Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytest: quality control for phylogenetic analyses

Abstract Motivation The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with the increase in genetic sequencing and the use of real-time pipelines e.g. in the SARS-CoV-2 era. Implementations of real-time phylogenetic analyses require automated testing to make sure that problems in the data are caught automatically within analysis pipelines and in a timely manner. Here, we present Phytest (version 1.1) a tool for automating quality control checks on sequences, trees and metadata during phylogenetic analyses. Results Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples. Availability and implementation Phytest source code is available on GitHub (https://github.com/phytest-devs/phytest) and can be installed via PyPI with the command ‘pip install phytest’. Extensive documentation can be found at https://phytest-devs.github. io/phytest/. Supplementary information Supplementary data are available at Bioinformatics online.
Dynamic contrast‐enhanced MRI and Doppler sonography in patients with squamous cell carcinoma of head and neck treated with induction chemotherapy

In view of the inherent limitations associated with performing dynamic contrast enhanced‐magnetic resonance imaging (DCE‐MRI) in clinical settings, current study was designed to provide a proof of principle that Doppler sonography and DCE‐MRI derived perfusion parameters yield similar hemodynamic information from metastatic lymph nodes in squamous cell carcinomas of head and neck (HNSCCs). Strong positive correlations between volume fraction of plasma space in tissues (Vp) and blood volume (r = 0.72, p = 0.02) and between Vp and %area perfused (r = 0.65, p = 0.04) were observed. Additionally, a moderate positive correlation trending towards significance was obtained between volume transfer constant (Ktrans) and %area perfused (r = 0.49, p = 0.09).
On the accretion properties of young stellar objects in the L1615/L1616 cometary cloud

We present the results of FLAMES/UVES and FLAMES/GIRAFFE spectroscopic observations of 23 low-mass stars in the L1615/L1616 cometary cloud, complemented with FORS2 and VIMOS spectroscopy of 31 additional stars in the same cloud. L1615/L1616 is a cometary cloud in which the star formation was triggered by the impact of massive stars in the Orion OB association. From the measurements of the lithium abundance and radial velocity, we confirm the membership of our sample to the cloud. We use the equivalent widths of the Hα, Hβ, and the He i λ5876, λ6678, λ7065 A emission lines to calculate the accretion luminosities, Lacc, and the mass accretion rates, Ṁacc. We find in L1615/L1616 a fraction of accreting objects (∼30%), which is consistent with the typical fraction of accretors in T associations of similar age (∼3 Myr). The mass accretion rate for these stars shows a trend with the mass of the central object similar to that found for other star-forming regions, with a spread at a given mass that depends on the evolutionary model used to derive the stellar mass. Moreover, the behavior of the 2MASS/WISE colors with Ṁacc indicates that strong accretors with log Ṁacc >∼ −8.5 dex show large excesses in the JHKs bands, as in previous studies. We also conclude that the accretion properties of the L1615/L1616 members are similar to those of young stellar objects in T associations, like Lupus.
PULSE PROFILES FROM THERMALLY EMITTING NEUTRON STARS

The problem of computing the pulse profiles from thermally emitting spots on the surface of a neutron star in general relativity is reconsidered. We show that it is possible to extend Beloborodov's approach to include (multiple) spots of finite size in different positions on the star surface. The results for the pulse profiles are expressed by comparatively simple analytical formulae which involve only elementary functions.
Instability of charged wormholes supported by a ghost scalar field

In previous work, we analyzed the linear and nonlinear stability of static, spherically symmetric wormhole solutions to Einstein's field equations coupled to a massless ghost scalar field. Our analysis revealed that all these solutions are unstable with respect to linear and nonlinear spherically symmetric perturbations and showed that the perturbation causes the wormholes to either decay to a Schwarzschild black hole or undergo a rapid expansion. Here, we consider charged generalization of the previous models by adding to the gravitational and ghost scalar field an electromagnetic one. We first derive the most general static, spherically symmetric wormholes in this theory and show that they give rise to a four-parameter family of solutions. This family can be naturally divided into subcritical, critical and supercritical solutions depending on the sign of the sum of the asymptotic masses. Then, we analyze the linear stability of these solutions. We prove that all subcritical and all critical solutions possess one exponentially in time growing mode. It follows that all subcritical and critical wormholes are linearly unstable. In the supercritical case we provide numerical evidence for the existence of a similar unstable mode.
Star formation, structure, and formation mechanism of cometary globules: near-infrared observations of CG 1 and CG 2

