Miracle-dz/UniFAR-FTUs huggingface dataset:
New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.
Distinct microcolony morphologies promote flow-dependent bacterial colonization

Fluid flows can impact bacterial behaviors in unexpected ways (1–3). The high shear rate in heart valves should reduce colonization, but in endocarditis, valves are often counter-intuitively colonized by Staphylococcus aureus and Enterococcus faecalis (4, 5). Here we discover bacteria-specific mechanisms for preferential surface colonization in higher shear rate environments. This behavior enables bacteria that are outcompeted in low flow to dominate in high flow. Flow-dependent colonization by S. aureus and E. faecalis are mediated by distinct mechanisms that depend on each species’ microcolony morphologies: transport of a dispersal signaling molecule for clustered S. aureus and mechanical forces for linear chains of E. faecalis. These results suggest that microcolony morphologies have previously unappreciated costs and benefits in different environments, like those introduced by flow. One-Sentence Summary Bacterial surface colonization in high fluid flow depends upon the species’ clustered or chained microcolony morphologies.
The unique Legionella longbeachae capsule favors intracellular replication and immune evasion

Legionella longbeachae and Legionella pneumophila cause Legionnaires’ disease despite species-specific differences in environmental niches, disease epidemiology, and genomic content. Here, we characterized a new L. longbeachae virulence factor, a capsule that is expressed in post-exponential growth phase as shown by electron microscopy. Analysis of the capsule composition via HLPC revealed the presence of a highly anionic polysaccharide absent in a capsule mutant. The capsule is crucial for replication and virulence in vivo in a mouse model of infection and in the natural host Acanthamoeba castellanii. It has anti-phagocytic function when encountering innate immune cells, it is involved in a low cytokine responses in mice and in human monocyte derived macrophages and helps to dampen the innate immune response. The L. longbeachae capsule is a novel virulence factor, unique among known Legionella species, that aids L. longbeachae to survive in specific niches and partly confers L. longbeachae its unique infection characteristics.
YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing

X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we integrate time-course data of gene silencing and decreasing inactive X (Xi) chromatin accessibility in mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs). Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results indicate that YY1 acts as barrier to Xist-mediated silencing that is removed only at late stages of the XCI process.
The role of IL-6 in dopamine dysregulation underlying anhedonia phenotype in rats

Aims To investigate the role of peripheral metabolic change and chronic low-grade inflammation on striatal dopamine dynamics and anhedonia-like behaviour induced by hypothalamic–pituitary–adrenal (HPA) axis disruption. Methods Wistar rats were trained in a progressive-ratio/concurrent effort-related choice paradigm to assess effort-related decision making. After reaching a stable baseline, animals received daily injections of adrenocorticotrophic hormone (ACTH) or saline for 24 days. On the 23rd and 24th day, animals received a bupropion challenge (10mg/kg and 20mg/kg respectively) 30 minutes prior to the behavioural testing session. On the 25th day, animals received a single injection of bupropion (20mg/kg) 30 minutes prior to euthanasia. Peripheral and central inflammatory markers were assessed through ELISA and In-Cell Western assay; glucose transport activity was assessed in peripheral blood mononuclear cells though a commercial assay kit; brain levels of dopaminergic and inflammatory markers were assessed in the nucleus accumbens (NAc) and prefrontal cortex (PFC) through immunohistochemistry; and serum central carbon metabolism metabolites were assessed through a metabolomics approach. Results ACTH induced an anhedonia-like phenotype, decreased tyrosine hydroxylase (TH) levels in the NAc, increased peripheral IL-6 levels, and decreased glucose transport activity and glucose metabolites when compared to control group. Bupropion treatment was not able to reverse the anhedonic phenotype. Glucose uptake was positively correlated to behaviour; TH levels were correlated to microglia volume; metabolites were correlated to TH levels; and IL6 was correlated to TH levels and metabolites. Conclusion Chronic ACTH treatment can induce treatment-resistant anhedonia in rats, and the interaction between peripheral immunometabolic state and central dopamine synthesis is a potential mechanism underlying this phenotype.
Stable isotopes disentangle niche partitioning and species co-occurrence in a multi-level marine mutualism

