Miracle-dz/UniFAR-FTUs huggingface dataset:
Ames mutagenicity, structural alerts of carcinogenicity, Hansch QSAR parameters (ClogP, CMR, MgVol), tumor site concordance/multiplicity, and tumorigenicity rank in NTP 2-year rodent studies

Since its inception in 1976, the National Toxicology Program (NTP) has conducted 594 2-year studies on rats and mice by a number of routes of administration including inhalation, feed, drinking water, dermal, and intraperitoneal injection. Of these studies, the results on 470 chemicals were of adequate technical quality to be incorporated into final technical reports. In this study, the 470 chemicals were categorized from 1 to 48 by the level of “clear” neoplastic evidence in male and female rats, and in male and female mice, and given an ordinal rank from 1 to 135 following additional considerations regarding tumor site concordance and tumor multiplicity. The resultant tumorigenicity category score and ordinal rank score were examined for associations with results in the Ames Salmonella mutagenicity assay; presence or absence of structural alerts of carcinogenicity; and three Hansch Quantitative Structure-Activity Relationship (QSAR) parameters, namely, calculated base 10 logarithm of the octanol–water partition coefficient (ClogP), calculated molar refractivity (CMR), and McGowan molecular volume (MgVol). Smaller molecular volumes were found to be associated with higher levels of tumorigenicity. Whereas lower rather than higher levels of lipophilicity were found to be associated with higher levels of tumorigenicity. Positive Ames test results were positively correlated with overall tumorigenicity and with possession of structural alerts. Since larger organic molecules have more chemical reaction centers, it was not surprising that higher ClogP values were positively correlated with the number of structural alerts. The results from this study demonstrate the ability to devise rational rules for relative tumorigenicity that correlate, in biologically plausible ways, with known parameters of toxicity.
siRNAs Derived from Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus Down-modulated the Expression Levels of Endogenous Genes in Phalaenopsis equestris

Interplay between Cymbidium mosaic virus (CymMV)/Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response–related genes, RNA interference core components, cytoskeleton-related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by real-time reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.
Still challenging: the ecological function of the cyanobacterial toxin microcystin – What we know so far

Abstract Microcystins (MCs) are the most commonly studied cyanotoxins. While these past studies have mainly focused on the toxicity of MCs, the evolutionary history of life has shown that toxicity can be considered as an assigned role to MCs. Nowadays, there is a growing interest in understanding the importance of cyanotoxins in any of the physiological processes or beyond at the ecological level. This review evaluates variously proposed intracellular and extracellular functions of MCs and how they benefit the producing cyanobacterium. However, the strain-specific and divergent laboratory and field results obtained to date have made it difficult to generalize.
Analyses of Climate Variations at Four Meteorological Stations on Remote Islands in the Croatian Part of the Adriatic Sea

The Mediterranean region is one of the regions in the world that is most vulnerable to the impact of imminent climate change. In particular, climate change has an adverse effect on both the ecosystem and socioeconomic system, influencing water availability for both human and environmental purposes. The most endangered water resources are along the coasts and on islands since they have relatively small volumes and are intensively exploited. We analyzed the time series of air temperature and precipitation measured at four meteorological stations (Komiža, Palagruža, Lastovo, and Biševo) located on small islands in the Croatian part of the Adriatic Sea in this study. The investigated time series extend from the 1950s to the present, being contemporaneous for approximately 50 years. Despite possessing discontinuity, they can be considered as representative for assessing climate change and variability in the scattered environment of the Croatian islands. The results showed increasing trends in the annual air temperature, while the annual cumulative precipitation did not show significant variations. In addition, the analyses of the monthly air temperature showed that statistically significant increasing trends occurred from April to August, suggesting a more severe impact during these months. These results are in accordance with regional and local studies and climate models. Although the climate variability during the analyzed period can be considered as moderate, the impact on water resources could be severe due to the combined effect of the increase in air temperature during warm periods and the intensive exploitation for tourism purposes.
Coevolution of dispersal-related traits: modelling and analysis

