Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibodies Produced in Response to a Live-Attenuated Dengue Vaccine Are Functional in Activating the Complement System

Abstract Background Antibody-driven complement system (CS) activation has been associated with protection against symptomatic dengue virus (DENV) infection. Aggregation, opsonization, lysis, and phagocytosis are mechanisms triggered by antibody-antigen immunocomplexes following fixation of the component 1q (C1q) and activation of the classical pathway. As a result, DENV neutralization and clearance are facilitated, whereas antibody-dependent enhancement of infection is inhibited. We investigated the ability of antibodies produced in response to Takeda's dengue vaccine candidate, TAK-003, to fix C1q and activate CS. Methods Serum samples were collected from seronegative and seropositive participants in a phase 2 clinical trial (DEN-203), pre- and postvaccination. Samples were evaluated for the presence of complement-fixing antibodies (CFAs) against DENV using a Luminex multiplex-based immunoassay. Results TAK-003 elicited production of CFAs against all 4 DENV serotypes, which persisted for 1 year postvaccination, irrespective of baseline serostatus. CFA levels were correlated with neutralizing antibody titers and virus-binding total IgG and IgG1 concentrations. Furthermore, efficiency of CFA fixation was greater in samples with higher polyclonal IgG avidity. Conclusions These results indicate that antibodies produced after TAK-003 vaccination are functional in both activating CS and neutralizing virus infection by all DENV serotypes, which may contribute to efficacy of TAK-003. Clinical Trials Registration NCT01511250.
Targeting peptide‐mediated interactions in omics

Peptide‐mediated interactions (PMIs) play a crucial role in cell signaling network, which are responsible for about half of cellular protein–protein associations in the human interactome and have recently been recognized as a new kind of promising druggable target for drug development and disease therapy. In this article, we give a systematic review regarding the proteome‐wide discovery of PMIs and targeting druggable PMIs (dPMIs) with chemical drugs, self‐inhibitory peptides (SIPs) and protein agents, particularly focusing on their implications and applications for therapeutic purpose in omics. We also introduce computational peptidology strategies used to model, analyze, and design PMI‐targeted molecular entities and further extend the concepts of protein context, direct/indirect readout, and enthalpy/entropy effect involved in PMIs. Current issues and future perspective on this topic are discussed. There is still a long way to go before establishment of efficient therapeutic strategies to target PMIs on the omics scale.
The human LAT1–4F2hc (SLC7A5–SLC3A2) transporter complex: Physiological and pathophysiological implications

LAT1 and 4F2hc form a heterodimeric membrane protein complex, which functions as one of the best characterized amino acid transporters. Since LAT1–4F2hc is required for the efficient uptake of essential amino acids and hormones, it promotes cellular growth, in part, by stimulating mTORC1 (mechanistic target of rapamycin complex 1) signalling and by repressing the integrated stress response (ISR). Gain or loss of LAT1–4F2hc function is associated with cancer, diabetes, and immunological and neurological diseases. Hence, LAT1–4F2hc represents an attractive drug target for disease treatment. Specific targeting of LAT1–4F2hc will be facilitated by the increasingly detailed understanding of its molecular architecture, which provides important concepts for its function and regulation. Here, we summarize (i) structural insights that help to explain how LAT1 and 4F2hc assemble to transport amino acids across membranes, (ii) the role of LAT1–4F2hc in key metabolic signalling pathways, and (iii) how derailing these processes could contribute to diseases.
Exact solution approaches for the discrete lot-sizing and scheduling problem with parallel resources

We consider a production planning problem known as the discrete lot-sizing and scheduling problem (DLSP) and study a variant of the DLSP involving several identical parallel resources. We show how to solve the resulting discrete optimisation problem as a mixed-integer linear program using a commercial MIP solver. To achieve this, we exhibit a family of strong valid inequalities for which the associated separation problem is efficiently solvable. Our computational results show that the proposed solution algorithm is capable of providing optimal solutions for medium-sized instances.
Gaussian geometric discord of two-mode systems in a thermal environment

