Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterising filamentous fungal biofilm in drinking water distribution systems using microscopic and molecular techniques

Microbial quality of drinking water has been one of the greatest concerns of governmental and privative water suppliers. Water distribution systems are complex environments where algae, bacterial, fungi and protozoa cohabit. Many of these microorganisms are pathogenic to human and are associated with loss of water quality. Once within a water distribution system, microorganisms can attach to pipe surface and form biofilms. Biofilms are microbial communities wherein theirs constituents present differentiate features when compared with their planktonic form, e.g. increased resistance against adverse factors such as dryness, high temperatures, oligotrophic conditions and biocides. Fungi are known to habit diverse aquatic environments. Their presence in water systems is associated with pipe blockage, produce of metabolites involved in organoleptic changes such as odour and turbidity, and consequently are linked with loss of water quality. Moreover, because of their ability to adhere to surfaces, fungi are able to grown as biofilms on different surfaces, including pipe walls. The present work aimed to study filamentous fungal biofilms in water distribution systems. For this, epifluorescence microscopy and fluorescent in situ hybridization (FISH) were applied intending to detect, monitor and characterise filamentous fungal biofilms in real and laboratorial water systems. Specific fluorescent dyes and probes were used, i.e. Calcofluor White R2R, DAPI, FUN-1, EUK516 and FUN1429 probes. Microspheres Adhesion Assay, Cristal Violet staining and MTT assay were also applied. Moreover, a device was designed for sampling fungal biofilms in situ. As results, was observed that filamentous fungal biofilms have differentiated behaviour concerning resistance against disinfectant and levels of cell hydrophobicity when compared with their planktonic form. Filamentous fungal biofilms were detected in replaced pipes, sampler devices and laboratorial water system. Moreover, filamentous fungi recovered from water systems were capable to form biofilms with specific morphological and physiological features. In conclusion, filamentous fungi are able to form biofilms under diverse real and laboratorial conditions. Fungi are likely to play an important role in microbial interactions within water biofilms and consequently in microbial water quality. Thus, fungi may be included as a consistent member of biofilms in drinking water systems. The results reported in this work represent new concepts in mycological research, and further studies in the area may lead to new insights in fungal biology.
GUIDELINES FOR USING DOUBLE SAMPLING IN AVIAN POPULATION MONITORING

Abstract Double sampling involves combining information from inexpensive rapid counts with intensive complete counts to provide an efficient population estimate. This technique is a valuable approach for calibrating population indices based on incomplete counts and improving the precision of monitoring studies. Data collected through a double-sampling protocol can be analyzed with either a ratio or a regression estimator. The ratio estimator is recommended when the relationship of the actual count to the rapid count is a straight line through origin, which may not be valid when surveying populations that have a small number of individuals per site and a low detection probability. In such situations, the regression estimator may be more appropriate. I investigated the properties of these two different estimators through a simulation study and tabulated sample sizes to control bias of the population average and standard error. Further, I used the results to evaluate when double sampling is a cost-effective design and how to design surveys that meet precision requirements. The design process is illustrated with the Spring Eastern Waterfowl Survey, which shows that double sampling is not always appropriate. Directives pour l’utilisation de l’échantillonnage double dans le suivi des populations d’oiseaux
Homozygote loss-of-function variants in the human COCH gene underlie hearing loss

Since 1999, the COCH gene encoding cochlin, has been linked to the autosomal dominant non-syndromic hearing loss, DFNA9, with or without vestibular abnormalities. The hearing impairment associated with the variants affecting gene function has been attributed to a dominant-negative effect. Mutant cochlin was seen to accumulate intracellularly, with the formation of aggregates both inside and outside the cells, in contrast to the wild-type cochlin that is normally secreted. While additional recessive variants in the COCH gene (DFNB110) have recently been reported, the mechanism of the loss-of-function (LOF) effect of the COCH gene product remains unknown. In this study, we used COS7 cell lines to investigate the consequences of a novel homozygous frameshift variant on RNA transcription, and on cochlin translation. Our results indicate a LOF effect of the variant and a major decrease in cochlin translation. This data have a dramatic impact on the accuracy of genetic counseling for both heterozygote and homozygote carriers of LOF variants in COCH .
Predation risk breaks size-dependent dominance in juvenile coho salmon (Oncorhynchus kisutch) and provides growth opportunities for risk-prone individuals

