Miracle-dz/UniFAR-FTUs huggingface dataset:
Strong stabilizing selection on timing of germination in a Mediterranean population of Arabidopsis thaliana

Premise Timing of germination can strongly influence plant fitness by affecting seedling survival and by having cascading effects on later life‐history traits. In seasonal environments, the period favorable for seedling establishment and growth is limited, and timing of germination is likely to be under stabilizing selection because of conflicting selection through survival and fecundity. Moreover, optimal germination time may vary among genotypes because of inherent differences in later life‐history traits. Methods To examine how germination time affects survival, fecundity, and the relative fitness of two genotypes differing in time to first flower, we conducted a field experiment in an Italian population of the winter annual Arabidopsis thaliana, in which seedling establishment occurs mainly in November. We transplanted seedlings of the local genotype and of a Swedish genotype monthly from August to December and monitored survival and fecundity. Results Only seedlings transplanted in November and December survived until reproduction, and fitness of the November cohort was 35 times higher than that of the December cohort, indicating strong stabilizing selection on timing of germination. There was no evidence of conflicting selection: seedling survival, adult survival, and fecundity were all highest in the November cohort. Moreover, the relative fitness of the two genotypes did not differ significantly between cohorts. Conclusions The very narrow window of opportunity for seedling establishment was related to rapid seasonal changes in soil moisture and temperature, suggesting that rate of seasonal change is an important aspect to consider for understanding spatiotemporal variation in selection on phenological traits.
Light-Induced Fluorescence-Based Device and Hybrid Mobile App for Oral Hygiene Management at Home: Development and Usability Study

Background Dental diseases can be prevented through the management of dental plaques. Dental plaque can be identified using the light-induced fluorescence (LIF) technique that emits light at 405 nm. The LIF technique is more convenient than the commercial technique using a disclosing agent, but the result may vary for each individual as it still requires visual identification. Objective The objective of this study is to introduce and validate a deep learning–based oral hygiene monitoring system that makes it easy to identify dental plaques at home. Methods We developed a LIF-based system consisting of a device that can visually identify dental plaques and a mobile app that displays the location and area of dental plaques on oral images. The mobile app is programmed to automatically determine the location and distribution of dental plaques using a deep learning–based algorithm and present the results to the user as time series data. The mobile app is also built with convergence of naive and web applications so that the algorithm is executed on a cloud server to efficiently distribute computing resources. Results The location and distribution of users’ dental plaques could be identified via the hand-held LIF device or mobile app. The color correction filter in the device was developed using a color mixing technique. The mobile app was built as a hybrid app combining the functionalities of a native application and a web application. Through the scrollable WebView on the mobile app, changes in the time series of dental plaque could be confirmed. The algorithm for dental plaque detection was implemented to run on Amazon Web Services for object detection by single shot multibox detector and instance segmentation by Mask region-based convolutional neural network. Conclusions This paper shows that the system can be used as a home oral care product for timely identification and management of dental plaques. In the future, it is expected that these products will significantly reduce the social costs associated with dental diseases.
Intrinsically disordered bacterial polar organizing protein Z, PopZ, interacts with protein binding partners through an N-terminal Molecular Recognition Feature.

The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. Although a large portion of the protein is predicted to be natively unstructured, in reconstituted systems PopZ can self-assemble into a macromolecular scaffold that directly binds to at least ten different proteins. Here we report the solution NMR structure of PopZΔ134-177, a truncated form of PopZ that does not self-assemble but retains the ability to interact with heterologous proteins. We show that the unbound form of PopZΔ134-177 is unstructured in solution, with the exception of a small amphipathic α-helix in residues M10-I17, which is included within a highly conserved region near the N-terminus. In applying NMR techniques to map the interactions between PopZΔ134-177 and one of its binding partners, RcdA, we find evidence that the α-helix and adjoining amino acids extending to position E23 serve as the core of the binding motif. Consistent with this, a point mutation at position I17 severely compromises binding. Our results show that a partially structured Molecular Recognition Feature (MoRF) within an intrinsically disordered domain of PopZ contributes to the assembly of polar microdomains, revealing a structural basis for complex network assembly in Alphaproteobacteria that is analogous to those formed by intrinsically disordered hub proteins in other kingdoms.
COVID-19 and Overall Mortality Inequities in the Surge in Death Rates by Zip Code Characteristics: Massachusetts, January 1 to May 19, 2020.

