Position In Sequence Research Articles

Modulation of memory by prism adaptation in healthy subjects

Recent findings suggest that prism adaptation can extend its effects beyond spatial attention, modulating the performance of different cognitive tasks by acting on cerebellar, parietal and temporal-frontal networks. We tested groups of healthy subjects to investigate the effects of rightward vs. leftward prism adaptation vs. neutral lenses exposure in a series of memory tasks, probing either short-term (Digit span, Corsi span) or long-term memory (Supraspan verbal and spatial learning). In the short-term memory tasks, leftward prism adaptation selectively increased verbal span, while rightward prism adaptation increased spatial span. In the long-term memory tasks, leftward prism adaptation selectively increased verbal supraspan, i.e., increased the number of digits in the correct sequence reproduced and reduced the number of repetitions needed to learn the supraspan sequence. On the other hand, rightward prism adaptation selectively increased spatial supraspan, i.e. it increased the number of spatial positions in the correct sequence reproduced and reduced the number of repetitions needed to learn the supraspan sequence. Moreover, rightward, but not leftward, prism adaptation selectively increased supraspan recall after a delay interval, regardless of the stimulus material, i.e., it increased the number of digits or spatial positions recalled after a delay interval. Neutral lenses exposure did not influence any memory task. These findings suggest that prism adaptation can induce both modality/hemispheric-specific and process-specific effects on short-term and long-term explicit memory.

Exploration of the Computational Predicted Internal Tagging Preferred Protein Properties

Protein tags are commonly used in many biological experiments, and adding a tag to an intolerant sequence position can significantly damage the functions of a protein and affect the outcome of an experiment. Recently, an in-house computational prediction method, TagScore, was developed which uses sequence homology to identify non-conservative regions of proteins permissive of tagging. The properties of the proteins that are predicted by TagScore to prefer internal tagging were explored using gene enrichment strategies. Proteins that prefer internal tagging were found to be related to GTPase-associated proteins and sequence features with disordered and polar regions, as predicted by TagScore.

A GCN and Transformer complementary network for skeleton-based action recognition

Graph Convolution Networks (GCNs) have been widely used in skeleton-based action recognition. Although there are significant progress, the inherent limitation still lies in the restricted receptive field of GCN, hindering its ability to extract global dependencies effectively. And the joints that are structurally separated can also have strong correlation. Previous works rarely explore local and global correlations of joints, leading to insufficiently model the complex dynamics of skeleton sequences. To address this issue, we propose a GCN and Transformer complementary network (GTC-Net) that allows parallel communications between GCN and Transformer domains. Specifically, we introduce a graph convolution and self-attention combined module (GAM), which can effectively leverage the complementarity of GCN and self-attention to perceive local and global dependencies of joints for the human body. Furthermore, in order to address the problems of long-term sequence ordering and position detection, we design a position-aware module (PAM), which can explicitly capture the ordering information and unique identity information for body joints of skeleton sequence. Extensive experiments on NTU RGB+D 60 and NTU RGB+D 120 datasets are conducted to evaluate our proposed method. The results demonstrate that our method can achieve competitive results on both datasets.

Semisynthetic Phage Display Library Construction: Design and Synthesis of Diversified Single-Chain Variable Fragments and Generation of Primary Libraries.

Display of antibody fragments on the surface of M13 filamentous bacteriophages is a well-established approach for the identification of antibodies binding to a target of interest. Here, we describe the first of a three-step method to construct Antibody Libraries for Therapeutic Antibody Discovery (ALTHEA) Libraries. The three-step method involves (1) primary library (PL) construction, (2) filtered library construction, and (3) secondary library construction. The first step, described here, entails design, synthesis, and cloning of four PLs. These PLs are designed with specific properties amenable to therapeutic antibody development using one universal variable heavy (VH) scaffold and four distinct variable light (VL) scaffolds. The scaffolds are diversified in positions that bind both protein and peptide targets identified in antibody-antigen complexes of known structure using the amino acid frequencies found in those positions in known human antibody sequences, avoiding residues that may lead to developability liabilities. The diversified scaffolds are combined with 90 synthetic neutral HCDR3 sequences designed with developable human diversity genes (IGHD) and joining heavy genes (IGHJ) in germline configuration, and assembled as single-chain variable fragments (scFvs) in a VL-linker-VH orientation. The four designed PLs are synthesized using trinucleotide phosphoramidites (TRIMs) and cloned independently into a phagemid vector for M13 pIII display. Quality control of the cloning of the four PLs is also described, which involves sequencing scFvs in each library.

