Miracle-dz/UniFAR-FTUs huggingface dataset:
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP‐CAPRI protein assembly prediction experiment. These targets comprised 12 homo‐oligomers and 3 hetero‐complexes. The bulk of the analysis focuses on 10 targets (of CAPRI Round 37), which included all 3 hetero‐complexes, and whose protein chains or the full assembly could be readily modeled from structural templates in the PDB. On average, 28 CAPRI groups and 10 CASP groups (including automatic servers), submitted models for each of these 10 targets. Additionally, about 16 groups participated in the CAPRI scoring experiments. A range of acceptable to high quality models were obtained for 6 of the 10 Round 37 targets, for which templates were available for the full assembly. Poorer results were achieved for the remaining targets due to the lower quality of the templates available for the full complex or the individual protein chains, highlighting the unmet challenge of modeling the structural adjustments of the protein components that occur upon binding or which must be accounted for in template‐based modeling. On the other hand, our analysis indicated that residues in binding interfaces were correctly predicted in a sizable fraction of otherwise poorly modeled assemblies and this with higher accuracy than published methods that do not use information on the binding partner. Lastly, the strengths and weaknesses of the assessment methods are evaluated and improvements suggested.
Association of networked flying platforms with small cells for network centric 5G+ C-RAN

5G+ systems expect enhancement in data rate and coverage area under limited power constraint. Such requirements can be fulfilled by the densification of small cells (SCs). However, a major challenge is the management of fronthaul links connected to an ultra dense network of SCs. A cost effective and scalable idea of using network flying platforms (NFPs) is employed here, where the NFPs are used as fronthaul hubs that connect the SCs to the core network. The association problem of NFPs and SCs is formulated considering a number of practical constraints such as backhaul data rate limit, maximum supported links and bandwidth by NFPs and quality of service requirement of the system. The network centric case of the system is considered that aims to maximize the number of associated SCs without any biasing, i.e., no preference for high priority SCs. Then, two new efficient greedy algorithms are designed to solve the presented association problem. Numerical results show a favorable performance of our proposed methods in comparison to exhaustive search.
Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments

The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.
Roughness vs. contrast in natural textures

We investigate the effect of contrast enhancement on the subjective roughness of visual textures. Our analysis is based on subjective experiments with seventeen images from the CUReT database in three variants: original, synthesized textures, and contrast-enhanced synthesized textures. In Experiment 1, participants were asked to adjust the contrast of a synthesized image so that it became similar in roughness to the original image. A new adaptive procedure that extends the staircase paradigm was used for efficient placement of the stimuli. In Experiment 2, the subjective roughness and the subjective contrast of the original, synthesized, and contrastenhanced synthesized images were determined using a pairwise comparison paradigm. The results of the two experiments show that although contrast enhancement of a synthesized image results in a similar subjective roughness as the original, the subjective contrast of that image is considerably higher than that of the original image. Future research should give more insights in the interaction between roughness and contrast.
Local and Global Structure Preservation for Robust Unsupervised Spectral Feature Selection

This paper proposes a new unsupervised spectral feature selection method to preserve both the local and global structure of the features as well as the samples. Specifically, our method uses the self-expressiveness of the features to represent each feature by other features for preserving the local structure of features, and a low-rank constraint on the weight matrix to preserve the global structure among samples as well as features. Our method also proposes to learn the graph matrix measuring the similarity of samples for preserving the local structure among samples. Furthermore, we propose a new optimization algorithm to the resulting objective function, which iteratively updates the graph matrix and the intrinsic space so that collaboratively improving each of them. Experimental analysis on 12 benchmark datasets showed that the proposed method outperformed the state-of-the-art feature selection methods in terms of classification performance.
Role of Antiseptics in the Prevention of Surgical Site Infections

BACKGROUND Antiseptics are chemical agents used to reduce the microbial population on the surface of the skin and are used in nearly every surgical procedure today. Despite this, there are currently no definitive guidelines on surgical preoperative antisepsis that indicate a specific regimen based on demonstration of superior efficacy. OBJECTIVE This review serves to examine preoperative antisepsis, including cutaneous bacteriology, preoperative hair removal, preoperative decolonization, surgical attire, and the antiseptic agents themselves. MATERIALS AND METHODS A review of the literature on surgical antiseptics was performed. RESULTS Although numerous studies have demonstrated differences in bacterial colonization rates, few well-controlled investigations have demonstrated superiority of a given regimen. The alcohol-based iodophor and chlorhexidine products seem to exhibit greater efficacy than their aqueous counterparts. CONCLUSION More randomized controlled trials will be needed to determine if any specific regimen is most effective. At this point in time, product usage should be based on specific attributes relating to the products, such as iodophors around the eyes and/or ears to avoid irritation and aqueous-based solutions in hair bearing areas because of concern for flammability. Ultimately, it is up to the individual surgeon to tailor the optimal antiseptic regimen for their specific scope of practice.
A Novel Method on Information Recommendation via Hybrid Similarity