Ecologists have long sought general explanations for the co-occurrence of ecologically similar taxa. Niche theory explains co-occurrence via functional differences among taxa that reduce competition and promote resource partitioning. Alternatively, the unified neutral theory of biodiversity and biogeography suggests that co-occurrence can be attributed to stochastic processes, and thus, presupposes that ecologically similar species that occur in sympatry are functionally analogous. We test these alternative hypotheses in multiple dimensions using the most diverse crustacean-sea anemone symbiosis from coral reefs in the Tropical Western Atlantic. δ13C and δ15N stable isotope analyses of six crustacean symbionts that co-occur around the host anemone Bartholomea annulata exhibit highly differentiated isotopic niche space spanning three trophic levels. As multiple crustacean species within the symbiosis have been documented as cleaners that remove parasites from reef fishes, we extended our investigation into the broader cleaner community. Our stable isotope analyses of cleaners shows that only Pederson’s cleaner shrimp Ancylomenes pedersoni exhibits δ15N isotopic signatures that are consistent with a dedicated cleaning lifestyle. Co-occurring species that have been previously described to clean reef fishes such as Periclimenes yucatanicus, Stenopus hispidus, and Stenorhynchus seticornis all occupy trophic levels well below An. pedersoni. Taken together, our data are consistent with the expectations of niche theory: co-occurring symbiotic crustaceans have highly partitioned niche space with low levels of functional redundancy. Finally, our findings reinforce and extend the ecological importance of An. pedersoni as likely the only dedicated cleaner shrimp on coral reefs in the Tropical Western Atlantic.
Comparison of the cyclic fatigue resistance of WaveOne Gold, Reciproc Blue, and 2Shape NiTi systems in the root canal manipulation

: Mechanical files have drastically altered the treatment protocol in endodontics, allowing for quicker and easier treatment times and a more thorough debridement of the canal system. Despite the advantages of the Nickel-Titanium (NiTi) alloy files, instrument separation remains a major concern when using these files.The study aimed to compare the cyclic fatigue resistance of WaveOne Gold, Reciprocation (Reciproc) Blue, and 2Shape NiTi systems having a different design and metallurgic properties. The instruments were rotated in an artificial canal made of stainless steel with 45°angles and a radius of curvature of 8 mmand 5mm of curvature until fracture occurred, the time to fracture was recorded in seconds. Also, the number of cycles to fracture was calculated. Data were statistically analyzed using one way ANOVA and Bonferroni test. Reciproc Blue had the highest cyclic fatigue resistance in time to fracture compared to WaveOne Gold and 2Shape ( P < 0.05), however, there was no significant difference between WaveOne Gold and 2Shape in terms of time to fracture ( P < 0.05). No significant in the number of cycles to fracture when comparing WaveOne Gold with Reciproc Blue and 2Shape and highly significant difference when comparing Reciproc Blue with 2Shape. No significant in the length of fracture among group tested. The present study, Reciproc Blue NiTi files showed statistically higher cyclic fatigue resistance than the other Ni-Ti files tested.
Diffusion coefficients in gravel under unsaturated conditions

Diffusion coefficients were experimentally determined in unsaturated gravel to evaluate the effectiveness of gravel as a diffusion barrier to ionic transport in the vadose zone. Water contents were fixed by use of an ultracentrifuge with an ultralow constant rate flow pump supplying solution to the sample via a rotating seal. Once the gravel was at hydraulic steady state, the electrical conductivity was measured, and the diffusion coefficient calculated using the Nernst-Einstein equation. Diffusion coefficient values for potassium ion (De) in four types of angular gravel ranged from 1.7 × 10−11 m2/s (1.7 × 10−7 cm2/s) for a 6.3–9.5 mm angular granitic gravel at a volumetric water content of 5.5% to 2.2 × 10−14 m2/s (2.2 × 10×10 cm2/s) in a 4.0–6.3 mm quartzite gravel at a volumetric water content of 0.47%. Variations in De values resulted primarily from differences in water content which depends on gravel type and particle size.
A Chronological Assessment of Ghana’s Forestry Policies in Precolonial and Colonial Era: Lessons for Forest Management in Contemporary Ghana

This article examines historical trends in the character of forest management in the Gold Coast (now Ghana). Relying on the Socio-Economic Approach to policy analysis, the paper discusses the influence of changing socio-economic factors and power structures on forest management in pre-colonial and colonial Ghana. In so doing, the article also interrogates the real motives behind the colonial forest reservation policy in the Gold Coast. Contrary to the belief that colonial reservation policy was a ploy take the management of lucrative forest resources from local people; the paper argues that centralised forest reservation policy was adopted by the British colonial administration in response to genuine environmental concerns. Finally, the effects of colonial forest policies on forest governance in modern Ghana are discussed.
Detection of long-term changes in precipitation and discharge in the Meuse basin

