Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian Control of Chloroplast Transcription by a Nuclear-Encoded Timing Signal

Synchronizing Photosynthetic Capacity Coordination of photosynthetic activity with sunlight benefits plant productivity. Noordally et al. (p. 1316) analyzed how the Arabidopsis circadian clock keeps the chloroplasts working in tune with the Sun. SIGMA FACTOR5 (SIG5) is encoded in the cell nucleus and reflects circadian cycles with changes in its own transcript abundance. SIG5 acts, however, in the chloroplast, where it supports photosystem II production. In plants, day/night information is communicated from a nuclear-encoded circadian oscillator to the chloroplast. Circadian timekeeping in plants increases photosynthesis and productivity. There are circadian oscillations in the abundance of many chloroplast-encoded transcripts, but it is not known how the circadian clock regulates chloroplast transcription or the photosynthetic apparatus. We show that, in Arabidopsis, nuclear-encoded SIGMA FACTOR5 (SIG5) controls circadian rhythms of transcription of several chloroplast genes, revealing one pathway by which the nuclear-encoded circadian oscillator controls rhythms of chloroplast gene expression. We also show that SIG5 mediates the circadian gating of light input to a chloroplast-encoded gene. We have identified an evolutionarily conserved mechanism that communicates circadian timing information between organelles with distinct genetic systems and have established a new level of integration between eukaryotic circadian clocks and organelles of endosymbiotic origin.
Photoperiod Can Entrain Circannual Rhythms in Pinealectomized European Hamsters

In mammals, the pineal hormone melatonin is thought to be essential to process environmental photoperiodic information. In this study, we demonstrate in a circannual species, the European hamster Cricetus cricetus, the existence of a melatonin-independent second pathway. In 4 physiological parameters (reproduction, body weight, activity pattern, body temperature), a large majority of pinealectomized European hamsters were entrained to an accelerated photoperiodic regime. It compressed the natural variations in the photoperiod to a 6-month cycle, which allowed us to record up to 6 complete physiological cycles during the life span of the individuals. We show further that whether a pinealectomized animal is able to entrain to changes in the photoperiod is influenced by the season of pinealectomy. The results do not disprove that melatonin is capable of entraining a circannual rhythm, but they show clearly that melatonin is not necessary, demonstrating another melatonin-independent pathway for circannual entrainment by the photoperiod. In view of these new insights, a revision of the original literature revealed that probably the melatonin-independent pathway plays an important role in most circannual mammals but only a minor role in photoperiodic species. Thus, the present work provides also the first evidence for different synchronization mechanisms in photoperiodic and circannual species.
Cardiomyocyte-Specific BMAL1 Plays Critical Roles in Metabolism, Signaling, and Maintenance of Contractile Function of the Heart

Circadian clocks are cell autonomous, transcriptionally based, molecular mechanisms that confer the selective advantage of anticipation, enabling cells/organs to respond to environmental factors in a temporally appropriate manner. Critical to circadian clock function are 2 transcription factors, CLOCK and BMAL1. The purpose of the present study was to reveal novel physiologic functions of BMAL1 in the heart, as well as to determine the pathologic consequences of chronic disruption of this circadian clock component. To address this goal, we generated cardiomyocyte-specific Bmal1 knockout (CBK) mice. Following validation of the CBK model, combined microarray and in silico analyses were performed, identifying 19 putative direct BMAL1 target genes, which included a number of metabolic (e.g., β-hydroxybutyrate dehydrogenase 1 [Bdh1]) and signaling (e.g., the p85α regulatory subunit of phosphatidylinositol 3-kinase [Pik3r1]) genes. Results from subsequent validation studies were consistent with regulation of Bdh1 and Pik3r1 by BMAL1, with predicted impairments in ketone body metabolism and signaling observed in CBK hearts. Furthermore, CBK hearts exhibited depressed glucose utilization, as well as a differential response to a physiologic metabolic stress (i.e., fasting). Consistent with BMAL1 influencing critical functions in the heart, echocardiographic, gravimetric, histologic, and molecular analyses revealed age-onset development of dilated cardiomyopathy in CBK mice, which was associated with a severe reduction in life span. Collectively, our studies reveal that BMAL1 influences metabolism, signaling, and contractile function of the heart.
Paramyxovirus V Proteins Disrupt the Fold of the RNA Sensor MDA5 to Inhibit Antiviral Signaling

