Steps In Experiment Research Articles

Garden of forking paths in ERP research - Effects of varying pre-processing and analysis steps in an N400 experiment.

This study tackles the Garden of Forking Paths, as a challenge for replicability and reproducibility of ERP studies. Here, we applied a multiverse analysis to a sample ERP N400 dataset, donated by an independent research team. We analyzed this dataset using 14 pipelines selected to showcase the full range of methodological variability found in the N400 literature using systematic review approach. The selected pipelines were compared in depth by looking into statistical test outcomes, descriptive statistics, effect size, data quality, and statistical power. In this way we provide a worked example of how analytic flexibility can impact results in research fields with high dimensionality such as ERP, when analyzed using standard null-hypothesis significance testing. Out of the methodological decisions that were varied, high-pass filter cut-off, artifact removal method, baseline duration, reference, measurement latency and locations, and amplitude measure (peak vs. mean) were all shown to affect at least some of the study outcome measures. Low-pass filtering was the only step which did not notably influence any of these measures. This study shows that even some of the seemingly minor procedural deviations can influence the conclusions of an ERP study. We demonstrate the power of multiverse analysis in both identifying the most reliable effects in a given study, and for providing insights into consequences of methodological decisions.

Cross-Modal Interactions Between Auditory Attention and Oculomotor Control.

Microsaccades are small, involuntary eye movements that occur during fixation. Their role is debated with recent hypotheses proposing a contribution to automatic scene sampling. Microsaccadic inhibition (MSI) refers to the abrupt suppression of microsaccades, typically evoked within 0.1 s after new stimulus onset. The functional significance and neural underpinnings of MSI are subjects of ongoing research. It has been suggested that MSI is a component of the brain's attentional re-orienting network which facilitates the allocation of attention to new environmental occurrences by reducing disruptions or shifts in gaze that could interfere with processing. The extent to which MSI is reflexive or influenced by top-down mechanisms remains debated. We developed a task that examines the impact of auditory top-down attention on MSI, allowing us to disentangle ocular dynamics from visual sensory processing. Participants (N = 24 and 27; both sexes) listened to two simultaneous streams of tones and were instructed to attend to one stream while detecting specific task "targets." We quantified MSI in response to occasional task-irrelevant events presented in both the attended and unattended streams (frequency steps in Experiment 1, omissions in Experiment 2). The results show that initial stages of MSI are not affected by auditory attention. However, later stages (∼0.25 s postevent onset), affecting the extent and duration of the inhibition, are enhanced for sounds in the attended stream compared to the unattended stream. These findings provide converging evidence for the reflexive nature of early MSI stages and robustly demonstrate the involvement of auditory attention in modulating the later stages.

Gait improvement with wearable cyborg HAL trunk unit for parkinsonian patients: five case reports

Cybernic treatment involves the generation of an interactive bio-feedback loop between an individual’s nervous system and the worn cyborg Hybrid Assistive Limb (HAL); this treatment has been applied for several intractable neuromuscular disorders. Thus, it is of interest to determine its potential for parkinsonian patients. This study confirmed the feasibility of using a HAL trunk unit to improve parkinsonian gait disturbance. HAL establishes functional and physical synchronization with the wearer by providing lateral cyclic forces to the chest in the form of somatosensory and motor cues. To confirm the feasibility of its use for improving parkinsonian gait disturbances, we conducted experiments with three Parkinson’s disease patients and two patients with progressive supranuclear palsy. During the experiments, the immediate effect of the intervention was assessed; all participants exhibited improvements in gait disturbance while wearing the HAL unit, and this improvement effect persisted without the HAL unit in two participants. Afterward, based on the assessment, we conducted a continuous intervention for one participant. In this intervention, the number of steps in the final experiment was significantly decreased compared with the initial state. These findings suggest that the proposed method is an option for treating parkinsonian patients to generate somatosensory and motor cues.

Evaluating two steps in transcription using a fluorescence-based electrophoretic mobility shift assay.

