Miracle-dz/UniFAR-FTUs huggingface dataset:
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.
Cryoballoon vs. radiofrequency contact force ablation for paroxysmal atrial fibrillation: a propensity score analysis

Background Radiofrequency and cryoballoon pulmonary vein isolation are common approaches for paroxysmal atrial fibrillation treatment, showing similar results in recent multicenter studies, including heterogeneous tools and protocols. The aim of this study is to compare prospectively in a single, high-volume center the outcome of paroxysmal atrial fibrillation ablation performed specifically by second-generation cryoballoon or contact force radiofrequency ablation. Methods Consecutive patients scheduled for paroxysmal atrial fibrillation transcatheter ablation have been included and prospectively followed up. Aiming to reduce potential bias deriving from baseline characteristics, a propensity score matching analysis has been performed to analyze safety and efficacy outcomes. Results Out of consecutive patients undergoing atrial fibrillation transcatheter ablation between January 2015 and December 2016, 46 patients approached by cryoablation were matched 1 : 1 by propensity score to a similar population treated by last-generation radiofrequency ablation. Freedom from atrial fibrillation after 12 months (76 vs. 78%, P = 0.804) and incidence of complications (4 vs. 6%, P = 0.168) did not differ between the two groups. Radiological exposure was higher for the cryoballoon group (11 vs. 4 min, P < 0.001), whereas procedural duration did not differ (P = 0.174). Aiming to assess the potential impact of a learning curve in patients undergoing cryoablation, the first-third of patients (n = 15) were compared with the remaining, reporting longer radiological exposure (P < 0.001), but similar safety and efficacy. Conclusion In this propensity score analysis, last-generation cryoballoon and radiofrequency catheters for atrial fibrillation ablation present similar efficacy and safety. Cryoablation requires longer fluoroscopy exposure compared with radiofrequency, although this is reduced by increased experience.
Sharing the Growth Dividend: Analysis of Inequality in Asia

This paper focusses on income inequality in Asia, its drivers and policies to combat it. It finds that income inequality has risen in most of Asia, in contrast to many regions. While in the past, rapid growth in Asia has come with equitable distribution of the gains, more recently fast-growing Asian economies have been unable to replicate the 'growth with equity' miracle. There is a growing consensus that high levels of inequality can hamper the pace and sustainability of growth. The paper argues that policies could have a substantial effect on reversing the trend of rising inequality. It is imperative to address inequality of opportunities, in particular to broaden access to education, health, and financial services. Also fiscal policy could combat rising inequality, including by expanding and broadening the coverage of social spending, improving tax progressivity, and boosting compliance. Further efforts to promote financial inclusion, while maintaining financial stability, can help.
Control and synchronization of the generalized Lorenz system with mismatched uncertainties using backstepping technique and time‐delay estimation

We propose a robust control technique for regulation and synchronization of the generalized Lorenz system (GLS) that covers the Lorenz system, Chen system and Lü system. The proposed control provides synergy through the combination of the backstepping control and time‐delay estimation (TDE) technique. TDE is used to estimate and cancel nonlinearities and uncertainties while the backstepping method is adopted to provide robustness against matched and mismatched uncertainties. As a result, we observe in numerical simulation that the proposed technique shows better performances in regulating and synchronizing the GLS with mismatched uncertainties, in comparison with existing schemes. The efficacy of the proposed technique is also validated with a circuit‐implemented chaotic system. Copyright © 2017 John Wiley & Sons, Ltd.
The choline-methionine interrelationship for growth of the chick.

Three experiments involving 1230 battery-reared crossbred chicks were conducted to evaluate the potential sparing effect of choline on methionine and vice versa. Experiment 1 employed a crystalline amino acid diet to establish the sulfur-amino acid (SAA) and choline requirement for maximal feed efficiency of chicks during the period 8 to 18 days posthatching. Six graded levels of DL-methionine (.20 to .45% in the presence of .20% L-cystine) and five of choline (0 to 1216 mg/kg) were employed in a 6 X 5 factorial treatment arrangement. Gain/feed ratio was maximized at 608 mg/kg choline at all levels of methionine and at . 30 to . 35% methionine at all levels of choline. Two identical experiments (8 to 25 days posthatching) with a corn-soybean meal diet were carried out to explore the relationship between supplemental methionine (0 to .20% in five equal increments) and supplemental choline (0, 217, and 434 mg/kg). Optimal performance occurred at . 10% supplemental methionine regardless of choline level and at 217 mg/kg choline at supplemental methionine levels of 0 and . 05%. At . 10, . 15, and . 20% supplemental methionine, no gain or gain/feed response to supplemental choline was observed. It was thus apparent that excess levels of choline had minimal capacity to reduce the dietary requirement for methionine. Excess levels of methionine, however, seemed to have a consistent, although small, effect on the chick's dietary need for choline.
Strategic Citations to Precedent on the U.S. Supreme Court

