Sequence Preference Research Articles

Comparison of the efficacy of neoadjuvant chemotherapy with FLOT regimen and adjuvant chemotherapy with XELOX/FOLFOX regimen in patients with locally advanced gastric cancer: A retrospective study

Background. To date, there is no consensus on the preferred sequence of combined treatment in patients with locally advanced gastric cancer (perioperative chemotherapy – POCT or primary surgical treatment). No direct comparison of these approaches had been conducted before. Aim. To compare, in retrospective analysis, 3-year relapse-free (RFS) and overall survival (OS) in patients receiving POCT FLOT or adjuvant chemotherapy XELOX/FOLFOX for locally advanced gastric cancer. Materials and methods. The assessment included 153 patients who underwent POCT FLOT and 171 patients who underwent surgical treatment at the first stage. When evaluating the initial characteristics, it was shown that patients with ECOG (The Eastern Cooperative Oncology Group) stage 1-2, clinical stage cT4a-b, cN2-3 and Bormann type 4 to were significantly more common in the POCT group. Morphological characteristics: grade, presence of signet cell carcinoma, HER2/neu overexpression, microsatellite instability, sensitivity to immunotherapy (Combined Positive Score) didn't differ. Results. With a median follow-up of 40 months, it was shown that the long-term results assessed in all included patients were better in the group with primary surgical treatment: 3-year RFS was 55 and 40% (risk ratio – RR 1.33, 95% confidence interval – CI 1.08–1.64; р=0.007). 3-year OS was 68 and 56% (RR 1.36, 95% CI 1.02–1.8; р=0.04), respectively. However, when evaluating patients who received surgical treatment in the POCT group (n=121, 79%), the results did not differ: 3-year RFS 55 and 50% (RR 0.9, 95% CI 0.71–1.16; р=0.97), 3-year OS 68 and 63% (RR 1.1, 95% CI 0.84–1.59; р=0.97). Insufficient volume of adjuvant chemotherapy (75% of the dose) significantly worsened long-term results (3-year OS 43 and 71%; p=0.002). Conclusion. The obtained data of a retrospective analysis did not reveal the advantages of any of the approaches provided that the surgical stage was performed in patients receiving POCT. To obtain more objective results, it is necessary to conduct randomized multicenter studies in the high volume centers, providing the necessary sample capacity, quality of diagnosis and treatment. Thus, the design of future studies should be based on the hypothesis of non-inferiority, which inevitably entails a significant increase in the required number of observations to obtain reliable sampling power.

DNA-Encoded Noncanonical Substrate Library for Protease Profiling.

Profiling the substrate sequence preferences of proteases is important for understanding both biological functions as well as for designing protease inhibitors. Several methods are available for profiling the sequence specificity of proteases. However, there is currently no rapid and high-throughput method to profile specificity of proteases for noncanonical substrates. In this study, we described a strategy to use a DNA-encoded noncanonical substrate library to identify the protease substrates composed of both canonical and noncanonical amino acids. This approach uses a DNA-encoded peptide library and introduces a biotin molecule at the N-terminus to immobilize the library on a solid support. Upon protease hydrolysis, the released DNA tag of the substrate peptides can be sequenced to identify the substrate structures. Using this approach, we profiled trypsin and fibroblast activation protein α and discovered noncanonical substrates that were more efficiently cleaved than the commonly used substrates. The identified substrates of FAP were further used to design corresponding covalent inhibitors containing non-canonical sequences with high potency for the target protease. Overall, our approach can aid in the development of new protease substrates and inhibitors.

Alternative substrate kinetics of SARS-CoV-2 Nsp15 endonuclease reveals a specificity landscape dominated by RNA structure.

Coronavirus endoribonuclease Nsp15 contributes to the evasion of host innate immunity by suppressing levels of viral dsRNA. Nsp15 cleaves both ssRNA and dsRNA in vitro with a strong preference for unpaired or bulged U residues, and its activity is stimulated by divalent ions. Here, we systematically quantified effects of RNA sequence and structure context that define its specificity. The results show that sequence preference for U↓A/G, observed previously, contributes only ca. 2-fold to kcat/Km. In contrast, dsRNA structure flanking a bulged U residue increases kcat/Km by an order of magnitude compared to ssRNA while base pairing in dsRNA essentially blocks cleavage. Despite enormous differences in multiple turnover kinetics, the effect of RNA structure on the cleavage step is minimal. Surprisingly, although divalent ion activation of Nsp15 is widely considered to be important for its biological function, the effect on kcat/Km is only ∼2-fold and independent of RNA structure. These results reveal a specificity landscape dominated by RNA structure and provide a quantitative framework for identifying interactions that underlie specificity, determining mechanisms of inhibition and resistance and defining targets important for coronavirus biology.