Transcription is the critical first step in expressing a gene, during which an RNA polymerase (RNAP) synthesizes an RNA copy of one strand of the DNA that encodes a gene. Here we describe a laboratory experiment that uses a single assay to probe two important steps in transcription: (1) RNAP binding to DNA, and (2) the transcriptional activity of the polymerase. Students probe both these steps in a single experiment using a fluorescence-based electrophoretic mobility shift assay (EMSA) and commercially available Escherichia coli RNAP. As an inquiry-driven component, students add the transcriptional inhibitor rifampicin to reactions and draw conclusions about its mechanism of inhibition by determining whether it blocks polymerase binding to DNA or transcriptional activity. Depending on the curriculum and learning goals of individual courses, this experimental module could be easily expanded to include additional experimentation that mimics a research environment more closely. After completing the experiment students understand basic principles of transcription, mechanisms of inhibition, and the use of EMSAs to probe protein/DNA interactions.

Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew?

Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry such as agriculture, biomanufacturing, and medicine. This technology is enabled by an ever-growing portfolio of biomolecular reagents that span the central dogma, from DNA to RNA to protein. In this paper, we draw from our unique perspective as the National Metrology Institute of the United States to bring attention to the importance of understanding and reporting genome editing formulations accurately and promoting concepts to verify successful delivery into cells. Achieving the correct understanding may be hindered by the way units, quantities, and stoichiometries are reported in the field. We highlight the variability in how editing formulations are reported in the literature and examine how a reference molecule could be used to verify the delivery of a reagent into cells. We provide recommendations on how more accurate reporting of editing formulations and more careful verification of the steps in an editing experiment can help set baseline expectations of reagent performance, toward the aim of enabling genome editing studies to be more reproducible. We conclude with a future outlook on technologies that can further our control and enable our understanding of genome editing outcomes at the single-cell level.

Modeling Atom Interferometry Experiments with Bose–Einstein Condensates in Power-Law Potentials

Recent atom interferometry (AI) experiments involving Bose–Einstein condensates (BECs) have been conducted under extreme conditions of volume and interrogation time. Numerical solution of the rotating-frame Gross–Pitaevskii equation (RFGPE), which is the standard mean-field theory applied to these experiments, is impractical due to the excessive computation time and memory required. We present a variational model that provides approximate solutions of the RFGPE for a power-law potential on a practical time scale. This model is well-suited to the design and analysis of AI experiments involving BECs that are split and later recombined to form an interference pattern. We derive the equations of motion of the variational parameters for this model and illustrate how the model can be applied to the sequence of steps in a recent AI experiment where BECs were used to implement a dual-Sagnac atom interferometer rotation sensor. We use this model to investigate the impact of finite-size and interaction effects on the single-Sagnac-interferometer phase shift.

An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis.

The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP‐Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome‐wide histone modification patterns and transcription factor‐binding sites alike. Here, we established a ChIP‐Seq framework for Chr. zofingiensis yielding over 20 million high‐quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA–protein cross‐linking. We used this ChIP‐Seq framework to generate a genome‐wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA‐Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP‐Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis.

Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates.

In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low-cost device is presented that functions as a cover for 96-well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi-crystal screening campaigns.

Using 3Ds Max Application Create An Eyeball

This paper represents an experiment report of VR (Virtual Reality) and AR (Augmented Reality) for medical learners. Four main purposes of this experiment through 3Ds Max application create an eyeball. The environment of experiment also be discussed. As well as the studies of organ in medical points of view. Two parts, two objects and three modifications as core activities for representing anatomical studies. More details about creation in experiment essential features demonstrated consequently. Thirty steps in experiment, descriptions show with screenshots. Output of this experiments would be able to understand medical learner’s anatomical perspective studies, as well as medical educators introduce organ and medical knowledge to no-medical learners. Combining VR and AR to medical learning activities, as well as clinical presentations. This paper no only practices the application 3Ds Max create organ models, but also medical learning perspective discussion.