Cometary globule (CG) 1 and CG 2 are "classic" CGs in the Gum Nebula. They have compact heads and long dusty tails that point away from the centre of the Gum Nebula. We study the structure of CG 1 and CG 2 and the star formation in them to find clues to the CG formation mechanism. The two possible mechanisms, radiation-driven implosion (RDI) and a supernova (SN) blast wave, produce a characteristic mass distribution where the major part of the mass is situated in either the head (RDI) or the tail (SN). CG 1 and CG 2 were imaged in the near infrared (NIR) JsHKs bands. NIR photometry was used to locate NIR excess objects and to create extinction maps of the CGs. The A_V maps allow us to analyse the large-scale structure of CG 1 and CG 2. Archival images from the WISE and Spitzer satellites and HIRES-processed IRAS images were used to study the small-scale structure. In addition to the previously known CG 1 IRS 1 we discovered three new NIR-excess objects, two in CG 1 and one in CG 2. CG 2 IRS 1 is the first detection of star formation in CG 2. Spectral energy distribution (SED) fitting suggests the NIR-excess objects are young low-mass stars. CG 1 IRS 1 is probably a class I protostar in the head of CG 1. CG 1 IRS 1 drives a bipolar outflow, which is very weak in CO, but the cavity walls are seen in reflected light in our NIR and in the Spitzer 3.6 and 4.5 mum images. Strong emission from excited polycyclic aromatic hydrocarbon particles and very small grains were detected in the CG 1 tail. The total mass of CG 1 in the observed area is 41.9 Msun of which 16.8 Msun lies in the head. For CG 2 these values are 31.0 Msun total and 19.1 Msun in the head. The observed mass distribution does not offer a firm conclusion for the formation mechanism of these CGs: CG 1 is in too evolved a state, and in CG 2 part of the globule tail was outside the observed area. (abridged)
Parallelized continuous flow dielectrophoretic separation of DNA

Numerous microfluidic separation applications have been shown in the past years providing a fast analysis of biological samples like DNA or proteins. Microfluidic separation based on dielectrophoresis (DEP), that is the migration of a polarizable object in an inhomogeneous electric field, provides numerous advantages. However, the main drawback of DEP separation devices is that they are not sufficient for large‐scale sample purification due to the lack of high sample throughput. In this work, we present for the first time a microfluidic device with two parallelized dielectrophoretic separations of (biological) samples smaller than 1 µm. The separation is carried out by means of insulator‐based DEP, that is an insulating ridge reduced the flow through height and thus created a nanoslit at which the selective DEP forces occur. The device consists of a cross injector, two parallel operation regions and separate harvesting reservoirs where the samples are collected. Each DEP operation region contains an insulating ridge. We successfully demonstrate the separation of 100 and 40 nm beads and 10 and 5 kbp DNA with a separation purity of more than 80%. This states the proof‐of‐concept for up‐scaling of dielectrophoretic separation by parallelization. As the present technique is virtually label‐free, it offers a fast purification, for example in the production of gene vaccines.
Detecting gravitational waves from the Galactic center with pulsar timing