Long records (>1911) of discharge and precipitation in the Meuse basin have been investigated by statistical methods for detection of non-homogeneity (trends and jumps) in the data series. Over the past century, annual total precipitation (November to October) in the basin has significantly increased since 1980 as well as k-day extreme precipitation depths (e.g. over 5 days and 10 days). No significant trend or change-point was identified for the annual average discharge of the Meuse River. However, a significant increase since 1984 was found for the annual and winter half-year maximum daily discharges, while a significant downward trend was identified for the low flows (e.g. annual minimum 10-day moving average), with an obvious decrease since 1933. The annual runoff coefficient of the river has also significantly decreased since 1933. The preliminary results suggest that the increase of flood peaks in the Meuse River since the early 1980s can broadly be ascribed to climatic variability.
Explicit iterative computation of diffusive vapour field in the 3-D snow matrix: preliminary results for low flux metamorphism

Abstract The metamorphism of seasonal snow is classically considered as limited by vapour diffusion in the pore phase. To account for the lack of knowledge of the ice–vapour reaction coefficient near 0 ° C, the assumption of a reaction-limited metamorphism was first tested in three-dimensional simulations at low and very low temperature gradients; however, the validity of such results is difficult to verify experimentally. By a reasoned use of traditional iterative schemes, vapour diffusion is now simulated in three dimensions on tomographic snow data, mapping the gradient of vapour pressure near the grains. Repeating this process may provide a way to simulate the isothermal metamorphism without grain packing at a reasonable expense of computation time. Preliminary results are compared with existing computations made within the reaction-limited hypothesis.
Complementing a Policy with a Different Observation Space

We consider the problem of improving upon a black-box policy which operates on a different observation space than the learner. Such problems occur when augmenting an existing hand-engineered system with a new machine learning model or in a shared autonomy / human-AI complementarity context. We prove that following the naive policy gradient can lead to a decrease in performance because of incorrect grounding in a different observation space. Then, if we have access to both sets of observation at train time, we derive a method for correctly estimating a policy gradient via an application of backdoor adjustment. If we don’t, we prove that under certain assumptions, we can use the proxy correction to correctly estimate a direction of improvement.
Analysis of terrestrial heat-flow profiles across the Rio Grande rift and southern Rocky Mountains in northern New Mexico

Every fall since 1950, the New Mexico Geological Society (NMGS) has held an annual Fall Field Conference that explores some region of New Mexico (or surrounding states). Always well attended, these conferences provide a guidebook to participants. Besides detailed road logs, the guidebooks contain many well written, edited, and peer-reviewed geoscience papers. These books have set the national standard for geologic guidebooks and are an essential geologic reference for anyone working in or around New Mexico.
A 7-Yr Climatology of the Initiation, Decay, and Morphology of Severe Convective Storms during the Warm Season over North China

: The present work established a 7-yr climatology of the initiation, decay, and morphology of severe convective storms (SCSs) during the warm seasons (May–September) of 2011–18 (except 2014) over North China. This was achieved by using severe weather reports,precipitation observations, and composite Doppler radar reﬂectivity data. A total of 371 SCSs were identiﬁed. SCSs primarily initiatedaround noon with the highest frequency over the high terrain of Mount Taihang, and they mostly decayed over the plains at night. The storm morphologies were classiﬁed into three types of cellular storms (individual cells, clusters of cells, and broken lines), six types of linear systems (convective lines with no stratiform, with trailing stratiform, leading stratiform, parallel stratiform, embedded lines, and bow echoes), and nonlinear systems. Three types of severe convective weather, namely, short-duration heavy rainfall, hail, and thunderstorm high winds, associated with these morphologies were investigated. A total of 1429 morphology samples from the 371 SCSs were found to be responsible for 15966 severe convective weather reports. Nonlinear systems were the most frequent morphology, followed by clusters of cells. Convective lines with trailing stratiform were the most frequent linear morphology. Linear(nonlinear)systemsproducedthemostshort-durationheavyrainfall(hailandthunderstormhighwind)reports.Bow echoesweremostefﬁcientinproducingbothshort-durationheavyrainfallandthunderstormhighwindreportswhereas brokenlineshadthehighestefﬁciency forhailproduction. Theresultsinthepresentstudyarehelpfulforlocalforecastersto better anticipate the storm types and associated hazardous weather.
Distinctive aerosol-cloud-precipitation interactions in marine boundary layer clouds from the 1 ACE-ENA and SOCRATES aircraft field campaigns 2

