Typical Sequence Research Articles

Negative target stimuli do not influence cross-modal auditory distraction.

The present study served to test whether emotion modulates auditory distraction in a serial-order reconstruction task. If auditory distraction results from an attentional trade-off between the targets and distractors, auditory distraction should decrease when attention is focused on targets with high negative arousal. Two experiments (with a total N of 284 participants) were conducted to test whether auditory distraction is influenced by target emotion. In Experiment 1 it was examined whether two benchmark effects of auditory distraction—the auditory-deviant effect and the changing-state effect—differ as a function of whether negative high-arousal targets or neutral low-arousal targets are used. Experiment 2 complements Experiment 1 by testing whether target emotion modulates the disruptive effects of reversed sentential speech and steady-state distractor sequences relative to a quiet control condition. Even though the serial order of negative high-arousal targets was better remembered than that of neutral low-arousal targets, demonstrating an emotional facilitation effect on serial-order reconstruction, auditory distraction was not modulated by target emotion. The results provide support of the automatic-capture account according to which auditory distraction, regardless of the specific type of auditory distractor sequence that has to be ignored, is a fundamentally stimulus-driven effect that is rooted in the automatic processing of the to-be-ignored auditory stream and remains unaffected by emotional-motivational factors.

A time series analysis model of the relationship between psychoacoustic parameters of urban soundscape spatial sequences and emotional changes.

A listening test was conducted with 32 participants to obtain data on emotional changes in response to three types of urban soundscape spatial sequences. By establishing a time series model, the relationship between psychoacoustic parameters of the sequence and changes in the two dimensions of emotion was determined. Results showed that psychoacoustic parameters can explain 44% and 40%-49% of the changes in the pleasantness and arousal dimensions of emotion, respectively. Roughness and fluctuation have the highest correlation with emotional changes, while loudness and articulation index have the lowest correlation with emotional changes. This research verified the lags between psychoacoustic changes in the soundscape and the associated perceived emotion. First, there was a 3-4 s lag between psychoacoustic parameters and emotional changes. Second, changes in roughness and loudness could cause synchronous changes in emotions, while other parameters could cause delayed changes in emotions. Finally, the lag of emotion had a strong and stable explanatory power for emotional changes. This research proves the effectiveness of the time series analysis technology in establishing the dynamic relationship between the acoustic parameters of soundscape sequences and the second-by-second perceived emotions and provides a new data analysis method for in-depth study of soundscape sequence perception.

Aging of galaxies along the morphological sequence, marked by bulge growth and disk quenching

Aims. We revisit the color bimodality of galaxies using the extensive EFIGI morphological classification of nearby galaxies. Methods. The galaxy profiles from the Sloan Digital Sky Survey (SDSS) gri images were decomposed as a bulge and a disk by controlled profile modeling with the Euclid SourceXtractor++ software. The spectral energy distributions from our resulting gri SDSS photometry complemented with Galaxy Evolution Explorer (GALEX) NUV photometry were fitted with the ZPEG software and PEGASE.2 templates in order to estimate the stellar masses and specific star formation rates (sSFR) of whole galaxies as well as their bulge and disk components. Results. The absolute NUV−r color versus stellar mass diagram shows a continuous relationship between the present sSFR of galaxies and their stellar mass, which spans all morphological types of the Hubble sequence monotonously. Irregular galaxies to intermediate-type Sab spirals make up the “Blue Cloud” across 4 orders of magnitude in stellar mass but a narrow range of sSFR. This mass build-up of spiral galaxies requires major mergers, in agreement with their frequently perturbed isophotes. At high mass, the Blue Cloud leads to the “Green Plain”, dominated by S0a and Sa early-type spirals. It was formerly called the “Green Valley”, due to its low density, but we rename it because of its wide stretch and nearly flat density over ∼2 mag in NUV−r color (hence sSFR), despite a limited range of stellar mass (1 order of magnitude). The Green Plain links up the “Red Sequence”, containing all lenticular and elliptical galaxies with a 2 order of magnitude mass interval, and systematically higher masses for the ellipticals. We confirm that the Green Plain cannot be studied using u − r optical colors because it is overlayed by the Red Sequence, hence NUV data are necessary. Galaxies across the Green Plain undergo a marked growth by a factor 2 to 3 in their bulge-to-total mass ratio and a systematic profile change from pseudo to classical bulges, as well as a significant reddening due to star formation fading in their disks. The Green Plain is also characterized by a maximum stellar mass of 1011.7 M⊙ beyond which only elliptical galaxies exist, hence supporting the scenario of ellipticals partly forming by major mergers of massive disk galaxies. Conclusions. The EFIGI attributes indicate that dynamical processes (spiral arms and isophote distortions) contribute to the scatter of the Main Sequence of star-forming galaxies (Blue Cloud), via the enhancement of star formation (flocculence, HII regions). The significant bulge growth across the Green Plain confirms that it is a transition region, and excludes a predominantly quick transit due to rapid quenching. The high frequency of bars for all spirals as well as the stronger spiral arms and flocculence in the knee of the Green Plain suggest that internal dynamics, likely triggered by flybys or (mainly minor) mergers, may be the key to the bulge growth of massive disk galaxies, which is a marker of the aging of galaxies from star forming to quiescence. The Hubble sequence can then be considered as an inverse sequence of galaxy physical evolution.