An interactional linguistics study of Shi ba in Mandarin conversation

From the perspective of interactional linguistics and adopting the methodology of conversation analysis, this study explores some fine-grained interactional uses of shi ba in Mandarin conversation. It first classifies shi ba into unmarked and marked forms generally in terms of their prosodic manifestations with the assistance of Praat, the speech analysis tool. Then it demonstrates that the unmarked shi ba fulfills three interactional functions: requesting confirmation, seeking affiliation and maintaining floor; the marked shi ba registers dissatisfaction and displays affiliation. However, shi ba is basically a tag question, and serves to invite the recipient to proffer certain interactional response. The specific function that shi ba performs in conversation is tied to three decisive factors – its prosodic manifestations, position in specific turns and sequences as well as the relative epistemic status of interlocutors. The study also suggests that there lies a common motivation for the emergence of various interactional functions of shi ba, that is – the demand for an on-line alignment, which reflects the cross-fertilization between language and interaction.

Expression of thermostable MMLV reverse transcriptase in Escherichia coli by directed mutation

The functionality of Moloney murine leukemia virus reverse transcriptase (MMLV RT) will increase with the improvement of its solubility and thermal stability. Introduce directed mutation at specific positions of the MMLV RT sequence and codon optimization is needed to achieve these properties. The two RT coding sequences with (rRT-K) and without directed mutations (rRT-L) were versatility optimized and expressed to analyze the ribonuclease H (RNase H) inactivity and thermostable polymerase activity. For this purpose, the five-point mutations (438–442aa) and three-point mutations (530, 568, and 659 aa) were done at the RT connection domain and RNase H active site, respectively. High expression levels of rRT-L and rRT-K were obtained in E. coli BL21(DE3) and BL21(shuffle) strains, 0.5 mM IPTG concentration at 37 °C, and 8 hours’ post-induction condition. Then, recombinant enzymes were purified and verified by Ni-NTA resin and western blotting. Insilico analysis (IUpred 3.0) showed that the directed mutation in the RNase H domain caused the formation of disorder regions or instability in the RNase H domain of rRT-K compared to rRT-L. The modified RT-PCR and the RT-LAMP reactions proved the RNase H inactivity of rRT-K. In addition, increasing of thermostability of rRT-K compared to rRT-L and commercial RT was evaluated by the RT-PCR and RT-LAMP reactions. The results showed that rRT-K could successfully tolerate 60 ºC in the two methods. This study revealed that the directed mutations and the versatile sequence optimization can promise to produce thermostable commercial enzymes to decrease non-specific one-step RT-PCR and RT-LAMP products.

Optimized design of annular ejector primary nozzle based on orthogonal test method

Abstract Annular ejectors are widely used in aerospace and other applications, and their performance has a significant impact on the overall system. In this paper, the effects of main nozzle area ratio, contraction section angle and diffusion section angle on the performance of annular ejector are investigated by using computational fluid dynamics combined with one-factor experiments, on the basis of which the L9(33) orthogonal table is established to optimise the structure of main nozzle and to screen the main influencing factors. The results show that the flow field inside the annular ejector is extremely complex. The influence of the main nozzle area ratio on the performance of the annular ejector is very great, and the change of the area ratio will lead to the change of the position of the second excitation sequence as well as the Mach number at the outlet of the main nozzle. However, as with the results of the one-way analysis, the effect of the angle of the constriction section on the exit Mach number is negligible.

