An In-depth Exploration of the Interplay between fMRI Methods and Theory in Cognitive Neuroscience.

Functional magnetic resonance imaging (fMRI) has been a cornerstone of cognitive neuroscience since its invention in the 1990s. The methods that we use for fMRI data analysis allow us to test different theories of the brain, thus different analyses can lead us to different conclusions about how the brain produces cognition. There has been a centuries-long debate about the nature of neural processing, with some theories arguing for functional specialization or localization (e.g., face and scene processing) while other theories suggest that cognition is implemented in distributed representations across many neurons and brain regions. Importantly, these theories have received support via different types of analyses; therefore, having students implement hands-on data analysis to explore the results of different fMRI analyses can allow them to take a firsthand approach to thinking about highly influential theories in cognitive neuroscience. Moreover, these explorations allow students to see that there are not clearcut "right" or "wrong" answers in cognitive neuroscience, rather we effectively instantiate assumptions within our analytical approaches that can lead us to different conclusions. Here, I provide Python code that uses freely available software and data to teach students how to analyze fMRI data using traditional activation analysis and machine-learning-based multivariate pattern analysis (MVPA). Altogether, these resources help teach students about the paramount importance of methodology in shaping our theories of the brain, and I believe they will be helpful for introductory undergraduate courses, graduate-level courses, and as a first analysis for people working in labs that use fMRI.

VirtMRI: A Tool for Teaching MRI.

Magnetic resonance image formation is not trivial and remains a difficult subject for teaching. Therefore, we saw an urgent need to facilitate teaching by developing a practical and easily accessible MR image generator. Due to the increasing interest in X-nuclei MRI, sodium image generation is also offered. The tool is implemented as a web application that is compatible with all standard desktop browsers and is open source. The user interface focuses on the parameters needed for the creation and display of the resulting images. Available MR sequences range from the standard Spin Echo and Inversion Recovery over steady-state to conventional sodium and more advanced single and triple quantum sequences. Additionally, the user interface has parameters to alter the resolution, the noise, and the k-space sampling. Our software is free to use and specifically suited for teaching purposes.

Toward a Structural Health Monitoring Methodology for Concrete Structures under Dynamic Loads Using Embedded FBG Sensors and Strain Mapping Techniques.

A data-driven-based methodology for SHM in reinforced concrete structures using embedded fiber optic sensors and pattern recognition techniques is presented. A prototype of a reinforced concrete structure was built and instrumented in a novel fashion with FBGs bonded directly to the reinforcing steel bars, which, in turn, were embedded into the concrete structure. The structure was dynamically loaded using a shaker. Superficial positive damages were induced using bonded thin steel plates. Data for pristine and damaged states were acquired. Classifiers based on Mahalanobis' distance of the covariance data matrix were developed for both supervised and unsupervised pattern recognition with an accuracy of up to 98%. It was demonstrated that the proposed sensing scheme in conjunction with the developed supervised and unsupervised pattern recognition techniques allows the detection of slight stiffness changes promoted by damages, even when strains are very small and the changes of these associated with the damage occurrence may seem negligible.

mmSIM: an open toolbox for accessible structured illumination microscopy.

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.

The case for free and open source software in research and scholarship.

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other 'open' initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability-including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of 'open source' as 'open code' is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Active fractions of mannoproteins derived from yeast cell wall stimulate innate and acquired immunity of adult and elderly dogs.

Nutritional intervention in older dogs aims to increase lifespan and improve life quality as well as delay the development of diseases related to ageing. It is believed that active fractions of mannoproteins (AFMs) obtained through extraction and fractionation of yeast cell walls (Saccharomyces cerevisiae) may beneficially modulate the immune system. However, studies that have evaluated this component and the effects of ageing on the immune system of dogs are scarce. This study aimed to evaluate the immunological effects of AFMs in adult and elderly dogs. Three extruded iso-nutrient experimental diets were formulated: without addition of AFM (T0); with AFM at 400 mg/kg (T400); and with AFM at 800 mg/kg (T800). Thirty-six beagle dogs were used, and six experimental treatments, resulting in combinations of age (adult and elderly) and diet (T0, T400, and T800), were evaluated. On days zero, 14, and 28, blood samples were obtained for leucocyte phenotyping and phagocytosis assays. On days zero and 28, a lymphoproliferation test, quantification of reactive oxygen (H2O2) and nitrogen (NO) intermediate production, evaluation of faecal immunoglobulin A (IgA) content, and a delayed cutaneous hypersensitivity test (DCHT) were performed. Statistical analyses were performed with SAS software. Repeated measure variance analyses were performed, and means were compared by the Tukey test. Values of P ≤ 0.05 were considered significant, and values of P ≤ 0.10 were considered tendencies. Dogs fed T400 tended to have higher neutrophilic phagocytic activity than dogs fed T800 (P = 0.073). Regarding reactive oxygen intermediates, bacterial lipopolysaccharide (LPS)-stimulated neutrophils from animals that were fed T400 had a tendency to produce more H2O2 than those from animals fed the control diet (P = 0.093). Elderly dogs, when compared to adult dogs, had lower absolute T and B lymphocyte counts, lower auxiliary T lymphocyte counts, and higher cytotoxic T lymphocyte counts (P < 0.05). A significant effect of diet, age, and time with saline inoculation was noted for the DCHT. There was no effect of diet or age on faecal IgA content in dogs. This study suggests beneficial effects of mannoproteins on the specific and nonspecific immune responses in adult and elderly dogs.