This thesis theoretically investigates dispersal evolution in a wider ecological context. It factors in ecological relevant dependencies e.g. trade-offs or spatial heterogeneity, and allows coevolutionary interactions between immigration and other traits. It extends well-known models to include more biological realism, reveals novel evolutionary mechanisms and helps to understand the complex dispersal patterns more accurately. In particular, this work studies the evolution of dispersal, i.e., natal emigration when it is under a trade-off with fecundity. Furthermore, dispersal is divided into its three phases and hence studied as emigration, transfer and immigration. Emigration and immigration are made dependent on the local conditions experienced by the individuals: the patch types. The coevolution of patch-type dependent immigration is investigated alone, but also the coevolution of patch-type dependent immigration and patch-type dependent emigration or local adaptation is studied. The evolutionary framework was chosen to be adaptive dynamics, a way of describing the long-term evolutionary outcomes of single populations that can lead to evolutionary diversification of strategies.
Strength-Based Flourishing Intervention to Promote Resilience in Individuals With Physical Disabilities in Disadvantaged Communities: A Randomized Controlled Trial

Purpose: The current study developed a strength-based flourishing intervention (SFI) and examined its efficacy on fostering the resilience of people with physical disabilities in poor areas, using a randomized (1:1) parallel-group controlled, and single-blind trial. Method: A total of 51 participants (M age = 42.16, standard deviation = 8.42; 43.14% males; 29 for the intervention group, whereas 22 for the control group) completed preintervention, postintervention, and 3-month follow-up tests. Results: The 2 × 3 mixed repeated measure analyses and post hoc analyses revealed a significant main group effect (F = 4.46, p = .04) and a short-term effect (i.e., 3 month; F = 6.35, p = .02) of the SFI. The results indicated that the SFI could significantly promote resilience in the intervention group. However, the effects of the intervention did not immediately appear. Discussion: The SFI could assist in providing research-based and cost-effective health services to promote flourishing and resilience in vulnerable populations.
The finer points of urban adaptation: intraspecific variation in lizard claw morphology

Human activity drastically transforms landscapes, generating novel habitats to which species must adaptively respond. Consequently, urbanization is increasingly recognized as a driver of phenotypic change. The structural environment of urban habitats presents a replicated natural experiment to examine trait–environment relationships and phenotypic variation related to locomotion. We use geometric morphometrics to examine claw morphology of five species of Anolis lizards in urban and forest habitats. We find that urban lizards undergo a shift in claw shape in the same direction but varying magnitude across species. Urban claws are overall taller, less curved, less pointed and shorter in length than those of forest lizards. These differences may enable more effective attachment or reduce interference with toepad function on smooth anthropogenic substrates. We also find an increase in shape disparity, a measurement of variation, in urban populations, suggesting relaxed selection or niche expansion rather than directional selection. This study expands our understanding of the relatively understudied trait of claw morphology and adds to a growing number of studies demonstrating phenotypic changes in urban lizards. The consistency in the direction of the shape changes we observed supports the intriguing possibility that urban environments may lead to predictable convergent adaptive change.
CONSTRUCCIÓN DEL SENTIDO DESDE LAS NARRATIVAS DE LOS MIEMBROS DE UNA ORGANIZACIÓN

This paper describes the construction of meaning in organizational practices using the naturalistic construction of meaning paradigm created by Kurtz and Snowden (2003) as a method of examining organizational events apart from the natural processes of control and expert opinion. Narratives, the stories and interactions, are fundamental elements of the cultural collective actions of an organization. Thus, organizational events are addressed beyond a positivist approach. A methodology for constructing meaning is proposed (narrative sensemaking). This method suggests listening to the different stories of the different actors in the organization and classifying them. Dyads or triads employ distinctive terms, allowing actors to tell their stories and describe their perceptions in a qualitative framework, and where possible a quantitative framework, depending on the computational tools to be used. This process allows a unique combination of statistical rigor (objectivity of numbers) along with the rich context provided by anecdotal evidence. Once the various narratives are collected, an interpretation workshop is organized. At this stage, consultants help to find emerging patterns captured from the number of story cues. Weak cues can help to anticipate future trends and help make decisions about future strategies and interventions.
The global COVID-19 pandemic at a crossroads: relevant countermeasures and ways ahead

