Miracle-dz/UniFAR-FTUs huggingface dataset:
Pervasive contingency and entrenchment in a billion years of Pervasive contingency and entrenchment in a billion years of Hsp90 evolution [preprint] Hsp90 evolution [preprint] document benefits you.

1 Interactions among mutations within a protein have the potential to make molecular 2 evolution contingent and irreversible, but the extent to which epistasis actually shaped historical 3 evolutionary trajectories is unclear. We addressed this question by identifying all amino acid 4 substitutions that occurred during the billion-year evolutionary history of the heat shock protein 5 90 (Hsp90) ATPase domain beginning from a deep eukaryotic ancestor to modern 6 Saccharomyces cerevisiae and then precisely measuring their fitness effects when introduced 7 into both extant and reconstructed ancestral Hsp90 proteins. We find a pervasive influence of 8 epistasis: of 98 derived states that evolved during history, most were deleterious at times before 9 they happened, and the vast majority also became subsequently entrenched, with the ancestral 10 state becoming deleterious after its substitution. This epistasis was primarily caused by specific 11 interactions among sites rather than a general permissive or restrictive effect on the protein’s 12 tolerance to mutation. Our results show that epistasis continually opens and closes windows of 13 mutational opportunity over evolutionary timescales, producing histories and biological states 14 that reflect the transient internal constraints imposed by a protein’s fleeting sequence states. 15
Targeted gene delivery to the enteric nervous system using AAV: a Targeted gene delivery to the enteric nervous system using AAV: a comparison across serotypes and capsid mutants comparison across serotypes and capsid mutants

Recombinant adeno-associated virus (AAV) vectors are one of the most widely used gene transfer systems in research and clinical trials. AAV can transduce a wide range of biological tissues, however to date, there has been no investigation on targeted AAV transduction of the enteric nervous system (ENS). Here, we examined the efficiency, tropism, spread, and immunogenicity of AAV transduction in the ENS. Rats received direct injections of various AAV serotypes expressing green fluorescent protein (GFP) into the descending colon. AAV serotypes tested included; AAV 1, 2, 5, 6, 8, or 9 and the AAV2 and AAV8 capsid mutants, AAV2-Y444F, AAV2-tripleY-F, AAV2-tripleY-F+T-V, AAV8-Y733F, and AAV8-doubeY-F+T-V. Transduction, as determined by GFP-positive cells, occurred in neurons and enteric glia within the myenteric and submucosal plexuses of the ENS. AAV6 and AAV9 showed the highest levels of transduction within the ENS. Transduction efficiency scaled with titer and time, was translated to the murine ENS, and produced no vector-related immune response. A single injection of AAV into the colon covered an area of ~47 mm 2 . AAV9 primarily transduced neurons, while AAV6 transduced enteric glia and neurons. This is the first report on targeted AAV transduction of neurons and glia in the ENS.
Compressive sampling system based on random demodulation for active and passive structural health monitoring

Structural health monitoring (SHM) is a revolutionary and innovative technique for determining structural integrity. It has broad application prospects in industrial equipment and infrastructure such as aircrafts, bridges and buildings. SHM system is used to monitor and diagnose the damages of these large structures, and it requires to install large sensor networks in or on large structures such as aircraft wings and airframes. The large number of sensors results in a very large amount of data for excited and received signals, especially for ultrasonic guided wave-based SHM with high frequency signals. According to the traditional Nyquist sampling theorem, the sampling rate is at least 2 times higher than the highest frequency of the received signal. The high sampling rate and the large amount of data pose a serious challenge on the signal acquisition, transmission, storage, and processing equipment, especially in the case that the signal needs to be transmitted to the base station for processing in real time. Therefore, how to compress and sample signals obtained by large sensor networks to improve monitoring efficiency and reduce costs is a research hotspot in current SHM. This paper adopts compressive sensing (CS) theory which has appeared in recent years to solve the big data and high frequency acquirement problem of SHM. The random demodulation system is chosen to realize CS, and the corresponding hardware and software systems are designed, which are achieved to compress and sample signal and reduce the sampling rate and the amount of data at the same time. The active and passive SHM signals based on piezoelectric sensor networks are compressed and sampled, and the new method are compared with the traditional Nyquist sampling in the experiment. The results show the effectiveness of the proposed method.
Wireless gas sensing based on a passive piezoelectric resonant sensor array through near-field induction