From raw measurements to human pose - a dataset with low-cost and high-end inertial-magnetic sensor data

Wearable technology is expanding for motion monitoring. However, open challenges still limit its widespread use, especially in low-cost systems. Most solutions are either expensive commercial products or lower performance ad-hoc systems. Moreover, few datasets are available for the development of complete and general solutions. This work presents 2 datasets, with low-cost and high-end Magnetic, Angular Rate, and Gravity(MARG) sensor data. Provides data for the complete inertial pose pipeline analysis, starting from raw data, sensor-to-segment calibration, multi-sensor fusion, skeleton-kinematics, to complete Human pose. Contains data from 21 and 10 participants, respectively, performing 6 types of sequences, presenting high variability and complex dynamics with almost complete range-of-motion. Amounts to 3.5 M samples, synchronized with a ground-truth inertial motion capture system. Presents a method to evaluate data quality. This database may contribute to develop novel algorithms for each pipeline’s processing steps, with applications in inertial pose estimation algorithms, human movement forecasting, and motion assessment in industrial or rehabilitation settings. All data and code to process and analyze the complete pipeline is freely available.

Sustaining shifts in science teaching through a research–practice partnership

AbstractThis study examines shifts in science teachers' (N = 15) beliefs and practices within the context of a research–practice partnership (RPP) that developed and implemented curriculum modules in middle school science classrooms. Interview, document, and observation data gathered over the course of the project indicate that the vast majority of teachers intended to continue using the curriculum modules in their classrooms for the foreseeable future. These data also documented potential shifts in teacher attitudes and practices inspired by the modules. Among teacher participants, there were clear examples of teachers modifying other lesson plans to resemble key components of the modules, using module implementation as a context for developing proficiency with inquiry‐oriented teaching, and revisiting or drawing connections to the modules when teaching other science content. The study also documented the typical sequence of shifts in teachers' beliefs and practices, with findings indicating that teacher beliefs were most powerfully influenced by their observations of student performance and engagement during module implementation. By following teachers' beliefs and practices beyond the official implementation timeline of the project, the study lends insight into the ways in which curriculum resources developed in the context of RPPs may have a lasting impact at the classroom level.

A study protocol to prepare an RBD protein for vaccine against COVID-19

Background: SARS-CoV-2 pandemic is a global threat to humans and the world’s economy. Effective and safe vaccines against this virus are essential to control and eradicate the pandemic. The currently applied vaccines carry SARS-CoV-2 spike-protein mRNA/cDNA. These vaccines go through several cellular processes in the recipients for producing antigens. On the contrary, the SARS-CoV-2 RBD (receptor binding domain)-protein is an antigen. It will directly stimulate antibody production against SARS-CoV-2. Hence, we propose to produce SARS-CoV-2 RBD-protein as a fast acting, effective and safe vaccine. Methods: We propose to reconstruct a plasmid carrying three types of DNA sequences: RBD cDNA, FP (fusion peptide) DNA and sfGFP(superfolder-green-fluorescent-protein), cDNA creating the RBD-FP-sfGFP DNA within an orf (open-reading-frame). Escherichia coli, C2566H, transformed with the reconstructed plasmid will express RBD-FP-sfGFP fusion protein producing green fluorescent cfu (colony forming unit). The RBD-protein will be separated from the sfGFP using an FP specific enterokinase, and eluted by HIC (hydrophobic-interaction-chromatography), detected with a BioVision-Elisa-Kit, and quantified by spectrophotometry at UV280nm and immune simulation will be carried out using C57BL mice. Results: The plasmid reconstruct will carry ampr (ampicillin-resistant) gene as a selective marker and a T7 promoter controlling the expression of RBD-FP-sfGFP fusion protein. The transformed Escherichia coli will efficiently express the RBD-FP-sfGFP fusion protein. The highly efficient sfGFP fused within the RBD-FP-sfGFP will produce green fluorescent cfu. The RBD-FP-sfGFP protein extract from the green cfu, digested by enterokinase and separated by the HIC will produce pure immunoreactive RBD protein. Conclusion: A positive BioVision-ELISA test detects <10 pg RBD protein/ml of the sample. A larger sample of the purified RBD protein can be used as a vaccine following a standard formulation and safety protocols. Once administered, the RBD protein will stimulate antibody production against the SARS-CoV-2 virus. The RBD protein has no potential to recombine with human genome.

