Miracle-dz/UniFAR-FTUs huggingface dataset:
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks

Motivation Spatial Analysis of Functional Enrichment (SAFE) is a popular tool for biologists to investigate the functional organisation of biological networks via highly intuitive 2D functional maps. To create these maps, SAFE uses Spring embedding to project a given network into a 2D space in which nodes connected in the network are near each other in space. However, many biological networks are scale-free, containing highly connected hub nodes. Because Spring embedding fails to separate hub nodes, it provides uninformative embeddings that resemble a “hairball”. In addition, Spring embedding only captures direct node connectivity in the network and does not consider higher-order node wiring patterns, which are best captured by graphlets, small, connected, non-isomorphic, induced subgraphs. The scale-free structure of biological networks is hypothesised to stem from an underlying low-dimensional hyperbolic geometry, which novel hyperbolic embedding methods try to uncover. These include coalescent embedding, which projects a network onto a 2D disk. Results To better capture the functional organisation of scale-free biological networks, whilst also going beyond simple direct connectivity patterns, we introduce Graphlet Coalescent (GraCoal) embedding, which embeds nodes nearby on a hyperbolic disk if they tend to touch a given graphlet together. We use GraCoal embedding to extend SAFE. Through SAFE-enabled enrichment analysis, we show that GraCoal embeddings captures the functional organisation of the genetic interaction networks of fruit fly, budding yeast, fission yeast and E. coli better than graphlet-based Spring embedding. We show that depending on the underlying graphlet, GraCoal embeddings capture different topology-function relationships. We show that triangle-based GraCoal embedding captures functional redundancy between paralogous genes. Availability https://gitlab.bsc. es/dtello/graphlet-based-SAFE Contact natasha@bsc.as Supplementary information Supplementary data are available at Bioinformatics online.
Interplay between harvesting, planting density and ripening time affects coffee leaf rust dispersal and infection

Coffee leaf rust (CLR; Hemileia vastatrix) is one of the principal coffee diseases and has caused devastating loss of production around the globe. This fungus disperses between plants or regions through direct contact, water splash, or local turbulent wind conditions. Some studies have proposed that coffee harvesters can also bear CLR during harvesting. Their different trajectories depend on management and coffee plant characteristics, like the planting density or the ripening synchronicity, but also on the social organization of the plantation. However, it is not clear how relevant these movements are for CLR dispersal and plot-level infection in plots with other modes of CLR dispersal and different planting densities. Here we present a qualitative computational model to explore the role of coffee ripening synchronicity and the number of workers per plot in reproducing the different movement trajectories observed in the field. We then evaluate how these trajectories modify rust dispersal and change CLR infection in plots with increasing planting densities. We found that interplant asynchronous ripening and tree scarcity generate trajectories with long steps. In our model, the number of workers does not modify the trajectories. The harvest dispersal significantly increases coffee plot infection (up to 15%) compared to scenarios where only local mechanisms for CLR dispersal (contact-mediated or splash) are present. This effect is maximal for trajectories with long steps and in plantations with medium planting densities. At larger planting densities, plants are all already infected due to the local CLR dispersal. Our results aim to spur discussion on practices that could reduce the impact of harvesting and specific trajectories, in scenarios where one can benefit from asynchronous maturation of berries and shaded plantations. Some examples of practices include reducing the long-distance movements during the same day, for instance, by avoiding harvesting at the end of the harvest season when trees ripening asynchronicity and CLR levels are higher.
Passive Acoustic Monitoring for Marine Mammals at Site D in Onslow Bay, July 2010 - February 2011

A High-frequency Acoustic Recording Package (HARP; Wiggins and Hildebrand 2007) was deployed between July 2010 and February 2011 in Onslow Bay at Site D in 338 m. This HARP sampled at 200 kHz for 5 minutes of every 10 minutes and recorded for 210 days between 30 July 2010 and 24 February 2011. Long-Term Spectral Averages (LTSAs) were created for two frequency bands (10 Hz – 1000 Hz and 1 kHz – 100 kHz) and scanned for marine mammal vocalizations. Calls of blue whales, fin whales, minke whales, possible sei whales, Kogia spp. , Risso’s dolphins, sperm whales, and unidentified odontocetes were detected in the data.
Is Topical Nasal Steroid Useful for Treatment of Otitis Media with Effusion in Children?