The aerosol-cloud-precipitating interaction within the cloud-topped Marine Boundary Layer 12 (MBL), are being examined using aircraft in-situ measurements from Aerosol and Cloud Experiments in 13 the Eastern North Atlantic (ACE-ENA) and Southern Ocean Clouds Radiation Aerosol Transport 14 Experimental Study (SOCRATES) field campaigns. SOCRATES clouds have a larger number of smaller 15 cloud droplets compared to ACE-ENA summertime and wintertime clouds. The ACE-ENA clouds, 16 especially in wintertime, exhibit pronounced drizzle formation and growth, attributed to the strong in-17 cloud turbulence that enhances the collision-coalescence process. Furthermore, the Aerosol-Cloud 18 Interaction (ACI) indices from the two aircraft field campaigns suggest distinct sensitivities. The aerosols 19 during ACE-ENA winter are more likely to be activated into cloud droplets due to more larger aerosols 20 and strong vertical turbulence. The enriched aerosol loading during SOCRATES generally leads to 21 smaller cloud droplets competing for available water vapor and exhibiting a stronger ACI. The ACI 22 calculated near the cloud base was noticeably larger than the layer-mean and near-cloud-top, owing to 23 the closer connection between the cloud layer and sub-cloud aerosols. Notably, the sensitivities of cloud 24 base precipitating rates to cloud-droplet number concentrations are more pronounced during the ACE-25
Modeling Coupled Climate, Ecosystems, and Economic Systems

Human economies and ecosystems form a coupled system coevolving in time and space, since human economies use ecosystems services and at the same time affect ecosystems through their production and consumption activities. The study of the interactions between human economies and ecosystems is fundamental for the efficient use of natural resources and the protection of the environment. This necessitates the development and use of models capable of tracing the main interactions, links and feedbacks. In developing this chapter, our objective was to focus on a segment of rapidly developing literature on coupled ecological/economic models with an emphasis on climate change. The advantage of this approach is that it introduces the reader to a very important current research topic, but it also allows, by using climate as the reference ecosystem, the exploration of new modeling approaches which are relevant and useful for the modeling of other types of coupled ecological/economic systems. These include modeling of deep structural uncertainty by using robust control methods, exploring modeling through cumulative carbon budgeting, studying spatial transport phenomena and spatial aspects in economic/ecological modelling.
Financial literacy and stock market participation :

This research studies the moderating effect of country-specific social connectedness on the relation between financial literacy and stock market participation. This is done by using the extensive and multi-country SHARE data. The positive relation between financial literacy and stock market participation is reconfirmed. Moreover, the findings show that country-specific social connectedness significantly moderates the relation between financial literacy and stock market participation. The findings are robust and indicate that the predictive power of financial literacy on stock market participation decreases if country-specific social connectedness increases. This research is following up on contemporary literature and contributes to the explanation of the stock market participation puzzle on a macroeconomic scale.
UvA-DARE (Digital Academic Repository) Salt stains from evaporating droplets

The study of the behavior of sessile droplets on solid substrates is not only associated with common everyday phenomena, such as the coffee stain effect, limescale deposits on our bathroom walls , but also very important in many applications such as purification of pharmaceuticals, de-icing of airplanes, inkjet printing and coating applications. In many of these processes, a phase change happens within the drop because of solvent evaporation, temperature changes or chemical reactions, which consequently lead to liquid to solid transitions in the droplets. Here we show that crystallization patterns of evaporating of water drops containing dissolved salts are different from the stains reported for evaporating colloidal suspensions. This happens because during the solvent evaporation, the salts crystallize and grow during the drying. Our results show that the patterns of the resulting salt crystal stains are mainly governed by wetting properties of the emerging crystal as well as the pathway of nucleation and growth, and are independent of the evaporation rate and thermal conductivity of the substrates.
Inﬂuence of anxiety on health outcomes in COPD

Background Psychological functioning is an important determinant of health outcomes in chronic lung disease. To better deﬁne the role of anxiety in chronic obstructive pulmonary disease (COPD), a study was conducted of the inter-relations between anxiety and COPD in a large cohort of subjects with COPD and a matched control group. Methods Data were used from the FLOW (Function, Living, Outcomes, and Work) cohort of patients with COPD (n ¼ 1202) and matched controls without COPD (n ¼ 302). Anxiety was measured using the Anxiety subscale of the Hospital Anxiety and Depression Scale. Results COPD was associated with a greater risk of anxiety in multivariable analysis (OR 1.85; 95% CI 1.072 to 3.18). Among patients with COPD, anxiety was related to poorer health outcomes including worse submaximal exercise performance (less distance walked during the 6-min walk test: (cid:2) 66.3 feet for anxious vs non-anxious groups; 95% CI (cid:2) 127.3 to (cid:2) 5.36) and a greater risk of self-reported functional limitations (OR 2.41; 95% CI 1.71 to 3.41). Subjects with COPD with anxiety had a higher longitudinal risk of COPD exacerbation in Cox proportional hazards analysis after controlling for covariates (HR 1.39; 95% CI 1.007 to 1.90). Conclusion