Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Recognition by a Polymorphic Cell Surface Receptor Governs Cooperative Behaviors in Bacteria

Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors. Some microbes, such as myxobacteria, build multicellular fruiting bodies from free-living cells. However, how bacterial cells recognize each other by contact is poorly understood. Here we show that myxobacteria engage in recognition through interactions between TraA cell surface receptors, which leads to the fusion and exchange of outer membrane (OM) components. OM exchange is shown to be selective among 17 environmental isolates, as exchange partners parsed into five major recognition groups. TraA is the determinant of molecular specificity because: (i) exchange partners correlated with sequence conservation within its polymorphic PA14-like domain and (ii) traA allele replacements predictably changed partner specificity. Swapping traA alleles also reprogrammed social interactions among strains, including the regulation of motility and conferred immunity from inter-strain killing. We suggest that TraA helps guide the transition of single cells into a coherent bacterial community, by a proposed mechanism that is analogous to mitochondrial fusion and fission cycling that mixes contents to establish a homogenous population. In evolutionary terms, traA functions as a rare greenbeard gene that recognizes others that bear the same allele to confer beneficial treatment.
Executable assertions for detecting data errors in embedded control systems

In order to be able to tolerate the effects of faults, we must first detect the symptoms of faults, i.e. the errors. This paper evaluates the error detection properties of an error detection scheme based on the concept of executable assertions aiming to detect data errors in internal signals. The mechanisms are evaluated using error injection experiments in an embedded control system. The results show that using the mechanisms allows one to obtain a fairly high detection probability for errors in the areas monitored by the mechanisms. The overall detection probability for errors injected to the monitored signals was 74%, and if only errors causing failure are taken into account we have a detection probability of over 99%. When subjecting the target system to random error injections in the memory areas of the application, i.e., not only the monitored signals, the detection probability for errors that cause failure was 81%.
Development and Clinical Evaluation of Two Chromogenic Substrate Methods for Monitoring Fondaparinux Sodium

This study was designed to develop methods for monitoring of the selective factor Xa inhibitor fondaparinux sodium (ARIXTRA®) based on standard laboratory methods for the chromogenic determination of the anti-factor Xa activity of low molecular weight heparin. To examine the biologic activity of fondaparinux in comparison to its plasma concentration, 2 methods were investigated: 1 working with the addition of antithrombin (AT), the other without exogenous AT. Both methods showed a linear relationship of fondaparinux concentration and OD/min on a log-lin scale in the range from 0.1 to 2 μg/mL. Inter- and intra-assay variability was <6% in all cases. The results of spiked samples from patients on vitamin K antagonists (VKA) were in good agreement with both methods, and the determination of the fondaparinux concentration was not influenced by reduced levels of factor X in plasma caused by VKA-intake. Ex vivo samples from orthopedic patients (n=18) on prophylactic treatment with fondaparinux showed concentrations between 0.2 to 0.7 μg/mL 3 hours after s.c. injection. No significant differences were detected between both methods with these samples. The presented methods are suitable tools for monitoring of fondaparinux. The linear calibration curve in the range 0.1 to 2 μg/mL is suitable for determination of prophylactic and therapeutic application of fondaparinux. Both methods, with and without addition of AT, can be performed fully automated in clinical routine on an automated coagulation analyzer (STA coagulation analyzer®). No significant differences were detected between both methods with these samples.
Role of imaging in evaluation of sudden cardiac death risk in hypertrophic cardiomyopathy

Purpose of review Hypertrophic cardiomyopathy (HCM) is the most common heritable cardiomyopathy and is associated with sudden cardiac death (SCD) – an uncommon but devastating clinical outcome. This review is designed to assess the role of imaging in established risk factor assessment and its role in emerging SCD risk stratification. Recent findings Recent publications have highlighted the crucial role of imaging in HCM SCD risk stratification. Left ventricular hypertrophy assessment remains the key imaging determinant of risk. Data continue to emerge on the role of systolic dysfunction, apical aneurysms, left atrial enlargement and left ventricular outflow tract obstruction as markers of risk. Quantitative assessment of delayed myocardial enhancement and T1 mapping on cardiac MRI continue to evolve. Summary Recent multicenter trials have allowed multivariate SCD risk assessment in large HCM cohorts. Given aggregate risk with presence of multiple risk factors, a single parameter should not be used in isolation to determine implantable cardiac defibrillator candidacy. Use of all available imaging data, including cardiac magnetic resonance tissue characterization, allows a comprehensive approach to SCD stratification and implantable cardiac defibrillator decision-making.
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which can be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been derived from structural alignments in the HOMSTRAD database (http://www-cryst.bioc. cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other cases. The gap penalty at each position of the structure is determined according to its solvent accessibility, its position relative to the secondary structure elements (SSEs) and the conservation of the SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy.
Insights into gas heating and cooling in the disc of NGC 891 from Herschel far-infrared spectroscopy

