Atomic Evolution Mechanism and Suppression of Edge Threading Dislocations in Nitride Remote Heteroepitaxy.

The majority of dislocations in nitride epilayers are edge threading dislocations (TDs), which diminish the performance of nitride devices. However, it is extremely difficult to reduce the edge TDs due to the lack of available slip systems. Here, we systematically investigate the formation mechanism of edge TDs and find that besides originating at the coalescence boundaries, these dislocations are also closely related to geometrical misfit dislocations at the interface. Based on this understanding, we propose a novel strategy to reduce the edge TD density of the GaN epilayer by nearly 1 order of magnitude via graphene-assisted remote heteroepitaxy. The first-principles calculations confirm that the insertion of graphene dramatically reduces the energy barrier required for interfacial sliding, which promotes a new strain release channel. This work provides a unique approach to directly suppress the formation of edge TDs at the source, thereby facilitating the enhanced performance of photoelectronic and electronic devices.

Bio-Sprayed/Threaded Microalgae Remain Viable and Indistinguishable from Controls.

Microalgae are increasingly playing a significant role in many areas of research and development. Recent studies have demonstrated their ability to aid wound healing by their ability to generate oxygen, aiding the healing process. Bearing this in mind, the capability to spray/spin deposit microalgae in suspension (solution) or compartmentalize living microalgae within architectures such as fibers/scaffolds and beads, would have significance as healing mechanisms for addressing a wide range of wounds. Reconstructing microalgae-bearing architectures as either scaffolds or beads could be generated via electric field (bio-electrospraying and cell electrospinning) and non-electric field (aerodynamically assisted bio-jetting/threading) driven technologies. However, before studying the biomechanical properties of the generated living architectures, the microalgae exposed to these techniques must be interrogated from a molecular level upward first, to establish these techniques, have no negative effects brought on the processed microalgae. Therefore these studies, demonstrate the ability of both these jetting and threading technologies to directly handle living microalgae, in suspension or within a polymeric suspension, safely, and form algae-bearing architectures such as beads and fibers/scaffolds.

Scheduling Framework for Accelerating Multiple Detection-Free Object Trackers.

In detection-free tracking, after users freely designate the location of the object to be tracked in the first frame of the video sequence, the location of the object is continuously found in the following video frame sequence. Recently, technologies using a Siamese network and transformer based on DNN modules have been evaluated as very excellent in terms of tracking accuracy. The high computational complexity due to the usage of the DNN module is not a preferred feature in terms of execution speed, and when tracking two or more objects, a bottleneck effect occurs in the DNN accelerator such as the GPU, which inevitably results in a larger delay. To address this problem, we propose a tracker scheduling framework. First, the computation structures of representative trackers are analyzed, and the scheduling unit suitable for the execution characteristics of each tracker is derived. Based on this analysis, the decomposed workloads of trackers are multi-threaded under the control of the scheduling framework. CPU-side multi-threading leads the GPU to a work-conserving state while enabling parallel processing as much as possible even within a single GPU depending on the resource availability of the internal hardware. The proposed framework is a general-purpose system-level software solution that can be applied not only to GPUs but also to other hardware accelerators. As a result of confirmation through various experiments, when tracking two objects, the execution speed was improved by up to 55% while maintaining almost the same accuracy as the existing method.

Assembly of Synaptic Protein-DNA Complexes: Critical Role of Non-Specific Interactions.

The synaptic protein-DNA complexes, formed by specialized proteins that bridge two or more distant sites on DNA, are critically involved in various genetic processes. However, the molecular mechanism by which the protein searches for these sites and how it brings them together is not well understood. Our previous studies directly visualized search pathways used by SfiI, and we identified two pathways, DNA threading and site-bound transfer pathways, specific to the site-search process for synaptic DNA-protein systems. To investigate the molecular mechanism behind these site-search pathways, we assembled complexes of SfiI with various DNA substrates corresponding to different transient states and measured their stability using a single-molecule fluorescence approach. These assemblies corresponded to specific-specific (synaptic), non-specific-non-specific (non-specific), and specific-non-specific (pre-synaptic) SfiI-DNA states. Unexpectedly, an elevated stability in pre-synaptic complexes assembled with specific and non-specific DNA substrates was found. To explain these surprising observations, a theoretical approach that describes the assembly of these complexes and compares the predictions with the experiment was developed. The theory explains this effect by utilizing entropic arguments, according to which, after the partial dissociation, the non-specific DNA template has multiple possibilities of rebinding, effectively increasing the stability. Such difference in the stabilities of SfiI complexes with specific and non-specific DNA explains the utilization of threading and site-bound transfer pathways in the search process of synaptic protein-DNA complexes discovered in the time-lapse AFM experiments.