BACKGROUND Otitis media with effusion is a common and important pediatric clinical problem; it is the leading cause of hearing impairment in children. Medical treatment remains controversial. AIM To evaluate the usefulness of using topical nasal steroids in the treatment of otitis media with effusion. PATIENTS AND METHODS Between November 2019 and October 2022, a prospective controlled clinical study was carried out in the department of otolaryngology at Al-Jerrahat Teaching Hospital in Medical City, Baghdad, Iraq. This study comprised 40 patients with bilateral otitis media with effusion (23 males, 17 females). Two groups were created for the patients. Patients in group A (20 patients) were treated with mometasone furoate nasal spray; 1 puff (50 µg) in each nostril daily for 2 weeks, while the 20 patients in group B were treated with saline nasal spray; 1 puff in each nostril daily for 2 weeks. At the end of the first and second weeks of treatment, otoscopic examination was used to monitor the patients. At the end of the second post-treatment week, pure tone audiometry and tympanometry were performed again. Normal otoscopic results, a type A tympanogram, and enhanced pure tone hearing threshold average to be ≤20 dB HL within 0, 5, 1, and 4 KHz were used to characterize resolution of OME. The association between two means was determined using an independent sample t-test, while the association between categorical variables was determined using an X2-test. RESULTS At the end of 2nd post-treatment week, there was no significant difference regarding improvement of otitis media with effusion regarding otoscopic, audiometric, and tympanometric results in both groups (P-value >0.05). CONCLUSION Topical nasal steroid is unuseful for the treatment of otitis media with effusion in the short-term.
Same-sex parent families and school progress of children: an association that disappeared over time

Previous research is divided as to whether children living in same-sex parent families achieve different outcomes compared to their peers. In this paper, we improve on earlier estimates of such differences and subsequently study whether and why the association between parental union sex-composition and children’s school progress changed over time. Data from the American Community Survey waves 2008-2015 (N=1,952,490 including 7,792 children living with a same-sex couple) indicates that children living with same-sex couples were more likely to be behind in school in the past, but that this association disappeared over time. Changes in socioeconomic characteristics of same-sex couples played a minor role. In 2008, it was only in areas with unfavorable laws and attitudes toward same-sex couples that children living with same-sex couples were more likely to be behind in school. This was especially the case for adopted children. In more recent periods, no effect of parental union sex composition on school progress is observed within any area or among any group studied. Based on where and when these changes took place, it is suggested that changing attitudes toward same-sex couples might have played an important role in equalizing school progress across groups.
THIC and OpenSPARC : Reducing Instruction Fetch Power in a Multithreading Processor

In the Edinburgh PASTA project we seek to automate the design and optimisation of customisable, ultra-low power, embedded processors. We do this by creating tools that are able to learn about the physical characteristics of the underlying silicon technology, and use that knowledge to synthesise the structure of an embedded processor. As the processor is now a flexible entity the compiler and instruction set simulator for that processor must be automatically extended or generated. Furthermore, the code optimisations that the compiler performs when translating from source code to the newly generated architecture must also be synthesised. The four main areas for automated synthesis are: The processor architecture, the micro-architecture, the instruction set simulator, and the compiler. In this talk we present an overview of our work on architecture/compiler co-design as part of the PASTA project.
Fundamental leaking mode (PL) propagation along the Tonga–Kermadec–Hikurangi–Macquarie margin