We present Herschel PACS and SPIRE spectroscopy of the most important far-infrared cooling lines in the nearby, edge-on spiral galaxy, NGC 891: [Cii] 158 μm, [Nii] 122, 205 μm, [Oi] 63, 145 μm, and [Oiii] 88 μm. We find that the photoelectric heating efficiency of the gas, traced via the ([Cii]+[Oi]63)/FTIR ratio, varies from a mean of 3.5 × 10-3 in the centre up to 8 × 10-3 at increasing radial and vertical distances in the disc. A decrease in ([Cii]+[Oi]63)/FTIR but constant ([Cii]+[Oi]63)/FPAH with increasing FIR colour suggests that polycyclic aromatic hydrocarbons (PAHs) may become important for gas heating in the central regions. We compare the observed flux of the FIR cooling lines and total IR emission with the predicted flux from a PDR model to determine the gas density, surface temperature and the strength of the incident far-ultraviolet (FUV) radiation field, G0. Resolving details on physical scales of ~0.6 kpc, a pixel-by-pixel analysis reveals that the majority of the PDRs in NGC 891’s disc have hydrogen densities of 1 < log (n/ cm-3) < 3.5 experiencing an incident FUV radiation field with strengths of 1.7 < log G0< 3. Although these values we derive for most of the disc are consistent with the gas properties found in PDRs in the spiral arms and inter-arm regions of M 51, observed radial trends in n and G0 are shown to be sensitive to varying optical thickness in the lines, demonstrating the importance of accurately accounting for optical depth effects when interpreting observations of high inclination systems. Increasing the coverage of our analysis by using an empirical relationship between the MIPS 24 μm and [Nii] 205 μm emission, we estimate an enhancement of the FUV radiation field strength in the far north-eastern side of the disc relative to the rest of the disc that coincides with the above-average star formation rate surface densities and gas-to-dust ratios. However, an accurate interpretation remains difficult due to optical depth effects, confusion along the line-of-sight and observational uncertainties.
Multiethnic Genetic Association Studies Improve Power for Locus Discovery

To date, genome-wide association studies have focused almost exclusively on populations of European ancestry. These studies continue with the advent of next-generation sequencing, designed to systematically catalog and test low-frequency variation for a role in disease. A complementary approach would be to focus further efforts on cohorts of multiple ethnicities. This leverages the idea that population genetic drift may have elevated some variants to higher allele frequency in different populations, boosting statistical power to detect an association. Based on empirical allele frequency distributions from eleven populations represented in HapMap Phase 3 and the 1000 Genomes Project, we simulate a range of genetic models to quantify the power of association studies in multiple ethnicities relative to studies that exclusively focus on samples of European ancestry. In each of these simulations, a first phase of GWAS in exclusively European samples is followed by a second GWAS phase in any of the other populations (including a multiethnic design). We find that nontrivial power gains can be achieved by conducting future whole-genome studies in worldwide populations, where, in particular, African populations contribute the largest relative power gains for low-frequency alleles (<5%) of moderate effect that suffer from low power in samples of European descent. Our results emphasize the importance of broadening genetic studies to worldwide populations to ensure efficient discovery of genetic loci contributing to phenotypic trait variability, especially for those traits for which large numbers of samples of European ancestry have already been collected and tested.
Visualization of web form submissions for security analysis

Purpose – The purpose of this paper is to propose novel information visualization and interaction techniques to help security administrators analyze past web form submissions, with the goals of searching, inspecting, verifying, and understanding about malicious submissions.Design/methodology/approach – The authors utilize well‐known visual design principles in the techniques to support the analysis process. They also implement a prototype and use it to investigate simulated normal and malicious web submissions.Findings – The techniques can increase analysts' efficiency by displaying large amounts of information at a time, help analysts detect certain kinds of anomalies, and support the analyzing process via provided interaction capabilities.Research limitations/implications – Due to resources constraints, the authors experimented on simulated data only, not real data.Practical implications – The techniques can be used to investigate past web form submissions, which is a first step in analysing and underst.
Throughput Analysis of the IEEE 802 . 11 Power Save Mode in Single Hop Ad hoc Networks

In the IEEE 802.11 Power Save Mode (PSM) specified for Independent Basic Service Set (IBSS), time is divided into beacon intervals. At the beginning of each beacon interval, each station in the power save mode periodically wakes up for a duration called announcement traffic indication message (ATIM) window. The stations that have successfully transmitted ATIM frame within the ATIM window will compete to transmit data frame in the rest of the beacon interval. The transmission of an ATIM frame depends on the CSMA/CA mechanism specified in the IEEE 802.11 DCF. The probability of a successful transmission of an ATIM frame has a great impact on the performance of IBSS in power save mode. This paper presents an analytical model to calculate the throughput using the success probability of an ATIM frame transmission in ATIM window of fixed size. The simulation results validate the accuracy of this analytical analysis.
Stabilizing information-driven exploration for bearings-only SLAM using range gating