Objectives. To address evidence gaps in COVID-19 mortality inequities resulting from inadequate race/ethnicity data and no socioeconomic data.Methods. We analyzed age-standardized death rates in Massachusetts by weekly time intervals, comparing rates for January 1 to May 19, 2020, with the corresponding historical average for 2015 to 2019 stratified by zip code social metrics.Results. At the surge peak (week 16, April 15-21), mortality rate ratios (comparing 2020 vs 2015-2019) were 2.2 (95% confidence interval [CI] = 1.4, 3.5) and 2.7 (95% CI = 1.4, 5.5) for the lowest and highest zip code tabulation area (ZCTA) poverty categories, respectively, with the 2020 peak mortality rate 1.1 (95% CI = 1.0, 1.3) times higher in the highest than the lowest poverty ZCTA. Similarly, rate ratios were significantly elevated for the highest versus lowest quintiles with respect to household crowding (1.7; 95% CI = 1.0, 2.9), racialized economic segregation (3.1; 95% CI = 1.8, 5.3), and percentage population of color (1.8; 95% CI = 1.6, 2.0). Conclusions. The COVID-19 mortality surge exhibited large inequities.Public Health Implications. Using zip code social metrics can guide equity-oriented COVID-19 prevention and mitigation efforts. (Am J Public Health. Published online ahead of print October 15, 2020: e1-e3. https://doi.org/10.2105/AJPH.2020.305913).
Comparison of physical, microstructural and antioxidative properties of pumpkin cubes cooked by conventional, vacuum cooking and sous vide methods.

BACKGROUND The current dietary guidelines recommend five or more fruits, vegetables and legumes servings per day. Often, these products are eaten cooked, resulting in organoleptic and nutritional changes. Vacuum cooking is gaining attention as alternative cooking technique, thanks to its ability to preserve or even enhance sensory and healthy properties of food. Its household application is however poorly explored. In this work, the effect of vacuum cooking, performed with a new patented system, was studied for the first time on pumpkin cubes and compared to sous vide and a traditional steam cooking, through a multidisciplinary approach. RESULTS All the cooking treatments damaged pumpkin microstructure, leading to cells separation and plasmolysis; vacuum cooking resulted the most aggressive method, as confirmed by the texture softening. Vacuum cooking resulted also the less impacting method on pumpkin colour, in relation to the largest extraction of some classes of carotenoids from the broken cells. A significant polyphenols extraction, especially of gallic acid and naringenin, was instead observed for sous vide and steamed pumpkins. Total antioxidant activity, ascribable to the effect of both carotenoids and polyphenols, resulted thus enhanced after cooking, mainly for vacuum cooked pumpkins, followed by the steamed and sous vide ones. CONCLUSIONS Vacuum cooking, followed by sous vide, has often shown better performances than traditional steam cooking on pumpkin cubes. The implementation of sous-vide and vacuum cooking at domestic level or in professional kitchens and in the food industry would allow the consumption of vegetables with improved nutritional and sensorial characteristics. This article is protected by copyright. All rights reserved.
Adaptation aftereffects reveal how categorization training changes the encoding of face identity