Contribution of ICTs to the Down Syndrome Children’s Language and Cognitive Development

Down syndrome is considered to be one of the most prevalent genetic causes of intellectual disability, derived from chromosomal disorder, which accounts for dysfunctions in many organs and has a characteristic phenotype, which consists of physical and behavioral features. Many studies have shown that language is one of the most impaired areas of function in Down syndrome and perhaps, the highest barrier for their substantial inclusion into formal education and community. The aim of this paper is to investigate the specific features of this linguistic phenotype, presenting the strengths and weaknesses of their language, as well as the factors that contribute to their formation, compared to normally developing children. In addition, it scopes to highlight the role of educational mobile apps, as innovative and interactive tools for the developmental learning of Down syndrome children. The results of the research indicate that their language goes through the same, with typical development sequences, but progressively erases a slowing trajectory and results in lower performance. However, the use of ICT tools can, significantly, improve language, literacy and sort-term memory skills, but also stimulate their cognitive and fine mobile functioning, in order to upgrade their quality of life.

The impact of bleaching on the yield of softwood kraft pulps obtained by high alkali impregnation

AbstractHigh alkali impregnation (HAI) increases the total yield of softwood pulps following kraft cooking. This yield improvement is also maintained after oxygen delignification. This study evaluates how bleaching with either chlorine dioxide or hydrogen peroxide affects the final yield of samples obtained with standard and HAI. The chemical composition, viscosity, brightness, mechanical and morphological properties were studied. Compared to cooking after standard impregnation the yield improvement achieved by HAI was preserved in both types of bleaching sequences (2 % units for chlorine dioxide and 4 % units for hydrogen peroxide). The introduction of charged groups into the cellulose fibers was higher with hydrogen peroxide bleaching than with chlorine dioxide however, no significant impact was seen on the swelling or mechanical properties. The brightness was higher for the pulps bleached with chlorine dioxide compared with hydrogen peroxide. Hydrogen peroxide bleaching resulted in similar brightness development for both standard and HAI. Fibers bleached with chlorine dioxide had the highest curl index (16–17 %) compared to the fibers bleached with hydrogen peroxide (15 %).

Change over time in interactions between unfamiliar toddlers

The frequency and length of games, conflicts, and contingency sequences that took place between toddlers as they got to know one another were studied using archival data. The sample consisted of 28 unfamiliar 20- and 30-month-old toddlers (predominantly White, 16 males) who met separately with each of two other toddlers for 18 play dates. The frequency of games increased over time, while the frequency of conflict and contingency sequences decreased. The length of games increased over time while the length of conflicts and contingency sequences were stable. Age and language ability predicted changes in frequency and length of the different types of sequences. Thus, toddlers engage in less structured interactions when they first meet; their interactions become increasingly more organized and positive as the relationship evolves.

Delta-band neural tracking primarily reflects rule-based chunking instead of semantic relatedness between words.

It is debated whether cortical responses matching the time scales of phrases and sentences mediate the mental construction of the syntactic chunks or are simply caused by the semantic properties of words. Here, we investigate to what extent delta-band neural responses to speech can be explained by semantic relatedness between words. To dissociate the contribution of semantic relatedness from sentential structures, participants listened to sentence sequences and paired-word sequences in which semantically related words repeated at 1Hz. Semantic relatedness in the 2 types of sequences was quantified using a word2vec model that captured the semantic relation between words without considering sentential structure. The word2vec model predicted comparable 1-Hz responses with paired-word sequences and sentence sequences. However, empirical neural activity, recorded using magnetoencephalography, showed a weaker 1-Hz response to paired-word sequences than sentence sequences in a word-level task that did not require sentential processing. Furthermore, when listeners applied a task-related rule to parse paired-word sequences into multi-word chunks, 1-Hz response was stronger than that in word-level task on the same sequences. Our results suggest that cortical activity tracks multi-word chunks constructed by either syntactic rules or task-related rules, whereas the semantic relatedness between words contributes only in a minor way.

