Intrinsic disorder is relatively common in proteins, plays important roles in numerous cellular activities, and its prevalence was implicated in various human diseases. However, annotations of the ...disorder lag behind the rapidly increasing number of known protein chains. The last decade observed development of a relatively large number of in-silico methods that predict the disorder using the protein sequence as their input. We perform a first-of-its kind comprehensive empirical evaluation of the disorder predictors which is characterized by three novel aspects, (1) we evaluate the quality of the disorder predictions at the residue, segment, and chain levels; (2) we consider a large number of published and accessible to the end user predictors that are evaluated on a relatively big dataset with close to 500 proteins; and (3) we assess statistical significance of differences between the considered methods. Our study reveals that there is no universally superior predictor and that the top-performing methods are complementary. We show that while recent consensus-based predictors outperform other considered methods for the residue-level predictions, some older methods perform better for the prediction of the disordered segments. Our analysis indicates that certain predictors are biased to under-predict the disorder, while some other solutions tend to over-predict the number of the disordered residues. We also evaluate the utility of the predicted residue-level disorder for prediction of proteins with long disordered segments and prediction of the chainlevel disorder content. Lastly, we provide recommendations concerning development of a new generation of consensusbased methods and specialized methods for improved prediction of the disorder content.
We propose and study a nonoverlapping and nonconforming domain decomposition method for the integral-equation-based solution of large, complex electromagnetic (EM) scattering problems. The continuity ...of the electric surface current across the boundary between adjacent subdomains is enforced by a skew-symmetric interior penalty formulation. A nonoverlapping additive Schwarz preconditioner is designed and analyzed for the solution of the linear system of equations resulting from Galerkin boundary-element discretization. We show that the preconditioned system exhibits a uniformly confined eigenspectrum with respect to changing problem and discretization parameters. Numerical examples are presented to demonstrate the fast convergence of iterative solvers and the superior accuracy of the solutions obtained by our method. The proposed work can be viewed as an effective preconditioning scheme that reduces the condition number of very large systems of equations in challenging EM scattering problems. The strength and capability of the proposed method will be illustrated by means of several examples of practical interest.
Simulating quantum contextuality with classical systems requires memory. A fundamental yet open question is what is the minimum memory needed and, therefore, the precise sense in which quantum ...systems outperform classical ones. Here, we make rigorous the notion of classically simulating quantum state-independent contextuality (QSIC) in the case of a single quantum system submitted to an infinite sequence of measurements randomly chosen from a finite QSIC set. We obtain the minimum memory needed to simulate arbitrary QSIC sets via classical systems under the assumption that the simulation should not contain any oracular information. In particular, we show that, while classically simulating two qubits tested with the Peres-Mermin set requires log_{2}24≈4.585 bits, simulating a single qutrit tested with the Yu-Oh set requires, at least, 5.740 bits.
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Sub-wavelength dielectric gratings have emerged recently as a promising alternative to distributed Bragg reflection dielectric stacks for broadband, high-reflectivity filtering applications. Such a ...grating structure composed of a single dielectric layer with the appropriate patterning can sometimes perform as well as 30 or 40 dielectric distributed Bragg reflection layers, while providing new functionalities such as polarization control and near-field amplification. In this Letter, we introduce an interesting property of grating mirrors that cannot be realized by their distributed Bragg reflection counterpart: we show that a non-periodic patterning of the grating surface can give full control over the phase front of reflected light while maintaining a high reflectivity. This new feature of dielectric gratings allows the creation of miniature planar focusing elements that could have a substantial impact on a number of applications that depend on low-cost, compact optical components, from laser cavities to CD/DVD read/write heads.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
In resource-constrained mobile ad hoc network, geographical routing algorithms are relatively attractive routing algorithms. Due to the movement of nodes, energy exhaustion and the presence of ...obstacles, routing holes may occur. The existing routing algorithm only considers bypassing routing void through right-hand or left-hand criteria, and forwards data at the boundary of the hole. However, such a routing algorithm may lead to the expansion of the routing hole and even cause the paralysis of the network. This paper proposes a new greedy forwarding improvement routing method for mobile ad hoc network. In the greedy forwarding phase, the reliable communication area is calculated, and then the quality of the link is evaluated according to the relative displacement between the nodes and the maintenance time of the link. Then, according to the quality of the link, the distance between the candidate node and the destination node, and the number of the neighbor nodes, the metric value is obtained, and the node with the large metric value is selected as the next hop. When a routing hole occurs, the waiting forwarding mode is used for a period of time. After a period of time, when the current node is still a routing hole node, we can use the right-hand rule and the left-hand criteria, and the bypass mode is performed simultaneously. By considering three factors of the deflection angle and the maintenance time of the link and the remaining energy of the node, the forwarding node as the next hop with the highest priority value is selected in each direction. The experimental results show that compared with the existing GPSR, EMGR and EDGR, the proposed algorithm reduces the energy consumption of the network, improves the delivery rate of data packets, reduces the network delay and prolongs the network lifetime.
