Publications by authors named "Vitor Sousa"

97 Publications

Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species.

Heredity (Edinb) 2021 Aug 30. Epub 2021 Aug 30.

cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.

Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers-Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis-using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.
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http://dx.doi.org/10.1038/s41437-021-00466-1DOI Listing
August 2021

Impact of Positive Surgical Margins After Partial Nephrectomy.

Eur Urol Open Sci 2020 Oct 2;21:41-46. Epub 2020 Oct 2.

Department of Urology and Renal Transplantation, Coimbra University Hospital Center, Coimbra, Portugal.

Background: The impact of positive surgical margins (PSMs) after partial nephrectomy (PN) is controversial.

Objective: To evaluate the risk factors for a PSM and its impact on overall survival.

Design Setting And Participants: This is a retrospective study of 388 patients were submitted to PN between November 2005 and December 2016 in a single centre. Two groups were created: PSM and negative surgical margin (NSM) after PN. A value of <0.05 was considered significant.

Outcome Measurements And Statistical Analysis: Relationships with outcome were assessed using univariable and multivariable tests and log-rank analysis.

Results And Limitations: The PSM rate was 3.8% ( = 16). The mean age at the time of surgery (PSM group: 64.1 ± 11.3 vs NSM group: 61.8 ± 12.8 yr,  =  0.5) and the mean radiological tumour size (4.0 ± 1.5 vs 3.4 ± 1.8 cm,  =  0.2) were similar. Lesion location ( =  0.3), surgical approach ( =  0.4), warm ischaemia time ( =  0.9), and surgery time ( =  0.06) had no association with PSM. However, higher surgeon experience was associated with a lower PSM incidence (2.6% if ≥30 PNs vs 9.6% if <30 PNs;  =  0.02). Higher operative blood loss ( =  0.02), higher-risk tumours ( =  0.03), and larger pathological size ( =  0.05) were associated with an increase in PSM. In the PSM group, recurrence rate (18.7% vs 4.2%,  =  0.007) and secondary total nephrectomy rate (25% vs 4.4%,  <  0.001) were higher. However, overall survival was similar. Multivariate analysis revealed that high-risk tumour ( =  0.05) and low experience ( =  0.03) could predict a PSM. Limitations include retrospective design and reduced follow-up time.

Conclusions: PSMs were mainly associated with high-risk pathological tumour ( =  0.05) and low-volume surgeon experience. Recurrence rate and need for total nephrectomy were higher in that group, but no impact on survival was noticed.

Patient Summary: The impact of positive surgical margins (PSMs) after partial nephrectomy is a matter of debate. In this study, we found that PSMs were mainly associated with aggressive disease and low surgeon experience.
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http://dx.doi.org/10.1016/j.euros.2020.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317835PMC
October 2020

Influence of Preoperative Pulp Inflammation in the Outcome of Full Pulpotomy Using a Dog Model.

J Endod 2021 Sep 3;47(9):1417-1426. Epub 2021 Jul 3.

Institute of Endodontics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Center for Innovation and Research in Oral Sciences, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.

Introduction: This study aimed to evaluate the impact of preoperative pulp inflammation on the histologic outcome of full pulpotomy performed in mature permanent posterior teeth using 4 different biomaterials.

Methods: Five beagle dogs (providing a total of 120 roots) were selected. Dentin exposure was performed in teeth from the second and third quadrants. One week later, full pulpotomy procedures were performed using 4 different bioactive materials (ProRoot MTA [MTA], TotalFill BC Putty [BC], Biodentine [BIO], and an experimental cement [ie, pulp capping material]). The hemostasis time was registered. After 14 weeks, the animals were killed. Pulp-dentin tissues were histologically and radiographically assessed. The significance level was set at .05.

Results: Teeth with previously exposed dentin revealed a statistically significant increase in the time required to achieve hemostasis (P < .001), therefore confirming the pulp inflammation status induced by 1-week exposure of occlusal dentin before performing full pulpotomy. There was no radiographic evidence of root resorption, periapical radiolucency, or lamina dura alterations. No statistically significant differences were observed between normal and inflamed pulp regardless of the evaluated histologic parameters. Moreover, histologic data concerning calcified barrier formation and the pulp tissue response show better results for BIO without statistical differences compared with MTA or BC (P > .05). The pulp capping material presented a lower performance, with statistically significant differences being detected in regard to the remaining 3 tested materials (P < .001).

