Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect

In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation (“nutrient-growth dysregulation”) can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine auxotrophic mutant lys- encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A sub-population repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). Organosulfurs, mainly glutathione and glutathione conjugates, were released by lys- cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys-orgS- by eliciting a proper slow growth program including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.
Integration of Cool-Season Annual Legumes and Dairy Manure Compost with Switchgrass

Annual cool-season legumes can contribute forage or green manure to warm-season grass pastures or biofuel crops but may interfere with subsequent grass development. Arrowleaf clover (Trifolium vesiculosum Savi cv. Yuchi), common vetch (Vicia sativa L.), and button medic [Medicago orbicularis (L.) Bartal cv. Estes] were oversown on 10-yr-old switchgrass (Panicum vfrgatum L.) in north-central Texas to evaluate dry matter (DM) yield and nutritive value. Legumes were no-till drilled into a Windthorst fine sandy loam in autumn of 2000 and 2001; plots either received no dairy manure compost or 30 Mg compost ha -1 . Forage was harvested when individual legume species reached flowering, when switchgrass regrowth reached boot stage, and at the end of the summer growing season. Switchgrass DM yields (3022-6630 kg ha -1 yr1) were not reduced by overseeded legumes. Arrowleaf clover had the greatest production among the legume species and yielded more in a monoculture (1762-1923 kg ha -1 yr1) than with switchgrass (757-814 kg). Cumulative yields increased the second year as a result of legumes, compost, and combinations of the two. Compost increased phosphorus concentrations in both the grass and legumes, but not crude protein or acid detergent fiber concentrations. Cool-season annual legumes may be beneficial in switchgrass forage and biofuel systems, especially in combination with manure compost.
Diversity and gene expression patterns of functional groups in sidestream and mainstream wastewater partial-nitritation anammox biofilms

Partial nitritation-anammox (PNA) is today used for nitrogen removal from highly concentrated wastewater after anaerobic sludge digestion (sidestream). However, implementation of PNA for treatment of municipal wastewater (mainstream), with its lower ammonium concentration and lower temperature is challenging, which might be due to differences in microbial community composition and/or activity. To investigate this, we compared side-by-side sidestream and mainstream PNA biofilms using amplicon sequencing of 16S rDNA and rRNA, hzsB DNA and mRNA, and the genes nxrB, and amoA. The two communities were different to each other with relatively more heterotrophic denitrifying bacteria and less anammox bacteria in the mainstream. With hzsB and nxrB we found microdiversity among Brocadia and Nitrospira, and turnover (taxa replacement) between sidestream and mainstream. However, in both environments Brocadia sapporoensis represented most of the hzsB DNA and mRNA reads, despite the different environmental conditions and nitrogen removal rates. All of those populations present in both sidestream and mainstream had no differences in their 16S rRNA:rDNA ratios, supporting recent findings that rRNA:rDNA ratios are poor indicators of bacterial activity. The observed diversity within functional groups and composition differences between sidestream and mainstream add complexity to our view of PNA communities with possible implication for reactor function.
Short-term relative invader growth rate predicts long-term equilibrium proportion in a stable, coexisting microbial community

The ability of species to mutually invade from rare is the defining measure of species coexistence. However, it is unknown whether invasion growth rates predict any characteristic of long-term community dynamics. Here, we use a model five-species microbial community to investigate the link between short-term growth rate and long-term relative abundance. We manipulated diversity and tested the ability of species to coexist in different combinations. Across all diversity levels and species combinations, populations re-established from rare in 71 of 75 combinations and all combinations were stable in long-term culture. Moreover, short-term relative invader growth rate was positively associated with long-term equilibrium proportion, despite large variation in interactions between species and communities. This finding was confirmed using a modelling approach and suggests that the short-term invasion growth rate can predict long-term relative abundance within that community.
TIME OF CONCENTRATION IN AN EXPERIMENTAL BASIN: METHODS FOR ANALYSIS, BACKWATER EFFECTS AND VEGETATION REMOVAL

There are several empirical and theoretical formulas used for the estimation of the time of concentration (Tc). However, it has been shown that the Tc estimation may vary in several orders of magnitude depending on the method. In this study we compare 10 different methods for the estimation of the Tc using sub-basins and backwater effects to analyze those results. We also analyzed if the vegetation removal changes the Tc in the basin. The study area is the basin of the Federal University of Santa Catarina (UFSC) campus in Joinville with a significant part in a wetland and there is backwater effect caused by the Piraí river. Applying the empirical and theoretical equations found a significant variation of Tc estimates, the standard deviation in relation to the general average was around 65%. The influence of vegetation removal and drainage of a canal had an effect of reducing the Tc by 50%.
Geographic and subsequent biotic isolations led to a diversity anomaly of Heterotropa (Aristolochiaceae) in insular versus continental regions of the Sino-Japanese Floristic Region