We developed a wireless and passive piezoelectric resonant sensor for contimuous volatile organic compound detection. An equivalent circuit is proposed to model the sensing system, and Lamb wave resonators are adopted to demonstrate the wireless interrogation achieved by near-field inductive coupling. The wireless sensing system is employed to monitor the ethanol vapor concentration, and the sensitivity of the wireless sensor barely degrades compared to that of the wired one. Further, we simultaneously and wirelessly tracked several resonance frequencies of a monolithic sensor array, which demonstrates its potential for high-throughput and real-time point-of-care test.
On the Modeling and Multi-objective Optimization Design of Compact Planar Ultra-wideband Impedance Transformer

A versatile scheme for design of planar ultra-wideband impedance transformer is proposed by using fragment-type structures (FTS) for modeling and MOEA/D-GO for optimization. To improve the optimization efficiency, non-uniform FTS cells are applied. To find the optimal planar FTS transformer, two objective functions characterizing the return loss and the insertion loss of the impedance transformer, respectively, are defined on a ultra-wide bandwidth. For demonstration, a 25-ohm to 50-ohm FTS impedance transformer is designed, which acquires reflection coefficient lower than -20 dB and extra insertion loss less than 0.27 dB in ultra-wide frequency band of 0.89-5.00 GHz.
Estimating the Injection Duration of 20 MeV Protons in Large Western Solar Energetic Particle Events

An ad hoc analytical calculation is presented to infer the duration of injection of 20 MeV protons in 21 selected western solar energetic particle (SEP) events. We convolve the solution of diffusion equation with a “triangle” source to model the time-intensity profiles over the onset and the peaking phase. The effects of “corotating” flux tubes and of solar wind convection are neglected. To accommodate these simplifications, only western events whose associated flares erupted between W15 and W90 are selected. The time-intensity profiles of these events are reconstructed from the timescales presented in Kahler (2005) and Kahler (2013) using the modified Weibull function. From the linear relation between the logarithm of the peak intensity and the logarithm of the fluence of 27–37 MeV protons presented in Kahler & Ling, we derive an optimal radial mean free path (λ mfp) of 0.08 au and adopt this value to fit all selected events. The inferred duration of injection for the selected events, which in general increases with the initial speed of the associated coronal mass ejection (CME) (V cme), is less than 1 hr for V cme < 1000 km s−1 and varies from a few to ∼10 hr for 1000 km s−1 < V cme < 2000 km s−1. We then estimate the distance that the associated CMEs have traveled over the duration of injection. Most CMEs in selected events have traveled to less than 60 solar radii by the time the majority of accelerated particles have been injected into the interplanetary space.
Heteromaterial-gate line tunnel field-effect transistor based on Si/Ge heterojunction*

A Si/Ge heterojunction line tunnel field-effect transistor (LTFET) with a symmetric heteromaterial gate is proposed. Compared to single-material-gate LTFETs, the heteromaterial gate LTFET shows an off-state leakage current that is three orders of magnitude lower, and steeper subthreshold characteristics, without degradation in the on-state current. We reveal that these improvements are due to the induced local potential barrier, which arises from the energy-band profile modulation effect. Based on this novel structure, the impacts of the physical parameters of the gap region between the pocket and the drain, including the work-function mismatch between the pocket gate and the gap gate, the type of dopant, and the doping concentration, on the device performance are investigated. Simulation and theoretical calculation results indicate that the gap gate material and n-type doping level in the gap region should be optimized simultaneously to make this region fully depleted for further suppression of the off-state leakage current.
Role of government and society in urban innovation system: A case study from Indonesia