Parainfluenza 5 and MDA5 Our immune system and the viruses that infect us are in a constant arms race, with one side always trying to outwit the other. One example is the inhibition of host protein MDA5, a member of the retinoic acid–inducible gene 1 (RIG-I)–like receptor (RLR) family of innate immune sensors, by the V protein expressed by parainfluenza virus 5 (PIV5). To better understand how this inhibition is accomplished, Motz et al. (p. 690, published online 17 January) solved the crystal structure of PIV5 V protein bound to the adenosine triphosphatase (ATPase) domain of porcine MDA5. This analysis, together with mutational studies using mouse and human versions of MDA5, revealed that the V protein unfolds the ATPase domain of MDA5 and replaces two β strands of this domain's structural core. These changes disrupt the ATPase hydrolysis site and prevent the formation of filaments by MDA5, which are important for transmitting downstream signals that activate antiviral immunity. Mutation of just two amino acids in RLR family member RIG-I also rendered this receptor susceptible to V protein–mediated inhibition. The crystal structure of a viral protein core complex reveals how paramyxoviruses inhibit the innate immune response. The retinoic acid–inducible gene I (RIG-I)–like receptor (RLR) melanoma differentiation–associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5′-triphosphate (ATP)–hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a β-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. The structure explains why V proteins inactivate MDA5, but not RIG-I, and mutating only two amino acids in RIG-I induces robust V protein binding. Our results suggest an inhibition mechanism of RLR signalosome formation by unfolding of receptor and inhibitor.
Robust predictive control for the management of multi-echelon distribution chains

The problem of robust inventory control for multi-echelon distribution chains is addressed by using predictive control. Since the future demand of goods is assumed to be uncertain, we focus on a worst-case planning strategy that is consistent with the demand predictions and minimizes the maximum of a performance objective function. The resulting optimal decisions concern the delivery of goods in such a way to reduce the overall costs as to holding, transportation, and backlogs. As compared with previous works, the proposed approach allows one to deal with distribution chains of much larger dimension because of its intrinsic scalability. Of course, such an appreciable feature is paid in terms of loss of optimality. However, a convenient tradeoff can be achieved, as shown by means of simulations.
Metamaterials with Quantum Gain

Integrating amplifying media with metamaterials allows loss-free plasmonic operation and opens a route for controlling nanoscale quantum emitters. Optical metamaterials and nanoplasmonics offer extreme control and localization of light within volumes that can be smaller than a cubic light wavelength by more than three orders of magnitude, but they suffer from appreciable dissipative losses. This weakness is thought to constitute the prime impediment before many of the envisaged applications can succeed in practice. However, recent breakthroughs in the theoretical understanding and experimental fabrication of gain-enhanced metamaterials and nanoplasmonic heterostructures promise to overcome these hindrances, while allowing for new ways to control spontaneous and stimulated emission of light on the nanoscale (1, 2).
Advanced quality of services with security integration in wireless sensor networks

In this paper, we focus on the coexistence between security and quality of services QoS guarantee in wireless sensor networks. The idea is to integrate the security services: authentication, integrity, confidentiality, and non-repudiation with QoS guarantee. In literature, the major proposed solutions consider QoS and security separately. In addition, it has been shown that it is difficult to offer the end-users multiple levels of security while offering a high level of QoS, because security and QoS are opposite parameters. To tackle this main issue, we propose a new model based on proportional integral derivative controller in order to dynamically select the security level adapted to QoS requirements while considering the energy consumption. The stability parameters in terms of security level and QoS are taken into account by using the principle of proportional integral derivative which is based on the past parameters history, the current system state present, and the predictable system change future. In order to evaluate the proposed model, we consider the case of routing protocol, and we introduce this model into the well-known ad-hoc on-demand distance vector AODV protocol called QwS-AODV protocol. Unlike the classical secure AODV, the QwS-AODV protocol aims at adding or removing security services dynamically according to the network performance. Moreover, the validation and the evaluation of the proposed solution are carried out by simulation. The performance evaluation is presented with different network parameters such as throughput, delay, energy consumption, and security services. In addition, the comparison with a classical secure AODV is carried out, and the results obtained with the simulation illustrate that the security is always ensured with lower costs in terms of QoS and energy consumption. Copyright © 2014 John Wiley & Sons, Ltd.
Behavioral Economics and the Retirement Savings Crisis

Behavioral economics can be scaled up to have a major, positive impact on certain behaviors, such as retirement savings. Many countries are facing a retirement savings crisis. In the United States, for example, the fraction of workers at risk of having inadequate funds to maintain their lifestyle through retirement is estimated to have increased from 31% to 53% from 1983 to 2010 (1). Roughly half of U.S. employees (78 million) have no access to retirement plans at their workplace (2). Fortunately, there are solutions to these problems. We simply have to change the choice architecture of retirement plans by utilizing the findings of behavioral economics research (3) and make such plans available to all workers. We describe a large-scale field demonstration of the potential impact of such research-based changes in how we save.
Evidence for Two Distinct Populations of Type Ia Supernovae