Link similarity is widely applied in measuring the similarity between such objects as Web pages, scientific papers, and social networks. However, there are some deficiencies in the existing methods to measure it. For example, they cannot handle some semantic-similar contents. Their computation may not lead to accurate results in some cases. This paper presents a novel method to do so. It introduces the semantic similarity to calculate the similarity between two given objects, and overcomes the drawback caused by the fact that the existing methods ignore the semantic information of objects. It also gives a novel computation function to make the computing result of similarity more accurate.
Improving the anti-diabetic activity of GLP-1 by fusion with globular adiponectin

Abstract Glucagon-like peptide-1 (GLP-1) as an endogenous glucose-lowering peptide has great potential in diabetes therapy, but its clinical utility is compromised by its limited activity in vivo. Herein to improve the anti-diabetic activity of GLP-1, we constructed a fusion protein (GLP-1-globular adiponectin, GAD) using this peptide and the globular adiponectin. Using recombinant expression, we prepared the GAD fusion protein with a purity of above 95%. In normal mice, we validated the acute glucose-lowering activity of GAD by performing intraperitoneal glucose tolerance test (IPGTT). After that, we evaluated the anti-diabetic activity of this fusion protein in a multiple-low-dose streptozotocin (STZ)-induced diabetic mice model. In this diabetic mice model, GAD treatment greatly reduced the elevated fasting glucose and improved their impaired glucose homeostasis as judged by oral glucose tolerance test (OGTT). After treatment, the fasting glucose was 15.34 ± 2.07 mmol/L and 9.47 ± 1.08 mmol/L for GLP-1-treated and GAD-treated diabetic mice, respectively. Moreover, GLP-1 treatment and GAD treatment improved the pancreas function of the diabetic mice by ~1.5-fold and ~4.2-fold, respectively. Furthermore, GAD treatment greatly reduced the tissue damage in the pancreas of the diabetic mice. These data suggest that GAD possesses an improved anti-diabetic activity in vivo compared with native GLP-1, and therefore it could be regarded as a potential candidate for the future development of anti-diabetic drugs.
Association Study of Serotonin 3 Receptor Subunit Gene Variants in Antipsychotic-Induced Weight Gain

Background: Schizophrenia (SCZ) is a chronic severe neuropsychiatric disorder, where pharmacological treatment has been hindered by adverse effects, including antipsychotic-induced weight gain (AIWG) and related complications. Genetic studies have been exploring the appetite regulation and energy homeostasis pathways in AIWG with some promising leads. The serotonin system has been shown to participate in these pathways. Methods: In the current study, we examined single nucleotide polymorphisms across the serotonin receptor genes HTR3A and HTR3B. Prospective weight change was assessed for a total of 149 SCZ patients of European ancestry. Results: We did not find the tested HTR3A or HTR3B gene markers to be associated with AIWG in our sample. Conclusion: Our preliminary findings suggest that these receptors may not play a major role in predicting AIWG.
Computational soundness without protocol restrictions

The abstraction of cryptographic operations by term algebras, called Dolev-Yao models, is essential in almost all tool-supported methods for verifying security protocols. Recently significant progress was made in establishing computational soundness results: these results prove that Dolev-Yao style models can be sound with respect to actual cryptographic realizations and security definitions. However, these results came at the cost of imposing various constraints on the set of permitted security protocols: e.g., dishonestly generated keys must not be used, key cycles need to be avoided, and many more. In a nutshell, the cryptographic security definitions did not adequately capture these cases, but were considered carved in stone; in contrast, the symbolic abstractions were bent to reflect cryptographic features and idiosyncrasies, thereby requiring adaptations of existing verification tools. In this paper, we pursue the opposite direction: we consider a symbolic abstraction for public-key encryption and identify two cryptographic definitions called PROG-KDM (programmable key-dependent message) security and MKE (malicious-key extractable) security that we jointly prove to be sufficient for obtaining computational soundness without imposing assumptions on the protocols using this abstraction. In particular, dishonestly generated keys obtained from the adversary can be sent, received, and used. The definitions can be met by existing cryptographic schemes in the random oracle model. This yields the first computational soundness result for trace-properties that holds for arbitrary protocols using this abstraction (in particular permitting to send and receive dishonestly generated keys), and that is accessible to all existing tools for reasoning about Dolev-Yao models without further adaptations.
Convolutional neural network transfer learning for robust face recognition in NAO humanoid robot

