Things you need to know if you are writing a scientific paper, thesis or report in Engineering or Science

This paper focuses on the common mistakes made by students at the early stages of research when writing scientific papers, thesis and reports. It points out mistakes to be avoided and the basic rules that can be inferred by reading a few scientific documents but are not usually clearly written and that we, as professors, end up teaching over and over again. The outcome of this paper will be, hopefully, that we will not need to correct the same common mistakes again and you, as a student, will have a faster lane to publishing. Starting with the abstract: it is composed of a single paragraph, does not contain acronyms or references and describes in short the work, main highlights and points out the results or main conclusions obtained from the work being presented. The abstract is an independent part of the paper and commonly has a character or word limit that you need to respect. It can be read as a “stand-alone” and the paper starts in the introduction, meaning that the introduction is not the sequence of the abstract and it can have some text in common if needed.info:eu-repo/semantics/publishedVersio

Fish communities in the lower Tagus inland wetlands: from anthropogenic pressures to conservation management

Inland wetlands are important biodiversity hotspots and amongst the most impacted ecosystems worldwide. Conservation management and restauration actions in wetlands are thus urgently needed to reverse trends in species loss and habitat degradation, particularly in regions harbouring already endangered endemic species. Inland wetlands may play an important role in supporting endemic endangered fishes in the Lower Tagus basin, where anthropogenic pressures have been increasing, but there is a lack of studies on fish communities, and few areas are identified as inland wetlands. Here, we aim to identify small inland wetlands in the Lower Tagus River and their potential role in supporting fish species, constituting the first study to identify and evaluate the most important fish communities. Inland wetlands were identified through the usage of remote sensing techniques and the calculation of a Normalized Difference Water Index (NDWI) with Sentinel-2 imagery for the Lower Tagus region. From a total of 486 locations identified, 31 were recognized as wetlands as having potential to host fish communities, with 11 being selected for sampling after in loco assessment. Fish sampling was conducted between 6 May and 11 June 2021. Furthermore, for each wetland, we evaluated anthropogenic stressors and land use changes between 2007 and 2018, using national land use data (i.e., Carta de Uso e Ocupação do Solo). A total of 7727 fishes from eight non-native and five native species were captured. Overall, fish communities were dominated by non-native species (97% catches), but both European eel (Anguilla anguilla) and Lisbon arched-mouth nase (Iberochondrostoma olisiponense), which are globally classified as critically endangered (CR), were found in at least two wetlands. Our results suggest that, over the last 10 years, intensive agriculture decreased (on average ≈ 3%) in the areas surrounding these wetlands, being replaced by extensive agriculture or natural uses. Despite non-native fish prevalence, some wetlands may act as refuge habitats for CR fish species. These results are important for guiding the restoration of inland wetlands and promoting conservation management actions to help reverse fish diversity loss.info:eu-repo/semantics/publishedVersio

Biomarkers of Presbycusis and Tinnitus in a Portuguese Older Population

Introduction: Presbycusis or age-related hearing loss (ARHL) is a ubiquitous health problem. It is estimated that it will affect up to 1.5 billion people by 2025. In addition, tinnitus occurs in a large majority of cases with presbycusis. Glutamate metabotropic receptor 7 (GRM7) and N-acetyltransferase 2 (NAT2) are some of the genetic markers for presbycusis. Objectives: To explore patterns of hearing loss and the role of GRM7 and NAT2 as possible markers of presbycusis and tinnitus in a Portuguese population sample. Materials and Methods: Tonal and speech audiometry, tinnitus assessment, clinical interview, and DNA samples were obtained from patients aged from 55 to 75 with or without tinnitus. GRM7 analysis was performed by qPCR. Genotyping of single nucleotide polymorphisms (SNPs) in NAT2 was performed by PCR amplification followed by Sanger sequencing or by qPCR. Results: We screened samples from 78 individuals (33 men and 45 women). T allele at GRM7 gene was the most observed (60.3% T/T and 33.3% A/T). Individuals with a T/T genotype have a higher risk for ARHL and 33% lower risk for tinnitus, compared to individuals with A/A and A/T genotype, respectively. Being a slow acetylator (53%) was the most common NAT2 phenotype, more common in men (55.8%). Intermediate acetylator was the second most common phenotype (35.9%) also more frequent in men (82.6%). Noise exposed individuals and individuals with ‘high frequency’ hearing loss seem to have a higher risk for tinnitus. Our data suggests that allele AT of GRM7 can have a statistically significant influence toward the severity of tinnitus. Conclusion: For each increasing year of age the chance of HL increases by 9%. The risk for ARHL was not significantly associated with GRM7 neither NAT2. However, we cannot conclude from our data whether the presence of T allele at GRM7 increases the odds for ARHL or whether the A allele has a protective effect. Genotype A/T at GRM7 could potentially be considered a biomarker of tinnitus severity. This is the first study evaluating the effect of GRM7 and NAT2 gene in tinnitus