Government innovation at the regional level needs to be encouraged to stimulate regional development. Technology can help drive the innovation process and organizational change. The innovation process involves interactive learning to create and disseminate knowledge. Positive impacts are also obtained from the success of this innovation, not only for local governments but also for the society. This paper aims to identify how local government innovation encourages urban innovation in the context of the Global South. We perform a case study to represent the digitalized innovation, namely Surakarta City. The data were collected from the Innovation Government Awards (IGA) organized by the Ministry of Home Affairs and interviews with the local governments. The analysis was conducted using qualitative methods which resulted in a typology of local government innovation in Indonesia at the city level. This paper shows the ideas of good governance, as revealed by local government innovation awards. In addition, there are role of actors in initiating the creation of new knowledge, imitating ideas, and socializing them to make government performance more effective.
“Winged” Radio Sources from the LOFAR Two-meter Sky Survey First Data Release (LoTSS DR1)

A small number of extragalactic radio sources disclose a pair of low-surface-brightness radio lobes, known as “wings,” aligned at a certain angle to the primary jets. Such exotic sources are known as “winged” radio sources. Here we report the new identification of a total of 26 “winged” radio sources from the LOFAR Two-meter Sky Survey First Data Release (LoTSS DR1). Out of the 26 “winged” sources, 14 are identified as X-shaped radio galaxies and the remaining 12 as Z-shaped radio galaxies. The available optical counterpart of each radio galaxy is cataloged along with its estimated redshift. Among the 26 sources, 15 candidates are classified as FR-II radio galaxies, and two are classified as FR-I type. For nine candidates, no conclusions are drawn due to their complex morphology. We also calculate the physical parameters such as spectral index, radio luminosity, and power of the sources. We have made a statistical study of the spectral index by combining our estimated value with the spectral index collected from previous works. A mean value of spectral index of 0.71 is obtained.
A Brief Tutorial On Recursive Estimation With Examples From Intelligent Vehicle Applications (Part III): Handling Nonlinear Estimation Problems And The Unscented Kalman Filter

This is the third article of the series "A brief tutorial on recursive estimation". In this article, we focus on the problem of how to handle model nonlinearity (concerning both the system model and the measurement model) in recursive estimation. We will review an important variant of the KF, i.e. the unscented Kalman filter (UKF), which is dedicated to nonlinear estimation problems.
Optimization and simulation of a bionic fish tail driving system based on linear hypocycloid with hydrodynamics

The tail driving system based on linear hypocycloid has the advantages of adjustable phase difference, no quick-return, and combining speed reducer with transformation mechanism. The plane complex movement of the driving system was realized via a motion triangle with a linear hypocycloid planetary gear train and a linkage. In this article, we approach the question of which kind of parameter design can make this driving system more efficient in swimming from a hydrodynamic perspective. First, dynamic and hydrodynamic models were established with momentum theorem, Lagrange theorem, and two-dimensional foil theory. And then, hydrodynamic optimization on kinematic parameters (i.e. caudal peduncle’s reciprocation velocity and caudal fin swing angle) and structural parameters (i.e. swing amplitude, V planetary carrier’s angle, and sun gear’s radius) for a better propulsive efficiency was developed in detail. Second, influences of structural parameters on vortex ring were further conducted by numerical simulation in FLUENT. Finally, the prototype and experimental platform of the designed driving system were established, and the theoretical derivation of lift and lateral forces was testified by experiment.
Research on Target Defect Detection Based on Machine Vision

The daily detection of highspeed electric multiple units (EMU) body is very important for China railway maintenance system. This paper proposes a new method based on machine vision to detect bolts and switches on EMU side skirt, which aims to replace manpower. Yolov3 network is used to identify and locate bolts and switches. After positioning, the status of bolts is detected through Alexnet network. Experiments show that the processing method can achieve the detection work efficiently and accurately. It is suitable for many cases such as insufficient illumination and non-vertical shooting of image samples, which has high robustness.
Rural renewable energy development: lessons learned from community-based renewable energy business model in East Sumba, Indonesia