SUMMARY High-quality digital data from the temporary Leeds Tararua broad-band array, North Island, New Zealand and the station SNZO at Wellington often record long-period oscillations within the body wave train from large, shallow events in the Tonga^ Kermadec and Macquarie seismic zones at regional distances (8 0 ^25 0 ) along the Australasian/Paci¢c plate boundary. These arrivals are dispersed typically from 40 s period to 25 s and exhibit prograde elliptical polarization, which is diagnostic of the regional leaking modePL.Theoretical dispersion curves are generatedwith the simplest structure of a slow layer overlying a faster half-space. We have analysed the group velocity dispersion characteristics of the recorded waveforms and successfully modelled it as purely fundamental mode propagation in a low-velocity waveguide. Our best¢tting structure north of New Zealand consists of a low-velocity layer within the mantle (b~4.1^4.3 km s ˇ1 ) with a thickness of 32^34 km overlying a typical mantle structure. A seismicity study for the period 1976^1992 at SNZO shows that those events generating PL are shallow (10^60 km), with the highest concentration along the Kermadec arc, suggesting that the low-velocity layer is connected with this feature. We suggest that a small degree of partial melt within the uppermost mantle is responsible for creating a low-velocity channel within the region of backarc spreading in the Havre Trough. Dispersion curves derived from waveforms travelling northwards from events on the Macquarie Ridge give a similar structure with a slow layer 31 km thick with b~3.8 km s ˇ1 . This is consistent with the continental crust of South Island, which lies along most of the event^station paths.
Going Beyond BEM with BEM: an Insight into Dynamic Inflow Effects on Floating Wind Turbines

Blade Element Momentum (BEM) theory is the backbone of many industry-standard wind turbine aerodynamic models. To be applied to a broader set of engineering problems, BEM models have been extended since their inception and now include several empirical corrections. These models have benefitted from decades of development and refinement and have been extensively used and validated, proving their adequacy in predicting aerodynamic forces of horizontal axis wind 10 turbine rotors in most scenarios. However, the analysis of Floating Offshore Wind Turbines (FOWTs) introduces new sets of challenges, especially if new-generation large and flexible machines are considered. In fact, due to the combined action of wind and waves and their interaction with the turbine structure and control system, these machines are subject to unsteady motion, and thus unsteady inflow on the wind turbine’s blades, which could put BEM models to the test. Consensus is not present yet on the accuracy limits of BEM in these conditions. This study contributes to the ongoing research on the topic by 15 systematically comparing four different aerodynamic models, ranging from BEM to Computational Fluid Dynamics (CFD), in an attempt to shed light on the unsteady aerodynamic phenomena that are at stake in FOWTs and whether BEM is able to model them appropriately. Simulations are performed on the UNAFLOW 1:75 scale rotor during imposed harmonic surge and pitch motion. Experimental results are available for these conditions and are used for baseline validation. The rotor is analysed both in rated operating conditions and in low wind speeds, where unsteady aerodynamic effects are expected to be more 20 pronounced. Results show how BEM, despite its simplicity, if augmented with a dynamic inflow model, is able to adequately model the aerodynamics of FOWTs in most conditions.
Magnetic viscosity by localized shear flow instability in magnetized accretion disks

Differentially rotating disks are subject to the axisymmetric instability for perfectly conducting plasma in the presence of poloidal magnetic fields. For nonaxisymmetric perturbations, the authors find localized unstable eigenmodes whose eigenfunction is confined between two Alfven singularities at {omega}{sub d} = {+-} {omega}{sub A}, where {omega}{sub d} is the Doppler-shifted wave frequency, and {omega}{sub A} = k{parallel}v{sub A} is the Alfven frequency. The radial width of the unstable eigenfunction is {Delta}x {approximately} {omega}{sub A}/(Ak{sub y}), where A is the Oort`s constant, and k{sub y} is the azimuthal wave number. The growth rate of the fundamental mode is larger for smaller value of k{sub y}/k{sub z}. The maximum growth rate when k{sub y}/k{sub z} {approximately} 0.1 is {approximately} 0.2{Omega} for the Keplerian disk with local angular velocity {Omega}. It is found that the purely growing mode disappears when k{sub y}/k{sub z} > 0.12. In a perfectly conducting disk, the instability grows even when the seed magnetic field is infinitesimal. Inclusion of the resistivity, however, leads to the appearance of an instability threshold. When the resistivity {eta} depends on the instability-induced turbulent magnetic fields {delta}B as {eta}([{delta}B{sup 2}]), the marginal stability condition self-consistently determines the {alpha} parameter of the angular momentum transportmore » due to the magnetic stress. For fully ionized disks, the magnetic viscosity parameter {alpha}{sub B} is between 0.001 and 1. The authors` three-dimensional MHD simulation confirms these unstable eigenmodes. It also shows that the {alpha} parameter observed in simulation is between 0.01 and 1, in agreement with theory. The observationally required smaller {alpha} in the quiescent phase of accretion disks in dwarf novae may be explained by the decreased ionization due to the temperature drop. « less
Silent Users in Online Social Networks and Delurking Mechanisms