The Sino-Japanese Floristic Region is highly diverse with respect to temperate plants. However, the reasons for this diversity are poorly understood because most studies have only considered geographic isolation caused by climatic oscillations. Heterotropa (genus Asarum; Aristolochiaceae) diverges here and shows high species diversity in insular systems (63 species) compared to continental areas (25 species). Heterotropa shows low dispersal ability with small distribution ranges, implying diversification by geographic events, and high floral diversity, implying pollinator-mediated diversification. To reveal how abiotic and biotic factors have shaped the diversity anomaly of Heterotropa, we conducted phylogenetic analysis using ddRAD-seq and chloroplast genome datasets including 79 species, estimation of floral trait evolution, and comparison of isolation factors within clades based on distribution range and floral trait analysis. Phylogenetic analysis indicates that Heterotropa originated in mainland China and expanded to the Japanese Archipelago in the Miocene, and the major clades almost correspond to geographic distributions. Floral traits evolved repeatedly in the tip nodes within the clades. Although the major clades include a high proportion of species pairs showing isolation by floral traits, there are no conditional relationships between two isolation factors, indicating that most species pairs with floral trait isolation are distributed allopatrically. The repeated exposure and submergence of land-bridges caused by climatic oscillations would have led to significant population fragmentation in insular systems. Thus, the diversity anomaly of Heterotropa would have resulted from geographic and climatic events during the Miocene, while subsequent repeated floral trait evolution would have followed geographic isolation during the Pleistocene.
Integrative Omics for Informed Drug Repurposing: Targeting CNS Disorders

The treatment of CNS disorders, and in particular psychiatric illnesses, lacks disease-altering therapeutics for many conditions. This is likely due to regulatory challenges involving the high cost and slow-pace of drug development for CNS disorders as well as due to limited understanding of disease causality. Repurposing drugs for new indications have lower cost and shorter development timeline compared to that of de novo drug development. Historically, empirical drug-repurposing is a standard practice in psychiatry; however, recent advances in characterizing molecules with their structural and transcriptomic signatures along with ensemble of data analysis approaches, provides informed and cost-effective repurposing strategies that ameliorate the regulatory challenges. In addition, the potential to incorporate ontological approaches along with signature-based repurposing techniques addresses the various knowledge-based challenges associated with CNS drug development. In this review we primarily discuss signature-based in silico approaches to drug repurposing, and its integration with data science platforms for evidence-based drug repurposing. We contrast various in silico and empirical approaches and discuss possible avenues to improve the clinical relevance. These concepts provide a promising new translational avenue for developing new therapies for difficult to treat disorders, and offer the possibility of connecting drug discovery platforms and big data analytics with personalized disease signatures.
Fine scale patterning of species distributions in a saxicolous lichen community at Jonas Rockslide, Canadian Rocky Mountains

Distinct patterns of species distribution upon individual rockfaces are found n a saxicolous lichen community growing on a rockslide in the Canadian Rockies. A grid system was used for sampling individual rockfaces and the likelihood of finding a species on particular parts of the rockface was analysed. Use of chemicals in the field and collection of apothecia allowed specific identification of individual lichen thalli. Lichens were divisible into three groups: those which are distributed apparently at random over the rockfaces, those which are more likely to occur on upper, outer and southerly portions of the rockfaces and those which are found more often on lower, inner and northerly portions of the rockfaces. The upper rockface surfaces are often snow-free in winter while the lower rockface group experiences deeper and more persistent snow cover. Simple microclimatic measurements suggest that temperature also differs across the surface of a rockface. It is hypothesised that lichen distributions are at least in part explained by ecophysiological adaptations to their particular microhabitat, while it is recognised that competition may also play a role in community organisation.
Influence of Dominant Follicle and Corpus luteum on Recovery of Good Quality Oocytes for In vitro Embryo Production in Cattle

The quality of oocytes is more critical for the success of bovine in vitro embryo production (IVP) than the conditions of in vitro culture of these structures. Despite knowledge about bovine follicular development, especially gonadotropin-dependent phase, be considerably wide, knowledge about effects of the estrous cycle phase, follicular or luteal, on recovery Mini -review Article
Sperm whale abundance estimates from acoustic surveys of the Ionian Sea and Straits of Sicily in 2003