Abstract Black holes orbiting the supermassive black hole (SMBH) Sgr A* in the Galactic center (GC) of the Milky Way generate gravitational waves (GW). The resulting spectrum, due to stars and black holes (BHs), is continuous below 40 nHz while individual BHs within about 200 AU of the central SMBH stick out in the spectrum at higher frequencies. The GWs can be detected by timing radio pulsars within a few parsecs of this region. Future observations with the Square Kilometer Array of such pulsars with sufficient timing accuracy may be sensitive to signals from intermediate mass BHs (IMBH) in a 3 year observation baseline. The recent detection of radio pulsations from the magnetar SGR J1745–29 very near the GC opens up the possibilities of detecting millisecond pulsars (which can be used as probes of the GWs) through lines of sight with only moderate pulse and angular broadening due to scattering.
Recent Apolipoprotein CIII trials

Purpose of review This review will briefly revise the evidence concerning the pharmacological inhibition of Apolipoprotein CIII (ApoCIII) in patients with hypertriglyceridemia. Recent findings ApoCIII is a plasma apolipoprotein playing a major role in the metabolism of triglyceride-rich lipoproteins, namely chylomicrons and very-low-density lipoproteins as well as in the pathological processes involved in atherosclerosis. Therefore, ApoCIII is a potential new target for reducing plasma levels of TRLs and, thereby, cardiovascular risk. In recent years, there have been extensive preclinical and clinical pharmacological studies aimed at testing drugs directed against ApoCIII. Summary In this review, firstly we will summarize the molecular function of ApoCIII in lipoprotein metabolism. Then, we will examine the lipid-lowering potential of the pharmacological inhibition of ApoCIII based on the results of clinical trial employing Volansesorsen, the first approved antisense therapeutic oligonucleotide against ApoCIII mRNA. The future perspectives for ApoCIII inhibition will be also revised.
A qualitative investigation of leisure benefits for social and psychological health among international volleyball players living in South Korea

ABSTRACT Purpose The proportion of foreign players in global sports industries has steadily increased in the last decade. This qualitative study aims to capture the benefits of leisure activities for the social and psychological health of international volleyball players affiliated with South Korean volleyball leagues. Method A purposeful criterion sampling strategy was employed in this qualitative study. Findings: Based on semi-structured interviews with 12 participants, in this study three major themes pertaining to leisure benefits are identified: (a) new leisure opportunities and coping, (b) inter-intra group friendships, and (c) acculturation. Conclusions These benefits can contribute to social and psychological health for the participants. Practical implications of this study and suggestions for health professionals, sports psychologists, and team counsellors are discussed.
Spatial Representations Without Spatial Computations

Cognitive maps are assumed to be fundamentally spatial and grounded only in perceptual processes, as supported by the discovery of functionally dedicated cell types in the human brain, which tile the environment in a maplike fashion. Challenging this view, we demonstrate that spatial representations—such as large-scale geographical maps—can be as well retrieved with high confidence from natural language through cognitively plausible artificial-intelligence models on the basis of nonspatial associative-learning mechanisms. More critically, we show that linguistic information accounts for the specific distortions observed in tasks when college-age adults have to judge the geographical positions of cities, even when these positions are estimated on real maps. These findings indicate that language experience can encode and reproduce cognitive maps without the need for a dedicated spatial-representation system, thus suggesting that the formation of these maps is the result of a strict interplay between spatial- and nonspatial-learning principles.
Examining the relative influence of dispersal and competition on co-occurrence and functional trait patterns in response to disturbance