Sumba Island is a remote region with great potential for renewable energy sources, as the Iconic Island of Renewable Energy designated through the Minister of Energy and Mineral Resources Decree No. 3051 K / 30 / MEM / 2015 is targeted to reach 100% of renewable energy usage with 95% of electrification by 2025. To reach this target, the participation of the community as the subject of every renewable energy project is essential. This paper aims to identify the lessons learned to enhance the community’s capacity in implementing the rural community-based renewable energy business model in Indonesia, with the case of the renewable energy business in Luku Wingir and Waimbidi Village - East Sumba. The result indicates that the Rural Community-based Renewable Energy Business Model in the case study need to be developed based on the fundamental strategies of building community capacity: (1) leadership development of the village community in East Sumba, (2) business organizational development in managing the renewable energy, (3) developing a significant role for the community in organizing renewable energy, and (4) adapting collaborative relations among multiple stakeholders in East Sumba.
Coevolution of Broad Emission Lines and X-Ray Spectrum in Changing-look AGNs

Changing-look active galactic nuclei (CLAGNs) show the disappearance and reappearance of broad emission lines in a few years, which challenges the orientation-based AGN unification model. We reduce the X-ray data for five well-studied CLAGNs that show a strong change in broad emission lines in the past several decades. We find that the X-ray photon index, Γ, and the Eddington-scaled X-ray luminosity, L 2–10 keV/L Edd, normally follow negative and positive correlations when the Eddington ratio is lower and higher than a critical value of ∼10−3. We find that the CLAGNs observed with broad Hβ emission lines stay in the positive part of the Γ–L 2–10 keV/L Edd correlation, while the broad Hβ lines become weak or disappear in the anticorrelation part of the Γ–L 2–10 keV/L Edd correlation, which suggests that the evolution of the broad lines should be correlated with the evolution of the underlying accretion process. We further find that the CLAGNs are consistent with the other different types of AGNs in the L bol–L bol/L Edd correlation. These results support that the CLAGNs belong to a special stage of AGNs with a bolometric Eddington ratio ∼1%, where the broad emission lines are easily affected by the strong variation in ionization luminosity that is caused by the transition of accretion modes.
Perkinsus marinus Protistan Parasite ) Is a Receptor for the Crassostrea virginica from Hemocytes of the Eastern Oyster ( A Galectin of Unique Domain Organization

Invertebrates display effective innate immune responses for defense against microbial infection. However, the protozoan parasite Perkinsus marinus causes Dermo disease in the eastern oyster Crassostrea virginica and is responsible for catastrophic damage to shellﬁsheries and the estuarine environment in North America. The infection mechanisms remain un-clear, but it is likely that, while ﬁlter feeding, the healthy oysters ingest P. marinus trophozoites released to the water column by the infected neighboring individuals. Inside oyster hemocytes, trophozoites resist oxidative killing, proliferate, and spread throughout the host. However, the mechanism(s) for parasite entry into the hemocyte are unknown. In this study, we show that oyster hemocytes recognize P. marinus via a novel galectin ( C. virginica galectin (CvGal)) of unique structure. The biological roles of galectins have only been partly elucidated, mostly encompassing embryogenesis and indirect roles in innate and adaptive immunity mediated by the binding to endogenous ligands. CvGal recognized a variety of potential microbial pathogens and unicellular algae, and preferentially, Perkinsus spp. trophozoites. Attachment and spreading of hemocytes to foreign surfaces induced localization of CvGal to the cell periphery, its secretion and binding to the plasma membrane. Exposure of hemocytes to Perkinsus spp. trophozoites enhanced this process further, and their phagocytosis could be partially inhibited by pretreatment of the hemocytes with anti-CvGal Abs. The evidence presented indicates that CvGal facil-itates recognition of selected microbes and algae, thereby promoting phagocytosis of both potential infectious challenges and phytoplankton components, and that P. marinus subverts the host’s immune/feeding recognition mechanism to passively gain entry into the hemocytes. The Journal of Immunology, 2007, 179: 3086–3098.
Co-simulation platform for integrated real-time power system emulation and wide area communication