Historical food-web changes in invaded fish communities in the lower Guadiana basin

Freshwater ecosystems are increasingly being reshaped by biological invasions, leading to biotic homogenization and biodiversity loss. However, the extent to which novel species may drive changes in food-web structure over time remains poorly understood. Clarifying changes in historical ecological processes is critical to inform conservation and restoration efforts in recipient ecosystems. Here, we address food-web changes associated with fish invasions in the Lower Guadiana Basin (LGB) over the past 40 years, by contrasting feeding relationships between museum-archived and contemporary specimens, using stable carbon (δ13C) and nitrogen (δ15N) ratios. Specifically, trophic niches of museum-archived fishes sampled throughout 1978–1987 and 1999–2004 corresponding to the initial establishment and spread of non-native fishes, respectively, were compared with those of fishes sampled in 2019, characterizing the integration of non-native species in the recipient ecosystem. We focused on five native species (Anaecypris hispanica, Cobitis paludica, Iberochondrostoma lemmingii, Squalius pyrenaicus and Squalius alburnoides) and four non-native species (Lepomis gibbosus, Australo heros facetus, Micropterus salmoides and Gambusia holbrooki) with potential to cover multiple trophic positions in the food-webs. We approached historical baseline resources using prey items in gut con tents of the museum-archived fishes and characterized primary producers and macroinvertebrates in 2019. Prior to analysis, samples were normalized for high lipid content and corrected for preservation. We found considerable asymmetries in niche partitioning among species as invasion progressed. Over time, native species tended to be displaced to lower trophic levels, while non-native species showed significantly higher trophic niches, driven mainly by increases in trophic (δ15N) range. Our study highlights that stable isotopes may provide important insights on historical food-web structure and particularly on processes underpinning ecological changes associated with anthropogenetic pressures on freshwater ecosystems.info:eu-repo/semantics/publishedVersio

Audiological biomarkers of tinnitus in an older Portuguese population

Copyright © 2022 Haider, Ribeiro, Ribeiro, Trigueiros, Caria, Borrego, Pinto, Papoila, Hoare and Paço.Tinnitus is a phantom sound perceived in the absence of external acoustic stimulation. It is described in a variety of ways (e.g., buzzing, ringing, and roaring) and can be a single sound or a combination of different sounds. Our study evaluated associations between audiological parameters and the presence or severity of tinnitus, to improve tinnitus diagnosis, treatment, and prognosis. Our sample included 122 older participants (63 women and 59 men), aged 55-75 years from the Portuguese population, with or without sensory presbycusis and with or without tinnitus. All participants underwent a clinical evaluation through a structured interview, Ear, Nose, and Throat observation, and audiological evaluation (standard and extended audiometry, psychoacoustic tinnitus evaluation, auditory brainstem responses, and distortion product otoacoustic emissions). The Tinnitus Handicap Inventory was used to measure tinnitus symptom severity. Our data confirmed that the odds of developing tinnitus were significantly higher in the presence of noise exposure and hearing loss. Also, participants who had abrupt tinnitus onset and moderate or severe hyperacusis featured higher odds of at least moderate tinnitus. However, it was in the ABR that we obtained the most exciting and promising results, namely, in wave I, which was the common denominator in all findings. The increase in wave I amplitude is a protective factor to the odds of having tinnitus. Concerning the severity of tinnitus, the logistic regression model showed that for each unit of increase in the mean ratio V/I of ABR, the likelihood of having at least moderate tinnitus was 10% higher. Advancing knowledge concerning potential tinnitus audiological biomarkers can be crucial for the adequate diagnosis and treatment of tinnitus.publishersversionpublishe

Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins

This work focused on the biodegradation of three structurally related fluoroacetates (FAs), mono- (MFA), di- (DFA) and trifluoroacetate (TFA), using as microbial inocula samples collected from a site with a long history of industrial contamination and activated sludge obtained from a municipal wastewater treatment plant. Biodegradation experiments were carried out under different modes of substrate supplementation, which included (i) FAs fed as sole carbon sources; (ii) FAs (only for DFA and TFA) fed in co-metabolism with sodium acetate; and (iii) mixtures of MFA with DFA or TFA. Biodegradation of the target compounds was assessed through fluoride ion release. Defluorination was obtained in the cultures fed with MFA, while DFA and TFA were recalcitrant in all tested conditions. When present in mixture, DFA was shown to inhibit biodegradation of MFA, while TFA had no effect. A total of 13 bacterial isolates obtained from MFA degrading cultures were found to degrade 20mgL-1 of this compound, as single strains, when supplemented as a sole carbon source. Sequencing of the 16S rRNA gene indicated that among these degrading bacteria only Delftia acidovorans had been previously reported to be able to degrade MFA. This work shows that, despite their similar chemical structures, biodegradation of the three tested FAs is very distinct and draws attention to the unknown impacts that the accumulation of DFA and TFA may have in the environment as a result of their high recalcitrance.info:eu-repo/semantics/publishedVersio