Disturbance gradients are particularly useful for understanding the relative influences of competition and dispersal. Shortly after disturbance, plant composition should be influenced more strongly by dispersal than competition; over time, this should reverse, with competition becoming more important. As such, we predicted that plant functional traits associated with high dispersal ability would be over-represented shortly after a disturbance event occurs, while those associated with high competitive ability would have increased representation as time progresses. Additionally, it has been suggested that competitive interactions may contribute to negative co-occurrence patterns; if this is the case, negative co-occurrence patterns should also increase as time-since-disturbance increases. Here, we examine how functional trait and co-occurrence patterns change over time following a herbicide-based disturbance, compared to undisturbed vegetation, in a temperate, old-field grassland dominated by herbaceous perennials. In our study system, negative co-occurrence patterns were most pronounced in disturbed plots one year after herbicide application, consistent with several lines of evidence that dispersal can strongly impact both composition and co-occurrence patterns. Over three years post-disturbance, co-occurrence patterns in disturbed plots decreased, becoming more similar to control plots. This pattern is inconsistent with the expectation that competition contributes to negative co-occurrence patterns, at least over three growing seasons. More pronounced negative co-occurrence patterns were associated with higher species evenness among plots. Functional traits related to increased dispersal (mean seed mass, and proportion of stoloniferous/rhizomatous species) and competitive ability (mean species height, and mean specific leaf area) did not differ significantly across treatments, with the exception of mean height in the third-year post-disturbance; however, the overall trajectory of this trait was inconsistent with theoretical expectations. Overall, co-occurrence patterns changed across the gradient of time-since disturbance, but not as expected; functional trait patterns (trait means, functional diversity measures) were not responsive to our experimental disturbance gradient.
Septin and actin contributions to endothelial cell–cell junctions and monolayer integrity

Septins in endothelial cells (ECs) have important roles supporting the integrity of the endothelial monolayer. Cell–cell junctions in EC monolayers are highly dynamic, with continuous retractions and protrusions. Depletion of septins in ECs leads to disruption of cell–cell junctions, which are composed of VE‐cadherin and other junctional proteins. In EC monolayers, septins are concentrated at the plasma membrane at sites of cell–cell contact, in curved‐ and scallop‐shaped patterns. These membrane‐associated septin accumulations are located in regions of positive membrane curvature, and those regions are often associated with and immediately adjacent to actin‐rich protrusions with negative membrane curvature. EC septins associate directly with plasma membrane lipids, based on findings with site‐specific mutations of septins in ECs, which is consistent with biochemical and cell biological studies in other systems. Loss of septins leads to disruption of the EC monolayer, and gaps form between cells. The number and breadth of cell–cell contacts and junctions decreases, and the number and frequency of retractions, ruffles, and protrusions at cell edges also decreases. In addition, loss of septins leads to decreased amounts of F‐actin at the cortical membrane, along with increased amounts of F‐actin in stress fibers of the cytoplasm. Endothelial monolayer disruption from loss of septins is also associated with decreased transendothelial electric resistance (TEER) and increased levels of transendothelial migration (TEM) by immune and cancer cells, owing to the gaps in the monolayer. A current working model is that assembly of septin filaments at regions of positive membrane curvature contributes to a mechanical footing or base for actin‐based protrusive forces generated at adjoining regions of the membrane. Specific molecular interactions between the septin and actin components of the cytoskeleton may also be important contributors. Regulators of actin assembly may promote and support the assembly of septin filaments at the membrane, as part of a molecular feedback loop between the assembly of septin and actin filaments.
A red wine intervention does not modify plasma trimethylamine N-oxide but is associated with broad shifts in the plasma metabolome and gut microbiota composition

ABSTRACT Background Gut microbiota profiles are closely related to cardiovascular diseases through mechanisms that include the reported deleterious effects of metabolites, such as trimethylamine N-oxide (TMAO), which have been studied as diagnostic and therapeutic targets. Moderate red wine (RW) consumption is reportedly cardioprotective, possibly by affecting the gut microbiota. Objectives To investigate the effects of RW consumption on the gut microbiota, plasma TMAO, and the plasma metabolome in men with documented coronary artery disease (CAD) using a multiomics assessment in a crossover trial. Methods We conducted a randomized, crossover, controlled trial involving 42 men (average age, 60 y) with documented CAD comparing 3-wk RW consumption (250 mL/d, 5 d/wk) with an equal period of alcohol abstention, both preceded by a 2-wk washout period. The gut microbiota was analyzed via 16S rRNA high-throughput sequencing. Plasma TMAO was evaluated by LC-MS/MS. The plasma metabolome of 20 randomly selected participants was evaluated by ultra-high-performance LC-MS/MS. The effect of RW consumption was assessed by individual comparisons using paired tests during the abstention and RW periods. Results Plasma TMAO did not differ between RW intervention and alcohol abstention, and TMAO concentrations showed low intraindividual concordance over time, with an intraclass correlation coefficient of 0.049 during the control period. After RW consumption, there was significant remodeling of the gut microbiota, with a difference in β diversity and predominance of Parasutterella, Ruminococcaceae, several Bacteroides species, and Prevotella. Plasma metabolomic analysis revealed significant changes in metabolites after RW consumption, consistent with improved redox homeostasis. Conclusions Modulation of the gut microbiota may contribute to the putative cardiovascular benefits of moderate RW consumption. The low intraindividual concordance of TMAO presents challenges regarding its role as a cardiovascular risk biomarker at the individual level. This study was registered at clinical trials.gov as NCT03232099.
Synthesis of graphene on gold