Fast and Young Type Ia supernovae are thought to result from the thermonuclear explosion of a white dwarf star accreting material from a companion star in a binary system. Their adoption as cosmic yardsticks has led to the discovery of the accelerated expansion of the universe. Wang et al. (p. 170, published online 7 March) show that supernovae with higher expansion velocities are located in the central, brighter regions of their host galaxies and are found in larger, more luminous galaxies, suggesting that they are associated with younger stellar populations. The spectral diversity of a particular type of stellar explosion is tied to the stellar environment. Type Ia supernovae (SNe Ia) have been used as excellent standardizable candles for measuring cosmic expansion, but their progenitors are still elusive. Here, we report that the spectral diversity of SNe Ia is tied to their birthplace environments. We found that those with high-velocity ejecta are substantially more concentrated in the inner and brighter regions of their host galaxies than are normal-velocity SNe Ia. Furthermore, the former tend to inhabit larger and more luminous hosts. These results suggest that high-velocity SNe Ia likely originate from relatively younger and more metal-rich progenitors than do normal-velocity SNe Ia and are restricted to galaxies with substantial chemical evolution.
Schraubenhalt-Verstärkung im Femurkopf durch Zementapplikation via Implantat - eine biomechanische Studie

Purpose: Osteoporosis reveals a higher risk of fractures. Due to the lack of possibilities to anchor fixation elements, fracture treatment often turns out to be complicated. An experimental study served to investigate the extent to which the application of bone cement through a modified gliding screw (Dynamic Hip Screw DHS) would improve the screw anchoring in osteorporotic femoral heads. Methods: Quasi-static compressive and torsional load tests were used to assess the desired improvement of the screw anchoring. Cadaver femur pairs served to compare the cement augmentation to the uncemented contralateral control. Results: The improvement of the holding strength of the screw under static compressive and torsional load depended on the cement flow into the adjacent bone tissue. The filling with additional cement was only successful after having created a small hollow space at the screw tip with a special instrument. Consequently, under compression as well as torsion, the cement application yielded improvements from 17% up to several times as much. Conclusion: In the application of gliding screws in osteoporotic femoral heads, the locally limited cement application through the implant has been shown to be a biomechanical possibility to improve screw fixation.
Nanoscale Nuclear Magnetic Resonance with a Nitrogen-Vacancy Spin Sensor

Nanoscale NMR with Diamond Defects Although nuclear magnetic resonance (NMR) methods can be used for spatial imaging, the low sensitivity of detectors limits the minimum sample size. Two reports now describe the use of near-surface nitrogen-vacancy (NV) defects in diamond for detecting nanotesla magnetic fields from very small volumes of material (see the Perspective by Hemmer). The spin of the defect can be detected by changes in its fluorescence, which allows proton NMR of organic samples only a few nanometers thick on the diamond surface. Mamin et al. (p. 557) used a combination of electron spin echoes and pulsed NMR manipulation of the proton spins to detect the very weak fields. Staudacher et al. (p. 561) measured statistical polarization of a population of about 104 spins near the NV center with a dynamical decoupling method. The optical response of the spin of a near-surface atomic defect in diamond can be used to sense proton magnetic fields. [Also see Perspective by Hemmer] Extension of nuclear magnetic resonance (NMR) to nanoscale samples has been a longstanding challenge because of the insensitivity of conventional detection methods. We demonstrated the use of an individual, near-surface nitrogen-vacancy (NV) center in diamond as a sensor to detect proton NMR in an organic sample located external to the diamond. Using a combination of electron spin echoes and proton spin manipulation, we showed that the NV center senses the nanotesla field fluctuations from the protons, enabling both time-domain and spectroscopic NMR measurements on the nanometer scale.
What's in the gap? Interaction transitions that make HRI work

This paper presents an in-depth analysis from a human robot interaction (HRI) study on spatial positioning and interaction episode transitions. Subjects showed a living room to a robot to teach it new places and objects. This joint task was analyzed with respect to organizing strategies for interaction episodes. Noticing the importance of transitions between interaction episodes, small adaptive movements in posture were observed. This finding needs to be incorporated into HRI modules that plan and execute robots' spatial behavior in interaction, e.g., through dynamic adaptation of spatial formations and distances depending on interaction episode
Sensing Precision of an Optical Three-axis Tactile Sensor for a Robotic Finger