Previous research suggests that learning to categorize faces along a novel dimension changes the perceptual representation of such dimension, increasing its discriminability, its invariance, and the information used to identify faces varying along the dimension. A common interpretation of these results is that categorization training promotes the creation of novel dimensions, rather than simply the enhancement of already existing representations. Here, we trained a group of participants to categorize faces that varied along two morphing dimensions, one of them relevant to the categorization task and the other irrelevant to the task. An untrained group did not receive such categorization training. In three experiments, we used face adaptation aftereffects to explore how categorization training changes the encoding of face identities at the extremes of the category-relevant dimension and whether such training produces encoding of the category-relevant dimension as a preferred direction in face space. The pattern of results suggests that categorization training enhances the already existing norm-based coding of face identity, rather than creating novel category-relevant representations. We formalized this conclusion in a model that explains the most important results in our experiments and serves as a working hypothesis for future work in this area.
The HRDC domain oppositely modulates the unwinding activity of E. coli RecQ helicase on duplex DNA and G-quadruplex.

RecQ family helicases are highly conserved from bacteria to humans and have essential roles in maintaining genome stability. Mutations in three human RecQ helicases cause severe diseases with the main features of premature aging and cancer predisposition. Most RecQ helicases shared a conserved domain arrangement which comprises a helicase core, an RQC domain, and an auxiliary element HRDC domain, the functions of which are poorly understood. In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3'-partial duplex and fork DNA with a moderate processivity, and periodically patrols on the ssDNA in the 5'-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core- and ssDNA- binding modes after RecQ association with DNA, we proposed a model to explain the modulation mechanism of the HRDC domain. Our findings not only provide new insights into the activities of RecQ on different substrates but also highlight the novel functions of the HRDC domain in DNA metabolisms.
Visual salience of 3D and 2D spoons determines S-R mapping and flanker effects

This study tested the hypothesis that affordances for grasping with the corresponding hand are activated more strongly by three-dimensional (3D) real objects than by two-dimensional (2D) pictures of the objects. In Experiment 1, participants made left and right keypress responses to the handle or functional end (tip) of an eating utensil using compatible and incompatible mappings. In one session, stimuli were spoons mounted horizontally on a blackboard with the sides to which the handle and tip pointed varying randomly. In the other, stimuli were pictures of spoons displayed on a black computer screen. Three-dimensional and 2D sessions showed a similar benefit for compatible mapping when the tip was relevant and a small cost of compatible mapping when the handle was relevant. Experiment 2 used a flanker task in which participants responded compatibly to the location of the handle or the tip, and spoons located above and below the target spoon could have congruent or incongruent orientations. The difference between 3D and 2D displays was not obtained in the flanker effect for reaction time. There was little evidence that 3D objects activate grasping affordances that 2D images do not. Instead, we argue that visual salience of the tip is the critical factor determining these correspondence effects.
Altered neuronal activity in the visual processing region of eye-fluke-infected fish

Abstract Fish, like most vertebrates, are dependent on vision to varying degrees for a variety of behaviours such as predator avoidance and foraging. Disruption of this key sensory system therefore should have some impact on the ability of fish to execute these tasks. Eye-flukes, such as Tylodelphys darbyi, often infect fish where they are known to inflict varying degrees of visual impairment. In New Zealand, T. darbyi infects the eyes of Gobiomorphus cotidianus, a freshwater fish, where it resides in the vitreous chamber between the lens and retina. Here, we investigate whether the presence of the parasite in the eye has an impact on neuronal information transfer using the c-Fos gene as a proxy for neuron activation. We hypothesized that the parasite would reduce visual information entering the eye and therefore result in lower c-Fos expression. Interestingly, however, c-Fos expression increased with T. darbyi intensity when fish were exposed to flashes of light. Our results suggest a mechanism for parasite-induced visual disruption when no obvious pathology is caused by infection. The more T. darbyi present the more visual stimuli the fish is presented with, and as such may experience difficulties in distinguishing various features of its external environment.
Characterizing the Role of Deubiquitination in Ribosome Biogenesis

