Miracle-dz/UniFAR-FTUs huggingface dataset:
Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species

Abstract Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. Here, we use publicly available RNA-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. Our RNA mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. In all cases, 85% or more of the organelle genome was recovered from the RNA data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding RNAs, and that organelle genome noncoding content might provide raw material for generating regulatory RNAs.
Structure of Extreme Correlated Equilibria

We exhibit the rich structure of the set of correlated equilibria by analyzing the simplest of polynomial games: the mixed extension of matching pennies. We show that while the correlated equilibrium set is convex and compact, the structure of its extreme points can be quite complicated. In finite games there can be a superexponential separation between the number of extreme Nash and extreme correlated equilibria. In polynomial games there can exist extreme correlated equilibria which are not finitely supported; we construct a large family of examples using techniques from ergodic theory. We show that in general the set of correlated equilibrium distributions of a polynomial game cannot be described by conditions on finitely many joint moments, in marked contrast to the set of Nash equilibria which is always expressible in terms of finitely many moments.
Experimental Platform for Characterizing a Nylon Thread Thermomechanical Actuator

The present work has as objective to develop and execute the project of an experimental platform to obtain the electro thermomechanical responses of a class of actuators based on nylon shing lines. The methodologies used for the hardware and software development were the Model-Based Design, automatic code generation, and the V Model methodology. The tests for validating the platform demonstrated a capacity of a 120 mm in length and 1 mm diameter actuator perform work and lift a load of 150 g, contracting up to 15.2 mm (12:67%), and to generate a force of up to 2.36 N, when submitted to a temperature of 156.4 C in response to an input signal of electric current of average value of 6.6 A controlled by PWM that owed through a 0.8 mm diameter copper wire wrapped on the actuator.
Collision Warning with Full Auto Brake and Pedestrian Detection - a practical example of Automatic Emergency Braking

More and more vehicles are being equipped with Automatic Emergency Braking (AEB) systems. These systems intend to help the driver avoid or mitigate accidents by automatically applying the brakes prior to an accident. Initially only rear-end collision were addressed but over time more accident types are incorporated and brakes are applied earlier and stronger, in order to increase the velocity reduction before the accident occurs. This paper describes one of the latest AEB systems called Collision Warning with Full Auto Brake and Pedestrian Detection (CWAB-PD). It helps the driver with avoiding both rear-end and pedestrian accidents by providing a warning and, if necessary, automatic braking using full braking power. A limited set of accident scenarios is selected to illustrate the theoretical and practical performance of this system. It is shown that the CWAB-PD system can avoid accidents up to 35 km/h and can mitigate accidents achieving an impact speed reduction of 35 km/h. To the best of the authors knowledge CWAB-PD is the only system on the market that automatically can avoid accidents with pedestrians.
The treatment of mild Alzheimer's disease post‐NICE

The efﬁcacy of cholinesterase inhibitors in treating cognitive, functional or neuropsychiatric symptoms in patients with Alzheimer ’ s disease (AD) has been established (Takeda et al ., 2006). By contrast trials of potential alternatives for improving cognition in mild AD, e.g. Akhondzadeh et al . (2003) have had small sample sizes or produced inconclusive and often conﬂicting results. Although ‘open label ’ studies of cognitive stimulation in mild dementia exist (Savorani et al ., 2004), and potential beneﬁts of maintenance cognitive stimulation are suggested (Orrell et al ., 2005), the study populations are very small and have no placebo control.
In vitro replication of adeno-associated virus DNA