Conclusions: Radiographic and histologic outcomes of full pulpotomy are not jeopardized by short-term preoperative pulp inflammation. Moreover, BIO, MTA, and BC cements present suitable alternatives to be used as pulp capping agents.
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http://dx.doi.org/10.1016/j.joen.2021.06.018DOI Listing
September 2021

fastsimcoal2: demographic inference under complex evolutionary scenarios.

Bioinformatics 2021 Jun 23. Epub 2021 Jun 23.

Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.

Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.

Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes.

Availability: fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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http://dx.doi.org/10.1093/bioinformatics/btab468DOI Listing
June 2021

Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin".

Nat Commun 2021 05 14;12(1):2807. Epub 2021 May 14.

Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1038/s41467-021-23096-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121787PMC
May 2021

The genomic history of the Aegean palatial civilizations.

Cell 2021 May 29;184(10):2565-2586.e21. Epub 2021 Apr 29.

Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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http://dx.doi.org/10.1016/j.cell.2021.03.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127963PMC
May 2021

Adaptation and convergence in circadian-related genes in Iberian freshwater fish.

BMC Ecol Evol 2021 03 8;21(1):38. Epub 2021 Mar 8.

cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.

Background: The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type.

Results: We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes.

Conclusions: Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.
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http://dx.doi.org/10.1186/s12862-021-01767-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7941933PMC
March 2021

Staphylococcus-induced glomerulonephritis: potential role for corticosteroids.

BMJ Case Rep 2021 Jan 27;14(1). Epub 2021 Jan 27.

Department of Nephrology, Centro Hospitalar e Universitario de Coimbra EPE, Coimbra, Portugal.

is a troublesome pathogen, responsible for a broad range of clinical manifestations, ranging from benign skin infections to life-threatening conditions such as endocarditis and osteomyelitis. The kidney can be affected through a rapidly progressive glomerulonephritis mediated by an inflammatory reaction against a superantigen deposited in the glomerulus during the infection's course. This glomerulopathy has a poor prognosis, often leading to chronically impaired kidney function, eventually progressing to end-stage renal disease. Treatment rests on antibiotherapy. Despite the inflammatory role in this disease's pathophysiology, most authors discourage a simultaneous immunosuppressive approach given the concomitant infection. However, there are some reports of success after administration of systemic corticosteroids in these patients. We present a 66-year-old man with a staphylococcus-induced glomerulonephritis brought on by a vascular graft infection, with rapidly deteriorating kidney function despite extraction of the infected graft and 3 weeks of antibiotherapy with achievement of infection control. Kidney function improved after the introduction of corticosteroids. This case highlights the potential role of corticosteroids in selected cases of staphylococcus-induced glomerulonephritis, particularly those in which the infection is under control.
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http://dx.doi.org/10.1136/bcr-2020-237011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843308PMC
January 2021

Subcutaneous Implantation Assessment of New Calcium-Silicate Based Sealer for Warm Obturation.

Biomedicines 2021 Jan 1;9(1). Epub 2021 Jan 1.

Coimbra Institute for Clinical and Biomedical Research (iCBR) and Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal.