Comparison of Echo Planar and Turbo Spin Echo Diffusion-Weighted Imaging in Intraoperative MRI.

Diffusion-weighted imaging (DWI) is routinely used in brain tumor surgery guided by intraoperative MRI (IoMRI). However, conventional echo planar imaging DWI (EPI-DWI) is susceptible to distortion and artifacts that affect image quality. Turbo spin echo DWI (TSE-DWI) is an alternative technique with minimal spatial distortions that has the potential to be the radiologically preferred sequence. To compare via single- and multisequence assessment EPI-DWI and TSE-DWI in the IoMRI setting to determine whether there is a radiological preference for either sequence. Retrospective. Thirty-four patients (22 female) aged 2-61 years (24 under 18 years) undergoing IoMRI during surgical resection of intracranial tumors. 3-T, EPI-DWI, and TSE-DWI. Patients were scanned with EPI- and TSE-DWI as part of the standard IoMRI scanning protocol. A single-sequence assessment of spatial distortion and image artifact was performed by three neuroradiologists blinded to the sequence type. Images were scored regarding distortion and artifacts, around and remote to the resection cavity. A multisequence radiological assessment was performed by three neuroradiologists in full radiological context including all other IoMRI sequences from each case. The DWI images were directly compared with scorings of the radiologists on which they preferred with respect to anatomy, abnormality, artifact, and overall preference. Wilcoxon signed-rank tests for single-sequence assessment, weighted kappa for single and multisequence assessment. A P-value <0.001 was considered statistically significant. For the blinded single-sequence assessment, the TSE-DWI sequence was scored equal to or superior to the EPI-DWI sequence for distortion and artifacts, around and remote to the resection cavity for every case. In the multisequence assessment, all radiologists independently expressed a preference for TSE-DWI over EPI-DWI sequences on viewing brain anatomy, abnormalities, and artifacts. The TSE-DWI sequences may be favored over EPI-DWI for IoMRI in patients with intracranial tumors. 2 TECHNICAL EFFICACY: Stage 5.

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.

SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5'-TCGGAT-3') of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B.

DNA methyltransferase 3B (DNMT3B) plays a crucial role in DNA methylation during mammalian development. Mutations in DNMT3B are associated with human genetic diseases, particularly immunodeficiency, centromere instability, facial anomalies (ICF) syndrome. Although ICF syndrome-related missense mutations in the DNMT3B have been identified, their precise impact on protein structure and function remains inadequately explored. Here, we delve into the impact of four ICF syndrome-linked mutations situated in the DNMT3B dimeric interface (H814R, D817G, V818M, and R823G), revealing that each of these mutations compromises DNA-binding and methyltransferase activities to varying degrees. We further show that H814R, D817G, and V818M mutations severely disrupt the proper assembly of DNMT3B homodimer, whereas R823G does not. We also determined the first crystal structure of the methyltransferase domain of DNMT3B-DNMT3L tetrameric complex hosting the R823G mutation showing that the R823G mutant displays diminished hydrogen bonding interactions around T775, K777, G823, and Q827 in the protein-DNA interface, resulting in reduced DNA-binding affinity and a shift in sequence preference of +1 to +3 flanking positions. Altogether, our study uncovers a wide array of fundamental defects triggered by DNMT3B mutations, including the disassembly of DNMT3B dimers, reduced DNA-binding capacity, and alterations in flanking sequence preferences, leading to aberrant DNA hypomethylation and ICF syndrome.

Regulation of bacterial virulence genes by PecS family transcription factors.

Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.

Vps4 substrate binding and coupled mechanisms of Vps4p substrate recruitment and release from autoinhibition.

The ESCRT pathway's AAA+ ATPase, Vps4p, remodels ESCRT-III complexes to drive membrane fission. Here, we use peptide binding assays to further the understanding of substrate specificity and the mechanism of autoinhibition. Our results reveal unexpected sequence preference to the substrate binding groove and an elegant mechanism of regulation that couples localization to substrate with release from autoinhibition.

Should the pricing or advertising decision come first in a supply chain with a network externality?