We are developing an optical three-axis tactile sensor capable of acquiring normal and shearing force, with the aim of mounting it on a robotic finger. The tactile sensor is based on the principle of an optical waveguide-type tactile sensor, which is composed of an acrylic hemispherical dome, a light source, an array of rubber sensing elements, and a CCD camera. The sensing element of silicone rubber comprises one columnar feeler and eight conical feelers. The contact areas of the conical feelers, which maintain contact with the acrylic dome, detect the three-axis force applied to the tip of the sensing element. Normal and shearing forces are then calculated from integration and centroid displacement of the gray-scale value derived from the conical feeler's contacts. To evaluate the present tactile sensor, we have conducted a series of experiments using a y-z stage, a rotational stage, and a force gauge, and have found that although the relationship between the integrated gray-scale value and normal force depends on the sensor's latitude on the hemispherical surface, it is easy to modify the sensitivity according to the latitude, and that the centroid displacement of the gray-scale value is proportional to the shearing force. When we examined repeatability of the present tactile sensor with 1,000 load-unload cycles, the respective error of the normal and shearing forces was 2 and 5%
Dynamical Structure Function and Granger Causality: Similarities and differences

Causal networks are essential in many applications to illustrate causal relations in dynamical systems. In a view of statistics, Granger Causality (GC) gives a definition for causal ordering of time series, which implies a parametric model for stationary processes. In a systematic view, Dynamical Structure Function (DSF) is proposed to provide a general parametric representation for linear causal networks based on state space representations. It is difficult to determine which definition should be adopted for a particular application. By introducing an intermediate form of DSF, this article connects GC for stationary processes with DSF. Both GC and DSF essentially represent the same notion of causality but with important differences with respect to how they encode latent variables. This article also addresses the relations between graphs defined by GC and DSF. Furthermore, the uniqueness of parametric representations is addressed, which is essential in network inference. Results from different fields are surveyed and categorized into two categories - networks with exogeneity and networks without exogeneity. Limitations on sufficient conditions to guarantee exact identification are discussed under different assumptions on systems. In the end, a figure is used to summarize the relationships between various representations of causal dynamical networks and their identifiability conditions in LTI systems.
Accumulation of clinically relevant antibiotic-resistance genes, bacterial load, and metals in freshwater lake sediments in Central Europe.

Wastewater treatment plants (WWTP) receive the effluents from various sources (communities, industrial, and hospital effluents) and are recognized as reservoir for antibiotic-resistance genes (ARGs) that are associated with clinical pathogens. The aquatic environment is considered a hot-spot for horizontal gene transfer, and lake sediments offer the opportunity for reconstructing the pollution history and evaluating the impacts. In this context, variation with depth and time of the total bacterial load, the abundance of faecal indicator bacteria (FIB; E. coli and Enterococcus spp. (ENT)), Pseudomonas spp. , and ARGs (blaTEM, blaSHV, blaCTX-M, blaNDM, and aadA) were quantified in sediment profiles of different parts of Lake Geneva using quantitative PCR. The abundance of bacterial marker genes was identified in sediments contaminated by WWTP following eutrophication of the lake. Additionally, ARGs, including the extended-spectrum ß-lactam- and aminoglycoside-resistance genes, were identified in the surface sediments. The ARG and FIB abundance strongly correlated (r ≥ 0.403, p < 0.05, n = 34) with organic matter and metal concentrations in the sediments, indicating a common and contemporary source of contamination. The contamination of sediments by untreated or partially treated effluent water can affect the quality of ecosystem. Therefore, the reduction of contaminants from the source is recommended for further improvement of water quality.
Tele-operation of a Mobile Robot Using a Force Reflection Joystick with a Single Hall Sensor

Though the final goal of mobile robot navigation is to be autonomous, operators' intelligent and skillful decisions are necessary when there are many scattered obstacles. There are several limitations even in the camera-based tele-operation of a mobile robot, which is very popular for the mobile robot navigation. For examples, shadowed and curved areas cannot be viewed using a narrow view-angle camera, especially in bad weather such as on snowy or rainy days. Therefore, it is necessary to have other sensory information for reliable tele-operations. In this paper, sixteen ultrasonic sensors are attached around a mobile robot in a ring pattern to measure the distances to obstacles. A collision vector is introduced in this paper as a new tool for obstacle avoidance, which is defined as a normal vector from an obstacle to the mobile robot. Based on this collision vector, a virtual reflection force is generated to avoid the obstacles and then the reflection force is transferred to an operator who is holding a joystick to control the mobile robot. Relying on the reflection force, the operator can control the mobile robot more smoothly and safely. For this bi-directional tele-operation, a master joystick system using a hall sensor was designed to resolve the existence of nonlinear sections, which are usual for a general joystick with two motors and potentiometers. Finally, the efficiency of a force reflection joystick is verified through the comparison of two vision-based tele-operation experiments, with and without force reflection.