Design and technological analysis of the multi-position progressive die for the clamp

Abstract The technological process of the clamp part is analyzed, the design of the stamping and bending process for the clamp is introduced, including determination of the operation sequence and operation position parts dimensions. The process is used side blade settles to distance, pilot pin was used in exact positioning, the blanking and bending of the part were carried out continuously. The design of the general structure, layout of the progressive and forming characteristics die for the clamp is introduced in detail, the method for designing and calculating the key parts.

Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning.

Despite the success of AlphaFold2 approaches in predicting single protein structures, these methods showed intrinsic limitations in predicting multiple functional conformations of allosteric proteins and have been challenged to accurately capture the effects of single point mutations that induced significant structural changes. We examined several implementations of AlphaFold2 methods to predict conformational ensembles for state-switching mutants of the ABL kinase. The results revealed that a combination of randomized alanine sequence masking with shallow multiple sequence alignment subsampling can significantly expand the conformational diversity of the predicted structural ensembles and capture shifts in populations of the active and inactive ABL states. Consistent with the NMR experiments, the predicted conformational ensembles for M309L/L320I and M309L/H415P ABL mutants that perturb the regulatory spine networks featured the increased population of the fully closed inactive state. The proposed adaptation of AlphaFold can reproduce the experimentally observed mutation-induced redistributions in the relative populations of the active and inactive ABL states and capture the effects of regulatory mutations on allosteric structural rearrangements of the kinase domain. The ensemble-based network analysis complemented AlphaFold predictions by revealing allosteric hotspots that correspond to state-switching mutational sites which may explain the global effect of regulatory mutations on structural changes between the ABL states. This study suggested that attention-based learning of long-range dependencies between sequence positions in homologous folds and deciphering patterns of allosteric interactions may further augment the predictive abilities of AlphaFold methods for modeling of alternative protein sates, conformational ensembles and mutation-induced structural transformations.

Energy landscapes of peptide-MHC binding.

Molecules of the Major Histocompatibility Complex (MHC) present short protein fragments on the cell surface, an important step in T cell immune recognition. MHC-I molecules process peptides from intracellular proteins; MHC-II molecules act in antigen-presenting cells and present peptides derived from extracellular proteins. Here we show that the sequence-dependent energy landscapes of MHC-peptide binding encode class-specific nonlinearities (epistasis). MHC-I has a smooth landscape with global epistasis; the binding energy is a simple deformation of an underlying linear trait. This form of epistasis enhances the discrimination between strong-binding peptides. In contrast, MHC-II has a rugged landscape with idiosyncratic epistasis: binding depends on detailed amino acid combinations at multiple positions of the peptide sequence. The form of epistasis affects the learning of energy landscapes from training data. For MHC-I, a low-complexity problem, we derive a simple matrix model of binding energies that outperforms current models trained by machine learning. For MHC-II, higher complexity prevents learning by simple regression methods. Epistasis also affects the energy and fitness effects of mutations in antigen-derived peptides (epitopes). In MHC-I, large-effect mutations occur predominantly in anchor positions of strong-binding epitopes. In MHC-II, large effects depend on the background epitope sequence but are broadly distributed over the epitope, generating a bigger target for escape mutations due to loss of presentation. Together, our analysis shows how an energy landscape of protein-protein binding constrains the target of escape mutations from T cell immunity, linking the complexity of the molecular interactions to the dynamics of adaptive immune response.

Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs

The inversion of substrate size specificity is an evolutionary roadblock for proteins. The Duf4243 dioxygenases GedK and BTG13 are known to catalyze the aromatic cleavage of bulky tricyclic hydroquinone. In this study, we discover a Duf4243 dioxygenase PaD that favors small monocyclic hydroquinones from the penicillic-acid biosynthetic pathway. Sequence alignments between PaD and GedK and BTG13 suggest PaD has three additional motifs, namely motifs 1-3, distributed at different positions in the protein sequence. X-ray crystal structures of PaD with the substrate at high resolution show motifs 1-3 determine three loops (loops 1-3). Most intriguing, loops 1-3 stack together at the top of the pocket, creating a lid-like tertiary structure with a narrow channel and a clearly constricted opening. This drastically changes the substrate specificity by determining the entry and binding of much smaller substrates. Further genome mining suggests Duf4243 dioxygenases with motifs 1-3 belong to an evolutionary branch that is extensively involved in the biosynthesis of natural products and has the ability to degrade diverse monocyclic hydroquinone pollutants. This study showcases how natural enzymes alter the substrate specificity fundamentally by incorporating new small motifs, with a fixed overall scaffold-architecture. It will also offer a theoretical foundation for the engineering of substrate specificity in enzymes and act as a guide for the identification of aromatic dioxygenases with distinct substrate specificities.

