Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of heat shock during grain filling on grain quality of bread and durum wheats

In southern Europe the Mediterranean climate is responsible for the remarkable variability in both yield and quality from year to year and also from location to location, but it offers also a unique opportunity for the production of high-quality wheats which are deficient in the European Economic Community. This study was conducted to determine the role of the fluctuation of temperatures during grain filling on the rheological properties of bread and durum wheats (Triticum aestivum and Triticum turgidum) as evaluated with a Chopin alveograph. During the 1991-92 season, four cultivars of bread and durum wheat were grown in several locations scattered along the Italian peninsula and the island of Sicily. In each location different temperature profiles were imposed during grain filling by anticipating or delaying sowing date or by covering the plots with plastic tunnels. Viscoelastic properties, evaluated by the variations in W, P and L alveograph parameters were significantly affected by the imposed treatments. In presence of a long period of temperature in the range of 30-35¦C a dough 'strengthening' effect was observed, while frequent episodes of daily maximum temperatures above 35¦C led to a dough 'weakening' effect. These results observed both in durum and bread wheat confirm those firstly detected on bread wheat in Australia in areas charcterized by a Mediterranean-like climate. The practical relevance of these effects differs in the two species: an increase of dough strength is considered detrimental in breadmaking quality, while it exerts a positive effect in pastamaking quality.
QuoVidi: a open-source web application for the organisation of large scale biological treasure hunts

Learning biology, and in particular systematics, requires learning a substantial amount of specific vocabulary, both for botanical and zoological studies. While crucial, the precise identification of structures serving as evolutionary traits and systematic criteria is not per se a highly motivating task for students. Teaching this in a traditional teaching setting is quite challenging especially with a large crowd of students to be kept engaged. This is even more difficult if, as during the COVID-19 crisis, students are not allowed to access laboratories for hands-on observation on fresh specimens and sometimes restricted to short-range movements outside their home. Here we present QuoVidi, a new open-source web platform for the organisation of large scale treasure hunts. The platform works as follows: students, organised in teams, receive a list of quests that contain morphologic, ecologic or systematic terms. They have to first understand the meaning of the quests, then go and find them in the environment. Once they find the organism corresponding to a quest, they upload a geotagged picture of their finding and submit this on the platform. The correctness of each submission is evaluated by the staff. During the COVID-19 lockdown, previously validated pictures were also submitted for evaluation to students that were locked in low-biodiversity areas. From a research perspective, the system enables the creation of large image databases by the students, similar to citizen-science projects. Beside the enhanced motivation of students to learn the vocabulary and perform observations on self-found specimens, this system allows faculties to remotely follow and assess the work performed by large numbers of students. The interface is freely available, open-source and customizable. It can be used in other disciplines with adapted quests and we expect it to be of interest in many classroom settings.
Shorebird Use of Managed Wetlands in the Mississippi Alluvial Valley

Abstract We assessed shorebird use of artificial wetlands within the Mississippi Alluvial Valley during the winters of 1991–1992 and 1992–1993 and during the autumn of 1994. On agricultural fields managed to provide habitat for waterfowl from November to March, mean shorebird density was 58.6 birds/100 ha, but shorebird densities were greater on soybean fields than on rice or moist-soil fields. Killdeer (Charadrius vociferus) and common snipe (Gallinago gallinago) were common throughout winter, but shorebird abundance and species richness along survey routes increased from November through April. During the late summer and autumn, wetlands on public lands in the Mississippi Alluvial Valley are managed by the U.S. Fish and Wildlife Service specifically to provide foraging habitat for shorebirds. From August through October 1994, we observed 14,564 individual shorebirds of 22 species using these anthropogenic wetlands. Mean shorebird density on wetlands managed by flooding previously dry, disked fields was 695 birds/100 ha, whereas mean density on wetlands managed by drawing down water reservoirs was 1224 birds/100 ha. We recommend increased shallow-water flooding of agricultural fields, particularly soybean fields, during winter to provide habitat for wintering and early spring migrant shorebirds. More importantly, we recommend continued water management on public wetlands from July through October, preferably by drawing down water reservoirs, to provide foraging habitat for southward migrating shorebirds.
Phenotypic variation in two widespread Caribbean corals — Porites astreoides and P. divaricata — between mangrove and lagoon habitats