Regularization is commonly used for alleviating overfitting in machine learning. For convolutional neural networks (CNNs), regularization methods, such as DropBlock and Shake-Shake, have illustrated ...the improvement in the generalization performance. However, these methods lack a self-adaptive ability throughout training. That is, the regularization strength is fixed to a predefined schedule, and manual adjustments are required to adapt to various network architectures. In this article, we propose a dynamic regularization method for CNNs. Specifically, we model the regularization strength as a function of the training loss. According to the change of the training loss, our method can dynamically adjust the regularization strength in the training procedure, thereby balancing the underfitting and overfitting of CNNs. With dynamic regularization, a large-scale model is automatically regularized by the strong perturbation, and vice versa. Experimental results show that the proposed method can improve the generalization capability on off-the-shelf network architectures and outperform state-of-the-art regularization methods.
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•The number of ARGs in estuarine sediments in summer is more than in winter.•ARG abundance, but not ARG diversity, is significantly impacted by seasonal changes.•Chemical pollution ...contributes to the emergence of estuarine sediment ARGs.•Chemical pollution is positively correlated with ARG diversity, but not ARG abundance.
Estuary sediments are chemically contaminated by adjacent coastal industrial cities, but the impact of organic pollutants on antibiotic resistance genes (ARGs) in estuarine sediments is unknown. We comprehensively analyzed the complex interactions between chemical pollutants (heavy metals and organic pollutants), mobile genetic elements (MGEs), and ARGs in estuarine sediments during various seasons. The results indicate that under the effects of the chemically polluted river water, the number of different estuarine sediment ARGs increased by 76.9%–92.3% in summer and 5.9%–35.3% in winter, and the abundance of these ARGs increased by 29–5195 times in summer and 48–239 times in winter. The abundance of sediment ARGs in distinct estuaries showed different seasonal trends. Seasonal changes had a greater impact on the abundance of estuarine sediment ARGs than on their diversity. The diversity of estuarine sediment ARGs was positively correlated with the chemical pollution levels. Furthermore, chemical pollution was positively correlated with MGEs, and MGEs were correlated with ARG abundance. These results indicate that ARGs are enriched in bacteria via horizontal gene transfer triggered by chemical pollution, promoting multi-antibiotic resistance in estuarine sediment bacteria. These findings have implications for our understanding of the distribution and propagation of ARGs in chemically polluted estuarine sediments.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We show that some sets of quantum observables are unique up to an isometry and have a contextuality witness that attains the same value for any initial state. We prove that these two properties make ...it possible to certify any of these sets by looking at the statistics of experiments with sequential measurements and using any initial state of full rank, including thermal and maximally mixed states. We prove that this "certification with any full-rank state" (CFR) is possible for any quantum system of finite dimension d≥3 and is robust and experimentally useful in dimensions 3 and 4. In addition, we prove that complete Kochen-Specker sets can be Bell self-tested if and only if they enable CFR. This establishes a fundamental connection between these two methods of certification, shows that both methods can be combined in the same experiment, and opens new possibilities for certifying quantum devices.
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To compare radiofrequency ablation (RFA) with or without transcatheter arterial chemoembolization (TACE) in the treatment of hepatocellular carcinoma (HCC).
A randomized controlled trial was ...conducted on 189 patients with HCC less than 7 cm at a single tertiary referral center between October 2006 and June 2009. Patients were randomly asssigned to receive TACE combined with RFA (TACE-RFA; n = 94) or RFA alone (n = 95). The primary end point was overall survival. The secondary end point was recurrence-free survival, and the tertiary end point was adverse effects.
At a follow-up of 7 to 62 months, 34 patients in the TACE-RFA group and 48 patients in the RFA group had died. Thirty-three patients and 52 patients had developed recurrence in the TACE-RFA group and RFA group, respectively. The 1-, 3-, and 4-year overall survivals for the TACE-RFA group and the RFA group were 92.6%, 66.6%, and 61.8% and 85.3%, 59%, and 45.0%, respectively. The corresponding recurrence-free survivals were 79.4%, 60.6%, and 54.8% and 66.7%, 44.2%, and 38.9%, respectively. Patients in the TACE-RFA group had better overall survival and recurrence-free survival than patients in the RFA group (hazard ratio, 0.525; 95% CI, 0.335 to 0.822; P = .002; hazard ratio, 0.575; 95% CI, 0.374 to 0.897; P = .009, respectively). There were no treatment-related deaths. On logistic regression analyses, treatment allocation, tumor size, and tumor number were significant prognostic factors for overall survival, whereas treatment allocation and tumor number were significant prognostic factors for recurrence-free survival.
TACE-RFA was superior to RFA alone in improving survival for patients with HCC less than 7 cm.
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