Background Since the outbreak of novel coronavirus disease (COVID-19) in Wuhan, China at the beginning of December 2019, there have been over 11,200,000 confirmed cases in the world as of the 3rd July 2020, affecting over 213 countries and regions with nearly 530,000 deaths. The pandemic has been sweeping all continents, North America, Latin America, Europe, Middle East and South Asia among others at an alarming rapidity. Here, we provide an estimate of the scale of the pandemic spread under different scenarios of variation in key influencing parameters with a hybrid model. Methods We developed a new hybrid model of infectious disease transmission based on Cellular Automata (CA)-configured SEIR to analyse the COVID-19 outbreak and estimate its transmission pattern. A probabilistic contamination network is embedded in the pandemic transmission model to capture the randomness feature of person-to-person spread of the novel virus. We used the improved SEIR model to quantify the population contact state with isolation measures under different continuous time series contact probability via CA. We adjusted the modelling parameters to verify the model performance in accordance to the data from the reports published by the Chinese Center for Disease Control and Prevention. We simulated several scenarios by varying such key parameters as number of isolation rate, average contact times of the population, number of infected people before taking prevention and control measures, medical level and number of imported cases. Results In the baseline model, we identified that the isolation control as the most influencing factor that had the largest impact on decreasing the speed of the reproductive number, accelerating the arrival of the “inflection point” of pandemic prevention and control, and the death rate reduction. We estimated that the probability of people contacts and the number of the onset infected cases before prevention measures also had significant effect on the infection rate reduction with appropriate prevention measures adoption, which partly reflects the impact of timely measure on the severity of the outbreak. We found that imported cases will risk the domestic prevention. Conclusions Our modelling results clearly indicate that early-stage preventive measures are the most effective way to contain the pandemic spread and a strong interventionist approach needs to be adopted by policymakers vis-à-vis of the highly contagious nature of the COVID-19. Human resources, intensified isolation and confinement as well as special hospital buildings should be prioritised in countries with large number of infections to constrain the global transmission of the virulent infection. To do so, internationally coordinated actions require to be taken to replicate good practices to less infected countries and regions immediately.
Vitreous Seed Classification and Regression Patterns in Eyes With Retinoblastoma

Purpose: This work subclassifies retinoblastoma vitreous seeds and evaluates the efficacy, regression patterns, and adverse effects of combination intravitreal melphalan and topotecan chemotherapy for resistant and recurrent vitreous seeds. Methods: A retrospective review of medical records was conducted of patients with retinoblastoma and resistant or recurrent vitreous seeds who were treated with intravitreal melphalan and topotecan injections from August 2014 to July 2018. Main outcome measures included regression pattern, time for regression, time for recurrence of seeds, treatment outcomes, and ocular toxicity. Results: Nineteen eyes received 138 intravitreal injections over 74 treatment sessions (mean, 7.26 injections per eye); vitreous seeds regressed in 18 eyes. Of cloud vitreous seeds, curvilinear (n = 2) and sphero-linear (n = 2) subtypes were observed. During regression, some sphere seeds showed an intermediary streak-like pattern and took longer to regress (mean, 11.13 ± 14.05 months and 11.67 ± 8.62 injections) than those without the intermediary streak-like pattern (mean, 3.55 ± 2.57 months and 4.2 ± 1.87 injections). Mean follow-up was 34.87 ± 21.09 months (median, 35 months; range, 11-96 months). Anterior segment toxicity was seen in 10 (53%) eyes and posterior segment toxicity in 5 (26%) eyes. Kaplan-Meier survival estimates for globe salvage at 2 years was 94% and 73% at 5 years. Kaplan-Meier survival for vitreous seed–free status was 94% at 2 years and 65% at 5 years. Conclusions: An expanded vitreous seed classification system that further subcategorizes hitherto unrecognized vitreous seed morphology is needed. An intermediate streaking process results in a prolonged regression time for sphere vitreous seeds.
Structural Evolution of a 1.6 Ga Orogeny Related to the Final Assembly of the Supercontinent Nuna: Coupling of Episodic and Progressive Deformation

The poly‐deformed Georgetown Inlier (GTI) in NE Australia has recently been suggested to record a 1.60 Ga orogenic event related to final Nuna assembly. However, the structural evolution of the inlier has remained poorly constrained at the regional scale, and major tectono‐thermal events occurred at circa 1.55 Ga. The GTI is the type region for conceptualization of crenulation cleavage development and where the foliation intersection axes (FIAs) approach has been applied. We reevaluated both concepts by combining a multiscale petrostructural analysis with recent petrological and geochronological data. Three main deformation events (D1–D3) and associated composite fabrics (S1–S3) are identified in the GTI. The original NE orientation of 1.60 Ga D1 compressional structures is preserved in the low‐grade western domain, and the associated composite S1 fabric is retained as microstructural relicts within circa 1.55 Ga D2 low‐strain domains to the east. Extensional D2 structures, characterized by a pervasive, high‐grade, composite S2 foliation throughout the central and eastern domains, are interpreted as the footwall of a regional N‐S trending, W dipping crustal‐scale detachment zone. Syn‐D2 S‐type granites formed at 1.55 Ga as the detachment evolved. D1 stage was associated with Nuna assembly, whereas D2 represents postcollisional extension. Progressive foliation development occurred twice in the GTI, at 1.60 (D1) and 1.55 Ga (D2), but the previous FIA analysis only records the 1.60 Ga event and cannot be easily reconciled with the regional structural analysis. This study highlights that a multiscale and multidisciplinary approach is required to unravel the structural history of orogenic belts.
Further expansion of methane metabolism in the Archaea