In the framework of the theory of open systems based on completely positive quantum dynamical semigroups, we give a description of the Gaussian geometric discord in terms of Hilbert-Schmidt distance and the rescaled form. The system consists of two non-interacting non-resonant bosonic modes embedded in a thermal environment. We take as initial state of the system a two-mode squeezed thermal state and describe the time evolution of the Gaussian geometric discord under the influence of the thermal bath. By tracing the distance between the state of the considered subsystem and the closest classical-quantum Gaussian state we evaluate the Gaussian geometric discord for all times and temperatures. The geometric discord has finite values between 0 and 1 and decreases asymptotically to zero at large times and temperatures, with oscillations on the time axis.
An update on post‐transcriptional regulation of retrotransposons

Retrotransposons, including LINE‐1, Alu, SVA, and endogenous retroviruses, are one of the major constituents of human genomic repetitive sequences. Through the process of retrotransposition, some of them occasionally insert into new genomic locations by a copy–paste mechanism involving RNA intermediates. Irrespective of de novo genomic insertions, retrotransposon expression can lead to DNA double‐strand breaks and stimulate cellular innate immunity through endogenous patterns. As a result, retrotransposons are tightly regulated by multi‐layered regulatory processes to prevent the dangerous effects of their expression. In recent years, significant progress was made in revealing how retrotransposon biology intertwines with general post‐transcriptional RNA metabolism. Here, I summarize current knowledge on the involvement of post‐transcriptional factors in the biology of retrotransposons, focusing on LINE‐1. I emphasize general RNA metabolisms such as methylation of adenine (m6A), RNA 3′‐end polyadenylation and uridylation, RNA decay and translation regulation. I discuss the effects of retrotransposon RNP sequestration in cytoplasmic bodies and autophagy. Finally, I summarize how innate immunity restricts retrotransposons and how retrotransposons make use of cellular enzymes, including the DNA repair machinery, to complete their replication cycles.
Habitat fragmentation matters more than habitat loss: The case of host–parasite interactions

While ecologists agree that habitat loss has a substantial negative effect on biodiversity it is still very much a matter of debate whether habitat fragmentation has a lesser effect and whether this effect is positive or negative for biodiversity. Here, we assess the relative influence of tropical forest loss and fragmentation on the prevalence of vector‐borne blood parasites of the genera Plasmodium and Haemoproteus in six forest bird species. We also determine whether habitat loss and fragmentation are associated with a rise or fall in prevalence. We sample more than 4000 individual birds from 58 forest sites in Guadeloupe and Martinique. Considering 34 host–parasite combinations independently and a fine characterization of the amount and spatial configuration of habitat, we use partial least square regressions to disentangle the relative effects of forest loss, forest fragmentation, landscape heterogeneity, and local weather conditions on spatial variability of parasite prevalence. Then we test for the magnitude and the sign of the effect of each environmental descriptor. Strikingly, we show that forest fragmentation explains twice as much of the variance in prevalence as habitat loss or landscape heterogeneity. In addition, habitat fragmentation leads to an overall rise in prevalence in Guadeloupe, but its effect is variable in Martinique. Both habitat loss and landscape heterogeneity exhibit taxon‐specific effects. Our results suggest that habitat loss and fragmentation may have contrasting effects between tropical and temperate regions and that inter‐specific interactions may not respond in the same way as more commonly used biodiversity metrics such as abundance and diversity.
Robust and simple adaptive control systems

This paper deals with two problems for the improvement of the control performance of simple adaptive control (SAC) techniques. First, it is discussed that the introduction of a robust adaptive control term much robustifies the SAC system concerning plant uncertainties such as state dependent disturbance. Second, a practical procedure is described for designing the parallel feedforward compensator, which is necessary for the actual realization of the SAC system, given prior information concerning the plant such that: (1) the plant is minimum phase; (2) an upper bound on the relative degree exists; and (3) approximate values of high and low frequency gains are known. The effectiveness of the proposed methods is confirmed through the simulation of typical examples of adaptive control systems.
Generative adversarial network for PCB defect detection with extreme low compress rate