Calcium silicate-based sealers were recently introduced as a new class of endodontic sealers, with potential further benefits due to their bioactivity. The aim of this study was to evaluate the biocompatibility of two new hydraulic calcium silicate-based sealers, TotalFill BC Sealer (FKG, La Chaux-des-Fonds, Switzerland) and TotalFill BC Sealer HiFlow (FKG, La Chaux-des-Fonds, Switzerland) through subcutaneous implantation in connective tissue of rats. Subcutaneous implantation was performed in 16 young Wistar rats. Four polyethylene tubes were implanted in each animal, one empty to serve as a control, and three filled with tested sealers: AH Plus as reference (Dentsply DeTrey, Konstanz, Germany), TotalFill BC Sealer (BC) and TotalFill BC Sealer HiFlow (HiFlow). Eight rats were euthanized at 8 days and the remaining eight at 30 days. Hematoxylin-eosin staining was used to score the inflammatory reaction, macrophage infiltrate and to measure the thickness of the fibrous capsule. von Kossa staining was performed to evaluate the mineralization level. Kruskal-Wallis test followed by Dunn's test was used to analyze non-parametric data. To analyze the influence of the implantation time within each material, a Mann-Whitney U test was performed. At eight days post-implantation, AH Plus induced a more intense inflammatory reaction when compared both with the control ( ≤ 0.001) and BC ( ≤ 0.01). HiFlow presented a higher score of macrophage infiltrate than control ( ≤ 0.01) and BC ( ≤ 0.05). The fibrous capsule thickness in this period was significantly higher for the BC group when compared to control ( ≤ 0.01) and AH Plus ( ≤ 0.05). The mineralization potential was higher for the HiFlow group when compared with the control ( ≤ 0.001) and AH Plus ( ≤ 0.001). At 30 days post-implantation, the score for the inflammatory reaction remained higher for the AH Plus group when compared both to control ( ≤ 0.01) and BC ( ≤ 0.001). The macrophage infiltrate of the HiFlow was significantly higher than control ( ≤ 0.001) and AH Plus groups ( ≤ 0.01), additionally, the fibrous capsule of the BC ( ≤ 0.001) and HiFlow ( ≤ 0.01) groups were both thicker than control. Mineralization potential was observed only on BC ( ≤ 0.05) and HiFlow groups ( ≤ 0.001), when compared to control). BC exhibited the best biocompatibility performance of all tested sealers and HiFlow provided the greatest induction of mineralized tissues. Both TotalFill BC Sealer and TotalFill BC Sealer HiFlow are biocompatible and show potential bioactivity when implanted in the subcutaneous tissue. Bioactivity was not found in AH Plus.
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http://dx.doi.org/10.3390/biomedicines9010024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824331PMC
January 2021

A structured methodology to understand municipal waste generation at local level with minimized effort: development and case study.

Environ Sci Pollut Res Int 2021 Mar 21;28(10):12597-12612. Epub 2020 Oct 21.

Research Centre for Natural Resources, Environment and Society (CERNAS), Instituto de Investigação Aplicada (IIA) - Instituto Politécnico de Coimbra (IPC), Coimbra, Portugal.

Understanding municipal solid waste (MSW) generation is a key requirement for designing and optimizing MSW collection services. The present contribution proposes a statistical methodology to identify MSW generation patterns from MSW collection records. The methodology aims at finding statistically distinct household waste generation patterns within the days of the week and within months (seasonal variation). It is based on standard statistical methods (ANOVA complemented by non-parametric tests and cluster analysis). The methodology was applied to a Portuguese neighbourhood to assist in the definition of a waste sampling campaign to support the implementation of a pilot PAYT. The results showed the existence of groups with statistically distinct MSW generation patterns both at the weekly and monthly time scales. Three clusters of days of the week, with high, medium and low generation, and two clusters of months, with high and low generation, were identified. These results allowed to design and implement a customized field waste sampling campaign to estimate the MSW generated at the study site with minimal field work. Instead of implementing a homogeneous sampling campaign (equal number of samples for every day of the week and for every month), the samples were collected from the days and months that showed statistically distinct MSW generation pattern. The systematic procedure can be easily adapted to any given location, thus being a useful tool that combines statistical analysis with field collected data.
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http://dx.doi.org/10.1007/s11356-020-11108-0DOI Listing
March 2021

Cutting Forces Assessment in CNC Machining Processes: A Critical Review.

Sensors (Basel) 2020 Aug 13;20(16). Epub 2020 Aug 13.

ISEP-School of Engineering, Polytechnic of Porto, R. Dr. Antº Bernardino de Almeida, 431, 4200-072 Porto, Portugal.

Machining processes remain an unavoidable technique in the production of high-precision parts. Tool behavior is of the utmost importance in machining productivity and costs. Tool performance can be assessed by the roughness left on the machined surfaces, as well as of the forces developed during the process. There are various techniques to determine these cutting forces, such as cutting force prediction or measurement, using dynamometers and other sensor systems. This technique has often been used by numerous researchers in this area. This paper aims to give a review of the different techniques and devices for measuring the forces developed for machining processes, allowing a quick perception of the advantages and limitations of each technique, through the literature research carried out, using recently published works.
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http://dx.doi.org/10.3390/s20164536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472627PMC
August 2020

Rapid host-plant adaptation in the herbivorous spider mite Tetranychus urticae occurs at low cost.