Common law evolves not only through the outcomes of cases but also through the reasoning and citations to precedent employed in judicial opinions. We focus on citations to precedent by the U.S. Supreme Court. We demonstrate how strategic interaction between justices during the Court’s bargaining process affects citations to precedent in the Court’s opinion. We find that the majority-opinion writer relies more heavily on precedent when the Court’s decision is accompanied by separate opinions. We also show that diversity of opinion on the Court, a factor often overlooked, has a significant relationship with citations to precedent. Finally, our results indicate that the ideology of the median justice influences citation practices more than ideology of the majority-opinion writer.
Series Elasticity in Linearly Actuated Humanoids

Recent advancements in actuator technologies, computation, and control have led to major leaps in capability and have brought humanoids ever closer to being feasible solutions for real-world applications. As the capabilities of humanoids increase, they will be called on to operate in unstructured real world environments. This realization has driven researchers to develop more dynamic, robust, and adaptable robots. Compared to state-of-the-art robots, biological systems demonstrate remarkably better efficiency, agility, adaptability, and robustness. Many recent studies suggest that a core principle behind these advantages is compliance, yet there are very few compliant humanoids that have demonstrated successful walking. The work presented in this dissertation is based on several years of developing novel actuators for two full-scale linearly actuated compliant humanoid robots, SAFFiR and THOR. Both are stateof-the-art robots intended to operate in the extremely challenging real world scenarios of shipboard firefighting and disaster response. The design, modeling, and control of actuators in robotics application is critical because the rest of the robot is often designed around the actuators. This dissertation seeks to address two goals: 1) advancing the design of compliant linear actuators that are well suited for humanoid applications, and 2) developing a better understanding of how to design and model compliant linear actuators for use in humanoids. Beyond just applications for compliant humanoids, this research tackles many of the same design and application challenges as biomechanics research so it has many potential applications in prosthetics, exoskeletons, and rehabilitation devices.
The KMOS Cluster Survey (KCS). II. The Effect of Environment on the Structural Properties of Massive Cluster Galaxies at Redshift 1.39 < z < 1.61

We present results on the structural properties of massive passive galaxies in three clusters at 1.39 < z < 1.61 from the KMOS Cluster Survey. We measure light-weighted and mass-weighted sizes from optical and near-infrared Hubble Space Telescope imaging and spatially resolved stellar mass maps. The rest-frame R-band sizes of these galaxies are a factor of ∼2–3 smaller than their local counterparts. The slopes of the relation between the stellar mass and the light-weighted size are consistent with recent studies in clusters and the field. Their mass-weighted sizes are smaller than the rest-frame R-band sizes, with an average mass-weighted to light-weighted size ratio that varies between ∼0.45 and 0.8 among the clusters. We find that the median light-weighted size of the passive galaxies in the two more evolved clusters is ∼24% larger than that for field galaxies, independent of the use of circularized effective radii or semimajor axes. These two clusters also show a smaller size ratio than the less evolved cluster, which we investigate using color gradients to probe the underlying gradients. The median color gradients are ∇z − H ∼ −0.4 mag dex−1, twice the local value. Using stellar populations models, these gradients are best reproduced by a combination of age and metallicity gradients. Our results favor the minor merger scenario as the dominant process responsible for the observed galaxy properties and the environmental differences at this redshift. The environmental differences support that clusters experience accelerated structural evolution compared to the field, likely via an epoch of enhanced minor merger activity during cluster assembly.
A Robust Traffic Sign Recognition System for Intelligent Vehicles

The recognition of traffic signs in natural environment is a challenging problem in computer vision because of the influence of weather conditions, illumination, locations, vandalism and other factors. In this paper, we propose a robust traffic signs recognition system for the real utilization of intelligent vehicles. The proposed system is divided into two phases. In the detection and coarse classification phase, we employ the Simple Vector Filter algorithm for color segmentation, Hough transform and curve fitting approaches in shape analysis to divide traffic signs into six categories according to the color and shape properties. In the refined classification phase, the Pseudo-Zernike moments features of traffic sign symbols are selected for classification by support vector machines. The rationality and effectiveness of the proposed system is validated from great number of experiments.
EXPERIMENTAL AND NUMERICAL STUDY OF DEFECTS IN PRESSURESED CYLINDRICAL SHELLS INSTRUMENTED BY ACOUSTIC EMISSION AND STRAIN GAUGES