Printed circuit board (PCB) manufacturing is one of the most important parts of electronic production, where a small defect may cause the final product to fail. Therefore, the industry urgently needs a system to detect and locate all manufacturing defects. In this paper, we propose Generative Adversarial Networks (GANs) based learning defect system with an extremely low bit per pixel (BPP) for feature compression. The system includes an encoder, generator, and multi-scale discriminator for generative learned compression and a comparator to distinguish defected components from a compressed feature map generated by GAN. The model synthesizes images at extreme low bitrates where traditional methods such as JPEG show strong artifacts, resulting in a proportional reduction in the storage of feature comparison. Experimental results demonstrate the effectiveness and efficiency of our model with 97.8% mAP at 72FPS.
Towards inspection and cleaning on the inner face of GIS pipelines: design, control, and implementation of negative omnidirectional wall-climbing robot

According to the needs of pipeline inspection and cleaning in power industry, an omni-directional motion robot with a negative pressure adsorption is proposed. The robot can not only achieve the stable adsorption and movement of the vertical walls, but also has a brief structure, and high flexibility. Firstly, in consideration of the actual performance requirements of the project, we determined the scheme selection of different modules of the robot. Secondly, Maxwell module of ANSYS finite element analysis software was used to study the adsorption device, and an adsorption device with stable adsorption was obtained, which ensured the safe and stable operation of the robot on the vertical wall. Thirdly, the hardware system and control system of the robot are determined and the construction of the robot system is completed. Then the dynamics of the robot are analyzed, and the simulation is carried out according to the analysis. It is verified that under the control of PID algorithm, the acceleration of the robot can be in a stable state finally, which ensures the robot is stable in the process of motion. Finally, we finished experiments of the robot and verified the robot is stable whenever it works on walls.
RCU-Net: a novel network for retinal vessel segmentation

The segmentation of fundus vascular images is a key step in retinal image processing and analysis. It plays an important role in the early prevention and diagnosis of eye diseases and blood system diseases. In view of the low accuracy of retinal blood vessel segmentation caused by the complex features of fundus images, the presence of soft, hard penetrant and bleeding noises, the low contrast between retinal blood vessels and background, uneven changes in width and curvature, small shape and blurred edges, this paper proposes a new network model RCU-Net for retinal vessel segmentation. Specifically, this paper proposes CBAM-Conv convolution block and RA-Conv convolution block based on visual attention mechanism (CBAM) and residual connection idea, which can make the network better use of the information at the spatial and channel levels. Experiments were carried out in public datasets DRIVE and CHASE_DB1. The accuracy, sensitivity, F1-Score and AUC of RCU-Net network on DRIVE datasets reached 96.75%, 82.02%, 81.45% and 98.33% respectively. Compared with the classical U-Net network, the proposed model can effectively improve the performance of retinal vessel segmentation.
SELF-SIMILARITY IN COMPLEX NETWORKS: FROM THE VIEW OF THE HUB REPULSION

Complex networks are widely used to model the structure of many complex systems in nature and society. Recently, fractal and self-similarity of complex networks have attracted much attention. It is observed that hub repulsion is the key principle that leads to the fractal structure of networks. Based on the principle of hub repulsion, the metric in complex networks is redefined and a new method to calculate the fractal dimension of complex networks is proposed in this paper. Some real complex networks are investigated and the results are illustrated to show the self-similarity of complex networks.
Service quality, company goodwill and customer perception are the stimuli to customer satisfaction for banks catering home loans