Towards Cell-Permeable Hepatitis B Virus Core Protein Variants as Potential Antiviral Agents.

Hepatitis B virus (HBV) infection remains a major health threat with limited treatment options. One of various new antiviral strategies is based on a fusion of Staphylococcus aureus nuclease (SN) with the capsid-forming HBV core protein (HBc), termed coreSN. Through co-assembly with wild-type HBc-subunits, the fusion protein is incorporated into HBV nucleocapsids, targeting the nuclease to the encapsidated viral genome. However, coreSN expression was based on transfection of a plasmid vector. Here, we explored whether introducing protein transduction domains (PTDs) into a fluorescent coreSN model could confer cell-penetrating properties for direct protein delivery into cells. Four PTDs were inserted into two different positions of the HBc sequence, comprising the amphiphilic translocation motif (TLM) derived from the HBV surface protein PreS2 domain and three basic PTDs derived from the Tat protein of human immunodeficiency virus-1 (HIV-1), namely Tat4, NP, and NS. To directly monitor the interaction with cells, the SN in coreSN was replaced with the green fluorescent protein (GFP). The fusion proteins were expressed in E. coli, and binding to and potential uptake by human cells was examined through flow cytometry and fluorescence microscopy. The data indicate PTD-dependent interactions with the cells, with evidence of uptake in particular for the basic PTDs. Uptake was enhanced by a triplicated Simian virus 40 (SV40) large T antigen nuclear localization signal (NLS). Interestingly, the basic C terminal domain of the HBV core protein was found to function as a novel PTD. Hence, further developing cell-permeable viral capsid protein fusions appears worthwhile.

En-route recharging scheduling strategy for electric trucks serving inter-terminal container transportation

ABSTRACT Container ports are increasingly deploying electric trucks (ETs) for inter-terminal transportation (ITT). However, en-route recharging activities, which reduce ITT efficiency, are necessary for ETs because of limited battery capacity. This study proposes a real-time strategy to schedule the en-route recharging activities for ETs. The strategy dynamically monitors the ITT system, and simultaneously designates charging piles for ETs and determines their positions in the service sequences. An ET may be designated to a remote but shorter-queued pile. The total queue time of the ETs served by a designated pile can be reduced by adjusting the service sequence. The effectiveness is demonstrated in comparison with an alternative strategy in a real-world case. The results indicate that the proposed strategy effectively reduces container throughput time by 21.8% and ET energy consumption by 12.3%. Sensitivity analyses suggest that the strategy is applicable for ports with multiple charging stations and moderate ET fleet size.

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins.

Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact of sequence-local versus sequence-nonlocal features of an IDP's charge pattern on its conformational dimensions and its phase-separation propensity, the charge "blockiness" κ and the nonlocality-weighted sequence charge decoration (SCD) parameters are compared for their correlations with isolated-chain radii of gyration (Rgs) and upper critical solution temperatures (UCSTs) of polyampholytes modeled by random phase approximation, field-theoretic simulation, and coarse-grained molecular dynamics. SCD is superior to κ in predicting Rg because SCD accounts for effects of contact order, i.e., nonlocality, on dimensions of isolated chains. In contrast, κ and SCD are comparably good, though nonideal, predictors of UCST because frequencies of interchain contacts in the multiple-chain condensed phase are less sensitive to sequence positions than frequencies of intrachain contacts of an isolated chain, as reflected by κ correlating better with condensed-phase interaction energy than SCD.