An open-source geospatial framework for beach litter monitoring.

Here, we present a framework for a beach litter monitoring process, based on free and open-source software (FOSS), which allows customization for any sampling design. The framework was developed by means of a GIS project (QGIS), a GIS collector (QField), and an R code, allowing further adjustments according to the area to be surveyed and research questions. The aim is to improve data collection, accessibility, and interoperability, as well as to help to fill the currently existing gap between fieldwork and data analysis, preventing typos and allowing better data processing. Therefore, it is expected to take less than an hour from ending fieldwork to obtaining up-to-date products. To test the developed open-source geospatial framework, it was applied in different sectors and dates on an important southern Brazilian touristic beach. Results obtained from the open-source geospatial framework application produce baseline information on beach litter issues, such as amounts, sources, and spatial and temporal patterns. Adoption of the framework can facilitate data collection by local and regional stakeholders, and the results obtained from it can be applied to support management strategies. For researchers, it produces spatialized data for each item in an already tidy format, which can be used for robust and complex models. A series of supplementary files support reproducibility and provide a guide to future users.

An overview of levan-degrading enzyme from microbes.

Functional carbohydrates are ideal substitutes for table sugar and make up a large share of the worldwide functional food market because of their numerous physiological benefits. Growing attention has been focused on levan, a ß-(2,6) fructan that possesses more favorable physicochemical properties, such as lower intrinsic viscosity and greater colloidal stability, than ß-(2,1) inulin. Levan can be used not only as a functional carbohydrate but also as feedstock for the production of levan-type fructooligosaccharides (L-FOSs). Three types of levan-degrading enzymes (LDEs), including levanase (EC 3.2.1.65), ß-(2,6)-fructan 6-levanbiohydrolase (LF2ase, EC 3.2.1.64), and levan fructotransferase (LFTase, EC 4.2.2.16), play significant roles in the biological production of L-FOSs. These three enzymes convert levan into different L-FOSs, levanbiose, and difructose anhydride IV (DFA IV), respectively. The prebiotic properties of both L-FOSs and DFA IV have been confirmed in recent years. Although levanase, LF2ase, and LFTase belong to the same O-glycoside hydrolase 32 family (GH32), their catalytic properties and product spectra differ significantly. In this paper, recent studies on these LDEs are reviewed, including those investigating microbial source and catalytic properties. Additionally, comparisons of LDEs, including those of their differing cleavage behavior and applications for different L-FOSs, are presented in detail.

Learning HL7 FHIR Using the HAPI FHIR Server and Its Use in Medical Imaging with the SIIM Dataset.

Health Level 7's (HL7's) new standard, FHIR (Fast Health Interoperability Resources), is setting healthcare information technology and medical imaging specifically ablaze with excitement. This paper aims to describe the protocol's advantages in some detail and explore an easy path for those unfamiliar with FHIR to begin learning the standard using free, open-source tools, namely the HL7 application programming interface (HAPI) FHIR server and the SIIM Hackathon Dataset.

Neuroimaging article reexecution and reproduction assessment system.