Groups of coho salmon (Oncorhynchus kisutch) fry in stream tanks formed size-determined dominance hierarchies, which were upheld through aggressive interactions and led to smaller fish occupying inferior feeding positions. Under simulated predation risk, the frequency of agonistic interactions was reduced, but more intensive aggressive behaviours were performed. This allowed small fish to gain access to better feeding positions. The effect of the predation threat on coho behaviour seemed to extend across a riffle into a second pool that served as a refuge. Smaller fry that chose to be in the exposed pool had greater growth rates than those that mainly occupied the refuge, while large fry that exposed themselves to predation did not grow better than their risk-avoiding counterparts. Differences in risk taking and growth among small coho fry in this experiment may support reports for Atlantic salmon (Salmo salar) of a split into different life history trajectories. The observations suggest that the presence.
Blind Inpainting after Log Transformation using Total Variation

In this paper, we propose a method for blind image inpainting, in which the locations of the pixels which are missing or corrupted with impulse noise are not known. A logarithmic transformation is applied to convert the multiplication between the image and binary mask into an additive problem. The image and mask terms are then estimated iteratively with total variation regularization applied on the image, and ‘ 0 regularization on the mask term. The resulting alternating minimization scheme simultaneously estimates the image and mask, in the same iterative process. Experimental results show that the proposed method can deal with a larger fraction of missing pixels than two phase methods which ﬁrst estimate the mask and then reconstruct the image.
Reduction of Douglas-fir beetle infestation of high-risk stands by antiaggregation and aggregation pheromones

A combination of antiaggregation and aggregation pheromones was tested for protecting stands of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) at high risk for infestation by the Douglas-fir beetle (Dendroctonuspseudotsugae Hopkins). The antiaggregation pheromone, 3-methylcyclohex-2-en-1-one (MCH), was applied in a bubble capsule formulation to the perimeter of 1-ha circular plots at a rate of 60 g/plot. Treated plots also had three or four clusters of four Lindgren funnel traps baited with frontalin, seudenol, 1-methylcyclohex-2-en-1-ol, and ethanol located outside of the plot but within 160 m of the boundary. Mean (±SE) accumulated catches in all traps per plot were 73 658 ± 19 721 Douglas-fir beetles and 12 892 ± 2 513 Thanasimusundatulus (Say), a predator of the Douglas-fir beetle. The mean percentage of Douglas-fir trees ≥20 cm DBH that were mass attacked was reduced by 80% within the treated plots compared with the untreated plots. However, there was an eightfold increase in the percentage of tre.
Thermal bottlenecks in the life cycle define climate vulnerability of fish

Some cope better than others Increasingly, research is revealing how organisms may, or may not, adapt to a changing climate. Understanding the limitations placed by a species's physiology can help to determine whether it has an immediate potential to deal with rapid change. Many studies have looked at physiological tolerance to climate change in fishes, with results indicating a range of responses. Dahlke et al. conducted a meta-analysis to explore how life stage may influence a species's ability to tolerate temperature change (see the Perspective by Sunday). They found that embryos and breeding adult fishes are much more susceptible to temperature change than those in other life stages and that this factor must therefore be considered in evaluations of susceptibility. Science, this issue p. 65; see also p. 35 Thermal tolerance metrics for 694 marine and freshwater fish species reveal that breeding stages are most vulnerable to climate warming. Species’ vulnerability to climate change depends on the most temperature-sensitive life stages, but for major animal groups such as fish, life cycle bottlenecks are often not clearly defined. We used observational, experimental, and phylogenetic data to assess stage-specific thermal tolerance metrics for 694 marine and freshwater fish species from all climate zones. Our analysis shows that spawning adults and embryos consistently have narrower tolerance ranges than larvae and nonreproductive adults and are most vulnerable to climate warming. The sequence of stage-specific thermal tolerance corresponds with the oxygen-limitation hypothesis, suggesting a mechanistic link between ontogenetic changes in cardiorespiratory (aerobic) capacity and tolerance to temperature extremes. A logarithmic inverse correlation between the temperature dependence of physiological rates (development and oxygen consumption) and thermal tolerance range is proposed to reflect a fundamental, energetic trade-off in thermal adaptation. Scenario-based climate projections considering the most critical life stages (spawners and embryos) clearly identify the temperature requirements for reproduction as a critical bottleneck in the life cycle of fish. By 2100, depending on the Shared Socioeconomic Pathway (SSP) scenario followed, the percentages of species potentially affected by water temperatures exceeding their tolerance limit for reproduction range from ~10% (SSP 1–1.9) to ~60% (SSP 5–8.5). Efforts to meet ambitious climate targets (SSP 1–1.9) could therefore benefit many fish species and people who depend on healthy fish stocks.
Teacher Education Professor Jeannie Herbert School of Indigenous Australian Studies

