Miracle-dz/UniFAR-FTUs huggingface dataset:
Faraday rotation in GRMHD simulations of the jet launching zone of M87

Non-VLBI measurements of Faraday rotation at mm wavelengths have been used to constrain mass accretion rates ($\mdot$) onto supermassive black holes in the centre of the Milky Way and in the centre of M87. We constructed general relativistic magnetohydrodynamics models for these sources that qualitatively well describe their spectra and radio/mm images invoking a coupled jet-disk system. Using general relativistic polarized radiative transfer, we now also model the observed mm rotation measure (RM) of M87. The models are tied to the observed radio flux, however, electron temperature and accretion rate are degenerate parameters and are allowed to vary. For the inferred low viewing angles of the M87 jet, the RM is low even as the black hole $\mdot$ increases by a factor of $\simeq100$. In jet-dominated models, the observed linear polarization is produced in the forward-jet, while the dense accretion disk depolarizes the bulk of the near-horizon scale emission which originates in the counter-jet. In the jet-dominated models, with increasing $\mdot$ and increasing Faraday optical depth one is progressively sensitive only to polarized emission in the forward-jet, keeping the measured RM relatively constant. The jet-dominated model reproduces a low net-polarization of $\simeq1$ per cent and RMs in agreement with observed values due to Faraday depolarization, however, with $\mdot$ much larger than the previously inferred limit of $9\times10^{-4}\,\mdotu$. All jet-dominated models produce much higher RMs for inclination angles $i\gtrsim30^\circ$, where the line-of-sight passes through the accretion flow, thereby providing independent constraints on the viewing geometry of the M87 jet.
Relationships within the aldehyde dehydrogenase extended family

One hundred‐forty‐five full‐length aldehyde dehydrogenase‐related sequences were aligned to determine relationships within the aldehyde dehydrogenase (ALDH) extended family. The alignment reveals only four invariant residues: two glycines, a phenylalanine involved in NAD binding, and a glutamic acid that coordinates the nicotinamide ribose in certain E‐NAD binary complex crystal structures, but which may also serve as a general base for the catalytic reaction. The cysteine that provides the catalytic thiol and its closest neighbor in space, an asparagine residue, are conserved in all ALDHs with demonstrated dehydrogenase activity. Sixteen residues are conserved in at least 95% of the sequences; 12 of these cluster into seven sequence motifs conserved in almost all ALDHs. These motifs cluster around the active site of the enzyme. Phylogenetic analysis of these ALDHs indicates at least 13 ALDH families, most of which have previously been identified but not grouped separately by alignment. ALDHs cluster into two main trunks of the phylogenetic tree. The largest, the “Class 3” trunk, contains mostly substrate‐specific ALDH families, as well as the class 3 ALDH family itself. The other trunk, the “Class 102” trunk, contains mostly variable substrate ALDH families, including the class 1 and 2 ALDH families. Divergence of the substrate‐specific ALDHs occurred earlier than the division between ALDHs with broad substrate specificities. A site on the World Wide Web has also been devoted to this alignment project.
Novel Microsatellite Markers Acquired from Rubus coreanus Miq. and Cross-Amplification in Other Rubus Species

The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.
Proactive Blacklisting for Malicious Web Sites by Reputation Evaluation Based on Domain and IP Address Registration

The objective of creating malicious software (i.e., malware), intruding computers and conducting malicious activities is shifted from showing off attacker's computer skills to earning money. Thus, recent attackers take more sophisticated and effective malware infection ways such as malware infection via malicious Web sites as well as the traditional exploitations like worm propagation. The malicious Web sites attempt to compromise machines by drive-by-download attack which redirects users to exploiting sites and install malware compulsorily in their machines by exploiting vulnerabilities of their Web browser or plugins. As a countermeasure for these malicious Web sites, blacklisting URLs or domains of them is significant. However, attackers tend to change the URLs or domains in a short period to avoid the blacklist. Thus, a blacklisting scheme which can filter even unknown malicious Web sites is critical. In this paper, we first analyze characteristics of malicious Web sites by their domain information such as AS (Autonomous System), IP address block, IP address, domain, and registrar. Second, we evaluate reputations of IP address blocks and registrars used by attackers. Then, we propose a blacklisting scheme constructed of the combination of IP address block and registrars with low reputation, that is, intensively used by attackers. From our experimental results, the Web sites with the same combination with low reputation appeared over long period, which indicates that our proposed blacklist has a certain capability of filtering unknown malicious Web sites.
A Simple Extension of Dirac's Theorem on Hamiltonicity