Phasor measurement units (PMUs) are increasingly being deployed in electric power systems in an attempt to improve grid reliability and make the grid smarter through real-time wide area situational awareness, monitoring, protection and control applications. PMU-based applications require communication networks in the transmission of synchrophasor measurements from the substations to the control centres. However, the quality-of-service of these synchrophasor measurements are not guaranteed when transmitted over a global wide area network especially in the presence of non-deterministic communication network conditions. This study presents the design, development, and integration of an IEEE Std. C37.118-based co-simulation platform comprising of power system hardware-in-the-loop simulations using the real-time digital simulator interfaced to a communication network. The impact of adverse communication network conditions such as latency, packet losses, and corruption on the exchange of data using the co-simulation platform and their impact on a centralised wide area monitoring, protection, and control (WAMPAC) system was investigated with software-in-the-loop simulations. Moreover, the maximum allowable adverse communication conditions are quantified with respect to the WAMPAC applications during emergency conditions.
This information is current as with Differential ICOS Expression Hyperproliferative and Death-Prone Subsets Murine Regulatory T Cells Contain

Regulatory T cells (Treg) are crucial for self-tolerance. It has been an enigma that Treg exhibit an anergic phenotype reﬂected by hypoproliferation in vitro after TCR stimulation but undergo vigorous proliferation in vivo. We report in this study that murine Treg are prone to death but hyperproliferative in vitro and invivo, which is different from conventional CD4 + Foxp3 2 T cells (Tcon). During in vitro culture, most Treg die with or without TCR stimulation, correlated with constitutive activation of the intrinsic death pathway. However, a small portion of the Treg population is more sensitive to TCR stimulation, particularly weak stimulation, proliferates more vigorously than CD4 + Tcon, and is resistant to activation-induced cell death. Treg proliferation is enhanced by IL-2 but is less dependent on CD28-mediated costimulation than that of Tcon. We demonstrate further that the surviving and proliferative Treg are ICOS + whereas the death-prone Treg are ICOS 2 . Moreover, ICOS + Treg contain much stronger suppressive activity than that of ICOS 2 Treg. Our data indicate that massive death contributes to the anergic phenotype of Treg in vitro and suggest modulation of Treg survival as a therapeutic strategy for treatment of autoimmune diseases and cancer. The Journal of Immunology , 2012, 188: 000–000.
Activated T Cells Lymphocytes Are Partially But Not Fully Intestinal Intraepithelial + Most Murine CD8

Murine small intestine intraepithelial lymphocytes (IELs) bear properties of both activated and nonactivated T cells, although the signiﬁcance of that dichotomy remains unclear. In this study, we show that although IELs express CD69 in situ and ex vivo, and have cytotoxic activity ex vivo, most CD8 (cid:1) IELs from normal mice are phenotypically similar to naive T cells in that they are CD45RB high , CD44 low/int , and lack or have low levels of expression of CD25, Ly-6C, OX40, Fas ligand (FasL), and intracellular IFN- (cid:2) synthesis. Unlike CD8 (cid:1) lymph node cells, IELs express high levels of the FasL gene, but do not express surface FasL until after CD3-mediated stimulation has occurred. Additionally, anti-CD3 stimulation of IELs in the presence of actinomycin-D did not inhibit FasL expression, suggesting that regulation FasL expression on IELs is controlled at least partially at the posttranscriptional level. Following CD3-mediated stimulation, IELs synthesize and secrete IFN- (cid:2) more rapidly and to greater levels than CD8 (cid:1) lymph node cells, and they acquire the phenotype of fully activated effector cells as seen by an up-regulation of CD44, Ly-6C, OX40, FasL, and CD25 with the kinetics of memory T cells, with down-regulation of CD45RB expression. These ﬁndings indicate that contrary to previous interpretations, most small intestine IELs are not fully activated T cells, but rather that they are semiactivated T cells ready to shift to a fully activated state once a CD3-mediated signal has been received. These data also imply that under appropriate conditions it is possible for T cells to be sustained in a state of partial activation. The Journal of Immunology, 2002, 169: 4717–4722. Short-term CD3-mediated stimulation of IELs results in a rapid shift to an activated memory phenotype