The notion of lurking is more and more used these days. Lurkers (also called silent users) are Online Social Networks (OSNs) members, who consciously decide to observe, but not to participate. There is an emerging need to delurk these users and utilize this knowledge in computer science fields. In our work, we present the notion of lurkers in on-line social networks and the different categories of delurking mechanisms, including influence maximization.
A comparative analysis of routes generated by Web Mapping APIs

Web Mapping APIs (WMAs), such as Google Maps API, are widely used by researchers across different fields to develop geospatial Web applications. Among maps and map functionalities provided through WMAs, route and direction are prominent and commonly available. Given that each WMA uses a different map database and a different set of assumptions, the routes they generate, for the same pairs of origin and destination addresses, are different. Considering the current void in literature on WMAs and the routes they generate, in this paper, select common WMAs are compared and analyzed based on their routing techniques. The results of these comparisons will benefit researchers by helping them better understand the behavior of WMAs in producing routes, which in turn can be used for selecting suitable WMAs for research projects or developing applications (such as navigation and location-based services). The process in which routes are evaluated can also be used as a guideline to help researchers explore behavior of WMAs in generating routes.
The Effect of Company Size, Leverage and Return on Asset on Earnings Management: Case Study Indonesian

: This paper aims to analyze the effect of company size, leverage and return on assets on earnings management. The research method uses descriptive methods with a quantitative approach. The research data used financial statement data on the Indonesia Stock Exchange from 2014 to 2018. Data sources were obtained from the Indonesia Stock Exchange website. The research findings explain that company size has no influence on earnings management, while leverage and return on assets have an influence on earnings management.
Reliable Anti-Cancer Drug Sensitivity Prediction and Prioritization

Abstract The application of machine learning (ML) to solve real-world problems does not only bear great potential but also high risk. One fundamental challenge in risk mitigation is to ensure the reliability of the ML predictions, i.e., the model error should be minimized, and the prediction uncertainty should be estimated. Especially for medical applications, the importance of reliable predictions can not be understated. Here, we address this challenge for anti-cancer drug sensitivity prediction and prioritization. To this end, we present a novel drug sensitivity prediction and prioritization approach guaranteeing user-speciﬁed certainty levels. The developed conformal prediction (CP) approach is applicable to classiﬁcation, regression, and simultaneous regression and classiﬁcation. Additionally, we propose a novel drug sensitivity measure that is based on clinically relevant drug concentrations and enables a straightforward prioritization of drugs for a given cancer sample.
SHORT REPORT Spatial and temporal patterning of bank vole demography and the epidemiology of the Puumala hantavirus in northeastern France

SUMMARY Epidemiological data from bank voles, Myodes glareolus , naturally infected by the hantavirus Puumala (PUUV) were collected by a capture–mark–recapture protocol from 2000 to 2002 in the French department of Ardennes. Four monitored trapping sites were established in two forests located in two cantons (Flize and Montherme´). We captured 912 bank voles corresponding to 557 diﬀerent individuals during 8820 trapping nights for an overall trapping success of 10.34%. The average PUUV seroprevalence was 22.4%. Characteristics of the system reported in North European countries are conﬁrmed in France. PUUV seroprevalence and abundance of rodents appeared weakly linked. Adult voles were more frequently antibody-positive,
(2021). A secondary analysis of the childhood obesity prevention Cochrane Review through a wider determinants of health lens: implications for research funders, researchers, policymakers and practitioners.