Abstract Customer retention has always challenged the service industry. Banks being a part of this industry have two different elements to satisfy, investors and borrowers. This study highlights the components that can enrich the customer satisfaction out of three major antecedents i.e. through service quality, customer perception and company goodwill. The study is conducted through a structured questionnaire with 329 respondents and validated through Cronbach’s Alpha and the relationship between the variables is measured through Pearson’s correlation and linear regression model. The result highlights that all the variables are positively correlated with each other while the customer perception and service quality has a significant relationship.
Attosecond control of optical waveforms

A new, monolithic scheme for stabilizing the phase between the carrier wave and the envelope (CE phase) in a train of few-cycle laser pulses is demonstrated. Self-phase modulation and second-harmonic generation or difference-frequency generation in a single periodically poled lithium niobate crystal, that transmits the main laser beam, allows for the CE-phase locking directly in the usable output. The monolithic scheme obviates the need for splitting off a fraction of the laser output for CE-phase control, coupling into microstructured fibre, as well as separation and recombination of spectral components. As a result, the CE-phase error integrated over the spectral range of 0.2 mHz–35 MHz is as small as 0.016 × 2π rad. This implies that the phase of the field oscillations (λ ∼ 830 nm) with respect to the pulse peak is locked to within 44 attoseconds, resulting in optical waveform control with subhundred attosecond fidelity for the first time.
Heavy Precipitation and High Streamflow in the Contiguous United States: Trends in the Twentieth Century.

Abstract Changes in several components of the hydrological cycle over the contiguous United States have been documented during the twentieth century: an increase of precipitation, especially heavy and very heavy precipitation, and a significant retreat in spring snow cover extent over western regions during the last few decades. These changes have affected streamflow, including the probability of high flow. In the eastern half of the United States a significant relationship is found between the frequency of heavy precipitation and high streamflow events both annually and during the months of maximum streamflow. Two factors contributed to finding such a relation: 1) the relatively small contribution of snowmelt to heavy runoff in the eastern United States (compared to the west), and 2) the presence of a sufficiently dense network of streamflow and precipitation gauges available for analysis. An increase of spring heavy precipitation events over the eastern United States indicates with high probability that.
PI 3-kinase isoform p110α controls smooth muscle cell functionality and protects against aortic aneurysm formation

Background Catalytic class IA PI 3-kinase isoform p110α is a crucial regulator of cellular proliferation and survival in numerous cell types. While p110α is critically involved in pathogenic vascular remodeling, its physiological role for vascular integrity under stress conditions has not been studied. We report a protective function of smooth muscle p110α against abdominal aortic aneurysm (AAA) formation. Methods & Results In mice lacking p110α in smooth muscle cells (sm-p110α-/-), perfusion of the infrarenal aorta with porcine pancreatic elastase (PPE) yielded substantially enhanced AAA formation compared to wild type controls. This disease phenotype is partly attributable to a subtle preexisting vascular phenotype under basal conditions, as sm-p110α-/- mice displayed a smaller media area, deranged aortic wall structure (detached smooth muscle cells, increased apoptotic cell death), and a diminished functional responsiveness of aortic rings to vasodilators. Furthermore, p110α is also implicated in regenerative processes during AAA development: Whereas wild type mice showed increased media hypertrophy, neointima formation and proliferation upon PPE intervention, these vascular remodeling processes were diminished in sm-p110α-/- mice. Concomitantly, increased numbers of elastic fiber breaks and ECM degradation were detected in sm-p110α-/- aorta. Mechanistically, we found that lack of p110α expression impaired smooth muscle cell proliferation, expression of contractile marker genes and production of elastin fibers. This phenotype largely depended on reduced phosphorylation and inactivation of FOXO1, as specific FOXO1 inhibition fully rescued proliferation of p110α-/- smooth muscle cells, and knockdown of FOXO1 increased expression of calponin and elastin. Conclusions Smooth muscle p110α protects against AAA disease by maintaining aortic wall homoeostasis and promoting SMC proliferation to compensate for cell loss during AAA development. Our findings have potential implications for current approaches aimed at p110α inhibition for cancer therapy and suggest new pharmacological strategies to activate p110α signaling in AAA disease.
Deep learning models of perceptual expertise support a domain-specific account