The value of research articles is increasingly contingent on complex data analysis results which substantiate their claims. Compared to data production, data analysis more readily lends itself to a higher standard of transparency and repeated operator-independent execution. This higher standard can be approached via fully reexecutable research outputs, which contain the entire instruction set for automatic end-to-end generation of an entire article from the earliest feasible provenance point. In this study, we make use of a peer-reviewed neuroimaging article which provides complete but fragile reexecution instructions, as a starting point to draft a new reexecution system which is both robust and portable. We render this system modular as a core design aspect, so that reexecutable article code, data, and environment specifications could potentially be substituted or adapted. In conjunction with this system, which forms the demonstrative product of this study, we detail the core challenges with full article reexecution and specify a number of best practices which permitted us to mitigate them. We further show how the capabilities of our system can subsequently be used to provide reproducibility assessments, both via simple statistical metrics and by visually highlighting divergent elements for human inspection. We argue that fully reexecutable articles are thus a feasible best practice, which can greatly enhance the understanding of data analysis variability and the trust in results. Lastly, we comment at length on the outlook for reexecutable research outputs and encourage re-use and derivation of the system produced herein.

Free and open-source software for object detection, size, and colour determination for use in plant phenotyping.

BACKGROUND: Object detection, size determination, and colour detection of images are tools commonly used in plant science. Key examples of this include identification of ripening stages of fruit such as tomatoes and the determination of chlorophyll content as an indicator of plant health. While methods exist for determining these important phenotypes, they often require proprietary software or require coding knowledge to adapt existing code. RESULTS: We provide a set of free and open-source Python scripts that, without any adaptation, are able to perform background correction and colour correction on images using a ColourChecker chart. Further scripts identify objects, use an object of known size to calibrate for size, and extract the average colour of objects in RGB, Lab, and YUV colour spaces. We use two examples to demonstrate the use of these scripts. We show the consistency of these scripts by imaging in four different lighting conditions, and then we use two examples to show how the scripts can be used. In the first example, we estimate the lycopene content in tomatoes (Solanum lycopersicum) var. Tiny Tim using fruit images and an exponential model to predict lycopene content. We demonstrate that three different cameras (a DSLR camera and two separate mobile phones) are all able to model lycopene content. The models that predict lycopene or chlorophyll need to be adjusted depending on the camera used. In the second example, we estimate the chlorophyll content of basil (Ocimum basilicum) using leaf images and an exponential model to predict chlorophyll content. CONCLUSION: A fast, cheap, non-destructive, and inexpensive method is provided for the determination of the size and colour of plant materials using a rig consisting of a lightbox, camera, and colour checker card and using free and open-source scripts that run in Python 3.8. This method accurately predicted the lycopene content in tomato fruit and the chlorophyll content in basil leaves.

Peatland dynamics: A review of process-based models and approaches.

Despite peatlands' important feedbacks on the climate and global biogeochemical cycles, predicting their dynamics involves many uncertainties and an overwhelming variety of available models. This paper reviews the most widely used process-based models for simulating peatlands' dynamics, i.e., the exchanges of energy and mass (water, carbon, and nitrogen). 'Peatlands' here refers to mires, fens, bogs, and peat swamps both intact and degraded. Using a systematic search (involving 4900 articles), 45 models were selected that appeared at least twice in the literature. The models were classified into four categories: terrestrial ecosystem models (biogeochemical and global dynamic vegetation models, n = 21), hydrological models (n = 14), land surface models (n = 7), and eco-hydrological models (n = 3), 18 of which featured "peatland-specific" modules. By analysing their corresponding publications (n = 231), we identified their proven applicability domains (hydrology and carbon cycles dominated) for different peatland types and climate zones (northern bogs and fens dominated). The studies range in scale from small plots to global, and from single events to millennia. Following a FOSS (Free Open-Source Software) and FAIR (Findable, Accessible, Interoperable, Reusable) assessment, the number of models was reduced to 12. Then, we conducted a technical review of the approaches and associated challenges, as well as the basic aspects of each model, e.g., spatiotemporal resolution, input/output data format and modularity. Our review streamlines the process of model selection and highlights: (i) standardization and coordination are required for both data exchange and model calibration/validation to facilitate intercomparison studies; and (ii) there are overlaps in the models' scopes and approaches, making it imperative to fully optimize the strengths of existing models rather than creating redundant ones. In this regard, we provide a futuristic outlook for a 'peatland community modelling platform' and suggest an international peatland modelling intercomparison project.

Tagging EEG features within exam reports to quickly generate databases for research purposes.