Characterizing the Role of Deubiquitination in Ribosome Biogenesis Lauren Alexandria Richardson Chair of Supervisory Committee: Assistant Professor Richard Gardner Department of Pharmacology Eukaryotic ribosome biogenesis requires hundreds of trans-acting factors and dozens of RNAs. Although most factors required for ribosome biogenesis have been identified, little is known about how they are regulated. Here, we reveal that the yeast deubiquitinating enzyme Ubp10 is predominantly localized to the nucleolus and ubp10! cells have a significant reduction in pre-rRNAs, mature rRNAs, and translating ribosomes. Through proteomic analyses, we found that Ubp10 interacts with proteins that function in rRNA production and ribosome biogenesis. In particular, we discovered that the largest subunit of RNA polymerase I (RNAPI) is stabilized via Ubp10-mediated deubiquitination, and this is required to achieve optimal levels of ribosomes and cell growth. USP36, the human homolog of Ubp10, similarly regulates RNAPI in human cells and complements the ubp10! allele for RNAPI stability and cell growth in yeast. Thus, stabilization of RNAPI through deubiquitination is conserved in eukaryotes. Additionally, we proposed other potential roles for Ubp10-mediated regulation in essential nucleolar functions. Our work now places Ubp10/USP36 as a key regulator of rRNA production.
Differentiation of Local Pink Salmon Stocks on the Basis of Variations in Their Scale Structure

One of the challenges facing Pacific salmon fisheries management is the differentiation of local populations in mixtures of prespawning or feeding aggregations. The problem of differentiating stocks is especially urgent for pink salmon, the most abundant species of Pacific salmon in Asia. One method for stock identification is based on scale pattern analysis. Investigations in recent decades have demonstrated that pink salmon scales, particularly the first-year zone, can be an informative marker to differentiate populations at the level of major regional groups (e.g., Grachev 1983; Temnykh 1998; Antonov et al. 2005). A general characteristic trait for pink salmon returning to spawn in evenor odd-numbered years is the capacity for significant phenotypic separation using scales collected from local stocks in the southern and northern portions of pink salmon distribution in Asia. The difference in the scale structure has been described by several fish biologists in earlier works. Moreover, some regional complexes can be identified within local stocks in the southern and northern groups. We expanded the baseline and have improved on procedures of scale pattern analysis since an earlier study by Shaporev et al. (2007). In this project our objective was to use Asian pink salmon scale samples from known populations to explore inter-population differences for fish that returned as adults in 2007-2009. Samples used for this investigation included adult pink salmon scales collected from 34 local areas of Hokkaido, Sakhalin, the Amur River system, continental shore of the Okhotsk Sea, and West and East Kamchatka (Fig. 1). The samples consisted of 8,777 individual adult pink salmon originating from 67 stocks. Scales were scanned at 10fold magnification and scanned images included the whole scale. From one to five scales were examined from each pink salmon, and the analysis was based on averaged scale variables. To discover the extent of characteristics differentiating the stocks, we computed the Mahalanobis distance between population centroids using multidimensional scaling. The resolving ability of the data was analyzed using the maximum likelihood estimation procedure available in the computer program SPAM (Statistics Program for Analyzing Mixtures; Masuda et al. 1991; Pella et al. 1996). 1 14
A review of potential alpine newt (Ichthyosaura alpestris) impacts on native frogs in New Zealand

ABSTRACT The alpine newt (Ichthyosaura alpestris) is an adaptable European amphibian occupying a range of habitats from low to high elevation within its native range. The Italian subspecies I. a. apuana, illegally introduced to New Zealand, has established geographically close to habitats of Archey’s frog (Leiopelma archeyi) and Hochstetter’s frog (L. hochstetteri). The newt’s introductions in Europe suggest competitive impacts on local amphibians were not severe, although as a disease and parasite vector its impact may have been underestimated in the past. The most identifiable risk to native frog populations in New Zealand is introduction of new diseases or parasites, although the newt may have wider ecological impact should it substantially invade native frog habitats. Alpine newts need eradicating from New Zealand as soon as possible, while the status of captive-held fire-bellied newts (Cynops spp.) also requires review, given their disease risk and their potential for release into the wild.
FIRST REPORT OF BACTERIAL PITH SOFT ROT CAUSED BY PECTOBACTERIUM CAROTOVORUM subsp. BRASILIENSE ON ARTICHOKE IN ITALY