DAT-MT Accelerated Graph Fusion Dependency Parsing Model for Small Samples in Professional Fields.

The rapid development of information technology has made the amount of information in massive texts far exceed human intuitive cognition, and dependency parsing can effectively deal with information overload. In the background of domain specialization, the migration and application of syntactic treebanks and the speed improvement in syntactic analysis models become the key to the efficiency of syntactic analysis. To realize domain migration of syntactic tree library and improve the speed of text parsing, this paper proposes a novel approach-the Double-Array Trie and Multi-threading (DAT-MT) accelerated graph fusion dependency parsing model. It effectively combines the specialized syntactic features from small-scale professional field corpus with the generalized syntactic features from large-scale news corpus, which improves the accuracy of syntactic relation recognition. Aiming at the problem of high space and time complexity brought by the graph fusion model, the DAT-MT method is proposed. It realizes the rapid mapping of massive Chinese character features to the model's prior parameters and the parallel processing of calculation, thereby improving the parsing speed. The experimental results show that the unlabeled attachment score (UAS) and the labeled attachment score (LAS) of the model are improved by 13.34% and 14.82% compared with the model with only the professional field corpus and improved by 3.14% and 3.40% compared with the model only with news corpus; both indicators are better than DDParser and LTP 4 methods based on deep learning. Additionally, the method in this paper achieves a speedup of about 3.7 times compared to the method with a red-black tree index and a single thread. Efficient and accurate syntactic analysis methods will benefit the real-time processing of massive texts in professional fields, such as multi-dimensional semantic correlation, professional feature extraction, and domain knowledge graph construction.

A novel hybrid multi-thread metaheuristic approach for fake news detection in social media.

In fake news detection, intelligent optimization seems to be a more effective and explainable solution methodology than the black-box methods that have been extensively used in the literature. This study takes the optimization-based method one step further and proposes a novel, multi-thread hybrid metaheuristic approach for fake news detection in social media. The most innovative feature of the proposed method is that it uses a supervisor thread mechanism, which simultaneously monitors and improves the performance and search patterns of metaheuristic algorithms running parallel. With the supervisor thread mechanism, it is possible to analyse different key attribute combinations in the search space. In addition, this study develops a software framework that allows this model to be implemented easily. It tests the performance of the proposed model on three different data sets, respectively containing news about Covid-19, the Syrian War, and daily politics. The proposed method is evaluated in comparison to the results of fifteen different well-known deep models and classification algorithms. Experimental results prove the success of the proposed model and that it can produce competitive results.

DisCovER: distance- and orientation-based covariational threading for weakly homologous proteins.

Threading a query protein sequence onto a library of weakly homologous structural templates remains challenging, even when sequence-based predicted contact or distance information is used. Contact-assisted or distance-assisted threading methods utilize only the spatial proximity of the interacting residue pairs for template selection and alignment, ignoring their orientation. Moreover, existing threading methods fail to consider the neighborhood effect induced by the query-template alignment. We present a new distance- and orientation-based covariational threading method called DisCovER by effectively integrating information from inter-residue distance and orientation along with the topological network neighborhood of a query-template alignment. Our method first selects a subset of templates using standard profile-based threading coupled with topological network similarity terms to account for the neighborhood effect and subsequently performs distance- and orientation-based query-template alignment using an iterative double dynamic programming framework. Multiple large-scale benchmarking results on query proteins classified as weakly homologous from the continuous automated model evaluation experiment and from the current literature show that our method outperforms several existing state-of-the-art threading approaches, and that the integration of the neighborhood effect with the inter-residue distance and orientation information synergistically contributes to the improved performance of DisCovER. DisCovER is freely available at https://github.com/Bhattacharya-Lab/DisCovER.

MTDCNet: A 3D multi-threading dilated convolutional network for brain tumor automatic segmentation.