Background: Randomised controlled trials (RCTs) are often regarded as the gold standard of evidence, and subsequently go on to inform policymaking. Cochrane Reviews synthesise this type of evidence to create recommendations for practice, policy, and future research. Here, we critically appraise the RCTs included in the childhood obesity prevention Cochrane Review to understand the focus of these interventions when examined through a wider determinants of health (WDoH) lens. Methods: We conducted a secondary analysis of the interventions included in the Cochrane Review on “ Interventions for Preventing Obesity in Children ” , published since 1993. All 153 RCTs were independently coded by two authors against the WDoH model using an adaptive framework synthesis approach. We used aspects of the Action Mapping Tool from Public Health England to facilitate our coding and to visualise our findings against the 226 perceived causes of obesity. Results: The proportion of interventions which targeted downstream (e.g. individual and family behaviours) as opposed to upstream (e.g. infrastructure, environmental, policy) determinants has not changed over time (from 1993 to 2015), with most intervention efforts (57.9%) aiming to change individual lifestyle factors via education-based approaches. Almost half of the interventions (45%) targeted two or more levels of the WDoH. Where interventions targeted some of the wider determinants, this was often achieved via upskilling teachers to deliver educational content to children. No notable difference in design or implementation was observed between interventions targeting children of varying ages (0 – 5 years, 6 – 12 years, 13 – 18 years).
Multicultural and

Political communication is very supportive in influencing voters' alignment with politicians in general election activities. Every politician must have an effective communication strategy to be able to win elections. This study aims to analyse the political communication strategy of ethnic minorities to the ethnic majority in the election of regional heads of South Sulawesi Province. The method used in this research is descriptive qualitative. Sources of primary data were obtained from interviews with informants, and to support the primary data were studied from documents related to this research. The results of this study indicate that the political communication strategy of ethnic minorities can be seen from both good and bad sides, both in this case, namely with the aim of improving natural and social conditions, it is considered bad by the community because political communication is used only for election purposes. Ethnic minorities are expected to be more adaptive to their political activities, and not leave a bad impression on society.
Kinematics of the Pacific Equatorial Undercurrent: An Eulerian and Lagrangian Approach from GCM Results

Abstract Three-dimensional monthly velocity fields from an ocean general circulation model are used to study the annual mean mass balance of the Pacific Equatorial Undercurrent (EUC). Eulerian diagnostics are used to evaluate the various meridional, vertical, and zonal mass fluxes related to the EUC. There are several distinct regimes along the equator, showing clear asymmetries between the western and eastern parts of the basin, and between the northern and southern edges of the EUC. Meridional fluxes are decomposed into pure Ekman divergence and geostrophic convergence, and it is shown that the asymmetries are mainly related to the spatial structure of the Ekman divergence, and thus to that of the trade winds. Lagrangian calculations are used to evaluate accurately the mass transfers between various sections of the EUC and between the EUC domain and the Tropics. The authors show that geostrophic convergence only ventilates the upper layers of the EUC and that the EUC really is a tongue of water flowing .
Indonesia: A Vulnerable Country in the Face of Climate Change

This article reviews the causes of Indonesia’s high greenhouse gas releases, the impacts climate change has on the country, and the effects of climate change. It shows that deforestation, forest fires and the degradation of peat land have been the main causes for Indonesia being the world’s third largest emitter of greenhouse gases. It summarizes some of the main impacts climate change has in Indonesia, which include, but are not limited to: temperature increase, intense rainfall, sea level rise, and a threat to food security. It examines the effects climate change has on (i) Indonesia’s economy and poor people, (ii) human health, and (iii) Indonesia’s environment and biodiversity.