Acoustic surveys for sperm whales, using line-transect methodology, were carried out in the Ionian Sea and Straits of Sicily, Mediterranean Sea, in 2003. A total of 17 whales were detected along 3846 km of designed survey track in the Ionian Sea, and no whales along 892 km in the Straits of Sicily. This total was insufficient to estimate a detection function, so further data were obtained from quasi-random passages made elsewhere in the western Mediterranean in the same year. The encounters included several tight aggregations with inter-animal spacing less than 1 km, primarily from the western Mediterranean. Including individuals from these aggregations distorted the detection function due to the small sample sizes. No such aggregations were found during formal survey of the two areas of interest, and the aggregations were therefore excluded from detection function estimation. The resultant effective strip half-width was 10.0 km (n=40). On the assumption that g(0)=1, the resulting abundance estimates for the Ionian Sea were 62 (with 95% lognormal confidence limits of [24,165]), and 0 for the Straits of Sicily. The low abundance estimate for the Ionian Sea indicates that careful monitoring of the population is needed in the future. During passages along the Hellenic Trench, that were not part of the designed survey, several sperm whales including two aggregations were detected, suggesting that this may be a higher density area and ought to be considered as a separate stratum when designing future surveys.
Influences of Thinning, Chipping, and Fire on Understory Vegetation in a Sierran Mixed Conifer Stand

Thinning implemented with a cut-to-length harvesting system coupled with on-site slash chipping and redistribution and followed by prescribed underburning were assessed for their impacts on a shrub understory in an uneven-aged Sierra Nevada mixed conifer stand. Overstory species consisted of California white fir (Abies concolor var. lowiana [Gord.] Lemm.), Jeffrey pine (Pinus jeffreyi Grev. & Balf.), sugar pine (Pinus lambertiana Dougl.), incense-cedar (Libocedrus decurrens Torr.), and red fir (Abies magnifica A. Murr.), while huckleberry oak (Quercus vacciniifolia Kellogg) was predominant among 10 understory shrubs. Herbaceous species were entirely absent from the site for the 4-yr duration of the study. The mechanized treatments exerted minimal detriment effects on overall understory cover and weight, and for prostrate ceanothus (Ceanothus prostratus Benth.) and creeping snowberry (Symphoricarpos mollis Nutt.)—two of the lesser shrubs—were stimulatory. In contrast, losses to the total understory from the underburn amounted to two-thirds of cover and weight in the absence of the mechanized treatments and more than three-quarters where they had been implemented, with huckleberry oak prevalence especially diminished. For almost all of the understory species individually as well as for the total, greater pretreatment abundance predisposed greater posttreatment prevalence. Results of this study provide insight into the understory impacts of restoration treatments that are deemed especially appropriate for sensitive sites in western U.S. forests.
Does seasonal reproduction occur at the optimal time for fertilization in the polychaetes Arenicola marina L. and Nereis virens Sars?

Summary Many marine invertebrates exhibit highly seasonal and synchronised reproduction, with offspring production often being confined to just two or three days each year. Several models have been proposed to explain the fitness benefits of this reproductive pattern, many of which assume enhanced offspring survival due to temperature constraints placed on fertilization and development at other times of the year. In this investigation the temperature limits and optimum for fertilization were determined for two polychaete species, Arenicola marina and Nereis virens. These two polychaete species are exposed to the same environmental conditions throughout the year, yet breed at very different times. Other seasonal impacts on fertilization, i.e., reduced salinity due to rainfall and the effect of sub-zero temperatures on sperm of A. marina, were also investigated. In both A. marina and N. virens fertilization success was significantly influenced by temperature, with the maximum success recorded at 15–18°C. The ambient seawater temperature at the time of natural spawning for both worms is around 10°C, which means that both species are spawning right at the lower limit for maximum fertilization. Salinity and exposure of A. marina sperm to sub-zero temperatures were also found to influence fertilization success, but only at levels that would not be experienced by these polychaetes under natural conditions at the time of spawning. These results suggest there must be additional selective pressures acting on the fitness of these two polychaetes causing A. marina to breed later than, and N. virens to breed earlier than, the optimum time for fertilization. A. marina apparently waits as late as possible to maximise adult fecundity and survival. N. virens breeds as soon as it can achieve high fertilization to maximise larval and juvenile competitiveness.
Comparative In Vitro Assessment of Hydrocarbon Degradation Potential of Pleurotus ostreatus MP 5 and Pleurotus ostreatus MTCC 1804

Mycoremediation, involving the use of fungus for bioremediation, is one of the promising cost-effective methods for cleaning up the carcinogenic and mutagenic polycyclic aromatic hydrocarbons present in the environment. The present study deals with the isolation of white rot fungus from Chhattisgarh forest, India followed by identification based on ITS sequencing. Identification revealed MP 5 closely related to Pleurotus ostreatus isolate 6689 with 99% sequence similarity. Comparative primary screening assay of both the wild isolate and reference strain of Pleurotus ostreatus MTCC 1804 was performed by measuring the growth diameter of mycelia on minimal salt media enriched with 2% used engine oil (v/v). The fungal isolate MP 5 showed highest average growth rate. Confirmatory test was conducted via orbital shaking method and spectroscopic study was carried out at 600 nm which displayed degradation within 7 days and percentage of degradation was calculated. Level of degradation was 69.7 ± 0.351% and 64.7 ± 1.153% respectively for Pleurotus ostreatus MP 5 and Pleurotus ostreatus MTCC 1804. Degradation potential of both the isolates were evaluated in terms of chemical characterization via Fourier transform infrared spectroscopy (FTIR) which revealed bands formation based on the presence of different functional groups indicating oxidative degradation of hydrocarbons.
Extrapolating feedback processes from the present to the past