Here we report chemical vapor deposition of graphene on gold surface at ambient pressure. We studied effects of the growth temperature, pressure, and cooling process on the growngraphene layers. The Raman spectroscopy of the samples reveals the essential properties of the graphenegrown on gold surface. In order to characterize the electrical properties of the growngraphene layers, we have transferred them on insulating substrates and fabricated field effect transistors. Owing to distinctive properties of gold, the ability to growgraphene layers on gold surface could open new applications of graphene in electrochemistry and spectroscopy.
Algebraic Solutions in Open String Field Theory – a Lightning Review

In this short paper we review basic ideas of string field theory with the emphasis on the recent developments. We show how without much technicalities one can look for analytic solutions to Witten’s open string field theory. This is an expanded version of a talk given by the author over the last year at a number of occasions1 and notably at the conference Selected Topics in Mathematical and Particle Physics in honor of Prof. JiˇrLi Niederle’s 70th birthday.
Facilitating Serverless Match-based Online Games with Novel Blockchain Technologies

Applying peer-to-peer (P2P) architecture to online video games has already attracted both academic and industrial interests, since it removes the need for expensive server maintenance. However, there are two major issues preventing the use of a P2P architecture, namely how to provide an effective distributed data storage solution, and how to tackle potential cheating behaviors. Inspired by emerging blockchain techniques, we propose a novel consensus model called Proof-of-Play (PoP) to provide a decentralized data storage system that incorporates an anti-cheating mechanism for P2P games, by rewarding players that interact with the game as intended, along with consideration of security measures to address the Nothing-at-stake Problem and the Long-range Attack. To validate our design, we utilize a game-theory model to show that under certain assumptions, the integrity of the PoP system would not be undermined due to the best interests of any user. Then, as a proof-of-concept, we developed a P2P game (Infinity Battle) to demonstrate how a game can be integrated with PoP in practice. Finally, experiments were conducted to study PoP in comparison with Proof-of-Work (PoW) to show its advantages in various aspects.
Statistical Mechanics: J Theory and Experiment Shock dynamics of two-lane driven lattice gases

Driven lattice gases such as those of the ASEP model are useful tools for the modelling of various stochastic transport processes carried out by self-driven particles, such as molecular motors or vehicles in road traﬃc. Often these processes take place in one-dimensional systems oﬀering several tracks to the particles, and in many cases the particles are able to change track with a given rate. In this work we consider the case of strong coupling where the rate of hopping along the tracks and the exchange rates are of the same order, and show how a phenomenological approach based on a domain wall theory can be used to describe the dynamics of the system. In particular, the domain walls on the diﬀerent tracks form pairs, whose dynamics dominate the behaviour of the system.
Relational Database Performance for Multimedia: A Case Study

This paper describes the performance optimisation of a state-of-the-art relational database to more efficiently serve data for multimedia visualisations in the ViRMA prototype. We describe the baseline database and queries, along with two major optimisation steps that improve query efficiency, at the cost of slowing down dynamic updates. We evaluate the optimisations with a case study of a lifelog collection of 182K images, showing that the time to produce complex visualisations is reduced by orders of magnitude.