This paper examines the problem of information-driven exploration for the purposes of simultaneous localization and mapping (SLAM) with a bearings-only sensor. In another work, we have demonstrated that employing an information-driven approach to exploration with an extended Kalman filter (EKF) can drive the robot to locations in the world where filter updates are ill-conditioned and linearization constraints are violated, potentially destabilizing the filter, and increasing the probability of divergence from the true state estimate. In this paper, we demonstrate an information-driven approach to exploration that preserves the stability of the EKF and produces maps that are significantly more accurate than a conventional information-driven approach. Our method is based on range-gating observations so as to avoid potentially destabilizing updates. We provide simulated experimental results demonstrating the superior performance of our approach over simple outlier gating and over heuristic-driven exploration.
Reply to Ulrike Wacker ’ s comments 22 May 2017 Response to Ulrike Wacker ( reviewer # 2 )

Ice clouds, so-called cirrus clouds, occur very frequently in the tropopause region. A special class are subvisible cirrus clouds with an optical depth lower than 0.03, associated with very low ice crystal number concentrations. The dominant pathway for the formation of these clouds is not known well. It is often assumed that heterogeneous nucleation on solid aerosol particles is the preferred mechanism although homogeneous freezing of aqueous solution droplets might be possible, 5 since these clouds occur in the low temperature regime T < 235K. For investigating subvisible cirrus clouds as formed by homogeneous freezing we develop a reduced cloud model from first principles, which is close enough to complex models but is also simple enough for mathematical analysis. The model consists of a three dimensional set of ordinary differential equations, and includes the relevant processes as ice nucleation, diffusional growth and sedimentation. We study the formation and evo10 lution of subvisible cirrus clouds in the low temperature regime as driven by slow vertical updraughts (0<w ≤ 0.05m s−1). The model is integrated numerically and also investigated by means of theory of dynamical systems. We found two qualitatively different states for the long-term behaviour of subvisible cirrus clouds. The first state is a stable focus, i.e. the solution of the differential equations performs damped oscillations and asymptotically reaches a constant value as an equilibrium 15 state. The second state is a limit cycle in phase space, i.e. the solution asymptotically approaches a one-dimensional attractor with purely oscillatory behaviour. The transition between the states is characterised by a Hopf bifurcation and is determined by two parameters – vertical updraught velocity and temperature. In both cases, the properties of the simulated clouds agree reasonably well with simulations from a more detailed model, with former analytical studies, and with observations 20 of subvisible cirrus, respectively. The reduced model can also provide qualitative interpretations of simulations with a complex and more detailed model at states close to bifurcation qualitatively. The results indicate that homogeneous nucleation is a possible formation pathway for subvisible cirrus
Initiation into the ugao: rethinking the structure of Tharaka symbolism

Abstract After analysing the myth of origin of ugao (Tharaka medicine) as the constitutional charter of its ‘jurisdiction’, the article describes the initiation of the author by three agao (healers) in the ‘territory’ of ugao during a period of seventeen days, and outlines the different kinds of teachings and ritual performances and its conclusion with a practical apprenticeship. In particular, a detailed account is given of the giciaro, the blood brotherhood sealed by the muma, the oath made with goat's blood between the masters and the novice, and, finally, the ritual handing over of the horns, the instruments of the mugao's healing art. In the second part of the article, the key symbols of the ugao therapeutic rituals are analysed in order to show the specific structure that defines the healing pattern. Here the author, on the basis of his results, questions the validity of ‘dual classification’ and discusses the shortcomings of the analysis of Meru symbolism proposed by Rodney Needham. It is suggested that a triadic classification can account better for the overall pattern of symbolic correspondences in the ugao and in the culture of Tharaka. Résumé Après avoir analysé le mythe d'origine de l'ugao—médecine tharaka—comme la charte constitutionnelle de sa ‘juridiction’, l'étude décrive l'initiation de l'auteur par trois agao (guérisseurs) au territoire réservé de l'ugao pendant une période de dixsept journées, par plusiers types d'enseignement et de performances rituelles et qui se conclu avec un apprentissage pratique. Dans le détail, une description complète est donné par le giciaro, la fraternité de sang schellée par le muma, le serment sur le sang de la chèvre entre les maîtres et le novice; et de la livraison rituelle des cornes, les instruments de l'art de la guérison du mugao. Dans le deuxième partie de l'étude, les principaux symboles dominant des rituels thérapeutiques de l'ugao sont analysé dans le détail dans le but de cueillir la particulière structure qui le met en ordre, en définant le modèle de guérison. A ce sujet, l'auteur met en discussion la validité d'une classification duel sur la base de ses résultats, en discutant les faiblesses de l'analyse proposée par Rodney Needham sur le symbolisme méru. Alternativement, il suggère quʼune classification triadique peut mieux considerer le modèle générale de la correspondance symbolique propre de l'ugao comme de la culture tharaka.
Multi level RTS in proton irradiated CMOS image sensors manufactured in deep submicron technology