As coral reefs experience dramatic declines in coral cover throughout the tropics, there is an urgent need to understand the role that non-reef habitats such as mangroves play in the ecological niche of corals. Mangrove habitats present a challenge to reef-dwelling corals as they can differ dramatically from adjacent reef habitats with respect to key environmental parameters such as temperature and light. As variation in temperature and light within reef habitats is known to drive intraspecific differences in coral phenotype, we hypothesized that coral species which can exploit both reef and mangrove habitats will exhibit predictable differences in phenotype between habitats. To investigate how intraspecific variation, driven by either local adaptation or phenotypic plasticity, might enable particular coral species to exploit these two qualitatively different habitat types, we compared the phenotypes of two widespread Caribbean corals — Porites divaricata and P. astreoides— in mangrove versus lagoon habitats on Turneffe Atoll, Belize. We document significant differences in colony size, color, structural complexity, and corallite morphology between habitats. In every instance, the difference between mangrove and lagoon corals was consistent in P. divaricata and P. astreoides. This study is the first to document intraspecific phenotypic diversity in corals occupying mangrove versus patch-reef habitats, and it provides a foundation for understanding why some “reef coral” species can exploit mangroves, while others cannot.
Structural basis of TRPC4 regulation by calmodulin and pharmacological agents

Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca2+ signaling. Inhibition of TRPCs by small molecules was shown to be promising in treating renal diseases. In cells, the channels are regulated by calmodulin. Molecular details of both calmodulin and drug binding have remained elusive so far. Here we report structures of TRPC4 in complex with a pyridazinone-based inhibitor and a pyridazinone-based activator and calmodulin. The structures reveal that both activator and inhibitor bind to the same cavity of the voltage-sensing-like domain and allow us to describe how structural changes from the ligand binding site can be transmitted to the central ion-conducting pore of TRPC4. Calmodulin binds to the rib helix of TRPC4, which results in the ordering of a previously disordered region, fixing the channel in its closed conformation. This represents a novel calmodulin-induced regulatory mechanism of canonical TRP channels.
Transcription-dependent domain-scale 3D genome organization in dinoflagellates

Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and contain genes organized into polycistronic arrays, with minimal transcriptional regulation. We analyze the 3D genome of Breviolum minutum, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (“dinoTADs). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
Epigenetic signatures associated with the observed link between maternal tobacco use during pregnancy, and offspring conduct problems in childhood and adolescence

Background Metastable epialleles (MEs) are loci at which epigenetic regulation is established during development and subsequently maintained throughout life. Consequently, individuals can have the same genetic sequence, yet their epigenetic regulation of the underlying sequence can vary. MEs can be independent of genetic variation and may be induced by environmental exposures. Maternal tobacco smoking during pregnancy can alter offspring DNA methylation, hence there is potential for MEs to be induced during development in response to maternal tobacco smoking during pregnancy. Furthermore, associations between maternal tobacco use during pregnancy and conduct problems (CP) in offspring exposed to tobacco smoke in utero, have been observed. However, currently, we do not know what molecular mechanism may link these associations. Results We investigated the observed link between maternal tobacco use during pregnancy and CP outcomes in exposed offspring. Individuals who were exposed to tobacco in utero via maternal smoking, and unexposed individuals, both with and without CP, were selected from the Christchurch Health and Development Study (CHDS), a longitudinal birth cohort studied for over 40 years in New Zealand. Bisulfite-based amplicon sequencing (BSAS) was used to investigate DNA methylation differences and potential MEs between the groups at high risk loci. We identified nominally significant differential DNA methylation at specific CpG sites in individuals with CP who were exposed to tobacco in utero. This differential methylation appears to be specific to in utero tobacco exposure, and interacts with CP. Given its association with the in utero environment we hypothesise that these methylation changes may represent MEs. Conclusion We conclude that environmentally-induced DNA methylation differences may play a role in the observed link between maternal smoking during pregnancy and childhood/adolescent CP, potentially via the generation of MEs. Larger sample sizes and a genome-wide approach are required to investigate this association further.
Characterization of Bacterial Isolates in Vermicompost Produced from a Mixture of Cow dung, Straw, Neem leaf and Vegetable Wastes

Vermicomposting is a non-thermophilic biological oxidation process of composting where certain species of earthworm are used to enhance the process of conversion of organic waste to compost. Earthworm helps in influencing the growth of certain microbial species, and also improves the physical and chemical properties of the soil. The microbial population present in vermicompost play an important role in increasing the productivity of crop as well as maintain the structural stability of the soil. Different types of bacteria found in vermicompost and is depends on the environmental condition and the raw materials used in vermicomposting. Owing to this, a study was carried out to identify the bacteria exist in vermicompost produced from cow dungs, straw, neem leafs and vegetable wastes. The phenotypic studies such as colony morphology, microscopic studies, and biochemical characterization have identified eight bacterial species namely Actinomyces israelli, Azotobacter, Micrococus luteus, Bacillus cereus, Bacillus subtillis, Pseudomonas aeruginosa, Enterobacter in the vermicompost. All these bacteria were present in the gut of Eesenia Foetida and found beneficial for the soil and crop plants.
The seasonal occupancy of overwintering monarch butterflies, Danaus plexippus plexippus (Linnaeus, 1758) (Lepidoptera: Nymphalidae), at four California winter groves reflects grove conditions for winter aggregations, survival, and contribution to the next generation of butterflies