Curr Opin Insect Sci 2019 12 19;36:82-89. Epub 2019 Aug 19.

cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal. Electronic address:

The herbivorous spider mite Tetranychus urticae is a generalist world crop pest. Early evidence for host races, its fully sequenced genome resolved to the chromosome level, and the development of other molecular tools in this species suggest that this arthropod can be a good model to address host plant adaptation and early stages of speciation. Here, we evaluate this possibility by reviewing recent studies of host-plant adaptation in T. urticae. We find that evidence for costs of adaptation are relatively scarce and that studies involving molecular-genetics and genomics are mostly disconnected from those with phenotypic tests. Still, with the ongoing development of genetic and genomic tools for this species, T. urticae is becoming an attractive model to understand the molecular basis of host-plant adaptation.
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http://dx.doi.org/10.1016/j.cois.2019.08.006DOI Listing
December 2019

Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback.

Nat Commun 2019 09 18;10(1):4240. Epub 2019 Sep 18.

Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.

Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.
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http://dx.doi.org/10.1038/s41467-019-12182-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751218PMC
September 2019

Assessing water, energy and emissions reduction from water conservation measures in buildings: a methodological approach.

Environ Sci Pollut Res Int 2020 Feb 9;27(5):4612-4629. Epub 2019 Sep 9.

CERIS, DECivil, IST-Universidade de Lisboa, Campus Alameda, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.

Water-energy nexus is a cornerstone in modern societies, with significant impacts at social, environmental, and economic levels. In addition to the issue of water scarcity that several regions of the world already face or are forecasted to face in the near future due to demand increase and availability reduction (e.g. pollution, climate changes), water consumption in buildings entails substantial energy consumption. In most cases, part of this energy is produced from non-renewable sources, encompassing greenhouse gas emissions. The present research effort presents a generic methodology to assess the cascade impact of water efficiency measures in buildings in terms of water, energy and emissions reduction. The methodology is applied to the Mediterranean climate zone context for two different types of non-residential buildings: university buildings and hotels, with very distinct water end use and consumption patterns. Lastly, are performed sensitivity analyses between the proposed methodology and simplified approaches. Is observed that assuming a linear relationship between flow rate and water consumption can lead to overestimations of up to 64% in water savings. Is also explored the relevance of the water consumption and energy mix seasonality typical of climates with marked dry and wet seasons, such as the Mediterranean region. The importance of the seasonality is discussed in terms of the time scale considered to apply the methodology, revealing that adopting a simplified (annual) approach, instead of the proposed approach, can lead to relative differences between - 62 and 233% in the presented case studies.
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http://dx.doi.org/10.1007/s11356-019-06377-3DOI Listing
February 2020

Granulomatous interstitial nephritis: a rare diagnosis with an overlooked culprit.

BMJ Case Rep 2019 Aug 10;12(8). Epub 2019 Aug 10.

Nephrology Department, Centro Hospitalar e Universitário de Coimbra EPE, Coimbra, Portugal.

Granulomatous interstitial nephritis (GIN) is a rare entity identified in <1% of native kidney biopsies. The most frequent aetiology is drug-related, followed by systemic granulomatous conditions. Among drugs implicated in GIN, antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) are the most frequent. We report the case of a 45-year-old white man referred to a nephrology consult due to chronic kidney disease. He had a history of arterial hypertension with 10 years of evolution, hyperuricaemia, medicated with allopurinol and NSAID abuse for at least 20 years. Urine sediment was blunt, without proteinuria. Renal ultrasound was normal. A kidney biopsy revealed well-defined epithelioid granulomas with glomerular wrinkling and collapse. Infectious and systemic conditions were excluded, favouring the hypothesis of drug-induced GIN, probably related to NSAIDs. Kidney biopsy remains the gold standard for the diagnosis of GIN. Facing a patient with renal failure without significant proteinuria or active sediment, one should look for causes of tubulointerstitial injury.
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http://dx.doi.org/10.1136/bcr-2018-229159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700544PMC
August 2019

Parvoviral infection with systemic impact and renal consequences.

BMJ Case Rep 2019 Jun 8;12(6). Epub 2019 Jun 8.

Nephrology, Centro Hospitalar e Universitario de Coimbra EPE, Coimbra, Portugal.