The classical Dirac theorem asserts that every graph $G$ on $n$ vertices with minimum degree $\delta(G) \ge \lceil n/2 \rceil$ is Hamiltonian. The lower bound of $\lceil n/2 \rceil$ on the minimum degree of a graph is tight. In this paper, we extend the classical Dirac theorem to the case where $\delta(G) \ge \lfloor n/2 \rfloor $ by identifying the only non-Hamiltonian graph families in this case. We first present a short and simple proof. We then provide an alternative proof that is constructive and self-contained. Consequently, we provide a polynomial-time algorithm that constructs a Hamiltonian cycle, if exists, of a graph $G$ with $\delta(G) \ge \lfloor n/2 \rfloor$, or determines that the graph is non-Hamiltonian. Finally, we present a self-contained proof for our algorithm which provides insight into the structure of Hamiltonian cycles when $\delta(G) \ge \lfloor n/2 \rfloor$ and is promising for extending the results of this paper to the cases with smaller degree bounds.
In Vitro Generation of Neuraminidase Inhibitor Resistance in A(H5N1) Influenza Viruses

ABSTRACT To identify mutations that can arise in highly pathogenic A(H5N1) viruses under neuraminidase inhibitor selective pressure, two antigenically different strains were serially passaged with increasing levels of either oseltamivir or zanamivir. Under oseltamivir pressure, both A(H5N1) viruses developed a H274Y neuraminidase mutation, although in one strain the mutation occurred in combination with an I222M neuraminidase mutation. The H274Y neuraminidase mutation reduced oseltamivir susceptibility significantly (900- to 2,500-fold compared to the wild type). However the dual H274Y/I222M neuraminidase mutation had an even greater impact on resistance, with oseltamivir susceptibility reduced significantly further (8,000-fold compared to the wild type). A similar affect on oseltamivir susceptibility was observed when the dual H274Y/I222M mutations were introduced, by reverse genetics, into a recombinant seasonal human A(H1N1) virus and also when an alternative I222 substitution (I222V) was generated in combination with H274Y in A(H5N1) and A(H1N1) viruses. These viruses remained fully susceptible to zanamivir but demonstrated reduced susceptibility to peramivir. Following passage of the A(H5N1) viruses in the presence of zanamivir, the strains developed a D198G neuraminidase mutation, which reduced susceptibility to both zanamivir and oseltamivir, and also an E119G neuraminidase mutation, which demonstrated significantly reduced zanamivir susceptibility (1,400-fold compared to the wild type). Mutations in hemagglutinin residues implicated in receptor binding were also detected in many of the resistant strains. This study identified the mutations that can arise in A(H5N1) under either oseltamivir or zanamivir selective pressure and the potential for dual neuraminidase mutations to result in dramatically reduced drug susceptibility.
Analysis and Design of Steel Silo using STAAD.ProV8i

Generally silo is a storage structure for heavy bulk materials such as cement coal, wood, food products and saw dust. Its design involves materials, geometry, and structural considerations. This research considered a special structure steel silo treated with myriad conventional and unconventional loading conditions, varied from some tonnes to many of tonnes which findings in uncommon modes of failure. Silo Specifications of 14m height and 3m diameter was designed with section ISMB 300 and ISA 70x70x10mm as per Indian standards. In addition, the plan and section of the silo wad done by the AutoCADD 2018 software. modelling, dynamic analysis and designs were completer in STAAD PRO V8i.Besides, the silo was designed as per Indian standards IS 800.The maximum axial force and shear force of the steel silo were 15.9 KN and 0.037 KN respectively. The aim of this paper was to determined the Plate stress, contour lines, and critical support of the silo, beam end force summary and steel take off of the silo structure. Generally silo is a storage structure for heavy bulk materials such as cement coal, wood, food products and saw dust. Its design involves materials, geometry, and structural considerations. This research considered a special structure steel silo treated with myriad conventional and unconventional loading conditions, varied from some tonnes to many of tonnes which findings in uncommon modes of failure. Silo Specifications of 14m height and 3m diameter was designed with section ISMB 300 and ISA 70x70x10mm as per Indian standards. In addition, the plan and section of the silo wad done by the AutoCADD 2018 software. modelling, dynamic analysis and designs were completer in STAAD PRO V8i.Besides, the silo was designed as per Indian standards IS 800.The maximum axial force and shear force of the steel silo were 15.9 KN and 0.037 KN respectively. The aim of this paper was to determined the Plate stress, contour lines, and critical support of the silo, beam end force summary and steel take off of the silo structure.
ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment

The 'model-free' screening engine ProPose implements a general method for performing simultaneous protein-ligand docking, ligand-ligand alignment, pharmacophore queries-and combinations thereof-in order to incorporate a priori information into screening protocols. In this manuscript we describe a case study on herpes simplex virus thymidine kinase, an important antiviral drug target, where we evaluate different approaches for handling a specific type of a priori information, i.e., multiple target structures. We demonstrate that a simultaneous alignment on two target structures--in conjunction with logic operations on interactions and docking constraints derived from protein structure--is an effective means of (i) improving the enrichment of chemical substructures that are compatible with the a priori known ligands, (ii) ensuring the steric fit into the target protein, and (iii) handling target flexibility. The combination of ligand- and receptor-based methods steers the virtual screening by ranking molecules according to the similarity of their interaction pattern with known ligands, thereby--to some extent--outweighing the deficiencies of simple scoring functions often used in initial virtual screening.
Market Response to Flood Risk: An Empirical Study of Housing Values Using Boundary Discontinuities

This paper presents one of the first studies on flood risk evaluation in the US Northeast - a region where we are likely going to see increasing precipitation variability and associated risk of flood in the coming decades. In the paper, a spatial difference-in-differences framework based on floodplain boundary discontinuities is proposed to control for unobserved heterogeneities. Using parcel-level data from Juniata County and Perry County in Pennsylvania, the paper finds that on average there is a 5-6 percent housing value reduction due to exposure to 1 percent annual chance of flooding within the FEMA (Federal Emergency Management Agency) 100-year flood zone. For Juniata County, it shows that on average there is a $3.28/sqft (in 2015 USD) discount for a full-time SFR (single family residential) property located within the flood zone. For an average housing unit of 1430 sqft living space in the sample, the estimate translates to a $4690 housing value reduction. For Perry County, the corresponding estimates are $4.00/sqft (in 2015 USD) and $6320 for an average housing unit of 1580 sqft. The paper also shows that with similar specifications, a standard hedonic price model underestimates the flood risk impact on housing value by a substantial amount as a result of failing to control for unobserved heterogeneities.
Wasserbilanzierung der Oberflächen-Abdichtung von Deponien unter Verwendung mathematischer Bilanzierungsmodelle

For alternative surface sealing systems, the TA-Si (Technical Instruction for Sanitary Waste) explicitly requires proof of equivalence. To provide that proof, a test field, including an integrated macro-scale lysimeter of 10 * 40 meters, has been installed at the sanitary landfill Karlsruhe-West. This lysimeter has been used to obtain water-balance data on the alternative sealing system for 13 years. The analysis of the water-balance of the lysimeter gives an overview of the efficiency of the sealing system. The here used sealing system consists of 2 m vegetation support layer, underlined by 15 cm gravel drainage layer, a 50 cm clay-liner and 45 cm capillary-barrier. Additionally, the water balance of the landfill is yearly calculated with the numerical model HELP (Hydrological Evaluation of Landfill Performance). HELP is a quasi two-dimensional model which is designed especially for water-balance of landfills and requires the input of weather, soil and structural data of a real system. A comparison between the HELP model results and the measured data of the lysimeter was carried out to test the ability of the HELP model to describe the natural system correctly. Based on the calculation of the model and the measured data of the lysimeter, an exhaustive evaluation of the water balance for the complete landfill sealing system was done. HELP is not able to calculate the effects of a capillary barrier. Therefore a correction factor based on the output data of the lysimeter is introduced. Due to this, a calculation of the amount of water percolating through the capillary barrier is possible. By said comparison it was found, that the calculated percolation water for the complete landfill sealing system is about three and a half times higher than the one measured with the lysimeter. The comparison showed, that those differences are proportional to the inclination and length of the slope. It turns out that results, obtained from a small area, can not be extrapolated on a big area without considering these geometrical parameters. For the calculation of the water balance of the sealing system of the landfill Karlsruhe-West, the HELP model is an essential tool. The calculation showed, that it is possible to create a water balance with the HELP model. (In this context it is essential to calibrate the HELP model using the measured data of a lysimeter.) Additionally, the water balance of the lysimeter was modelled with hydrological computer based model Hydrus 2D. With Hydrus 2D it is possible to include the effect of cappillary barrier. That means, this model can be used for modelling the complete sealing system of the landfill. Finally, an array of temperature sensors was distributed in the mineral sealing layer, located in a septh of 2 m. Measurements in 2004 and 2005 show that the temperature is
Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.