Applications of transfer learning for convolutional neural networks (CNNs) have shown to be an efficient alternative for solving recognition tasks rather than designing and training a new neural network from scratch. However, there exists several popular CNN architectures available for various recognition tasks. Therefore, choosing an appropriate network for a specific recognition task, specifically designed for a humanoid robotic platform, is often challenging. This study evaluates the performance of two well-known CNN architectures; AlexNet, and VGG-Face for a face recognition task. This is accomplished by applying the transfer learning concept to the networks pre-trained for different recognition tasks. The proposed face recognition framework is then implemented on a humanoid robot known as NAO to demonstrate the practicality and flexibility of the algorithm. The results suggest that the proposed pipeline shows excellent performance in recognizing a new person from a single example image under varying distance and resolution conditions usually applicable to a mobile humanoid robotic platform.
An Integrated Switched Reluctance Motor Drive Topology With Voltage-Boosting and On-Board Charging Capabilities for Plug-In Hybrid Electric Vehicles (PHEVs)

This paper presents a new topology of switched reluctance motor (SRM) drives for plug-in hybrid electric vehicles. Six operating modes can be achieved as a result. Three of those modes are applied for driving and the others for charging. During the driving mode, the topology can be converted to a four-level one. During the charging mode, two battery packs are charged in parallel with the boost circuit by the external ac source or generators. The main contributions of the proposed topology are as follows. First, a four-level converter is formed by adopting different ways of connection (series or parallel) of the two battery packs (or the two capacitors), which can accelerate the excitation and demagnetization procedures of SRMs. Moreover, the topology contributes to decreasing the switching losses and extending the constant torque region to improve the drive performance as well. Second, the state of charge of the two battery packs (or the voltages of two capacitors) can keep balance on their own by parallel operation of the two battery packs. Furthermore, a detailed comparison between two drive modes of the proposed topology and asymmetric half bridge inverters is undertaken with simulation and experimental studies, the results of which demonstrate the validity of the proposed topology.
Procyanidin B2 attenuates neurological deficits and blood-brain barrier disruption in a rat model of cerebral ischemia.

SCOPE Disruption of the blood-brain barrier (BBB) is a major pathogenic mechanism of neurological dysfunction and death after ischemic stroke. The aim of our study was to investigate the effect of procyanidin B2 (PB), a bioactive food compound, on BBB disruption induced by ischemic stroke and explore the underlying mechanism. METHODS AND RESULTS PB was administrated intragastrically once a day starting at 3 h after transient middle cerebral artery occlusion (MCAO). PB treatment significantly decreased the infarction volume, brain edema, and neurological deficits after MCAO. PB prevented BBB disruption against ischemic stroke, as indicated by the reduction of Evans blue leakage and IgG levels. These results were also corroborated by immunofluorescence staining and Western blot analysis of ZO-1. Additionally, levels of reactive oxygen species and malondialdehyde were lessened in the ipsilateral ischemic area of brain by PB. The activities of antioxidant enzymes were elevated. Meanwhile, PB reversed the suppression of NF-E2-related factor nuclear translocation, and increased the protein expression of HO-1, GSTα, and NQO1 in the ipsilateral ischemic area of brain. CONCLUSION PB attenuates neurological deficits and BBB disruption in a rat model of cerebral ischemia, and the neuroprotection of PB is associated with activation of NF-E2-related factor pathway.
A Novel Method for Rapid Molecular Subgrouping of Medulloblastoma

Purpose: The classification of medulloblastoma into WNT, SHH, group 3, and group 4 subgroups has become of critical importance for patient risk stratification and subgroup-tailored clinical trials. Here, we aimed to develop a simplified, clinically applicable classification approach that can be implemented in the majority of centers treating patients with medulloblastoma. Experimental Design: We analyzed 1,577 samples comprising previously published DNA methylation microarray data (913 medulloblastomas, 457 non-medulloblastoma tumors, 85 normal tissues), and 122 frozen and formalin-fixed paraffin-embedded medulloblastoma samples. Biomarkers were identified applying stringent selection filters and Linear Discriminant Analysis (LDA) method, and validated using DNA methylation microarray data, bisulfite pyrosequencing, and direct-bisulfite sequencing. Results: Using a LDA-based approach, we developed and validated a prediction method (EpiWNT-SHH classifier) based on six epigenetic biomarkers that allowed for rapid classification of medulloblastoma into the clinically relevant subgroups WNT, SHH, and non-WNT/non-SHH with excellent concordance (>99%) with current gold-standard methods, DNA methylation microarray, and gene signature profiling analysis. The EpiWNT-SHH classifier showed high prediction capacity using both frozen and formalin-fixed material, as well as diverse DNA methylation detection methods. Similarly, we developed a classifier specific for group 3 and group 4 tumors, based on five biomarkers (EpiG3-G4) with good discriminatory capacity, allowing for correct assignment of more than 92% of tumors. EpiWNT-SHH and EpiG3-G4 methylation profiles remained stable across tumor primary, metastasis, and relapse samples. Conclusions: The EpiWNT-SHH and EpiG3-G4 classifiers represent a new simplified approach for accurate, rapid, and cost-effective molecular classification of single medulloblastoma DNA samples, using clinically applicable DNA methylation detection methods. Clin Cancer Res; 24(6); 1355–63. ©2018 AACR.
Adding reality to the virtual