Parvovirus infection is usually asymptomatic especially in immunocompetent adults. When symptomatic it can range from mild to life threatening depending on the patient's age and comorbidities. We report a case of a 40-year-old male patient with parvovirus infection who presented a purpuric rash in distal extremities, acute kidney injury, type II mixed cryoglobulinaemia and hypocomplementaemia. His renal biopsy showed a mesangioproliferative glomerulonephritis with positive immunoreactivity to C3, IgM and C1q. Parvovirus B19 was detected in the biopsy tissue by PCR. He was treated with prednisolone with total remission after 1 month. We discuss the diagnosis of kidney lesion due to parvovirus in an immunocompetent person, which is a very rare condition and its association with the cryoglobulinaemia diagnosis.
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http://dx.doi.org/10.1136/bcr-2019-229622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557350PMC
June 2019

The population history of northeastern Siberia since the Pleistocene.

Nature 2019 06 5;570(7760):182-188. Epub 2019 Jun 5.

Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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http://dx.doi.org/10.1038/s41586-019-1279-zDOI Listing
June 2019

Author Correction: Ancient admixture from an extinct ape lineage into bonobos.

Nat Ecol Evol 2019 Jun;3(6):988

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.

In the version of this article originally published, a funding acknowledgement was missing for Tomas Maques-Bonet. The original funding statement was: "T.M.-B. was supported by MINECO BFU2014-55090-P (FEDER), a U01 MH106874 grant, the Howard Hughes International Early Career programme, Obra Social 'La Caixa' and Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya." It has been updated to: "T.M.-B. was supported by BFU2017-86471-P (MINECO/FEDER, UE), a U01 MH106874 grant, the Howard Hughes International Early Career programme, Obra Social 'La Caixa' and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880)." The error has been corrected in the HTML and PDF versions of this article.
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http://dx.doi.org/10.1038/s41559-019-0919-xDOI Listing
June 2019

Ancient admixture from an extinct ape lineage into bonobos.

Nat Ecol Evol 2019 06 29;3(6):957-965. Epub 2019 Apr 29.

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.

Admixture is a recurrent phenomenon in humans and other great ape populations. Genetic information from extinct hominins allows us to study historical interactions with modern humans and discover adaptive functions of gene flow. Here, we investigate whole genomes from bonobo and chimpanzee populations for signatures of gene flow from unknown archaic populations, finding evidence for an ancient admixture event between bonobos and a divergent lineage. This result reveals a complex population history in our closest living relatives, probably several hundred thousand years ago. We reconstruct up to 4.8% of the genome of this 'ghost' ape, which represents genomic data of an extinct great ape population. Genes contained in archaic fragments might confer functional consequences for the immunity, behaviour and physiology of bonobos. Finally, comparing the landscapes of introgressed regions in humans and bonobos, we find that a recurrent depletion of introgression is rare, suggesting that genomic incompatibilities arose seldom in these lineages.
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http://dx.doi.org/10.1038/s41559-019-0881-7DOI Listing
June 2019

Are municipal waste utilities becoming sustainable? A framework to assess and communicate progress.

Environ Sci Pollut Res Int 2019 Dec 23;26(35):35305-35316. Epub 2019 Apr 23.

Research Centre for Natural Resources, Environment and Society (CERNAS) & Polytechnic Institute of Coimbra (IPC), 3045-601, Coimbra, Portugal.

A framework of indicators to assess the progress towards sustainability of municipal waste management utilities is developed. Its purpose is to fulfil the need for assessing the performance of municipal waste (MW) management in a simple but comprehensive way-unlike indicators based on individual aspects such as recycling-and including aspects not well considered before, such as waste prevention. The framework is composed of a set of six single indicators, concerning the three dimensions of sustainability: reduction of effectively landfilled MW and reduction of MW generation (environmental component), balance between expenses and revenues and reduction of costs (economic component), accessibility to separate collection and number of complaints (social component). Each indicator consists of an evaluation of the current status of the variable in contrast to a previous situation, with a positive value in case of improvement or negative in case of decline. Then, the values of the individual indicators are combined to obtain a global result. This approach focuses on dynamic progress towards sustainability, complementing the common static indicators. Contrarily to the existing performance indicator schemes, the proposed framework aims at measuring the progress and not the absolute or relative achievement of a waste management utility. The framework was tested on two Portuguese municipalities, proving to be a straightforward application and reliable in guiding stakeholders. Results for the case study showed good performance on economic sustainability, while environmental and social performance were lower due to a lack of strategies for waste prevention and low source separation, affected by poor accessibility to separate collection.
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http://dx.doi.org/10.1007/s11356-019-05102-4DOI Listing
December 2019

Genomic signatures of introgression between commercial and native bumblebees, , in western Iberian Peninsula-Implications for conservation and trade regulation.