The recent discovery of key methane-metabolizing genes in the genomes from the archaeal phyla Bathyarchaeota and Verstraetearchaeota has expanded our understanding of the distribution of methane metabolism outside of the phylum Euryarchaeota. Here, we recovered two near-complete crenarchaeotal metagenome-assembled genomes (MAGs) from circumneutral hot springs that contain genes for methanogenesis, including the genes that encode for the key methyl-coenzyme M reductase (MCR) complex. These newly recovered archaea phylogenetically cluster with Geoarchaeota (deep lineage of archaeal order Thermoproteales), and the MCR-encoding genes clustered with the recently reported methanogens within the Verstraetearchaeota. In addition, genes encoding hydroxybutyryl-CoA dehydratase were identified in the newly recovered methanogens, indicating they might carry out the β-oxidation process. Together, our findings further expanded the methane metabolism outside the phylum Euryarchaeota.
Large-scale Data Exploration Using Explanatory Regression Functions

Analysts wishing to explore multivariate data spaces, typically issue queries involving selection operators, i.e., range or equality predicates, which define data subspaces of potential interest. Then, they use aggregation functions, the results of which determine a subspace’s interestingness for further exploration and deeper analysis. However, Aggregate Query (AQ) results are scalars and convey limited information and explainability about the queried subspaces for enhanced exploratory analysis. Analysts have no way of identifying how these results are derived or how they change w.r. t query (input) parameter values. We address this shortcoming by aiding analysts to explore and understand data subspaces by contributing a novel explanation mechanism based on machine learning. We explain AQ results using functions obtained by a three-fold joint optimization problem which assume the form of explainable piecewise-linear regression functions. A key feature of the proposed solution is that the explanation functions are estimated using past executed queries. These queries provide a coarse grained overview of the underlying aggregate function (generating the AQ results) to be learned. Explanations for future, previously unseen AQs can be computed without accessing the underlying data and can be used to further explore the queried data subspaces, without issuing more queries to the backend analytics engine. We evaluate the explanation accuracy and efficiency through theoretically grounded metrics over real-world and synthetic datasets and query workloads.
Hermite-Hadamard inequality for new generalized conformable fractional operators

This paper is concerned to establish an advanced form of the well-known Hermite-Hadamard (HH) inequality for recently-defined Generalized Conformable (GC) fractional operators. This form of the HH inequality combines various versions (new and old) of this inequality, containing operators of the types Katugampula, Hadamard, Riemann-Liouville, conformable and Riemann, into a single form. Moreover, a novel identity containing the new GC fractional integral operators is proved. By using this identity, a bound for the absolute of the difference between the two rightmost terms in the newly-established Hermite-Hadamard inequality is obtained. Also, some relations of our results with the already existing results are presented. Conclusion and future works are presented in the last section.
Research on the Posture Control Method of Hexapod Robot for Rugged Terrain

This paper proposes a hexapod robot posture control method for rugged terrain to solve the problem of difficulty in realizing the posture control of a foot robot in rough terrain. The walking gait and original position of a six-legged robot is planned, and the Layer Identification of Tracking (LIT) strategy is developed to enable the robot to distinguish mild rugged terrain and severe rugged terrains automatically. The virtual suspension dynamic model is established. In mild rugged terrain, the posture maintenance strategy is adopted to keep the stability of the torso. In severe rugged terrain, the posture adjustment strategy is adopted to ensure the leg workspace and make it more widely adapt to the changing terrain, and a gravity center position adjustment method based on foot force distribution is designed to use foot force as feedback to control the position and attitude. The experiment of posture control in rough terrain and climbing experiment in the ladder terrain shows that the hexapod robot has good posture maintenance and posture adjustment effects when traversing complex terrain through the posture maintenance strategy and the posture adjustment strategy. Combined with the terrain identification method based on LIT, the hexapod robot can successfully climb the ladder terrain through the identification of the changing ladder terrain, and the movement of the posture adjustment process is stable.