In order to conduct a comprehensive study on the harmfulness of defects in the pressure vessels, and in order to propose simple rules to characterize the harmfulness of existing defects in pressurized installations. An experimental study based on the monitoring of deformations by strain gauges in the vicinity of defects. In parallel, during pressure testing, the evolution of defects is detected and followed by the acoustic emission method. The specific instrumentation has been designed and implemented. Ministructures ( models) have therefore been carried out with positional defects and different orientation. These experimental results validated by a numerical model of finite elements.
Network Traffic Classification Using Correlation Information

Traffic classification has wide applications in network management, from security monitoring to quality of service measurements. Recent research tends to apply machine learning techniques to flow statistical feature based classification methods. The nearest neighbor (NN)-based method has exhibited superior classification performance. It also has several important advantages, such as no requirements of training procedure, no risk of overfitting of parameters, and naturally being able to handle a huge number of classes. However, the performance of NN classifier can be severely affected if the size of training data is small. In this paper, we propose a novel nonparametric approach for traffic classification, which can improve the classification performance effectively by incorporating correlated information into the classification process. We analyze the new classification approach and its performance benefit from both theoretical and empirical perspectives. A large number of experiments are carried out on two real-world traffic data sets to validate the proposed approach. The results show the traffic classification performance can be improved significantly even under the extreme difficult circumstance of very few training samples.
Multicomponent Injectable Hydrogels for Antigen‐Specific Tolerogenic Immune Modulation

Biomaterial scaffolds that enrich and modulate immune cells in situ can form the basis for potent immunotherapies to elicit immunity or reëstablish tolerance. Here, the authors explore the potential of an injectable, porous hydrogel to induce a regulatory T cell (Treg) response by delivering a peptide antigen to dendritic cells in a noninflammatory context. Two methods are described for delivering the BDC peptide from pore‐forming alginate gels in the nonobese diabetic mouse model of type 1 diabetes: encapsulation in poly(lactide‐co‐glycolide) (PLG) microparticles, or direct conjugation to the alginate polymer. While particle‐based delivery leads to antigen‐specific T cells responses in vivo, PLG particles alter the phenotype of the cells infiltrating the gels. Following gel‐based peptide delivery, transient expansion of endogenous antigen‐specific T cells is observed in the draining lymph nodes. Antigen‐specific T cells accumulate in the gels, and, strikingly, ≈60% of the antigen‐specific CD4+ T cells in the gels are Tregs. Antigen‐specific T cells are also enriched in the pancreatic islets, and administration of peptide‐loaded gels does not accelerate diabetes. This work demonstrates that a noninflammatory biomaterial system can generate antigen‐specific Tregs in vivo, which may enable the development of new therapies for the treatment of transplant rejection or autoimmune diseases.
CCN1/Cyr61 enhances the function of hepatic stellate cells in promoting the progression of hepatocellular carcinoma

Hepatic stellate cells (HSCs) are the main extracellular matrix (ECM)-producing cells in liver fibrosis. Activated HSCs stimulate the proliferation and migration of hepatocellular carcinoma (HCC) cells. Cysteine-rich 61 (CCN1/Cyr61) is an ECM protein. Our previous studies demonstrated that the expression of CCN1 was significantly higher in benign hepatic cirrhosis tissue and cancer-adjacent hepatic cirrhosis tissues. CCN1 is a target gene of β-catenin in HCC and promotes the proliferation of HCC cells. The present study aimed to examine whether CCN1 can activate HSCs and affect the function of activated HSCs in promoting the progression of HCC. CCN1 expression was determined during the progression of liver fibrosis in a mouse model. LX-2 cells, which were infected with adenoviruses AdCCN1 or AdRFP, and HepG2 cells were co-cultured or subcutaneously co-implanted into in nude mice. MTT assay, Crystal Violet staining, Boyden chamber, matrigel invasion and monolayer scratch assays were used to analyze the proliferation, migration and invasion capability of HepG2 cells. Xenograft sizes were measured and histological analyses were performed by hematoxylin and eosin, immunohistochemical, immunefluorescence and Sirius Red staining. It was demonstrated that the expression of CCN1 was continually increased in liver fibrosis and the that expression may be correlated with the progression of liver fibrosis. CCN1 affected the function of LX-2 and enhanced the effect of LX-2 on promoting the viability, migration and invasion of HepG2 cells in vitro. CCN1 enhanced the effect of LX-2 on promoting the growth of HepG2 xenografts in vivo. CCN1 also affected the function of activated HSCs and regulated the formation of the xenograft microenvironment, including fibrogenesis and angiogenesis, which are beneficial for the progression of HCC. These findings demonstrated that CCN1 may be involved in the progression of the hepatic cirrhosis-HCC axis through regulating HSCs.
SIR Meta Distribution of  $K$ -Tier Downlink Heterogeneous Cellular Networks With Cell Range Expansion