OBJECTIVE: assess the effectiveness of a new method for classifying EEG recording features through the use of tags within reports. We present feature prevalence in a sample of patients with toxic-metabolic encephalopathy and discuss the advantages of this approach over existing classification systems. METHODS: during EEG report creation, tags reflecting background activity, epileptiform features and periodic discharges were selected according to the findings of each recording. Reports including the tags have been collected and processed by the EEG report parser script written in PHP language. The resulting spreadsheet was analysed to calculate the prevalence and type of EEG features in a sample group of patients with toxic-metabolic encephalopathy. RESULTS: tag checking and extraction were very little time-consuming processes. Considering 5784 EEG recordings performed either in inpatients or outpatients over 2 years, toxic-metabolic aetiology was tagged in 218 (3.8 %). The most frequent background feature was severe slowing (5-6 Hz frequency), occurring in 79 (36.2 %). Epileptiform abnormalities were rare, reaching a maximum of 10 (4.6 %). Triphasic waves were tagged in 43 (19.7 %) recordings. CONCLUSIONS: tagging and parsing processes are very fast and integrated into the daily routine. Sample analysis in patients with toxic-metabolic encephalopathies showed EEG slowing as the prevalent feature, while triphasic waves occurred in a minority of recordings. Existing software such as "SCORE" (Holberg EEG) requires the replacement of the currently used software for EEG reporting, minimizing additional costs and training. EEG Report Parser is free and open-source software, so it can be freely adopted, modified and redistributed, allowing further improvement and adaptability.

An Automated Open-Source Workflow for Standards-Compliant Integration of Small Animal Magnetic Resonance Imaging Data.

Large-scale research integration is contingent on seamless access to data in standardized formats. Standards enable researchers to understand external experiment structures, pool results, and apply homogeneous preprocessing and analysis workflows. Particularly, they facilitate these features without the need for numerous potentially confounding compatibility add-ons. In small animal magnetic resonance imaging, an overwhelming proportion of data is acquired via the ParaVision software of the Bruker Corporation. The original data structure is predominantly transparent, but fundamentally incompatible with modern pipelines. Additionally, it sources metadata from free-field operator input, which diverges strongly between laboratories and researchers. In this article we present an open-source workflow which automatically converts and reposits data from the ParaVision structure into the widely supported and openly documented Brain Imaging Data Structure (BIDS). Complementing this workflow we also present operator guidelines for appropriate ParaVision data input, and a programmatic walk-through detailing how preexisting scans with uninterpretable metadata records can easily be made compliant after the acquisition.

Fructo-oligosaccharides from Morinda officinalis remodeled gut microbiota and alleviated depression features in a stress rat model.

BACKGROUND: Inulin-type fructo-oligosaccharides (FOSs) purified from Morinda officinalis How., an effective oral antidepressant for mild to moderate depression, have a largely unknown efficacy and poor bioavailability. PURPOSE: Therefore, the microbiota-gut-brain axis was used to investigate the antidepressive properties of FOSs at the interface of the gut microbiota (GM). STUDY DESIGN AND METHODS: FOSs was introduced via intragastric gavage to rats exposed to chronic unpredictable mild stress (CUMS), and the antidepressive effects were investigated through behavioral tests, intestinal morphology and corticosterone levels. Bacterial genomic DNA was extracted from feces, and the GM was profiled for using enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis, partial least squares-discriminant analysis (PLS-DA) and 16S rRNA gene pyrosequencing. RESULTS: It was observed that FOSs alleviated depression-like behaviors and repaired intestinal epithelia damages. FOSs treatment lowered corticosterone levels in the plasma and urine of the model rats. Moreover, the GM compositions of normal and model rats were distantly clustered and were mainly related to the disappearance of beneficial bacteria (e.g., Acinetobacter, Barnesiella, Coprococcus, Dialister, Lactobacillus, and Paenibacillus) and appearance of depression-associated bacteria (e.g., Anaerostipes, Oscillibacter, Proteobacteria, and Streptococcus) in depressive rats. Interestingly, the dysbiosis in depressive rats' gut was reinstated with FOSs treatments. Notably, FOSs promoted the abundance of the bacterial phylum Cyanobacteria, a group of bacteria known for the secretion of pharmacologically important metabolites, such as H2S, that exhibit antidepressant-like properties. Apparently, FOSs-induced modulation of GM was more antidepressive compared to a component of FOSs, degrees of polymerization (DP) 5, and fluoxetine, the standard antidepressant drug. CONCLUSION: In conclusion, this study implied that antidepressant efficacy of FOSs was inseparable from and strongly associated with the modulation of the host' s GM.

Comment on Experimental Determination of the Threshold Dose for Bifidogenic Activity of Dietary 1-Kestose in Rats. Foods 2020, 9, 4.