Evol Appl 2019 Apr 11;12(4):679-691. Epub 2019 Jan 11.

Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências Universidade de Lisboa Lisboa Portugal.

Human-mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies and ), our aim was to assess their putative introgression with the native Iberian subspecies We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome-wide restriction-site-associated DNA markers (RAD-seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD-seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies , preferably with local production, should be evaluated.
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http://dx.doi.org/10.1111/eva.12732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6439495PMC
April 2019

A scale-adaptive method for urban rainwater harvesting simulation.

Environ Sci Pollut Res Int 2020 Feb 10;27(5):4557-4570. Epub 2019 Apr 10.

CERIS, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal.

At a building or dwelling scale, accurate evaluation of the water savings potential from rainwater harvesting (RWH) can be achieved by simulating the performance of the RWH system using a balance equations model. At an urban scale, water savings potential is usually estimated from the balance between the annual rainfall and annual water consumption. This approach has limited accuracy since it assumes an infinite storage capacity and it disregards the variability of the ratio between the water collected and water consumed in each building. This paper presents a methodology to evaluate rainwater harvesting potential at an urban level taking into consideration buildings' characteristics and consumption pattern. The complexity of the model is balanced with the format and detail of the information available to allow fast and easy implementation with few resources. The proposed methodology is applied to the city of Lisbon, Portugal, located on the Atlantic coast of the Mediterranean climate region. The results demonstrate water savings potential ranging from 16 to 86% depending on the buildings and occupancy characteristics. The spatial variability of the rainfall in the city of Lisbon was found to be negligible for rainwater harvesting potential evaluation.
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http://dx.doi.org/10.1007/s11356-019-04889-6DOI Listing
February 2020

Dataset of socio-economic and waste collection indicators for Portugal at municipal level.

Data Brief 2019 Feb 28;22:658-661. Epub 2018 Dec 28.

Research Centre for Natural Resources, Environment and Society (CERNAS), College of Agriculture (ESAC), Polytechnic Institute of Coimbra, Bencanta, 3045-601 Coimbra, Portugal.

This data article presents demographic, socio-economic and waste-related data at municipal level for Portugal. The dataset includes raw data collected from 4 main sources: (i) the annual reports of waste management companies; (ii) the database of the Portuguese water, sanitation and waste regulatory entity; (iii) the Portuguese Environmental Agency; and (iv) national statistical data. Relevant indicators for waste generation and for the separate collection of waste are proposed and calculated using the raw data. The dataset comprises municipalities with high, medium and low separate collection yields, providing socio-economic and waste infrastructures data that can be used for benchmarking. The dataset can also be used to define a baseline against which the progress of the collection of packaging waste can be assessed over time, or else serve as input to mathematical models predicting waste generation and collection. Moreover, data can serve as the base to calculate new waste-related indicators. In addition to being a valuable input to the waste topic, the dataset can also be used in a large range of other topics where demographic and socio-economic parameters are relevant. The data presented herein are associated with the research articles "Model for the separate collection of packaging waste in Portuguese low-performing recycling regions" [1] and "Artificial neural network modelling of the amount of separately-collected household packaging waste" [2].
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http://dx.doi.org/10.1016/j.dib.2018.12.069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327732PMC
February 2019

15 years of BMC Biology.

BMC Biol 2018 11 1;16(1):135. Epub 2018 Nov 1.

Springer Nature, New York, USA.

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http://dx.doi.org/10.1186/s12915-018-0602-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219252PMC
November 2018

Modeling driver cells in developing neuronal networks.

PLoS Comput Biol 2018 11 2;14(11):e1006551. Epub 2018 Nov 2.

CNR - Consiglio Nazionale delle Ricerche - Istituto dei Sistemi Complessi, Sesto Fiorentino, Italy.