Heterogeneous cellular networks (HCNs) constitute a necessary step in the evolution of cellular networks. In this paper, we apply the signal-to-interference ratio (SIR) meta distribution framework for a refined SIR performance analysis of HCNs, focusing on <inline-formula> <tex-math notation="LaTeX">$K$ </tex-math></inline-formula>-tier heterogeneous cellular networks based on the homogeneous independent Poisson point process (PPP) model, with range expansion bias (offloading bias) in each tier. Expressions for the <inline-formula> <tex-math notation="LaTeX">$b$ </tex-math></inline-formula>-th moment of the conditional success probability for both the entire network and each tier are derived, based on which the exact meta distributions and the beta approximations are evaluated and compared. Key performance metrics, including the mean success probability, the variance of the conditional success probability, the mean local delay, and the asymptotic SIR gains of each tier are obtained. The results show that the biases are detrimental to the overall mean success probability of the whole network and that the <inline-formula> <tex-math notation="LaTeX">$b$ </tex-math></inline-formula>-th moment curve of the conditional success probability of each tier can be tightly approximated by the horizontal shifted versions of the first moment curve of the single-tier PPP network. We also provide lower bounds for the region of the active probabilities of the base stations to keep the mean local delay of each tier finite.
Genetic susceptibility to autoimmune thyroid disease: past, present, and future.

BACKGROUND Autoimmune thyroid diseases (AITD), including Graves' disease and Hashimoto's thyroiditis, arise due to complex interactions between environmental and genetic factors. There are sound data coming from epidemiological, family, and twin studies demonstrating a strong genetic influence on the development of AITD. In this review we summarize the new findings on the genetic susceptibility to AITD focusing on emerging mechanisms of susceptibility. SUMMARY Candidate gene analysis, whole-genome linkage screening, genome-wide association studies, and whole-genome sequencing are the major technologies that have advanced this field, leading to the identification of at least seven genes whose variants have been associated with AITD. One of the major ones is the HLA-DR gene locus. Recently, it was shown that substitution of the neutral amino acids Ala or Gln with arginine at position beta 74 in the HLA-DR peptide-binding pocket is key to the etiology of both Graves' disease and Hashimoto's thyroiditis. Several other genes have also been shown to confer susceptibility to AITD. These can be classified into two groups: (i) immune regulatory genes (cytotoxic T lymphocyte-associated protein 4, CD40, protein tyrosine phosphatase-22, and CD25) and (ii) thyroid-specific genes (thyroglobulin and thyrotropin receptor genes). The influence of individual genes on the development of AITD when assessed in a population appears to be weaker than would be expected from the data showing strong genetic susceptibility to AITD. Two possible mechanisms explaining this discrepancy are gene-gene interactions and subset effects. CONCLUSIONS Significant progress has been made in our understanding of the immunogenetic mechanisms leading to thyroid autoimmunity. For the first time we are beginning to unravel these mechanisms at the molecular level. It is hoped that these new data will be translated into novel therapies and prevention strategies in AITD, such as costimulatory blockade.
Effects of egg and yolk weights on yolk antibody (IgY) production in laying chickens.

Twenty 35-wk-old chickens, including 10 Single Comb White Leghorn (SCWL) and 10 Rhode Island Red (RIR) hens, were used to examine the effects of egg and yolk weights on egg yolk antibody (IgY) production in the two strains of chickens immunized with BSA. The SCWL chickens had a greater (P < 0.01) percentage hen-day production and greater egg and yolk weights than did the RIR chickens. However, the anti-BSA antibody activities determined by ELISA in the serum and the egg yolk were similar (P > 0.05) between the SCWL and RIR chickens. Similarities between the two strains of hens were also observed in protein and total IgY contents (expressed as the percentage of wet weight of yolk) and the percentage of BSA-specific antibody in the total IgY. It was concluded that both the SCWL and RIR chickens immunized with BSA can produce egg yolk IgY containing similar proportions of BSA-specific antibodies. Therefore, the egg yolk weight and the percentage hen-day production, both of which are greater in the SCWL hens, are considered to be important factors for the efficient production of IgY.