Rock lithology classification algorithm based on improved self-attention mechanism VIT

Abstract When applying VIT to image classification, although good accuracy has been achieved, there is a limitation on the number of stacked layers. The similarity between different tokens increases as the model deepens, leading to low accuracy in shallow VIT models and wasting computational resources in deep VIT models. To address this issue, a multi-valued self-attention mechanism is proposed. By introducing an additional clue “V,” that does not vary arbitrarily, the dot product similarity observes each position in the token sequence more, reducing the depth of the attention mechanism network and avoiding the problem of similarity disappearing between deep tokens. Additionally, the loss function is improved by combining the Focal Loss function with Label Smoothing, enhancing the model’s handling of uncertain images while retaining the category focus of Focal Loss. Experiments are conducted on a rock lithology classification dataset, showing that compared to the VGG model and ResNet-18, the accuracy of the ResNet-50 model improves by 17.6%, 12%, and 4.9%, respectively. This paper also demonstrates the effectiveness of the multi-valued self-attention mechanism, which significantly reduces depth and parameter count while maintaining comparable accuracy. Finally, generalization experiments on the CIFAR-10 dataset further validate these conclusions.

A Markovian dynamics for Caenorhabditis elegans behavior across scales

How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode worm Caenorhabditis elegans, we show that a single dynamics connects posture-scale fluctuations with trajectory diffusion and longer-lived behavioral states. We take short posture sequences as an instantaneous behavioral measure, fixing the sequence length for maximal prediction. Within the space of posture sequences, we construct a fine-scale, maximum entropy partition so that transitions among microstates define a high-fidelity Markov model, which we also use as a means of principled coarse-graining. We translate these dynamics into movement using resistive force theory, capturing the statistical properties of foraging trajectories. Predictive across scales, we leverage the longest-lived eigenvectors of the inferred Markov chain to perform a top-down subdivision of the worm's foraging behavior, revealing both "runs-and-pirouettes" as well as previously uncharacterized finer-scale behaviors. We use our model to investigate the relevance of these fine-scale behaviors for foraging success, recovering a trade-off between local and global search strategies.

A hidden element governing immunogenicity in tumoral neoepitopes

The search for what characteristics define an epitope as either an immunogenic or a non-responsive target for immunotherapy has eluded researchers for years. Several studies demonstrate that certain positions in the peptide sequences, the major histocompatibility complex (MHC) anchor residues, have a preferential composition of amino acids (allelic motifs), being those epitopes more likely to display a better immunogenic response. First of all, not all MHC ligands are immunogenic, considering that unnumbered self-epitopes are continuously presented on the cell surfaces. In this work, we analyzed data to evaluate an additional element, central to our hypothesis that alterations in tumor protein sequences result in a structural change that shifts the electrostatic surface of the peptide-major histocompatibility complex (pMHC) molecules, pivotal for T-Cell receptor (TCR) recognition and the initiation of an immunogenic response. Firstly, previously neoepitope sequences presenting differential immune responses when compared with their wild-type counterparts were recovered. Even though the sequences were very similar, they triggered responses that were considerably different, and currently, there is no well-established explanation for why they conspicuously differ in immunogenic aspects from each other. The pMHCs structures harboring the epitope sequences were modeled and then used to generate images of their electrostatic surfaces, looking for qualitative differences that indicate the distinct responses. We noticed that no significant alteration occurred between immunogenic tumor peptides and their wild-type non-immunogenic counterparts when comparing their electrostatic surface. An additional comparison was made against structures of pMHCs containing immunogenic epitopes recovered from the Crosstope Database (https://crosstope.com.br/). In this sense, it was also possible to verify if immunogenic tumor epitopes were similar to viral immunogenic ones. Surprisingly, both wild-type (WT) sequences and neoepitopes shared an electrostatic surface distribution with pathogen targets, which could indicate their immunogenic predisposition. So we theorized that a “hidden element” may be responsible for the immunogenicity shift in neoepitopes.