Extant terrestrial vegetation alters its physical environment via its albedo, and its influence on immediate temperature via stomatal and boundary–layer influences of energy dissipation as sensible and latent heat; aquatic vegetation also controls albedo (e.g. coccolithophorids) and, by competing with water for electromagnetic energy absorption, the depth of the mixed layer and hence the quantity of nutrients trapped for the spring bloom. Both aquatic and terrestrial vegetation have had, together with microbial and geological processes, an influence on O2 and CO2 levels, and hence on the availability and biological functioning of Fe, Mn, Cu, Zn, Se and P, and the relative competitive advantage of C3 versus C4, crassulacean acid metabolism (CAM) and carbon concentration mechanism (CCM) organisms. Less directly, changes in primary productivity impact on the production of CH4 and N2O which, like CO2, are greenhouse gases, while some (marine) primary producers yield dimethyl sulphide (and hence cloud condensation nuclei, with effects on cloudiness) and halocarbons (via, in part, O2–dependent processes), partly negating the O3 attenuation of UV–B radiation. These effects can be related to the terrestrial embryophytic vegetation back to ca. 450 Ma, and to eukaryotic marine vegetation back to at least 1.7, and probably 2.1 Ga, with implications for inter alia C3 versus C4, CAM and CCM photosynthesis, and Fe acquisition mechanisms. Even earlier (3.8 Ga onwards) prokaryotes may have influenced CO2 levels and hence controlled (as they did later) surface temperature. By producing O2, they led to decreasing availability of Fe, Mn and P (and utility of Se? ), and increasing availability of Cu (and Zn? ) that shaped the biochemistry on which later biogeochemistry was based.
Influence of Matrix Composition on the Bioaccessibility of Copper, Zinc, and Nickel in Urban Residential Dust and Soil

ABSTRACT This study examines factors affecting oral bioaccessibility of metals in household dust, in particular metal speciation, organic carbon content, and particle size, with the goal of addressing risk assessment information requirements. Investigation of copper (Cu) and zinc (Zn) speciation in two size fractions of dust (< 36 μ m and 80–150 μ m) using synchrotron X-ray absorption spectroscopy (XAS) indicates that the two metals are bound to different components of the dust: Cu is predominately associated with the organic phase of the dust, while Zn is predominately associated with the mineral fraction. Total and bioaccessible Cu, nickel (Ni), and Zn were determined (on dry weight basis) in the < 150 μ m size fraction of a set of archived indoor dust samples (n = 63) and corresponding garden soil samples (n = 66) from the City of Ottawa, Canada. The median bioaccessible Cu content is 66 μ g g−1 in dust compared to 5 μ g g−1 in soil; the median bioaccessible Ni content is 16 μ g g−1 in dust compared to 2 μ g g−1 in soil; and the median bioaccessible Zn content is 410 μ g g−1 in dust compared to 18 μ g g−1 in soil. For the same data set, the median total Cu content is 152 μ g g−1 in dust compared to 17 μ g g−1 in soil; the median total Ni content is 41 μ g g−1 in dust compared to 13 μ g g−1 in soil; and the median total Zn content is 626 μ g g−1 in dust compared to 84 μ g g−1 in soil. Organic carbon is elevated in indoor dust (median 28%) compared to soil (median 5%), and is a key factor controlling metal partitioning and therefore bioaccessibility. The results show that house dust and soil have distinct geochemical signatures and should not be treated as identical media in exposure and risk assessments. Separate measurements of the indoor and outdoor environment are essential to improve the accuracy of residential risk assessments.
Image classification and analysis during the additive manufacturing process based on deep convolutional neural networks

In the advanced industrial manufacturing (3D printing), the assembly quality of parts has a tight relationship with the strength and the stiffness of products. Deep convolutional neural network for the image classification is an effective analysis approach for controlling the surface quality of parts and monitoring defects during this process. In this paper, a novel Artificial Intelligence (AI) method to classify and analyze numerous metal images during the manufacturing process is proposed. We exploit the visual-based feature classification method and deep convolutional neural network (DCNN) to analyze the quality of manufacturing parts, which is widely used in the defect detection for Additive Manufacturing. Two types of self-made industrial manufacturing datasets are collected, based on which we train the DCNN model to run the image classification tasks. Experiment results show that this method can achieve the state-of-art classification accuracy.