Glioma is one of the most threatening tumors and the survival rate of the infected patient is low. The automatic segmentation of the tumors by reliable algorithms can reduce diagnosis time. In this paper, a novel 3D multi-threading dilated convolutional network (MTDC-Net) is proposed for the automatic brain tumor segmentation. First of all, a multi-threading dilated convolution (MTDC) strategy is introduced in the encoder part, so that the low dimensional structural features can be extracted and integrated better. At the same time, the pyramid matrix fusion (PMF) algorithm is used to integrate the characteristic structural information better. Secondly, in order to make the better use of context semantical information, this paper proposed a spatial pyramid convolution (SPC) operation. By using convolution with different kernel sizes, the model can aggregate more semantic information. Finally, the multi-threading adaptive pooling up-sampling (MTAU) strategy is used to increase the weight of semantic information, and improve the recognition ability of the model. And a pixel-based post-processing method is used to prevent the effects of error prediction. On the brain tumors segmentation challenge 2018 (BraTS2018) public validation dataset, the dice scores of MTDC-Net are 0.832, 0.892 and 0.809 for core, whole and enhanced of the tumor, respectively. On the BraTS2020 public validation dataset, the dice scores of MTDC-Net are 0.833, 0.896 and 0.797 for the core tumor, whole tumor and enhancing tumor, respectively. Mass numerical experiments show that MTDC-Net is a state-of-the-art network for automatic brain tumor segmentation.

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects.

Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote "longitudinal breathing" and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an "open hole" population on the order of 10-2 compared to 10-4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.

VHH Structural Modelling Approaches: A Critical Review.

VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.

Conformational Effects on the Threading Kinetics of Dumbbell-Shaped Guests into the Cavity of Oxatub[4]arene.

Unprecedented threading kinetics were revealed between viologen-based guests and conformationally adaptive oxatub[4]arene. Three representative conformations of oxatub[4]arene are involved in the kinetic and thermodynamic products which follow the opposite orders in their rankings. Consequently, error correction was involved and a complex kinetic process was observed in a simple two-component system. Moreover, it was found that some viologen-based guests have much faster threading kinetics than those of DABCO-based with the same stoppers. This was enabled by an unprecedented threading mechanism in which a tilted conformation of the guests is adopted by involving one linear alkyl group on the 3,5-dialkoxybenzyl stoppers, the viologen core, and the methylene spacers in the transition states. This new mechanism even allows the viologen-based guests with the 3,5-dicetyloxybenzyl stoppers to form a pseudorotaxane with oxatub[4]arene.

Membrane orientation and oligomerization of the melanocortin receptor accessory protein 2.

The melanocortin receptor accessory protein 2 (MRAP2) plays a pivotal role in the regulation of several G protein-coupled receptors that are essential for energy balance and food intake. MRAP2 loss-of-function results in obesity in mammals. MRAP2 and its homolog MRAP1 have an unusual membrane topology and are the only known eukaryotic proteins that thread into the membrane in both orientations. In this study, we demonstrate that the conserved polybasic motif that dictates the membrane topology and dimerization of MRAP1 does not control the membrane orientation and dimerization of MRAP2. We also show that MRAP2 dimerizes through its transmembrane domain and can form higher-order oligomers that arrange MRAP2 monomers in a parallel orientation. Investigating the molecular details of MRAP2 structure is essential for understanding the mechanism by which it regulates G protein-coupled receptors and will aid in elucidating the pathways involved in metabolic dysfunction.

Hair Removal Practices: A Literature Review.

Hair removal practices have evolved from adhering to social, cultural, and religious traditions to meeting aesthetic standards. Hair removal methods can be divided into two categories: 1) depilation, which involves removing the hair shaft and includes shaving and chemical depilatories, and 2) epilation, which involves removing the hair shaft, follicle, and bulb, and includes plucking, threading, waxing, sugaring, lasers, intense pulsed light system, electrolysis, and photodynamic therapy. Furthermore, an eflornithine hydrochloride 13.9% cream (Vaniqa®, neither an epilatory or depilatory technique), has been US FDA- and Health Canada-approved to slow the rate of facial hair growth and to be used in combination with other hair removal methods. All methods are temporary except for electrolysis, and each technique has advantages and disadvantages in terms of efficacy and adverse events. Importantly, most studies examining the efficacy of hair removal techniques are limited to darker hair and fairer skin, and further research is required especially for those with light-colored hair.

Site-Search Process for Synaptic Protein-DNA Complexes.

The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualized sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.

Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics.

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

A Minimal Load-and-Lock RuII Luminescent DNA Probe.

Threading intercalators bind DNA with high affinities. Here, we describe single-molecule studies on a cell-permeant luminescent dinuclear ruthenium(II) complex that has been previously shown to thread only into short, unstable duplex structures. Using optical tweezers and confocal microscopy, we show that this complex threads and locks into force-extended duplex DNA in a two-step mechanism. Detailed kinetic studies reveal that an individual stereoisomer of the complex exhibits the highest binding affinity reported for such a mono-intercalator. This stereoisomer better preserves the biophysical properties of DNA than the widely used SYTOX Orange. Interestingly, threading into torsionally constrained DNA decreases dramatically, but is rescued on negatively supercoiled DNA. Given the "light-switch" properties of this complex on binding DNA, it can be readily used as a long-lived luminescent label for duplex or negatively supercoiled DNA through a unique "load-and-lock" protocol.