Abstract. When viewed over a period of years, the frequency and type of seasonal occupancy of overwintering monarch butterflies, Danaus plexippus plexippus (Linnaeus, 1758), at California winter groves are good indicators of whether grove conditions are being maintained, declining, or recovering. The contribution of a winter grove to the next generation of butterflies depends on the stability of grove conditions for winter aggregations. Knowing the trend of grove conditions allows proactive management of winter groves for overwintering butterflies.
Analysis of Complex DNA Rearrangements during Early Stages of HAC Formation

Human Artificial Chromosomes (HACs) are important tools for epigenetic engineering, for measuring chromosome instability (CIN) and possible gene therapy. However, their use in the latter is potentially limited because the input HAC-seeding DNA can undergo an unpredictable series of rearrangements during HAC formation. As a result, after transfection and HAC formation, each cell clone contains a HAC with a unique structure that cannot be precisely predicted from the structure of the HAC-seeding DNA. Although it has been reported that these rearrangements can happen, the timing and mechanism of their formation has yet to be described. Here we synthesized a HAC-seeding DNA with two distinct structural domains and introduced it into HT1080 cells. We characterized a number of HAC-containing clones and subclones to track DNA rearrangements during HAC establishment. We demonstrated that rearrangements can occur early during HAC formation. Subsequently, the established HAC genomic organization is stably maintained across many cell generations. Thus, early stages in HAC formation appear to at least occasionally involve a process of DNA shredding and shuffling that resembles chromothripsis, an important hallmark of many cancer types. Understanding these events during HAC formation has critical implications for future efforts aimed at synthesizing and exploiting synthetic human chromosomes.
Incorporating grazing behaviour measurements in models to predict herbage intake by grazing dairy cows

Models to predict herbage intake were constructed using 168 dairy cow records from three grazing experiments. Variables included fell into three categories: animal state, sward state and animal behaviour. Linear regression models of varying complexity were obtained by removing variables from the best fitting model to reflect progressive lack of information availability on farms. Thus, behavioural variables were removed first, followed by sward surface height and milk fat concentration. Models were subject to outlier analysis and collinearity tests. Equivalent models were constructed using ridge regression to minimize collinearity problems. They were tested using 20 Holstein–Friesian dairy cows continuously stocked on a perennial ryegrass sward. A `best practice' treatment [7 cm sward surface height (SSH), 6 kg day−1 concentrate (C)] was used together with treatments of SSH5/C6, SSH7/C8, SSH7/C0 and SSH9/C6. The best model accounted for 0.37 of the variance in the estimation data and contained the following variables: concentrate intake, milk yield, milk fat concentration, days in milk, sward surface height and chewing rate while ruminating. Model performance against test data was generally poor. This was mainly because of consistent underprediction of herbage intake, caused in part by the higher average herbage intakes in the test data compared with the estimation data.
Accelerating Artificial Intelligence on the Grid

In this work, we present an ongoing, three year project funded by the Advanced Research Project Agency (ARPA-E) to develop an infrastructure to accelerate the development and deployment of artificial intelligence solutions for the electric grid. The project addresses the critical issues that we have identified as hampering the deployment of AI on electric grid measurements. These issues have stymied the potential for insight from high resolution grid measurements and generally hindered artificial intelligence innovation in the utility industry. The project consists of three main components. The first is the deployment of a diverse set of grid sensors to capture a variety of grid behaviour, both from the field and in simulation. The second is the deployment of a highly performant, scalable, cloud-based data management and AI platform designed for time series data to enable the easy storage, processing and analysis of grid sensor data. The third is the cultivation of an open research community of experts around the platform and data through useful educational material, code and data sharing, and data science competitions. Overall, the project will accelerate the development of analytics, machine learning, and AI by addressing existing gaps in data, tools, and people, with the aim of improving the electric grid.
Extreme body size variability in the golden silk spider ( Nephila edulis ) does not extend to genitalia

Nephila edulis is a spider with large body size variability in males and females. Genital characters show negative allometric values compared to somatic characters. In males, the embolus (the most important structure for sperm transfer) had a significantly lower coefficient of variation than body size. This suggests that male genitalia are under stabilizing selection favouring intermediate size. Female N. edulis showed a trend similar to males regarding allometric values in genitalia. In females, however, the variation coefficient in a specific genital character crucial for successful copulation did not differ from that of indicators for overall body size. This suggests that in Nephila the genitalia of the females experience less stabilizing selection than those of the males. In male and female genitalia, the mode of selection seems to cause developmental instability not in degrees of fluctuating asymmetry but in the degree of data scatter which indicates a lower coefficient of determination.
Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model

Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to the dissemination of antibiotic-resistance genes in the gut microbiota and the development of antibiotic-resistant bacterial infection, a significant threat to animal and public health. Food or water may be contaminated with multiple resistant bacteria, but animal models on gene transfer were mainly based on single-strain infections. In this study, we investigated the mobility of β-lactam resistance following infection with single- versus multi-strain of resistant bacteria under ampicillin treatment. We characterized three bacterial strains isolated from food-animal production systems, Escherichia coli O80:H26 and Salmonella enterica serovars Bredeney and Heidelberg. Each strain carries at least one conjugative plasmid that encodes a β-lactamase. We orally infected mice with each or all three bacterial strain(s) in the presence or absence of ampicillin treatment. We assessed plasmid transfer from the three donor bacteria to an introduced E. coli CV601gfp recipient in the mouse gut, and evaluated the impacts of the bacterial infection on gut microbiota and gut health. In the absence of ampicillin treatment, none of the donor or recipient bacteria established in the normal gut microbiota and plasmid transfer was not detected. In contrast, the ampicillin treatment disrupted the gut microbiota and enabled S. Bredeney and Heidelberg to colonize and transfer their plasmids to the E. coli CV601gfp recipient. E. coli O80:H26 on its own failed to colonize the mouse gut. However, during co-infection with the two Salmonella strains, E. coli O80:H26 colonized and transferred its plasmid to the E. coli CV601gfp recipient and a residential E. coli O2:H6 strain. The co-infection significantly increased plasmid transfer frequency, enhanced Proteobacteria expansion and resulted in inflammation in the mouse gut. Our findings suggest that single-strain infection models for evaluating in vivo gene transfer may underrepresent the consequences of multi-strain infections following the consumption of heavily contaminated food or water.
Physicochemical Salt Solution Parameters Limit the Survival of Planococcus halocryophilus in Martian Cryobrines

Microorganisms living in sub-zero environments can benefit from the presence of dissolved salts, as they significantly increase the temperature range of liquid water by lowering the freezing point. However, high concentrations of salts can reduce microbial growth and survival, and can evoke a physiological stress response. It remains poorly understood how the physicochemical parameters of brines (e.g. water activity, ionic strength, solubility and hydration shell strength between the ions and the surrounding water molecules) influence the survival of microorganisms. We used the cryo− and halotolerant bacterial strain Planococcus halocryophilus as a model organism to evaluate the degree of stress different salts assert. Cells were incubated in liquid media at −15°C containing single salts at eutectic concentrations (CaCl2, LiCl, LiI, MgBr2, MgCl2, NaBr, NaCl, NaClO4 and NaI). Four of these salts (LiCl, LiI, MgBr2 and NaClO4) were also investigated at concentrations with a low water activity (0.635) and, separately, with a high ionic strength (8 mol/L). Water activity of all solutions was measured at −15°C. This is the first time that water activity has been measured for such a large number of liquid salt solutions at constant sub-zero temperatures (−15°C). Colony-Forming Unit (CFU) counts show that the survival of P. halocryophilus has a negative correlation with the salt concentration, molecular weight of the anion and anion radius; and a positive correlation with the water activity and anions’ hydration shell strength. The survival of P. halocryophilus did not show a significant correlation with the ionic strength, the molecular weight of the cation, the hydrated and unhydrated cation and hydrated anion radius, and the cations’ hydration bond length. Thus, the water activity, salt concentration and anion parameters play the largest role in the survival of P. halocryophilus in concentrated brines. These findings improve our understanding of the limitations of microbial life in saline environments, which provides a basis for better evaluation of the habitability of extraterrestrial environments such as Martian cryobrines.
Reproductive effort decreases antibody responsiveness

The prevalence and intensity of parasitic infection often increases in animals when they are reproducing. This may be a consequence of increased rates of parasite transmission due to reproductive effort. Alternatively, endocrine changes associated with reproduction can lead to immunosuppression. Here we provide support for a third potential mechanism: reduced immunocompetence as a consequence of adaptive reallocation of resources in times of increased energetic demand. In captive zebra finches Taeniopygia guttata, reproductive effort was manipulated through brood size. Enhanced effort was found to affect the production of antibodies towards sheep red blood cells. In addition, activity of zebra finches was manipulated independently of parental care. Experimentally increased daily workloads in activity reward schedules also suppressed antibody production. Thus, we show that not just the reproductive state, but the increased activity that accompanies reproduction is associated with immunocompetence. This mechanism may be sufficient to explain the increased parasitism observed in reproducing animals. We suggest that reduced immunocompetence as a consequence of increased reproductive effort may be an important pathway for the life history cost of reproduction.