Modification of the Step Potential Electrochemical Spectroscopy Analysis Protocol to Improve Outcomes

Here we present an improved methodology for the analysis of i-t transients collected as part of step potential electrochemical spectroscopy (SPECS) experiments. This approach is improved over previous methodologies because it takes into consideration interactions between i-t transients resulting from subsequent potential steps in the SPECS experiment. The improved output of the new methodology is demonstrated with simulated and experimental data. The revised methodology also highlights the independence of non-faradaic charge storage processes, as compared to faradaic processes in which case i-t transients are demonstrated to have an inherent contribution from previous steps in the SPECS experiment.

SpliceTAPyR — An Efficient Method for Transcriptome Alignment

RNA-Seq is a Next-Generation Sequencing (NGS) protocol for sequencing the messenger RNA in a cell and generates millions of short sequence fragments, reads, in a single run. These reads can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS reads to the reference genome. Because RNA-Seq reads can span over more than one exon in the genome, this task is challenging. In the last decade, tools for RNA-Seq alignment have emerged, but most of them run in two phases. First, the pipeline only maps reads that have a direct match in the reference, and the remaining are set aside as initially unmapped reads. Then, they use heuristics based approaches, clustering or even annotations, to decide where to align the later. This work presents an efficient computational solution for the problem of transcriptome alignment, named SpliceTAPyR. It identifies signals of splice junctions and relies on compressed full-text indexing methods and succinct data structures to efficiently align RNA-Seq reads in a single phase. This way it achieves the same or better accuracy than other tools while using considerably less memory and time to the most competitive tools.

Syringe-injectable Mesh Electronics for Stable Chronic Rodent Electrophysiology

Implantable brain electrophysiology probes are valuable tools in neuroscience due to their ability to record neural activity with high spatiotemporal resolution from shallow and deep brain regions. Their use has been hindered, however, by mechanical and structural mismatches between the probes and brain tissue that commonly lead to micromotion and gliosis with resulting signal instability in chronic recording experiments. In contrast, following the implantation of ultraflexible mesh electronics via syringe injection, the mesh probes form a seamless, gliosis-free interface with the surrounding brain tissue that enables stable tracking of individual neurons on at least a year timescale. This protocol details the key steps in a typical mouse neural recording experiment using syringe-injectable mesh electronics, including the fabrication of mesh electronics in a standard photolithography-based process possible at many universities, loading mesh electronics into standard capillary needles, stereotaxic injection in vivo, connection of the mesh input/output to standard instrumentation interfaces, restrained or freely moving recording sessions, and histological sectioning of brain tissue containing mesh electronics. Representative neural recordings and histology data are presented. Investigators familiar with this protocol will have the knowledge necessary to incorporate mesh electronics into their own experiments and take advantage of the unique opportunities afforded by long-term stable neural interfacing, such as studies of aging processes, brain development, and the pathogenesis of brain disease.

Syringe-injectable Mesh Electronics for Stable Chronic Rodent Electrophysiology.

Implantable brain electrophysiology probes are valuable tools in neuroscience due to their ability to record neural activity with high spatiotemporal resolution from shallow and deep brain regions. Their use has been hindered, however, by mechanical and structural mismatches between the probes and brain tissue that commonly lead to micromotion and gliosis with resulting signal instability in chronic recording experiments. In contrast, following the implantation of ultraflexible mesh electronics via syringe injection, the mesh probes form a seamless, gliosis-free interface with the surrounding brain tissue that enables stable tracking of individual neurons on at least a year timescale. This protocol details the key steps in a typical mouse neural recording experiment using syringe-injectable mesh electronics, including the fabrication of mesh electronics in a standard photolithography-based process possible at many universities, loading mesh electronics into standard capillary needles, stereotaxic injection in vivo, connection of the mesh input/output to standard instrumentation interfaces, restrained or freely moving recording sessions, and histological sectioning of brain tissue containing mesh electronics. Representative neural recordings and histology data are presented. Investigators familiar with this protocol will have the knowledge necessary to incorporate mesh electronics into their own experiments and take advantage of the unique opportunities afforded by long-term stable neural interfacing, such as studies of aging processes, brain development, and the pathogenesis of brain disease.