Template-based prediction of protein structure with deep learning.

BACKGROUND: Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. RESULTS: We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. ThreaderAI formulates the task of aligning query sequence with template as the classical pixel classification problem in computer vision and naturally applies deep residual neural network in prediction. ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residue-residue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. We evaluated our methods both in generating accurate template-query alignment and protein threading. Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56, 13, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. And on CASP13's TBM-hard data, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 16, 9 and 8% in terms of TM-score, respectively. CONCLUSIONS: These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins.

Failure to restore the calcar and locking screw cross-threading predicts varus collapse in proximal humerus fracture fixation.

BACKGROUND: Varus collapse is a common failure mode of proximal humerus fracture (PHF) fixation. The purpose of this study was to analyze predictors of varus collapse of PHF after open reduction, internal fixation (ORIF). METHODS: All patients who underwent ORIF of a PHF from January 2008 to July 2018 were identified. Known predictors of fixation failure were assessed, including calcar distance, calcar ratio, and calcar restoration. Additionally, the presence of cross-threaded screws was determined. The primary outcome analyzed was varus collapse of the fracture defined as a change in neck shaft angulation to less than 120°. RESULTS: There were 112 patients identified who underwent ORIF of a PHF that met inclusion criteria. The population was 75.0% female (84/112), average age was 62.5 ± 10.4 years (range 40.0-87.9), and average body mass index was 28.0 ± 5.5 (17.5-46.4). There were 17 with varus collapse. In 11 of the 17 patients (64.7%), there was screw cross-threading (vs. 31/95 [32.6%] in those that did not collapse); P = .012. In addition, 8 of the 17 (47.1%) did not have restoration of the calcar (vs. 16/95 [16.8%]; P = .005). CONCLUSION: This study identifies 2 surgeon-controlled variables that can contribute to varus collapse after ORIF of PHFs. Cross-threading of locking screws and failure to restore the medial calcar can be a function of implant design, surgeon technical skill, and/or bone quality.

Molecular Threading-Dependent Mass Transport in Paper Origami for Single-Step Electrochemical DNA Sensors.

Molecular transport controls the efficiency of complex biological network systems such as cellular signaling system and cascade biomedical reaction. However, device fabrication for molecular sensing is often restricted by a low transport efficiency and complicated processing. Here, we report a molecular threading-dependent transport system using three-dimensional (3D) paper origami enabling the directional transport of biomolecules. We demonstrate that framework nucleic acid-based interface engineering allows orthogonal molecular recognition and enzymatic reaction with programmed order on site. We thus develop a single-step electrochemical DNA sensor for quantitative analysis with 1 picomolar sensitivity within 60 min. Our sensor can discriminate a mismatched target at the level of a single base mismatch. Our study shows a great potential toward the development of a biomimetic molecular transport system for point-of-care and precision diagnosis.

Study on the Influence of Chirality in the Threading of Calix[6]arene Hosts with Dialkylammonium Axles.

: The influence of chirality in calixarene threading has been studied by exploiting the "superweak anion approach". In particular, the formation of chiral pseudo[2]rotaxanes bearing a classical stereogenic center in their axle and/or wheel components has been considered. Two kind of pseudo[2]rotaxane stereoadducts, the "endo-chiral" and "exo-chiral" ones, having the stereogenic center of a cationic axle inside or outside, respectively, the calix-cavity of a chiral calixarene were preferentially formed with specifically designed chiral axles by a fine exploitation of the so-called "endo-alkyl rule" and a newly defined "endo-α-methyl-benzyl rule" (threading of a hexaalkoxycalix[6]arene with a directional (α-methyl-benzyl)benzylammonium axle occurs with an endo-α-methyl-benzyl preference). The obtained pseudorotaxanes were studied in solution by 1D and 2D NMR, and in the gas-phase by means of the enantiomer-labeled (EL) mass spectrometry method, by combining enantiopure hosts with pseudoracemates of one deuterated and one unlabeled chiral axle enantiomer. In both instances, there was not a clear enantiodiscrimination in the threading process with the studied host/guest systems. Possible rationales are given to explain the scarce reciprocal influence between the guest and host chiral centers.