PurposeThis paper aims to study how the timing of these decisions affects the total profit and the individual profits of the two agents.Design/methodology/approachThis paper study a supply chain for a network good where there is a manufacturer and a retailer. The manufacturer determines its wholesale price and its share in the retailer’s advertising cost while the retailer decides the retail price and the advertising cost.FindingsThis paper finds that a stronger network externality leads to higher prices and higher advertising efforts. This increases the profits of both manufacturer and retailer, but the manufacturer’s share of advertising costs depends on the order in which the supply chain enterprise make their decisions, the strength of network externality and the effect of advertising determines which decision timeline results in a higher price and greater advertising effort. The manufacturer prefers the price decision to be made before the advertising decision, while the retailer prefers these decisions to be made simultaneously.Research limitations/implicationsAlthough this paper studies the price and advertising decision-making order preferences of channel members based on network externalities, this research can also be expanded from the following aspects based on network effects. First, network externality affects advertising cooperation between both parties in the situation such that the pricing power of retail prices is transferred from the retailer to the manufacturer and the retailer relies on revenue sharing (revenue sharing contract, nonwholesale price contract. Second, the manufacturer dominates the issues in the supply chain, but in reality, a retailer can also be the dominator or there are no dominators (Nash equilibrium). Finally, it is possible to consider pricing and advertising decisions in situations where two manufacturers or retailers compete.Practical implicationsWhen the price is reasonable, advertising investment is the main determinant of product sales. The greater the intensity of network externalities the more retailers will be willing to invest in advertising. An increase in the intensity of network externalities may not necessarily enhance manufacturers’ motivation or cooperative advertising, but it depends on the decision-making sequence. The strength of network externalities determines the decision-making sequence preferences of supply chain channel members whose preferences vary leading to conflicts of interest.Originality/valueThe impact of cooperative advertising or decision sequence on corporate decision-making has not been considered. To fill this gap, the paper integrates network externality and supply chain cooperative advertising models, focusing on the impact of network externality on pricing and advertising decisions, as well as on the sequence of decisions.

Heritable Tissue-Culture-Free Gene Editing in Nicotiana benthamiana through Viral Delivery of SpCas9 and sgRNA.

Conventional plant gene editing requires laborious tissue-culture-mediated transformation, which restricts the range of applicable plant species. In this study, we developed a heritable and tissue-culture-free gene editing method in Nicotiana benthamiana using tobacco ringspot virus (TRSV) as a vector for in planta delivery of Cas9 and single-guide RNA (sgRNA) to shoot apical meristems. Agrobacterium-mediated inoculation of the TRSV vector induced systemic and heritable gene editing in NbPDS. Transient downregulation of RNA silencing enhanced gene editing efficiency, resulting in an order of magnitude increase (0.8% to 13.2%) in the frequency of transgenerational gene editing. While the TRSV system had a preference for certain sgRNA sequences, co-inoculation of a TRSV vector carrying only Cas9 and a tobacco rattle virus vector carrying sgRNA successfully introduced systemic mutations with all five tested sgRNAs. Extensively gene-edited lateral shoots occasionally grew from plants inoculated with the virus vectors, of which the transgenerational gene editing frequency ranged up to 100%. This virus-mediated heritable gene editing method makes plant gene editing easy, requiring only the inoculation of non-transgenic plants with a virus vector(s) to obtain gene-edited individuals.

Tensile properties and damage behaviors of the prepreg-RTM co-cured composite bolted T-joint with a novel configuration

The tensile properties and damage behaviors of prepreg-resin transfer molding (RTM) co-cured composite bolted T-joints, consisting of an internal skeleton and an external skin, were investigated through experimental and numerical methods. With the validated finite element model, the effects of adding load-carrying beams, the corner radius and the stacking sequence were investigated. Results indicate that the novel T-joint, weighing only 55.7% of an equivalent sized 2A12 aluminum T-joint, can achieve 82% of the aluminum T-joint’s tensile stiffness and 107% of its proportional limit load. Damage in the joint initiates near the bolt holes and leads to delamination failure within the skeleton. With load-carrying beams including bolt holes, the tensile stiffness and ultimate load increase to 1.11 and 1.51 times that of the original configuration, respectively, with the final failure mode shifting to the fracture of the base panel. With the final failure mode unchanged, the ultimate load remains essentially unchanged with increasing the corner radius. Under tensile loads, the preferred stacking sequence for the skeleton is [0/+45/90/−45]nS. For the skin, the greater the number of ±45° plies, the higher the ultimate load, while the greater the number of 90° plies, the higher the tensile stiffness.