Without quality teacher training, both pre-service and in-service, teachers will not be adequately prepared to teach Indigenous learners within diverse settings. The failure to provide teachers with the understanding, skills and confidence to teach across cultures results in teachers struggling to adopt culturally inclusive, appropriate and effective approaches to teaching, In addition, teachers need ongoing support, leadership and professional development if they are to adopt productive pedagogy and effective teaching and learning strategies and ultimately achieve equitable and appropriate learning outcomes for all students. This research project examined current programs in teacher education and ongoing professional development in Queensland. All eight Queensland universities and twenty three schools across State, Catholic and Independent schools were included in the study. This paper will present the results of this research project. _________________________________________________________________________ __
Système rénine-angiotensine et remodelage vasculaire

Le systeme renine-angiotensine, l’un des principaux complexes de regulation de la pression sanguine, est distribue entre le sang circulant et l’espace pericellulaire de l’interstium tissulaire. Il participe en physiologie et en pathologie de la regulation de la vasomotricite et du remodelage tissulaire dans le systeme cardiovasculaire. Dans le cadre de ces effets, le systeme renine-angiotensine tissulaire agit sur les cellules musculaires lisses vasculaires et les fibroblastes, tandis que le systeme renine-angiotensine plasmatique a pour cibles les cellules endotheliales et les leucocytes circulants. L’angiotensine II, peptide actif du systeme, declenche differentes voies de signalisation aboutissant a une reponse fonctionnelle immediate (hypertension arterielle), puis a une reponse structurale hypertrophiante et, enfin, a des reponses pro-inflammatoires et procoagulantes. Dans des modeles experimentaux d’atherosclerose, la perfusion d’angiotensine II induit la formation d’anevrismes, qui a ete reliee a l’activation des leucocytes circulants. Des antagonistes de l’angiotensine II ont, dans ce type de modele, un effet benefique sur le ralentissement de la formation des lesions d’atherosclerose.
Deciphering New Players in the Neurogenic Adult Hippocampal Niche

In the mammalian adult hippocampus, new neurons are continuously generated throughout life in the subgranular zone of the dentate gyrus. Increasing evidence point out the contribution of adult-born hippocampal granule cells (GCs) to cognitive processes such as learning and memory, indicating the relevance of understanding the molecular mechanisms that control the development of these new neurons in the preexisting hippocampal circuits. Cell proliferation and functional integration of adult-born GCs is a process highly regulated by different intrinsic and extrinsic factors. In this review, we discuss recent advances related with cellular components and extrinsic signals of the hippocampal neurogenic niche that support and modulate neurogenesis under physiological conditions.
Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes

Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
Perspective: Pragmatic Exercise Recommendations for Older Adults: The Case for Emphasizing Resistance Training

Optimal health benefits from exercise are achieved by meeting both aerobic and muscle strengthening guidelines, however, most older adults (OAs) do not exercise and the majority of those who do only perform one type of exercise. A pragmatic solution to this problem may be emphasizing a single exercise strategy that maximizes health benefits. The loss of muscle mass and strength at an accelerated rate are hallmarks of aging that, without intervention, eventually lead to physical disability and loss of independence. Additionally, OAs are at risk of developing several chronic diseases. As such, participating in activities that can maintain or increase muscle mass and strength, as well as decrease chronic disease risk, is essential for healthy aging. Unfortunately, there is a widely held belief that adaptations to aerobic and resistance exercise are independent of each other, requiring the participation of both types of exercise to achieve optimal health. However, we argue that this assertion is incorrect, and we discuss crossover adaptations of both aerobic and resistance exercise. Aerobic exercise can increase muscle mass and strength, though not consistently and may be limited to exercise that overloads a particular muscle group, such as stationary bicycling. In contrast, resistance exercise is effective at maintaining muscle health with increasing age, and also has significant effects on cardiovascular disease (CVD) risk factors, type 2 diabetes (T2D), cancer, and mortality. We posit that resistance exercise is the most effective standalone exercise strategy for improving overall health in OAs and should be emphasized in future guidelines.
Borealization of the Arctic Ocean in Response to Anomalous Advection From Sub-Arctic Seas