Protein-protein interaction (PPI) is at the core of the entire interactomic system of any living organism. Although there are many human protein-protein interaction links being experimentally determined, the number is still relatively very few compared to the estimation that there are ∼300,000 protein-protein interactions in human beings. Hence, it is still urgent and challenging to develop automated computational methods to accurately and efficiently predict protein-protein interactions. In this paper, we propose a novel hierarchical LDA-RF (latent dirichlet allocation-random forest) model to predict human protein-protein interactions from protein primary sequences directly, which is featured by a high success rate and strong ability for handling large-scale data sets by digging the hidden internal structures buried into the noisy amino acid sequences in low dimensional latent semantic space. First, the local sequential features represented by conjoint triads are constructed from sequences. Then the generative LDA model is used to project the original feature space into the latent semantic space to obtain low dimensional latent topic features, which reflect the hidden structures between proteins. Finally, the powerful random forest model is used to predict the probability for interaction of two proteins. Our results show that the proposed latent topic feature is very promising for PPI prediction and could also become a powerful strategy to deal with many other bioinformatics problems. As a web server, LDA-RF is freely available at http://www.csbio. sjtu.edu. cn/bioinf/LR_PPI for academic use.
1,4-Dimethylpiperazine-1,4-diium dibromide dihydrate

In the title hydrated molecular salt, C6H16N2 2+·2Br−·2H2O, the complete 1,4-dimethylpiperazine-1,4-diium dication is generated by crystallographic inversion symmetry and both exocyclic C—N bonds are in equatorial orientations. In the crystal, the components are linked by N—H⋯O and O—H⋯Br hydrogen bonds, generating chains propagating in [110].
Inductive power transmission to millimeter-sized biomedical implants using printed spiral coils

The operation frequency (f) has been a key parameter in optimizing wireless power transmission links for biomedical implants with millimeter (mm) dimensions. This paper studies the feasibility of using printed spiral coils (PSCs) for powering mm-sized implants with high power transmission efficiency (PTE) at different fps. Compared to wire-wound coils (WWCs), using a PSC in the implant side allows batch fabrication on rigid or flexible substrates, which can also be used as a platform for integrating implant components. For powering an implant with 1 mm diameter, located 10 mm inside the tissue, the geometries of transmitter (Tx) and receiver (Rx) PSCs were optimized at different fPs of 50 MHz, 200 MHz, and 500 MHz using a commercial field solver (HFSS). In simulations, PSC- and WWC-based links achieved maximum PTE of 0.13% and 3.3%, and delivered power of 65.7 μW and 720 μW under specific absorption rate (SAR) constraints at the optimal fp of 50 MHz and 100 MHz, respectively, suggesting that the performance of the PSC-based link is significantly inferior to that of the WWC-based link.
Optimization by Simulated Annealing

There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.
Internet-based support for self-management strategies for people with COPD–protocol for a controlled pragmatic pilot trial of effectiveness and a process evaluation in primary healthcare

Introduction The use of adequate self-management strategies for people with chronic obstructive pulmonary disease (COPD) reduces healthcare use, improves health-related quality of life (HRQoL) and recovery after acute exacerbations. However, not many people with COPD receive support that promotes the use of such strategies and therefore new methods to facilitate and promote the use of self-management strategies are highly warranted. This pilot trial aims to evaluate the feasibility of the study design and study procedures considering effectiveness of the novel intervention, the COPD-web. Methods and analysis The overall design is a pragmatic controlled pilot trial with preassessments and postassessments and a parallel process evaluation. Patients with the diagnosis of COPD will be eligible for the study. The intervention group will be recruited when visiting one of the six participating primary care units in Sweden. The control group will be identified from the unit's computerised registers. The intervention, the COPD-web, is an interactive web page with two sections; one directed at people with COPD and one at healthcare professionals. The sections aim to support patients’ self-management skills—and to facilitate the provision of support for self-management strategies, respectively. Effectiveness with regard to patients’ symptoms, HRQoL, knowledge of and readiness for COPD-related self-management, health literacy, self-efficacy for physical activity and time spent in physical activity and time being sedentary, and further, healthcare professionals’ knowledge of and readiness to support COPD-related self-management strategies will be assessed using questionnaires at 3 and 12 months. The process evaluation will include observations and interviews. Ethics and dissemination Ethical approval has been obtained. Findings will be presented at conferences, submitted for publication in peer-reviewed publications and presented to the involved healthcare professionals, patients and to patient organisations. Trial registration number ClinicalTrials.gov: NCT02696187
Social emotional data analysis. The map of Europe

In this paper we present an investigation of the emotional content conveyed by words in online conversations captured on Twitter. A multivariate technique applied to co-occurence of words together with Correspondence Analysis is adopted in order to find clusters of meaningful words detecting emotional categories that provide meaning to everyday events. Specifically, given the current historical period, where the European Union has to gain trust in its citizens, a corpus of 155000 tweets selected through the Italian keywords "Europa" and "EU" is analyzed. Results show clearly how the textual content is structured according to the different emotional expressions.