A new automated method able to detect multi level random telegraph signals in pixel arrays and to extract their main characteristics is presented. The proposed method is applied to several proton irradiated pixel arrays manufactured using a 0.18 μm CMOS process dedicated to imaging. Despite the large proton energy range and the large fluence range used, similar exponential RTS amplitude distributions are observed. A universal mean amplitude is extracted from these distributions and the number of RTS defects appears to scale well with total NIEL. These conclusions allow the prediction of RTS amplitude distributions. The effect of electric field on RTS amplitude is also studied and no significant relation between electric field and RTS amplitude is observed.
Close range ship noise cross correlations with a vector sensor in view of geoacoustic inversion

Distant ship noise has been utilized for geoacoustic inversion and ocean monitoring for many years. In a shallow water experiment, Makai 2005, a 4-element acoustic vector sensor array was deployed at the stern of the research vessel R/V Kilo Moana. The recorded engine noise of R/V Kilo Moana during its dynamic positioning was analyzed by the DEMON (Detection of Envelope Modulation on Noise) method. The strongest modulation frequency band of the ship noise was found by a group of band-pass filters for further data processing. Multipath arrivals in the vertical particle velocity have higher signal-to-noise ratios than those in the horizontal particle velocities because of steep arrival directions. By exploiting this advantage, the cross-correlation of broadband ship noise between the pressure and the vertical particle velocity can be used for multipath information exploration. Since ship noise is often characterized as continuous broadband noise plus strong tonal noise, the cross-correlation of tonal noise would dominate that of broadband noise, and consequently cover the multipath arrival pattern. Therefore, spectral weighting functions are applied in order to reduce the noise contamination and ensure sharp multipath peaks in the cross-correlation. For engine noise emitted by the dynamically positioned ship, a short correlation time of 0.4s was used in order to keep the time delay fluctuation details of multipath arrivals. Clear multiple arrivals are seen in the cross-correlation of different arrivals, and verified by the ray tracing program TRACEO. The results demonstrate the potential of only one acoustic vector sensor in applications of source localization and geoacoustic inversion.
Over the Long Haul: The Persistent Economic Consequences of Single Motherhood

Purpose – This chapter examines change over time in income, human capital, and socio-demographic attributes for married, divorced, and never-married mothers Methodology/approach – The chapter consists of descriptive analysis of data from the National Longitudinal Survey of Youth's 1979 cohort. Respondents were followed from 1979 to 2006. Findings – The economic consequences of single motherhood are persistent. Women who have once been divorced or never-married mothers remain poorer through middle age, no matter how their family structure subsequently changes. Social implications – A critical feature of the modern economic and demographic landscape is the intersection of individual and family characteristics. Many divorced and, especially, never-married mothers experience profound disadvantage even before they become mothers. Single mothers in general are far less likely to have college degrees, and, in the case of never-married mothers less likely to even have a high school diploma. Never-married mothers are also much less likely to be employed. Single mothers have less educated parents, and are themselves more likely to come from nonintact families. All of these disadvantages contribute to the economic costs – and the economic stress – of single motherhood. Originality/value of paper – The chapter demonstrates that single mothers comprise two very different populations, divorced and never-married mothers. However, both are at a substantial disadvantage compared to married mothers.
Energy Production from Marine Biomass ( Ulva lactuca ) PSO Project No

Project Team: Lars Nikolaisen, Danish Technological Institute Peter Daugbjerg Jensen, Danish Technological Institute Karin Svane Bech, Danish Technological Institute Jonas Dahl, Danish Technological Institute Jørgen Busk, Danish Technological Institute Torben Brødsgaard, Danish Technological Institute Michael Bo Rasmussen, Aarhus University, Dept. of Bioscience Annette Bruhn, Aarhus University, Dept. of Bioscience Anne-Belinda Bjerre (Thomsen), Risø DTU/ Danish Technological Institute Henrik Bangsøe Nielsen, Risø DTU Kristian Rost Albert, Risø DTU Per Ambus, Risø DTU Zsofia Kadar, Risø DTU Stefan Heiske Risø DTU Bo Sander, DONG Energy Erik Ravn Schmidt, DONG Energy