The study of eukaryotic viral DNA replication in vitro has led to the identification of cellular enzymes involved in DNA replication. Adeno-associated virus (AAV) is distinct from previously reported systems in that it is believed to replicate entirely by leading-strand DNA synthesis and requires coinfection with adenovirus to establish completely permissive replication. In previous work, we demonstrated that two of the AAV nonstructural proteins, Rep78 and -68, are site-specific endonucleases and DNA helicases that are capable of resolving covalently closed AAV termini, a key step in AAV DNA replication. We have now cloned the AAV nonstructural proteins Rep78, Rep68, and Rep52 in the baculovirus expression system. Using the baculovirus-expressed proteins, we have developed an efficient in vitro AAV DNA replication system which mimics the in vivo behavior of AAV in every respect. With no-end AAV DNA as the starting substrate, the reaction required an adenovirus-infected cell extract and the presence of either Rep78 or Rep68. Rep52, as expected, did not support DNA replication. A mutant in the AAV terminal resolution site (trs) was defective for DNA replication in the in vitro assay. Little, if any, product was formed in the absence of the adenovirus-infected HeLa cell extract. In general, uninfected HeLa extracts were less efficient in supporting AAV DNA replication than adenovirus-infected extracts. Thus, the requirement for adenovirus infection in vivo was partially duplicated in vitro. The reduced ability of uninfected HeLa extracts to support complete DNA replication was not due to a defect in terminal resolution but rather to a defect in the reinitiation reaction or in elongation. Rep78 produced a characteristic monomer-dimer pattern of replicative intermediates, but surprisingly, Rep68 produced little, if any, dimer replicative form. The reaction had a significant lag (30 min) before incorporation of 32P-deoxynucleoside triphosphate could be detected in DpnI-resistant monomer replicative form and was linear for at least 4 h after the lag. The rate of incorporation in the reaction was comparable to that in the simian virus 40 in vitro system. Replication of the complete AAV DNA molecule was demonstrated by the following criteria. (i) Most of the monomer and dimer product DNAs were completely resistant to digestion with DpnI. (ii) Virtually all of the starting substrate was converted to heavy-light or heavy-heavy product DNA in the presence of bromo-dUTP when examined on CsCl density gradients. (ABSTRACT TRUNCATED AT 400 WORDS)
Multi-dimensional Data Analysis in Electron Microscopy

This thesis discusses various large multi-dimensional dataset analysis methods and their applications. Particular attention is paid to non-linear optimization analyses and general processing algorithms and frameworks when the datasets are significantly larger than the available computer memory. All new presented algorithms and frameworks were implemented in the HyperSpy analysis toolbox. A novel Smart Adaptive Multi-dimensional Fitting (SAMFire) algorithm is presented and applied across a range of scanning transmission electron microscope (STEM) experiments. As a result, the Stark effect in quantum disks was mapped in a cathodoluminescence STEM experiment, and fully quantifiable 3D atomic distributions of a complex boron nitride core-shell nanoparticle were reconstructed from an electron energy loss spectrum (EELS) tilt-series. The EELS analysis also led to the development of two new algorithms to extract EELS near-edge structure fingerprints from the original dataset. Both approaches do not rely on standards, are not limited to thin or constant thickness particles and do not require atomic resolution. A combination of the aforementioned fingerprinting techniques and SAMFire allows robust quantifiable EELS analysis of very large regions of interest. A very large dataset loading and processing framework, “LazySignal”, was developed and tested on scanning precession electron diffraction (SPED) data. A combination of SAMFire and LazySignal allowed efficient analysis of large diffraction datasets, successfully mapping strain across an extended (ca. 1 μm × 1 μm) region and classifying the strain fields around precipitate needles in an aluminium alloy.
Sprayed Concrete Lined Tunnels

Stefanie.Aschmann@tandf.co.uk 020 33773301 Practising engineers on site, in the design office or in client organizations will find this book an excellent introduction to the design and construction of sprayed concrete lined (SCL) tunnels. The complex behaviour of the early age behaviour of the sprayed concrete requires careful management. This book covers all aspects of SCL tunnelling – from the constituents of sprayed concrete to detailed design and management during construction. Although there is a close interdependence between all the facets of sprayed concrete, few engineers have the right breadth of experience and expertise, and this urgently needs to be transferred to the wider engineering community.
Robust and Noise Resistant Wrapper Induction

Wrapper induction is the problem of automatically inferring a query from annotated web pages of the same template. This query should not only select the annotated content accurately but also other content following the same template. Beyond accurately matching the template, we consider two additional requirements: (1) wrappers should be robust against a large class of changes to the web pages, and (2) the induction process should be noise resistant, i.e., tolerate slightly erroneous (e.g., machine generated) samples. Key to our approach is a query language that is powerful enough to permit accurate selection, but limited enough to force noisy samples to be generalized into wrappers that select the likely intended items. We introduce such a language as subset of XPATH and show that even for such a restricted language, inducing optimal queries according to a suitable scoring is infeasible. Nevertheless, our wrapper induction framework infers highly robust and noise resistant queries. We evaluate the queries on snapshots from web pages that change over time as provided by the Internet Archive, and show that the induced queries are as robust as the human-made queries. The queries often survive hundreds sometimes thousands of days, with many changes to the relative position of the selected nodes (including changes on template level). This is due to the few and discriminative anchor (intermediately selected) nodes of the generated queries. The queries are highly resistant against positive noise (up to 50%) and negative noise (up to 20%).
Trusting the Bankers: A New Look at the Credit Channel of Monetary Policy