Chemoradiotherapy plus induction or consolidation chemotherapy as total neoadjuvant therapy for locally advanced rectal cancer: Pooled analysis of the CAO/ARO/AIO-12 and the OPRA randomized phase 2 trials

Total neoadjuvant therapy (TNT) has been used for patients with locally advanced rectal cancer. The optimal sequence of chemoradiotherapy (CRT) and chemotherapy (CT) is a matter of debate. We performed a pooled analysis of the CAO/ARO/AIO-12 and OPRA multicenter, randomized phase 2 trials to identify patient subsets that could benefit from one TNT sequence over the other regarding disease-free survival (DFS). Patients with stage II/III rectal cancer were randomized to CRT (50.4-54Gy) with either induction (INCT-CRT) or consolidation CT (CRT-CNCT) with fluorouracil, leucovorin, oxaliplatin (CAO/ARO/AIO-12 and OPRA) or capecitabine and oxaliplatin (OPRA) followed by mandatory total mesorectal excision (TME) (CAO/ARO/AIO-12) or selective watch-and-wait surveillance (OPRA). 311 and 324 patients were recruited from June 15, 2015 to January 31, 2018; and from April 12, 2014 to March 30, 2020 in the two trials, respectively. Pretreatment clinical and tumor characteristics included were age, sex, ECOG, cT-category, cN-category, clinical UICC stage, location from anal verge, and tumor grade. In total, 628 eligible patients were included in the pooled analysis (CAO/ARO/AIO-12, n=304; OPRA, n=324). Of those, 313 were randomly assigned to the INCT-CRT group, and 315 to the CRT-CNCT group. Median follow-up was 43 months (IQR, 35-49) months in the CAO/ARO/AIO-12 trial and 61,2 months (IQR, 42-68,4) in the OPRA trial. Pooled analysis of baseline clinical and tumor characteristics did not identify any subgroups of patients that would benefit by the one TNT sequence over the other with regard to DFS. To our knowledge, this is the first pooled analysis of two randomized trials after direct head-to-head comparison of both TNT sequences. Both trials reported higher rates of complete response with CRT-CNCT, and this should be considered the preferred TNT sequence if organ preservation is a priority.

Customized decentralized autonomous organization based optimal energy management for smart buildings

In recent years, the unprecedented rising urbanization level and proliferation of distributed energy sources (DES) are motivating the transition of smart building from consumer to prosumer. In the context of mitigating upstream emission via reducing reliance on utility grids, the key challenge becomes realizing autonomous and economically optimal energy management within smart buildings. This paper innovatively proposes a Decentralized Autonomous Organization (DAO)-based energy management framework for smart buildings, where the mechanism of day-ahead scheduling DAO considering peer-to-peer (P2P) energy sharing is specifically investigated. Besides, a sequential preference satisfaction mechanism is designed to customize participants’ special demands, thereby achieving effective energy matching. Considering potential communication failures between buildings in practical operations, this study develops a communication failure robust distributed algorithm to minimize operational costs and safeguard building’s privacy. Extensive numerical studies for highly DES penetrated smart buildings successfully offers an operation cost reduction of 33.7% when considering preference satisfaction and P2P energy sharing in the day-ahead scheduling problem. Simulation results also demonstrates that the algorithm in this work excels in resisting potential communication failure during operation.

Expanding the Genome-Editing Toolbox with Abyssicoccus albus Cas9 Using a Unique Protospacer Adjacent Motif Sequence.

The genome-editing efficiency of the CRISPR-Cas9 system hinges on the recognition of the protospacer adjacent motif (PAM) sequence, which is essential for Cas9 binding to DNA. The commonly used Streptococcus pyogenes (SpyCas9) targets the 5'-NGG-3' PAM sequence, which does not cover all the potential genomic-editing sites. To expand the toolbox for genome editing, SpyCas9 has been engineered to recognize flexible PAM sequences and Cas9 orthologs have been used to recognize novel PAM sequences. In this study, Abyssicoccus albus Cas9 (AalCas9, 1059 aa), which is smaller than SpyCas9, was found to recognize a unique 5'-NNACR-3' PAM sequence. Modification of the guide RNA sequence improved the efficiency of AalCas9-mediated genome editing in both plant and human cells. Predicted structure-assisted introduction of a point mutation in the putative PAM recognition site shifted the sequence preference of AalCas9. These results provide insights into Cas9 diversity and novel tools for genome editing.

Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.

Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.

VOC Characterization of Byasa hedistus (Lepidoptera: Papilionidae) and Its Visual and Olfactory Responses during Foraging and Courtship.

Color and odor are crucial cues for butterflies during foraging and courtship. While most sexual dimorphic butterflies rely more on vision, our understanding of how butterflies with similar coloration use different signals remains limited. This study investigated the visual and olfactory behavioral responses of the similarly colored butterfly Byasa hedistus during foraging and courtship. While visiting artificial flowers of different colors, we found that B. hedistus exhibits an innate color preference, with a sequence of preferences for red, purple, and blue. The frequency of flower visits by B. hedistus significantly increased when honey water was sprayed on the artificial flowers, but it hardly visited apetalous branches with honey water. This proves that locating nectar sources by odor alone is difficult in the absence of floral color guides. During courtship, males are active while females hardly chase; only two models were observed: males chasing males and males chasing females. The courtship process includes four behaviors: slowing approach, straight chasing, hovering, and spinning. B. hedistus cannot distinguish between sexes based on color, as there is no significant difference in color and shape between them. Twenty-three VOCs (>1%) were identified in B. hedistus, with 21 shared by both sexes, while ketones are specific to males. These VOCs are principally represented by cineole, β-pinene, and linalool. When cineole was added to butterfly mimics, many butterflies were attracted to them, but the butterflies did not seem to distinguish between males and females. This suggests that cineole may be the feature VOC for identifying conspecific groups. Adding β-pinene and linalool to mimics induced numerous butterflies to chase, hover, spin around, and attempt to mate with them. This suggests that β-pinene and linalool are crucial cues indicating the presence of females.

Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations.

Human topoisomerase III beta (hTOP3B) is the only topoisomerase in the human cell that can act on both DNA and RNA substrates. Recent findings have emphasized the physiological importance of hTOP3B and consolidated it as a valuable drug target for antiviral and anticancer therapeutics. Although type IA topoisomerases of different organisms have been studied over the years, the step-by-step interaction of hTOP3B and nucleic acid substrates is still not well understood. Due to the lack of hTOP3B-RNA structures as well as DNA/RNA covalent complexes, computational investigations have been limited. In our study, we utilized molecular dynamics (MD) simulations to study the interactions between hTOP3B and nucleic acids to get a closer look into the residues that play a role in binding DNA or RNA and facilitate catalysis, along with the differences and similarities when hTOP3B interacts with DNA compared to RNA. For this, we generated multiple models of hTOP3B complexed with DNA and RNA sequences using the hTOP3B crystal structure and 8-mer single-stranded DNA and RNA sequences. These models include both covalent and noncovalent complexes, which are then subjected to MD simulations and analyzed. Our findings highlight the complexes' stability, sequence preference, and interactions of the binding pocket residues with different nucleotides. Our work demonstrates that hTOP3B forms stable complexes with both DNA and RNA and provides a better understanding of the enzyme's interaction with different nucleic acid substrate sequences.

Sequence-specific targeting of intrinsically disordered protein regions.

A general approach to design proteins that bind tightly and specifically to intrinsically disordered regions (IDRs) of proteins and flexible peptides would have wide application in biological research, therapeutics, and diagnosis. However, the lack of defined structures and the high variability in sequence and conformational preferences has complicated such efforts. We sought to develop a method combining biophysical principles with deep learning to readily generate binders for any disordered sequence. Instead of assuming a fixed regular structure for the target, general recognition is achieved by threading the query sequence through diverse extended binding modes in hundreds of templates with varying pocket depths and spacings, followed by RFdiffusion refinement to optimize the binder-target fit. We tested the method by designing binders to 39 highly diverse unstructured targets. Experimental testing of ∼36 designs per target yielded binders with affinities better than 100 nM in 34 cases, and in the pM range in four cases. The co-crystal structure of a designed binder in complex with dynorphin A is closely consistent with the design model. All by all binding experiments for 20 designs binding diverse targets show they are highly specific for the intended targets, with no crosstalk even for the closely related dynorphin A and dynorphin B. Our approach thus could provide a general solution to the intrinsically disordered protein and peptide recognition problem.