Methods for processing high-throughput RNA sequencing data.

High-throughput sequencing (HTS) methods for analyzing RNA populations (RNA-Seq) are gaining rapid application to many experimental situations. The steps in an RNA-Seq experiment require thought and planning, especially because the expense in time and materials is currently higher and the protocols are far less routine than those used for other high-throughput methods, such as microarrays. As always, good experimental design will make analysis and interpretation easier. Having a clear biological question, an idea about the best way to do the experiment, and an understanding of the number of replicates needed will make the entire process more satisfying. Whether the goal is capturing transcriptome complexity from a tissue or identifying small fragments of RNA cross-linked to a protein of interest, conversion of the RNA to cDNA followed by direct sequencing using the latest methods is a developing practice, with new technical modifications and applications appearing every day. Even more rapid are the development and improvement of methods for analysis of the very large amounts of data that arrive at the end of an RNA-Seq experiment, making considerations regarding reproducibility, validation, visualization, and interpretation increasingly important. This introduction is designed to review and emphasize a pathway of analysis from experimental design through data presentation that is likely to be successful, with the recognition that better methods are right around the corner.

Attenuated and Protease-Profile Modified Sendai Virus Vectors as a New Tool for Virotherapy of Solid Tumors

Multiple types of oncolytic viruses are currently under investigation in clinical trials. To optimize therapeutic outcomes it is believed that the plethora of different tumor types will require a diversity of different virus types. Sendai virus (SeV), a murine parainfluenza virus, displays a broad host range, enters cells within minutes and already has been applied safely as a gene transfer vector in gene therapy patients. However, SeV spreading naturally is abrogated in human cells due to a lack of virus activating proteases. To enable oncolytic applications of SeV we here engineered a set of novel recombinant vectors by a two-step approach: (i) introduction of an ubiquitously recognized cleavage-motive into SeV fusion protein now enabling continuous spreading in human tissues, and (ii) profound attenuation of these rSeV by the knockout of viral immune modulating accessory proteins. When employing human hepatoma cell lines, newly generated SeV variants now reached high titers and induced a profound tumor cell lysis. In contrast, virus release from untransformed human fibroblasts or primary human hepatocytes was found to be reduced by about three log steps in a time course experiment which enables the cumulation of kinetic differences of the distinct phases of viral replication such as primary target cell infection, target cell replication, and progeny virus particle release. In a hepatoma xenograft animal model we found a tumor-specific spreading of our novel recombinant SeV vectors without evidence of biodistribution into non-malignant tissues. In conclusion, we successfully developed novel tumor-selective oncolytic rSeV vectors, constituting a new tool for virotherapy of solid tumors being ready for further preclinical and clinical development to address distinct tumor types.

Natural and synthetic zeolites in adsorption/oxidation processes to remove surfactant molecules from water

Iron-containing zeolites were studied as adsorbents and heterogeneous Fenton-like catalysts for the removal of the non-ionic surfactant Triton® X-100 (TX-100) from water. Adsorption tests included a variety of zeolites with different structure types (ZSM5, Beta and Y) and SiO2/Al2O3 ratios. Zeolites with 12-membered-ring channels and high molar ratio of SiO2/Al2O3, indicating higher surface hydrophobicity, proved to be the most suitable adsorbents for TX-100. For preparation of iron-loaded zeolites, a Beta zeolite with a molar ratio of SiO2/Al2O3 of 200 was selected, based on its excellent adsorption properties, and compared with a natural zeolite of clinoptilolite type. Batch experiments indicated that both Fe-zeolites are active in the heterogeneous Fenton-like oxidation of TX-100 at neutral pH. However, the synthetic Fe-Beta zeolite was preferable compared to the Fe-loaded natural zeolite with respect to catalytic activity and H2O2 utilization efficiency, which was interpreted in terms of differences in iron speciation and adsorption properties towards TX-100. Fe-Beta (200) was successfully applied in two cycles of adsorption/oxidation steps in a column experiment. This study shows that Fe-loaded Beta zeolites with high hydrophobicity can be suitable materials for a combined approach of adsorption/wet peroxide oxidation of chemicals with relatively high molecular weight and chain-like molecule structure, such as the non-ionic surfactant TX-100.