Impact of Patellar Tendinopathy on Knee Proprioception

Objective: To determine whether high-level athletes with patellar tendinopathy have diminished knee proprioceptive acuity. Design: Cross-sectional study. Setting: University research laboratory (institutional). Participants: Twenty-one basketball and volleyball players with patellar tendinopathy (13 men and 8 women; mean age 24.5 6 3.6; body mass index = 22.5 6 2.0 kg/m2) and an equal number of athletes without symptoms of patellar tendinopathy injury were included in this study. Assessments: Participants underwent knee proprioception assessments on a single day. Furthermore, age, sex, height, weight, VISAP (Victorian Institute of Sport Assessment) questionnaire sports participation, medical history, knee injuries, previous treatment, and medication were obtained. Main Outcome Measures: Knee proprioception was evaluated by assessing sense of resistance, using a weight discrimination protocol, and joint position sense (JPS). Results: No significant differences were observed in JPS at 30 and 60 degrees of knee flexion between groups (P = 0.165 and 0.481, respectively). In regard to the ability to discriminate weight, significant differences between the 2 groups were found with the tendinopathy group showing a higher percentage of error (P = 0.009), namely when the set of incremental weights varied by 10% from the standard weight. Conclusions: Athletes with patellar tendinopathy have a diminished perception of force signals required for weight discrimination, whereas JPS remains unaffected in these athletes.info:eu-repo/semantics/publishedVersio

Tinnitus, hearing loss and inflammatory processes in an older Portuguese population

Objective: Tinnitus is associated with various conditions such as presbycusis, infectious, autoimmune and many other diseases. Our study aims to identify an association between inflammatory markers and the presence of tinnitus or hearing loss (HL).Design: Exploratory study including a structured interview, complete ENT observation, audiological and inflammatory markers evaluation.Study Sample: Sixty women and 54 men (55 to 75 years) from the Portuguese population, with or without sensory presbycusis and/or tinnitus.Results: IL10 levels were significantly lower in participants with tinnitus than in those without tinnitus. Moreover, TGF-β was lower in older participants (p = 0.034), IL1α was higher in participants with tonal tinnitus (p = 0.033), and IL2 was lower in participants who reported partial or complete residual inhibition (p = 0.019). Additionally, we observed a negative correlation between tinnitus duration and IL10 levels (r= −.281), and between HSP70 levels and tinnitus loudness (r= −.377). TNF-α and HSP70 levels appears to be sensitive to the time when samples were collected (morning or afternoon).Conclusions: The results of our study showing fluctuations in inflammatory markers along the hearing loss process, reinforce the idea that inflammatory mechanisms are involved in hearing loss pathogenesis but also in tinnitus. IL10 levels appear significantly altered in tinnitus but not in hearing loss

Actinobacteria from arctic and atlantic deep-sea sediments—biodiversity and bioactive potential

The deep-sea covers over 70% of the Earth’s surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.info:eu-repo/semantics/publishedVersio

Effects of Chlorella vulgaris as a feed ingredient on the quality and nutritional value of weaned piglets' meat

Chlorella vulgaris (CH) is usually considered a feed supplement in pig nutrition, and its use as an ingredient is poorly studied. Among many interesting characteristics, this microalga has high protein levels and can be a putative alternative for soybean meal. Our aim was to study the effect of a 5% CH incorporation in the diet, individually or combined with two carbohydrases, on meat quality traits and nutritional value. Forty-four post-weaned male piglets individually housed, with an initial live weight of 11.2 0.46 kg, were randomly distributed into four experimental groups: control (n = 11, without CH) and three groups fed with 5% CH incorporation, plain (n = 10), with 0.005% Rovabio® Excel AP (n = 10), and with 0.01% of a pre-selected four-CAZyme mixture (n = 11). After two weeks of trial, piglets were slaughtered and longissimus lumborum collected. CH had no effect on piglets’ growth performance. In turn, incorporation of CH improved the nutritional value of meat by increasing total carotenoids and n-3 PUFA content, thus contributing to a more positive n-6/n-3 fatty acid ratio. The supplementation with Rovabio® benefited tenderness and increased overall acceptability of pork. Our results show beyond doubt the viability of the utilization of this microalga as a feed ingredient for swine productioninfo:eu-repo/semantics/publishedVersio