Spontaneous emergence of synchronized population activity is a characteristic feature of developing brain circuits. Recent experiments in the developing neo-cortex showed the existence of driver cells able to impact the synchronization dynamics when single-handedly stimulated. We have developed a spiking network model capable to reproduce the experimental results, thus identifying two classes of driver cells: functional hubs and low functionally connected (LC) neurons. The functional hubs arranged in a clique orchestrated the synchronization build-up, while the LC drivers were lately or not at all recruited in the synchronization process. Notwithstanding, they were able to alter the network state when stimulated by modifying the temporal activation of the functional clique or even its composition. LC drivers can lead either to higher population synchrony or even to the arrest of population dynamics, upon stimulation. Noticeably, some LC driver can display both effects depending on the received stimulus. We show that in the model the presence of inhibitory neurons together with the assumption that younger cells are more excitable and less connected is crucial for the emergence of LC drivers. These results provide a further understanding of the structural-functional mechanisms underlying synchronized firings in developing circuits possibly related to the coordinated activity of cell assemblies in the adult brain.
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http://dx.doi.org/10.1371/journal.pcbi.1006551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235603PMC
November 2018

Phylogeny Estimation by Integration over Isolation with Migration Models.

Mol Biol Evol 2018 11;35(11):2805-2818

Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ.

Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
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http://dx.doi.org/10.1093/molbev/msy162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231491PMC
November 2018

Mixed extragonadal germ cell tumour of the prostate.

BMJ Case Rep 2018 Jul 10;2018. Epub 2018 Jul 10.

Department of Urology and Renal Transplantation, Centro Hospitalar e Universitario de Coimbra EPE, Coimbra, Portugal.

Extragonadal germ cell tumours (EGGCTs) originated in prostate are extremely rare, with <20 cases described in the literature. We report a case of a patient with a primary prostatic mixed EGGCT. A 47-year-old man presenting severe low urinary tract symptoms and signs of prostatic enlargement, with no malignancy suspicion, underwent transurethral resection of the prostate. The histopathological evaluation suggested the diagnosis of a retroperitoneal sarcoma. The patient underwent neoadjuvant chemotherapy and then was submitted to radical cystoprostatectomy. Histology revealed a mixed EGGCT of the prostate with yolk sac tumour and seminoma components. No testicular abnormalities were identified on the postoperative scrotal ultrasound. The patient went through four cycles of chemotherapy with bleomycin, etoposide and cisplatin. After 12 months of follow-up, the patient is alive and free of recurrence.
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http://dx.doi.org/10.1136/bcr-2017-223603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047698PMC
July 2018

Life-cycle cost as basis to optimize waste collection in space and time: A methodology for obtaining a detailed cost breakdown structure.

Waste Manag Res 2018 Sep 19;36(9):788-799. Epub 2018 May 19.

5 RISCO, Department of Civil Engineering, University of Aveiro, Portugal.

Extensive research has been carried out on waste collection costs mainly to differentiate costs of distinct waste streams and spatial optimization of waste collection services (e.g. routes, number, and location of waste facilities). However, waste collection managers also face the challenge of optimizing assets in time, for instance deciding when to replace and how to maintain, or which technological solution to adopt. These issues require a more detailed knowledge about the waste collection services' cost breakdown structure. The present research adjusts the methodology for buildings' life-cycle cost (LCC) analysis, detailed in the ISO 15686-5:2008, to the waste collection assets. The proposed methodology is then applied to the waste collection assets owned and operated by a real municipality in Portugal (Cascais Ambiente - EMAC). The goal is to highlight the potential of the LCC tool in providing a baseline for time optimization of the waste collection service and assets, namely assisting on decisions regarding equipment operation and replacement.
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http://dx.doi.org/10.1177/0734242X18774618DOI Listing
September 2018

Heterogeneity in Lung Cancer.

Pathobiology 2018 10;85(1-2):96-107. Epub 2018 Apr 10.

Institute of Anatomical and Molecular Pathology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.

Lung cancer diagnosis is a challenge since it is also one of the most frequently diagnosed cancers. Diagnostic challenges are deeply related to the development of personalized therapy and molecular and precise histological characterizations of lung cancer. When addressing these features, it is very important to acknowledge the issue of tumour heterogeneity, as it imposes several questions. First of all, lung cancer is a very heterogeneous disease, at a cellular and histological level. Cellular and histological heterogeneity are addressed with emphasis on the diagnosis, pre-neoplastic lesions, and cell origin, trying to contribute to a better knowledge of carcinogenesis. Molecular intra-tumour and inter-tumour heterogeneity are also addressed as temporal heterogeneity. Lung cancer heterogeneity has implications in pathogenesis understanding, diagnosis, selection of tissue for molecular diagnosis, as well as therapeutic decision. The understanding of tumour heterogeneity is crucial and we must be aware of the implications and future developments regarding this field.
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http://dx.doi.org/10.1159/000487440DOI Listing
October 2018
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