General guidelines for CRISPR/Cas-based genome editing in plants.

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T2 generation.

Ritualized disbelief in Mexican Spanish talk-in-interaction

Abstract The present investigation is a conversation-analytic study that examines a particular type of informing sequence where the new information is received with a turn displaying ritualized disbelief. In this paper, I analyze a range of ritualized disbelief and news-confirmation turn designs in Mexican Spanish talk: I describe the trajectory that different ritualized disbeliefs have, the composition of the disbelief they display, and how news-producers deal with ritualized disbelief turns. I argue that a speaker’s knowledge about the matter at hand relates to the type of disbelief expressed in his or her disbelieving turn; that is, the social actions involved in this type of sequences show a relationship between turn design, epistemics and disbelief.

Efficacy and Safety of Combined Brain Stereotactic Radiotherapy and Immune Checkpoint Inhibitors in Non-Small-Cell Lung Cancer with Brain Metastases.

Background: To analyze the outcomes of patients with brain metastases (BM) from non-small cell lung cancer (NSCLC) treated with immunotherapy (IT) and stereotactic radiotherapy (SRT) and to study the impact of the sequence between the two modalities. Methods: The authors reviewed the records of 51 patients with 84 BM from NSCLC treated at Institut Curie with IT and SRT. BM were categorized into three groups: ‘SRT before IT’, ‘concurrent SRT and IT’, and ‘SRT after IT.’ Regional progression-free interval (R-PFI) and overall survival (OS) were estimated using the Kaplan–Meier method. Results: After a median follow-up from SRT of 22.5 months (2.7–47.3), the 1-year and 2-year OS were 69.7% (95%CI [58.0–83.8]) and 44.0% [30.6–63.2], respectively. Concerning distant intracranial control, the 1-year and 2-year R-PFI were 40.1% [30.1–53.3] and 35.2% [25.1–49.4], respectively. Moreover, one-year R-PFI in ‘SRT before IT’, ‘concurrent SRT and IT’, and ‘SRT after IT’ groups were 24.1%, 49.6%, and 34.2%, respectively (p = 0.094). The type of therapeutic sequence did not appear to impact the risk of brain necrosis. Conclusions: The concurrent administration of SRT and IT appeared to offer the best locoregional control, without increasing the risk of toxicity, compared to patients treated with SRT before or after IT.

Digital Games for Down Syndrome Children’s Language and Cognitive Development

Down syndrome is considered to be one of the most prevalent genetic causes of intellectual disability, derived from chromosomal disorder, which accounts for dysfunctions in many organs and has a characteristic phenotype, which consists of physical and behavioral features. Many studies have shown that language is one of the most impaired areas of function in Down syndrome and perhaps, the highest barrier for their substantial inclusion into formal education and community. The aim of this paper is to investigate the specific features of this linguistic phenotype, presenting the strengths and weaknesses of their language, as well as the factors that contribute to their formation, compared to normally developing children. In addition, it scopes to highlight the role of educational mobile apps, as innovative and interactive tools for the developmental learning of Down syndrome children. The results of the research indicate that their language goes through the same, with typical development sequences, but progressively erases a slowing trajectory and results in lower performance. However, the use of digital games, especially virtual reality video games, can, significantly, improve their cognitive and fine mobile functioning and also the acquisition of literacy, language and math skills, in order to upgrade their quality of life.

Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics

AbstractNucleic acids play essential roles in some biological processes and nanotechnology. Understanding their structural elasticity is very important for biological functions. Differences in structural elasticity of RNA and DNA duplexes are investigated by all‐atom molecular dynamics in this work. Two models double‐strand (ds) B‐DNA and A‐RNA short sequences are used. For two typical sequences, bending persistence length, stretch, and twist modulus are analyzed and compared in detail. These results demonstrate that dsDNA has a smaller bending persistence length value than dsRNA, however, the former has about 2.6 times stretch modulus than the latter one and the twist modulus in the former is smaller than the latter. Furthermore, the microstructural parameter analysis indicates that the inclination angle of a single base pair and the dihedral angle between two bases in a base pair, as well as the slide between adjacent base pairs, influences the structural elasticities of these two types of nucleic acids. Results also show that the dsDNA has a positive stretch‐twist coupling parameter while the dsRNA has a negative stretch‐twist coupling parameter. Results offer research comprehensive comparing and understanding about structural elasticity of RNA and DNA and provide novel perspectives for grasping nucleic acids' elastic properties.

Mechanical Timer-Actuated Fluidic Dispensing System: Applications to an Automated Multistep Lateral Flow Immunoassay with High Sensitivity.