Monetary policy has real effects through credit supply and demand, and since these changes are mostly unobserved, the complete identification of the credit channel is generally unfeasible. Bank lending surveys by central banks, however, contain reliable quarterly information on changes in loan conditions due to bank, firm and household balance sheet strength and on changes in loan demand. Using the U.S. and the unique Euro area surveys, we find that the credit channel amplifies a monetary policy shock on GDP and prices through the balance-sheets of households, firms and banks. For corporate loans, amplification is highest through the bank lending and the borrower's balance sheet channel; for households, demand is the strongest channel (Copyright: Elsevier)
Booming far: the long-range vocal strategy of a lekking bird

The pressures of selection acting on transmission of information by acoustic signals are particularly high in long-distance communication networks. Males of the North African houbara bustard (Chlamydotis undulata undulata) produce extremely low-frequency vocalizations called ‘booms’ as a component of their courtship displays. These displays are performed on sites separated by a distance of on average 550 m, constituting exploded leks. Here, we investigate the acoustic features of booms involved in species-specific identity. We first assessed the modifications of acoustic parameters during boom transmission at long range within the natural habitat of the species, finding that the frequency content of booms was reliably transmitted up to 600 m. Additionally, by testing males' behavioural responses to playbacks of modified signals, we found that the presence of the second harmonic and the frequency modulation are the key parameters for species identification, and also that a sequence of booms elicited stronger responses than a single boom. Thus, the coding–decoding process relies on redundant and propagation-resistant features, making the booms particularly well adapted for the long-range transmission of information between males. Moreover, by experimentally disentangling the presentation of visual and acoustic signals, we showed that during the booming phase of courtship, the two sensory modalities act in synergy. The acoustic component is dominant in the context of intra-sexual competition. While the visual component is not necessary to induce agonistic response, it acts as an amplifier and reduces the time of detection of the signaller. The utilization of these adaptive strategies allows houbara males to maximize the active space of vocalizations emitted in exploded leks.
Methicillin-Resistant Staphylococcus aureus Colonization of the Groin and Risk for Clinical Infection among HIV-infected Adults

Data on the interaction between methicillin-resistant Staphylococcus aureus (MRSA) colonization and clinical infection are limited. During 2007–2008, we enrolled HIV-infected adults in Atlanta, Georgia, USA, in a prospective cohort study. Nares and groin swab specimens were cultured for S. aureus at enrollment and after 6 and 12 months. MRSA colonization was detected in 13%–15% of HIV-infected participants (n = 600, 98% male) at baseline, 6 months, and 12 months. MRSA colonization was detected in the nares only (41%), groin only (21%), and at both sites (38%). Over a median of 2.1 years of follow-up, 29 MRSA clinical infections occurred in 25 participants. In multivariate analysis, MRSA clinical infection was significantly associated with MRSA colonization of the groin (adjusted risk ratio 4.8) and a history of MRSA infection (adjusted risk ratio 3.1). MRSA prevention strategies that can effectively prevent or eliminate groin colonization are likely necessary to reduce clinical infections in this population.
Depth-aware motion deblurring

Motion deblurring from images that are captured in a scene with depth variation needs to estimate spatially-varying point spread functions (PSFs). We tackle this problemwith a stereopsis configuration, using depth information to help blur removal. We observe that the simple scheme to partition the blurred images into regions and estimate their PSFs respectively may make small-size regions lack necessary structural information to guide PSF estimation and accordingly propose region trees to hierarchically estimate them. Erroneous PSFs are rejected with a novel PSF selection scheme, based on the shock filtering invariance of natural images. Our framework also applies to general single-image spatially-varying deblurring.
Accretion shocks and cold filaments in galaxy formation