Perceptual expertise is an acquired skill that enables fine discrimination of members of a homogenous category. The question of whether perceptual expertise is mediated by general-expert or domain-specific processing mechanisms has been hotly debated for decades in human behavioral and neuroimaging studies. To decide between these two hypotheses, most studies examined whether expertise for different domains is mediated by the same mechanisms used for faces, for which most humans are expert. Here we used deep convolutional neural networks (DCNNs) to test whether perceptual expertise is best achieved by computations that are optimized for face or object classification. We re-trained a face-trained and an object-trained DCNNs to classify birds at the sub-ordinate or individual-level of categorization. The face-trained DCNN required deeper retraining to achieve the same level of performance for bird classification as an object-trained DCNN. These findings indicate that classification at the subordinate- or individual-level of categorization does not transfer well between domains. Thus, fine-grained classification is best achieved by using domain-specific rather than domain-general computations.
High‐frequency longitudinal white matter diffusion‐ and myelin‐based MRI database: Reliability and variability

Assessing the consistency of quantitative MRI measurements is critical for inclusion in longitudinal studies and clinical trials. Intraclass coefficient correlation and coefficient of variation were used to evaluate the different consistency aspects of diffusion‐ and myelin‐based MRI measures. Multi‐shell diffusion and inhomogeneous magnetization transfer data sets were collected from 20 healthy adults at a high‐frequency of five MRI sessions. The consistency was evaluated across whole bundles and the track‐profile along the bundles. The impact of the fiber populations on the consistency was also evaluated using the number of fiber orientations map. For whole and profile bundles, moderate to high reliability of diffusion and myelin measures were observed. We report higher reliability of measures for multiple fiber populations than single. The overall portrait of the most consistent measurements and bundles drawn from a wide range of MRI techniques presented here will be particularly useful for identifying reliable biomarkers capable of detecting, monitoring and predicting white matter changes in clinical applications and has the potential to inform patient‐specific treatment strategies.
Talin and vinculin combine their activities to trigger actin assembly

Focal adhesions (FAs) strengthen their link with the actin cytoskeleton to resist force. Talin-vinculin association could reinforce actin anchoring to FAs by controlling actin polymerization. However, the actin polymerization activity of the talin-vinculin complex is not known because it requires the reconstitution of the mechanical and biochemical activation steps that control the association of talin and vinculin and the exposure of their actin-binding domains. By combining kinetic and binding assays with single actin filament observations in TIRF microscopy, we show that the association of talin and vinculin mutants, mimicking different degrees of activation, results in a variety of activities. In particular, mechanically stretched talin and activated vinculin combine to stimulate actin assembly synergistically through a sequential mechanism in which filaments are nucleated, capped and released to elongate. Our findings suggest a versatile mechanism for the regulation of actin assembly in FAs subjected to various combinations of biochemical and mechanical cues.
Biologically plausible unsupervised learning in neural networks with sparse and asymmetric connectivity

In the search for biologically plausible but mathematically precise theories of learning in the brain, recent studies have begun to investigate how key assumptions underlying algorithms for supervised learning in artificial neural networks can be relaxed in biologically plausible ways. Turning to unsupervised learning, we develop biologically more plausible variants of the restricted Boltzmann machine (RBM), and benchmark their performance on MNIST. We show that RBMs with asymmetric connectivity can still be successfully trained with contrastive divergence, even if no two units are reciprocally connected. Furthermore, RBMs are able to learn if the forward, visible-to-hidden layer weights are kept constant and only the backward, hidden-to-visible layer weights are updated. These findings indicate that neural networks with biologically plausible connectivity support contrastive learning.