Distributed interactive simulation provides an environment for realistic participation in virtual worlds. Humans interact with the virtual world through interface devices such as switches and knobs, keyboards and mice, touch screens and data gloves. The time has come for the seamless integration of these physical, real-world human interface devices with the systems that generate and display the virtual environments. The merging of these two areas will result in virtual world experiences more realistic than any available today. <<ETX>>
Nondestructive Evaluation of Damaged and As-Fabricated Encapsulated Ceramic Panels

Abstract : X-ray computed tomography (XCT) and ultrasonic testing (UT) are two major nondestructive evaluation (NDE) methods used to inspect a wide variety of materials and components. Current work in the NDE of materials at the U.S. Army Research Laboratory includes inspection and analysis of individual ceramic targets and ceramic panels. A number of samples have been evaluated using XCT and UT, including encapsulated panels. XCT and UT results from NDE studies of damaged and as-fabricated encapsulated ceramic panels will be shown and discussed. The results from the two NDE methods will be compared and contrasted.
Approximation of the robust domain of attraction for uncertain polynomial systems

The main purpose of this paper is to present methods for the approximation of the robust domain of attraction (RDA). We consider polynomial systems where the uncertainty is given by a polynomial mapping of an interval into the uncertainties. Using Lyapunovs stability theory as a basis we develop methods to compute in a constructive way based on Bézout matrices and the theorem of Ehlich and Zeller an approximation to RDA. We illustrate the effectiveness of the method with three examples.
Treatment and Management of Obesity: Is Surgical Intervention the Answer?

Obesity is rapidly becoming a major health concern and could be considered equal to smoking as a preventable cause of premature death. The National Institute for Health and Clinical Excellence (NICE 2006) estimated that 1.1 billion people are overweight, a number rivalling those who are underweight globally. Recent statistics for England from the National Health Service (NHS 2011) report that in 2009/10 there were 7,214 bariatric surgical procedures performed on people of varying ages.
No association of multiple sclerosis activity and progression with EBV or tobacco use in BENEFIT

We read with interest the article by Munger et al.1 The authors were incorrect that “(only) one study among patients with multiple sclerosis (MS) has found no association between smoking and progression, …”1 In a study of 205 women with MS of 5-year mean duration, we also found no association between smoking and progression.2 Nevertheless, this work suggested that APOE …
Spindle-E Acts Antivirally Against Alphaviruses in Mosquito Cells

Mosquitoes transmit several human- and animal-pathogenic alphaviruses (Togaviridae family). In alphavirus-infected mosquito cells two different types of virus-specific small RNAs are produced as part of the RNA interference response: short-interfering (si)RNAs and PIWI-interacting (pi)RNAs. The siRNA pathway is generally thought to be the main antiviral pathway. Although an antiviral activity has been suggested for the piRNA pathway its role in host defences is not clear. Knock down of key proteins of the piRNA pathway (Ago3 and Piwi5) in Aedes aegypti-derived cells reduced the production of alphavirus chikungunya virus (CHIKV)-specific piRNAs but had no effect on virus replication. In contrast, knock down of the siRNA pathway key protein Ago2 resulted in an increase in virus replication. Similar results were obtained when expression of Piwi4 was silenced. Knock down of the helicase Spindle-E (SpnE), an essential co-factor of the piRNA pathway in Drosophila melanogaster, resulted in increased virus replication indicating that SpnE acts as an antiviral against alphaviruses such as CHIKV and the related Semliki Forest virus (SFV). Surprisingly, this effect was found to be independent of the siRNA and piRNA pathways in Ae. aegypti cells and specific for alphaviruses. This suggests a small RNA-independent antiviral function for this protein in mosquitoes.
Application of electrorheological fluid in a hydrodynamic clutch

In this paper, the test results of a prototype hydrodynamic clutch with electrorheological fluid as a working fluid are presented. The hydrodynamic clutch with electrorheological fluid is controlled by flow resistance modulation in the pump and turbine channels created by electrodes connected to a high voltage source. The main aim of the performed study is to investigate practical ranges of the hydrodynamic clutch control by applying an electric field. The test results show that the concept of hydrodynamic clutch control is sound. For the tested clutch both the maximum change of speed and the maximum change of torque during the control are about 80% of the clutch input values.