A generic expectation for gas accreted by high-mass haloes is that it is shock-heated to the virial temperature of the halo. In low-mass haloes, or at high redshift, however, the gas cooling rate is sufficiently rapid that an accretion shock is unlikely to form close to the virial radius. Instead, the accretion shock will form at smaller radii, perhaps close to the central galaxy. Semi-analytic models have always made a clear distinction between the regimes in which accretion is limited by the cooling time of hot gas and by the dynamical time-scale of the halo, using simple estimates of the mass-scale at which the transition from rapid to slow cooling occurs. In this work, we revisit this issue using the latest understanding and calibration of accretion shock formation. Starting from the well-established Galform code, we investigate the effect of accounting for the presence or otherwise of an accretion shock close to the virial radius using the shock stability model of Birnboim & Dekel. As expected, when we modify the code so that there is no effective feedback from galaxy formation, we find that so-called ‘cold-mode’ accretion is the dominant channel for feeding gas into the galaxies at high redshifts, such that 90 per cent of baryons in galaxies (averaged over all galaxies) arrive via this channel. The mass-scale at which the rapid to slow cooling transition occurs is significantly affected at high redshifts and accretion rates become dominated by cold-mode accretion. However, the impact of this change in the cooling channel on galaxies properties is mitigated by compensating effects in the star formation and feedback cycle. When effective feedback, which reheats gas from galaxies to the virial temperature but which allows no gas to escape from a halo, is included in the model, we find that the ‘cold mode’ is even less apparent because of the presence of gas ejected from the galaxy's disc, although it can still contribute almost 50 per cent of the net inflow rate when averaged over all galaxies. Thus, the inclusion of the latest calibration of accretion shock physics makes little difference to basic results from earlier semi-analytic models, which used a simpler treatment. We conclude that this ‘cold-mode’ physics is already adequately accounted for in semi-analytic models and that feedback represents a much larger uncertainty than any of these effects.
A Chain Observer for Nonlinear Systems with Multiple Time-Varying Measurement Delays

This paper presents a method for designing state observers with exponential error decay for nonlinear systems whose output measurements are affected by known time-varying delays. A modular approach is followed, where subobservers are connected in cascade to achieve a desired exponential convergence rate (chain observer). When the delay is small, a single-step observer is sufficient to carry out the goal. Two or more subobservers are needed in the the presence of large delays. The observer employs delay-dependent time-varying gains to achieve the desired exponential error decay. The proposed approach allows to deal with vector output measurements, where each output component can be affected by a different delay. Relationships among the error decay rate, the bound on the measurement delays, the observer gains, and the Lipschitz constants of the system are presented. The method is illustrated on the synchronization problem of continuous-time hyperchaotic systems with buffered measurements.
Quasi-Variational Inequalities with Dirichlet Boundary Condition Related to Exit Time Problems for Impulse Control

We study degenerate-elliptic quasi-variational inequalities with Dirichlet boundary condition, which are related to the value function of the exit time problem for stochastic impulse control by means of the dynamic programming principle. The boundary condition in the viscosity solutions sense does not identify a unique solution, because in this nonlocal problem the boundary layer gives rise to a loss of information also at the interior points. The eventual discontinuities of solutions at the boundary of the domain play an essential role and cannot be removed. Therefore we superimpose a selection criterion which, enforcing the information coming from the boundary datum, picks up the value function among all possible viscosity solutions. As a result, we attain the continuity of the value function up to the boundary. In addition, we produce a monotone iterative scheme approximating the value function.
The Major Symptoms of Hysteria

interesting manner, that one gains pleasure as well as profit from reading them. Those who are not already acquainted with . the author's views should procure this book, which presents them mcst lucidly, and at moderate length. Professor Janet's work has done much to elucidate hysteria by a process of analysis of the psychical phenomena which lie at its root. We may remind our readers that according to his view these phenomena comprise the occurrence of certain somnambulistic states? that is, of states which may roughly be called " absent-mindedness ; ""
Implementation of trot-to-gallop transition and subsequent gallop on the MIT Cheetah I

This paper presents a demonstration of the trot-to-gallop transition and subsequent stable gallop in a robotic quadruped. The MIT Cheetah I, a planar quadruped platform for high-speed running, achieves these tasks with a speed of 3.2 m/s (Froude number of 2.1) on a treadmill. The controller benefits from clues from biological findings and it incorporates (1) a gait pattern modulation that imposes predefined gait patterns with a proprioceptive touchdown feedback, (2) tunable equilibrium-point foot-end trajectories for four limbs that intentionally modulate ground reaction forces, and (3) programmable leg compliance that provides instantaneous reflexes to leg–ground interaction. An inertial measurement unit sensor is integrated with the controller in order to regulate leg angles of attack at touchdown. We reduce the dimension of the control parameters which describe temporal/spatial characteristics of quadruped locomotion, and the values are tuned via dynamic simulation and then experiment. Given a pre-defined virtual leg compliance and a desired angle of attack of legs, the equilibrium-point foot-end trajectories and phase relationships between four legs for stable trot and gallop gaits are found independently. We propose a simple throw-and-catch gait transition strategy which connects two stable limit cycles, the trot and the gallop, by linearly varying control parameters during the transition period. Successful gait transition is achieved in both simulation and experiment. Comprehensive analysis on the characteristics of the MIT Cheetah I experimental trot-to-gallop transition is provided. The phase portraits imply that stable limit cycles are achieved with the proposed controller in both trot and gallop, which enables the trot-to-gallop gait transition at high speed.