Natural noise management in collaborative recommender systems over time-related information

Recommender systems are currently a suitable alternative for providing easy and appropriate access to information for users in today’s digital information-overloaded world. However, an important drawback of these systems is the inconsistent behavior of users in providing item preferences. To address this issue, several natural noise management (NNM) approaches have been proposed, which positively influence recommendation accuracy. However, a major limitation of such previous works is the disregarding of the time-related information coupled to the rating data in RSs. Based on this motivation, this paper proposes two novel methods, named SeqNNM and SeqNNM-p for NNM focused on an incremental, time-aware recommender system scenario that has not yet been considered, by performing a classification-based NNM over specific preference sequences, driven by their associated timestamps. Such methods have been evaluated by simulating a real-time scenario and using metrics such as mean absolute error, root-mean-square error, precision, recall, NDCG, number of modified ratings, and running time. The obtained experimental results show that in the used settings, it is possible to achieve better recommendation accuracy with a low intrusion degree. Furthermore, the main innovation associated with the overall contribution is the screening of natural noise management approaches to be used on specific preferences subsets, and not over the whole dataset as discussed by previous authors. These proposed approaches allow the use of natural noise management in large datasets, in which it would be very difficult to correct the entire data.

Advances in mapping analysis of ribonucleic acid modifications through sequencing

Over 170 chemical modifications have been discovered in various types of ribonucleic acids (RNAs), including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). These RNA modifications play crucial roles in a wide range of biological processes such as gene expression regulation, RNA stability maintenance, and protein translation. RNA modifications represent a new dimension of gene expression regulation known as the "epitranscriptome". The discovery of RNA modifications and the relevant writers, erasers, and readers provides an important basis for studies on the dynamic regulation and physiological functions of RNA modifications. Owing to the development of detection technologies for RNA modifications, studies on RNA epitranscriptomes have progressed to the single-base resolution, multilayer, and full-coverage stage. Transcriptome-wide methods help discover new RNA modification sites and are of great importance for elucidating the molecular regulatory mechanisms of epitranscriptomics, exploring the disease associations of RNA modifications, and understanding their clinical applications. The existing RNA modification sequencing technologies can be categorized according to the pretreatment approach and sequencing principle as direct high-throughput sequencing, antibody-enrichment sequencing, enzyme-assisted sequencing, chemical labeling-assisted sequencing, metabolic labeling sequencing, and nanopore sequencing technologies. These methods, as well as studies on the functions of RNA modifications, have greatly expanded our understanding of epitranscriptomics. In this review, we summarize the recent progress in RNA modification detection technologies, focusing on the basic principles, advantages, and limitations of different methods. Direct high-throughput sequencing methods do not require complex RNA pretreatment and allow for the mapping of RNA modifications using conventional RNA sequencing methods. However, only a few RNA modifications can be analyzed by high-throughput sequencing. Antibody enrichment followed by high-throughput sequencing has emerged as a crucial approach for mapping RNA modifications, significantly advancing the understanding of RNA modifications and their regulatory functions in different species. However, the resolution of antibody-enrichment sequencing is limited to approximately 100-200 bp. Although chemical crosslinking techniques can achieve single-base resolution, these methods are often complex, and the specificity of the antibodies used in these methods has raised concerns. In particular, the issue of off-target binding by the antibodies requires urgent attention. Enzyme-assisted sequencing has improved the accuracy of the localization analysis of RNA modifications and enables stoichiometric detection with single-base resolution. However, the enzymes used in this technique show poor reactivity, specificity, and sequence preference. Chemical labeling sequencing has become a widely used approach for profiling RNA modifications, particularly by altering reverse transcription (RT) signatures such as RT stops, misincorporations, and deletions. Chemical-assisted sequencing provides a sequence-independent RNA modification detection strategy that enables the localization of multiple RNA modifications. Additionally, when combined with the biotin-streptavidin affinity method, low-abundance RNA modifications can be enriched and detected. Nevertheless, the specificity of many chemical reactions remains problematic, and the development of specific reaction probes for particular modifications should continue in the future to achieve the precise localization of RNA modifications. As an indirect localization method, metabolic labeling sequencing specifically localizes the sites at which modifying enzymes act, which is of great significance in the study of RNA modification functions. However, this method is limited by the intracellular labeling of RNA and cannot be applied to biological samples such as clinical tissues and blood samples. Nanopore sequencing is a direct RNA-sequencing method that does not require RT or the polymerase chain reaction (PCR). However, challenges in analyzing the data obtained from nanopore sequencing, such as the high rate of false positives, must be resolved. Discussing sequencing analysis methods for various types of RNA modifications is instructive for the future development of novel RNA modification mapping technologies, and will aid studies on the functions of RNA modifications across the entire transcriptome.