A severe soft rot disease was observed in some commercial artichoke crops (F1-hybrid cultivars) during 2014 in the Bari, Foggia (Apulia, Southern Italy) and Matera (Basilicata, Southern Italy) provinces. Symptoms were chlorosis and wilting of the older leaves accompanied by dark-green to dark-brown soft rotting of the pith. Several bacterial isolates were obtained from affected plants by culturing on semi-selective crystal violet pectate agar medium. Biochemical, physiological and molecular analyses and pathogenicity tests, performed using five selected isolates, identified three of them as Pectobacterium carotovorum subsp. brasiliense. To the best of our knowledge, this is the first report of a bacterial soft rot caused by P. carotovorum subsp. brasiliense in Italy and the first finding of this bacterial subspecies on artichoke.
Why invasive Patagonian beavers thrive in unlikely habitats: a demographic perspective

Understanding the demography of an invasive species is crucial to better guide managers seeking to slow the spread of the invader. Habitat differences can affect demographic rates, which may in turn impact the speed of the invasion, but this has been rarely addressed. We studied the demography of invasive North American beavers (Castor canadensis) in 2 contrasting habitat types of the island, forest and steppe, on Tierra del Fuego in southern Patagonia. We used repeated observations, mark-resight methods, telemetry, and camera traps to estimate colony size and demographic rates of beavers in the 2 habitats. Colony size and the number of offspring (“kits”) produced per colony per year were higher in the steppe, contrary to the belief that forest is better habitat. This may be the result of the longer time since invasion in the forests of Tierra del Fuego and that the forest subpopulation is showing density-dependent regulation. Survival of beavers was high in all age classes and was higher than survival rates recorded in North America. Our work shows that plasticity of habitat use and predator release have likely facilitated beaver invasion in Patagonia. The higher productivity and detectability of beavers in the steppe call for active management in a habitat previously assumed to be subprime.
dLipin-A Link between Lipid Metabolism, Glucose Homeostasis and Growth in Drosophila melanogaster

Lipins are a family of highly conserved proteins found from yeasts to humans. Lipins have dual functions, serving as phosphatidate phosphatase enzymes (PAP) in the synthesis of neutral fats (triacylglycerols, TAG) and as transcriptional co-regulators that affect the expression of genes involved in lipid and fatty acid metabolism. Thus, they play central roles in metabolic control. Disruption of Lipin function has been implicated in lipodystrophy, obesity and insulin resistance. Using dLipin, the Drosophila homolog of Lipin, as a model, I aimed to elucidate the relationship between the two biochemical functions of Lipin and metabolic homeostasis. I discovered there is a strong interconnection between TAG synthesis and insulin pathway activity. Reduced activity of dLipin and other enzymes involved in TAG synthesis disrupted insulin pathway activity by interfereing with phosphatidylinositol (3,4,5)-trisphosphate (PIP3) synthesis. Mosaic analysis revealed that cell-autonomous loss of dLipin activity in fat the body negatively affects cell growth. Genetic interaction experiments indicated that dLipin and the insulin pathway regulate adipogenesis in an interdependent fashion. Furthermore, I found that the nutrient sensing complex TORC1 regulates dLipin activity in lipid metabolism by controlling dLipin’s subcellular localization. Hence, the insulin pathway as well as the TORC1 pathway each appears to be a central regulator of dLipin activity and its functions in lipid metabolism. Nuclear functions of dLipin did not seem to have an effect on insulin pathway activity. Thus, metabolic disturbances observed after dLipin knockdown seem to be primarily caused by reduced PAP activity provided by dLipin. Taken together, the results position dLipin as a central target to further study the link between TAG synthesis and insulin and TORC1 pathway activity.