A map of glycation and glycoxidation sites in collagen I of human cortical bone: Effects of sex and type 2 diabetes

Complications of diabetes is a major health problem affecting multiple organs including bone, where the chronic disease increases the risk of fragility fractures. One hypothesis suggests a pathogenic role for hyperglycemia-induced modification of proteins, a.k.a. advanced glycation end products (AGEs), resulting in structural and functional damage to bone extracellular matrix (ECM). Evidence supporting this hypothesis has been limited by the lack of comprehensive information about the location of AGEs that accumulate in vivo at specific sites within the proteins of bone ECM. Analyzing extracts from cortical bone of cadaveric femurs by liquid chromatography tandem mass spectrometry, we generated a quantitative AGE map of human collagen I for male and female adult donors with and without diabetes. The map describes the chemical nature, sequence position, and levels of four major physiological AGEs, e.g. carboxymethyllysine, and an AGE precursor fructosyllysine within the collagen I triple-helical region. The important features of the map are: 1) high map reproducibility in the individual bone extracts, i.e. 20 male and 20 female donors; 2) localization of modifications to distinct clusters: 10 clusters containing 34 AGE sites in male donors and 9 clusters containing 28 sites in female donors; 3) significant increases in modification levels in diabetes at multiple sites: 26 out of 34 sites in males and in 17 out of 28 sites in females; and 4) generally higher modification levels in male vs. female donors. Moreover, the AGE levels at multiple individual sites correlated with total bone pentosidine levels in male but not in female donors. Molecular dynamics simulations and molecular modeling predicted significant impact of modifications on solvent exposure, charge distribution, and hydrophobicity of the triple helix as well as disruptions to the structure of collagen I fibril. In summary, the AGE map of collagen I revealed diabetes-induced, sex-specific non-enzymatic modifications at distinct triple helical sites that can disrupt collagen structure, thus proposing a specific mechanism of AGE contribution to diabetic complications in human bone.

Multidimensional regularity processing in music: an examination using redundant signals effect.

Music is based on various regularities, ranging from the repetition of physical sounds to theoretically organized harmony and counterpoint. How are multidimensional regularities processed when we listen to music? The present study focuses on the redundant signals effect (RSE) as a novel approach to untangling the relationship between these regularities in music. The RSE refers to the occurrence of a shorter reaction time (RT) when two or three signals are presented simultaneously than when only one of these signals is presented, and provides evidence that these signals are processed concurrently. In two experiments, chords that deviated from tonal (harmonic) and acoustic (intensity and timbre) regularities were presented occasionally in the final position of short chord sequences. The participants were asked to detect all deviant chords while withholding their responses to non-deviant chords (i.e., the Go/NoGo task). RSEs were observed in all double- and triple-deviant combinations, reflecting processing of multidimensional regularities. Further analyses suggested evidence of coactivation by separate perceptual modules in the combination of tonal and acoustic deviants, but not in the combination of two acoustic deviants. These results imply that tonal and acoustic regularities are different enough to be processed as two discrete pieces of information. Examining the underlying process of RSE may elucidate the relationship between multidimensional regularity processing in music.

MORPHOLOGICAL AND NRDNA-ITS SEQUENCES-BASED IDENTIFICATION AND DISTRIBUTION OF VOLVOPLUTEUS EARLEI IN PAKISTAN

Volvopluteus is represented by seven species distributed in America, Asia and Europe. They occur in the tropical regions growing as saprobes on wood debris and leaves, in grassy fields and forests. To explore the macrofungal diversity, different localities in Punjab were visited and collections were made. Among these several collections were found similar to Volvopluteus species. They were analyzed morphologically and phylogenetically using ITS sequences of nrDNA. Comparative analysis on the basis of morphological and anatomical features revealed that these collections represent V. earlei . Maximum likelihood phylogeny also showed the position of current sequences in a same clade with already known V. earlei sequences with 74% bootstrap value. Volvopluteus earlei is being described from different areas of Pakistan with variety of climatic conditions from warm semi-arid climate of Kasur, Lahore and Sheikhupura districts, humid subtropical climate of Sialkot district, in Punjab and warm semi-arid to humid subtropical climate of Swat district, Khyber Pakhtunkhwa. The occurrence of V. earlei in different climatic zones represents its wide distribution range and ecological amplitude in the country.