An important yet still not well documented aspect of recent changes in the Arctic Ocean is associated with the advection of anomalous sub-Arctic Atlantic- and Pacific-origin waters and biota into the polar basins, a process which we refer to as borealization. Using a 37-year archive of observations (1981–2017) we demonstrate dramatically contrasting regional responses to atlantification (that part of borealization related to progression of anomalies from the Atlantic sector of sub-Arctic seas into the Arctic Ocean) and pacification (the counterpart of atlantification associated with influx of anomalous Pacific waters). Particularly, we show strong salinification of the upper Eurasian Basin since 2000, with attendant reductions in stratification, and potentially altered nutrient fluxes and primary production. These changes are closely related to upstream conditions. In contrast, pacification is strongly manifested in the Amerasian Basin by the anomalous influx of Pacific waters, creating conditions favorable for increased heat and freshwater content in the Beaufort Gyre halocline and expansion of Pacific species into the Arctic interior. Here, changes in the upper (overlying) layers are driven by local Arctic atmospheric processes resulting in stronger wind/ice/ocean coupling, increased convergence within the Beaufort Gyre, a thickening of the fresh surface layer, and a deepening of the nutricline and deep chlorophyll maximum. Thus, a divergent (Eurasian Basin) gyre responds altogether differently than does a convergent (Amerasian Basin) gyre to climate forcing. Available geochemical data indicate a general decrease in nutrient concentrations Arctic-wide, except in the northern portions of the Makarov and Amundsen Basins and northern Chukchi Sea and Canada Basin. Thus, changes in the circulation pathways of specific water masses, as well as the utilization of nutrients in upstream regions, may control the availability of nutrients in the Arctic Ocean. Model-based evaluation of the trajectory of the Arctic climate system into the future suggests that Arctic borealization will continue under scenarios of global warming. Results from this synthesis further our understanding of the Arctic Ocean’s complex and sometimes non-intuitive Arctic response to climate forcing by identifying new feedbacks in the atmosphere-ice-ocean system in which borealization plays a key role.
Association Between Heart Rate Variability and Decompression-Induced Physiological Stress

The purpose of this study was to analyze the correlation between decompression-related physiological stress markers, given by inflammatory processes and immune system activation and changes in Heart Rate Variability, evaluating whether Heart Rate Variability can be used to estimate the physiological stress caused by the exposure to hyperbaric environments and subsequent decompression. A total of 28 volunteers participated in the experimental protocol. Electrocardiograms were performed; blood samples were obtained for the quantification of red cells, hemoglobin, hematocrit, neutrophils, lymphocytes, platelets, aspartate transaminase (AST), alanine aminotransferase (ALT), and for immunophenotyping and microparticles (MP) research through Flow Cytometry, before and after each experimental protocol from each volunteer. Also, myeloperoxidase (MPO) expression and microparticles (MPs) deriving from platelets, neutrophils and endothelial cells were quantified. Negative associations between the standard deviation of normal-to-normal intervals (SDNN) in the time domain, the High Frequency in the frequency domain and the total number of circulating microparticles was observed (p-value = 0.03 and p-value = 0.02, respectively). The pre and post exposure ratio of variation in the number of circulating microparticles was negatively correlated with SDNN (p-value = 0.01). Additionally, a model based on the utilization of Radial Basis Function Neural Networks (RBF-NN) was created and was able to predict the SDNN ratio of variation based on the variation of specific inflammatory markers (RMSE = 0.06).
Total arsenic accumulation in yabbies (Cherax destructor clark) exposed to elevated arsenic levels in victorian gold mining areas, Australia

Arsenic is a proven carcinogen often found at high concentrations in association with gold and other heavy metals. The freshwater yabby, Cherax destructor Clark (Decapoda, Parastacidae), is a ubiquitous species native to Australia's central and eastern regions, with a growing international commercial market. However, in this region of Australia, yabby farmers often harvest organisms from old mine tailings dams with elevated environmental arsenic levels. Yabbies exposed to elevated environmental arsenic were found to accumulate and store as much as 100 μg/g arsenic in their tissues. The accumulation is proportional to the concentration of arsenic in the sediment and is high enough to be of concern for people who eat the yabbies. A comparison of arsenic levels in wild and lab‐fed animals also was performed. Although there was no significant difference in the level of arsenic in the various organs of the wild animals, the animals purchased from a yabby farm showed a significantly higher arsenic concentration in their hepatopancreas (3.7 ± 0.9 μg/g) compared to other organs (0.6–1.8 μg/g). Furthermore, after a 40‐d exposure to food containing 200 to 300 μg/g inorganic arsenic, arsenate (As[V])‐exposed animals showed a significant increase in tissue‐specific arsenic accumulation, whereas arsenite (As[III])‐exposed animals showed a lower, nonsignificant increase in As uptake, primarily in the hepatopancreas. These results have important implications for yabby growers and consumers alike.