable of solving the problem for railway lines longer than any existing real railway lines.

Doutor, P., R. Castelhano, M. C. Soares, B. V. Guerrero, N. Stollenwerk, M. Aguiar, and P. Patrício. "Complex Dynamics in an Epidemic Model with Imitation-Driven Vaccination Strategy." SIAM Journal on Applied Dynamical Systems. 24.4 (2025): 3045-3062.
Rotatori, Filippo Maria, Fernando Escaso, Bruno Camilo, Filippo Bertozzo, Elisabete Malafaia, Octávio Mateus, Pedro Mocho, Francisco Ortega, and Miguel Moreno-Azanza and. "Evidence of large-sized ankylopollexian dinosaurs (Ornithischia: Iguanodontia) in the Upper Jurassic of Portugal." Journal of Systematic Palaeontology. 23 (2025): 2470789. Abstractevidence_of_large-sized_ankylopollexian_dinosaurs__ornithischia__iguanodontia__in_the_upper_jurassic_of_portugal.pdfWebsite

The Upper Jurassic beds of the Lusitanian Basin in central Portugal yield diverse dinosaurian fauna, dated to the Kimmeridgian–Tithonian interval. Saurischian dinosaurs are, overall, more abundant than their ornithischian counterparts, in terms of both specimens collected and species recognized. Iguanodontians are so far represented by the styracosternan Draconyx loureiroi, the dryosaurid Eousdryosaurus nanohallucis and the enigmatic dryomorphan Hesperonyx martinhotomasorum. Here we aim to highlight the diversity of this clade in the Late Jurassic of Portugal, presenting evidence for yet another species of ankylopollexian iguanodontian dinosaur, represented by the specimen SHN.JJS.015, which is housed at the Sociedade de História Natural, Torres Vedras. Detailed comparisons rule out attribution to previously known taxa, and phylogenetic analyses that include SHN.JJS.015 indicate early-diverging ankylopollexian affinities for this specimen. As there is no robust diagnosis, we do not erect a new formal species for it at this stage. Nevertheless, this specimen represents a previously unreported taxon that highlights greater diversity than previously estimated among the iguanodontians of the Late Jurassic and highlights the importance of Europe in diversification and dispersal events of this clade. A series of smaller, isolated femora from the same sub-basin as SHN.JJS.015 may represent the same taxon, presenting evidence of thriving communities of ankylopollexians during the Kimmeridgian–Tithonian interval in Portugal.

Ayık, H., Vítor H. Fernandes, and E. Korkmaz. "On monoids of monotone partial transformations of a finite chain whose domains and ranges are intervals." Algebra and Discrete Mathematics (DOI 10.12958/adm2403). 40.1 (2025): 1-13. AbstractWebsite

In this note, we consider the monoid PIM_n of all partial monotone transformations on a chain with n elements whose domains and ranges are intervals and its submonoid IM_n constituted by the full transformations. For both of these monoids, our aim is to determine their cardinalities and ranks and define them by means of presentations. We also calculate the number of nilpotent elements of PIM_n.

Costa-Camilo, Eduardo, Fátima Cardoso, Isabel Duarte, Graça P. Carvalho, João M. G. C. F. de Almeida, Rita G. Sobral, and Carla Pinheiro. "Mediterranean Diet as a Nutraceutical and Sustainable Model for Health and Environmental Wellbeing." Gastronomy. 3 (2025): 17. AbstractWebsite
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