In this study, we present a fluidic dispensing system that can automate the sequential fluidic delivery of multiple reagents for lateral flow assays. Highly sensitive assays typically require multiple solution-based sequences, including washing steps and signal amplification. However, implementation of these types of sequences on an automated and highly sensitive point-of-care testing (POCT) platform remains challenging. Our platform consists of two disposable cartridges with reagent chambers and a test strip and an instrument that has a mechanical timer to actuate the cam-follower-gear components. The timer rotation sequentially shifts the position of the chambers and loads the reagents to the test paper strip. The dispensing intervals are controlled at a variation of <1% within a total actuation time of 60 min. Unlike other POCT devices, the timing of fluid delivery in our timer-actuated platform is not dependent on the selection of substrates and reagents, and the unique approach to fluidic delivery results in no reagent overlap or carryover, minimal reagent loss, and highly accurate fluidic timing control for highly sensitive solution-based assays. As a model application, the proposed platform applies a gold enhancement solution to amplify the detection signal and detect prostate-specific antigen with a limit of detection of 86 pg/mL within 27 min. This platform provides an opportunity for solution-based POCT applications with high sensitivity, thereby satisfying the requirement for user-friendly operations in resource-limited settings.

Estimating tree-based dynamic treatment regimes using observational data with restricted treatment sequences.

A dynamic treatment regime (DTR) is a sequence of decision rules that provide guidance on how to treat individuals based on their static and time-varying status. Existing observational data are often used to generate hypotheses about effective DTRs. A common challenge with observational data, however, is the need for analysts to consider "restrictions" on the treatment sequences. Such restrictions may be necessary for settings where (1) one or more treatment sequences that were offered to individuals when the data were collected are no longer considered viable in practice, (2) specific treatment sequences are no longer available, or (3) the scientific focus of the analysis concerns a specific type of treatment sequences (eg, "stepped-up" treatments). To address this challenge, we propose a restricted tree-based reinforcement learning (RT-RL) method that searches for an interpretable DTR with the maximum expected outcome, given a (set of) user-specified restriction(s), which specifies treatment options (at each stage) that ought not to be considered as part of the estimated tree-based DTR. In simulations, we evaluate the performance of RT-RL versus the standard approach of ignoring the partial data for individuals not following the (set of) restriction(s). The method is illustrated using an observational data set to estimate a two-stage stepped-up DTR for guiding the level of care placement for adolescents with substance usedisorder.

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.

Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10-25 kilobases), accurate 'HiFi' reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus generation, pbccs, uses a hidden Markov model. We introduce DeepConsensus, which uses an alignment-based loss to train a gap-aware transformer-encoder for sequence correction. Compared to pbccs, DeepConsensus reduces read errors by 42%. This increases the yield of PacBio HiFi reads at Q20 by 9%, at Q30 by 27% and at Q40 by 90%. With two SMRT Cells of HG003, reads from DeepConsensus improve hifiasm assembly contiguity (NG50 4.9 megabases (Mb) to 17.2 Mb), increase gene completeness (94% to 97%), reduce the false gene duplication rate (1.1% to 0.5%), improve assembly base accuracy (Q43 to Q45) and reduce variant-calling errors by 24%. DeepConsensus models could be trained to the general problem of analyzing the alignment of other types of sequences, such as unique molecular identifiers or genome assemblies.

Using Excel Mapper to Design Chromosome Idiograms

Idiograms are graphical representations in which chromosomes appear ordered by their relative size, homology groups, and the presence of cytogenetic landmarks such as centromeres, secondary constrictions, and banding patterns. They have become crucial elements in cytogenetic research. Here, we describe a simple protocol for spreadsheet software to draw idiograms and map any type of sequence onto them. These graphs can be easily used to present research results and can become the basis to raise and resolve questions related to different biological issues. The methodology is inexpensive, easy to follow, and allows customization to meet a wide range of educational scenarios focused in genetics and evolution.

Transition metal-free fluorocyclization of unsaturated N-methoxyamides gives cyclic N-methoxyimidates

A new class of fluorinated, cyclic N-methoxyimidates was prepared by the intramolecular fluorocyclization of unsaturated N-methoxyamides. The reaction combined unsaturated amides, a monofluoroiodane, and HFIP as the activator, and this induced an intramolecular fluorocyclization expeditiously at room temperature, giving the products in up to 81% yield in a single step. Two product isomers were chemoselectively produced, depending on whether or not an α-arene substituent was present, in which case the typical reaction sequence was interrupted by a 1,2-phenyl shift prior to the final fluorination step.