The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards

The apparent handedness of an EM-tomography reconstruction depends on a number of conventions and can be confused in many ways. As the number of different hardware and software combinations being used for electron tomography continue to climb, and the reconstructions being produced reach higher and higher resolutions, the need to verify the hand of the results has increased. Here we enumerate various steps in a typical tomography experiment that affect handedness and show that DNA origami gold nanoparticle helices can be used as convenient and fail-safe handedness standards.

Shelter effect evaluation of the willow works bank protection method: a case study for Beinan River Reach 2009 Typhoon Morakot event

Beinan River is one of the rivers with perfect ecology and full of culture values in Taiwan. It is also the habitat of many freshwater fish species. Besides, the local agricultural crops are famous for exports due to its natural environment, too. Therefore, for these reasons, the hydraulic associations set a series of ecological constructions for waterfowl and fish species around the agricultural water intake areas. For instance, the river bank protection designs the willow works and the fascine mattress by the 8th River Management Bureau for ecological function and hydraulic protection in flood season. In this study, the concept and the methodology of the fish protection habitat predicted model is revealed. Beside the simulated hydraulic models, the indoor experiments of the willow works were conducted to gain the roughness. The hydraulic methods by one- and two-dimensional are used for simulation in flood season (2009 Typhoon Morakot event) to bring up the habitat protection locations. The experimental results showed that for the Manning’s n of the willow works is between 0.1322 and 0.1333 which corresponding height to the real field is about 144–176 cm. Therefore, it provided the revetment roughness data during the shelter effect evaluation. From the velocity distribution, it proves that the vegetated revetment can reduce the flow velocity. Fulfilling previous two main steps in experiment and model calibration, the shelter effect is made good going on discussion. Most of references indicated that the vegetated revetment provided suitable and excellent habitat condition, but rare of them provided the proof in data. This study presents that the WUA is 34,939.94 m2 and PUA is 1.53% at the highest discharge of Typhoon Morakot. The whole protection concepts, simulation methods, and results can be utilized for future plan and design of river engineering.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

BackgroundSince its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology.ResultWe introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site.This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser.ConclusionsTargeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html

Stabilities of Trityl‐Protected Substrates: The Wide Mechanistic Spectrum of Trityl Ester Hydrolyses

Ionization rates of para-substituted triphenylmethyl (trityl) acetates, benzoates, and para-nitrobenzoates have been determined in aqueous acetonitrile and aqueous acetone at 25 degrees C. Conventional and stopped-flow techniques have been used to evaluate rate constants ranging from 1.38 x 10(-5) to 2.15 x 10(2) s(-1) by conductimetry and photospectrometry methods. The varying stabilities of the differently substituted tritylium ions account for a gradual change of reaction mechanism. Poorly stabilized carbocations are generated slowly by the ionization of their covalent precursors and trapped fast by water. Better stabilized carbocations are generated more rapidly and accumulate, so that ionization and trapping by water can be observed as separate steps in a single experiment. Finally, highly stabilized tritylium ions do not react with water, and only the rates of their formation could be measured. The ionization rate constants correlate linearly with Winstein's ionizing powers Y; the low slopes (0.17<m<0.58) indicate non-carbocation-like transition states. While the correlation between the ionization rates and Hammett-Brown's sigma(+) parameters is excellent for symmetrically substituted tritylium derivatives, deviations for unsymmetrically substituted systems are observed. The failing rate-equilibrium relationship between the rates of ionizations (log k(ion)) and the stabilities of the carbocations in aqueous solution (pK(R(+))) may be explained by the late development of resonance between a p-amino group and the carbocationic center of the tritylium ion during the ionization process.