Currently, our group is undertaking a program trying to evaluate the bifidogenic effect/activity of different prebiotics and their dose-effect relationships [...].

Bottom-illuminated orbital shaker for microalgae cultivation.

A bottom-illuminated orbital shaker designed for the cultivation of microalgae suspensions is described in this open-source hardware report. The instrument agitates and illuminates microalgae suspensions grown inside flasks. It was optimized for low production cost, simplicity, low power consumption, design flexibility, consistent, and controllable growth light intensity. The illuminated orbital shaker is especially well suited for low-resource research laboratories and education. It is an alternative to commercial instruments for microalgae cultivation. It improves on typical do-it-yourself microalgae growth systems by offering consistent and well characterized illumination light intensity. The illuminated growth area is 20 cm × 15 cm, which is suitable for three T75 tissue culture flasks or six 100 ml Erlenmeyer flasks. The photosynthetic photon flux density, is variable in eight steps ( 26 - 800 µ mol · m - 2 · s - 1 ) and programmable in a 24-h light/dark cycle. The agitation speed is variable ( 0 - 210 RPM ). The overall material cost is around £300, including an entry-level orbital shaker. The build takes two days, requiring electronics and mechanical assembly capabilities. The instrument build is documented in a set of open-source protocols, design files, and source code. The design can be readily modified, scaled, and adapted for other orbital shakers and specific experimental requirements. The instrument function was validated by growing fresh-water microalgae Desmodesmus quadricauda and Chlorella vulgaris. The cultivation protocols, microalgae growth curves, and doubling times are included in this report.

Economic savings for scientific free and open source technology: A review.

Both the free and open source software (FOSS) as well as the distributed digital manufacturing of free and open source hardware (FOSH) has shown particular promise among scientists for developing custom scientific tools. Early research found substantial economic savings for these technologies, but as the open source design paradigm has grown by orders of magnitude it is possible that the savings observed in the early work was isolated to special cases. Today there are examples of open source technology for science in the vast majority of disciplines and several resources dedicated specifically to publishing them. Do the tremendous economic savings observed earlier hold today? To answer that question, this study evaluates free and open source technologies in the two repositories compared to proprietary functionally-equivalent tools as a function of their use of Arduino-based electronics, RepRap-class 3-D printing, as well as the combination of the two. The results of the review find overwhelming evidence for a wide range of scientific tools, that open source technologies provide economic savings of 87% compared to equivalent or lesser proprietary tools. These economic savings increased slightly to 89% for those that used Arduino technology and even more to 92% for those that used RepRap-class 3-D printing. Combining both Arduino and 3-D printing the savings averaged 94% for free and open source tools over commercial equivalents. The results provide strong evidence for financial support of open source hardware and software development for the sciences. Given the overwhelming economic advantages of free and open source technologies, it appears financially responsible to divert funding of proprietary scientific tools and their development in favor of FOSH. Policies were outlined that provide nations with a template for strategically harvesting the opportunities provided by the free and open source paradigm.

The chemfp project.

The chemfp project has had four main goals: (1) promote the FPS format as a text-based exchange format for dense binary cheminformatics fingerprints, (2) develop a high-performance implementation of the BitBound algorithm that could be used as an effective baseline to benchmark new similarity search implementations, (3) experiment with funding a pure open source software project through commercial sales, and (4) publish the results and lessons learned as a guide for future implementors. The FPS format has had only minor success, though it did influence development of the FPB binary format, which is faster to load but more complex. Both are summarized. The chemfp benchmark and the no-cost/open source version of chemfp are proposed as a reference baseline to evaluate the effectiveness of other similarity search tools. They are used to evaluate the faster commercial version of chemfp, which can test 130 million 1024-bit fingerprint Tanimotos per second on a single core of a standard x86-64 server machine. When combined with the BitBound algorithm, a k = 1000 nearest-neighbor search of the 1.8 million 2048-bit Morgan fingerprints of ChEMBL 24 averages 27 ms/query. The same search of 970 million PubChem fingerprints averages 220 ms/query, making chemfp one of the fastest CPU-based similarity search implementations. Modern CPUs are fast enough that memory bandwidth and latency are now important factors. Single-threaded search uses most of the available memory bandwidth. Sorting the fingerprints by popcount improves memory coherency, which when combined with 4 OpenMP threads makes it possible to construct an N × N similarity matrix for 1 million fingerprints in about 30 min. These observations may affect the interpretation of previous publications which assumed that search was strongly CPU bound. The chemfp project funding came from selling a purely open-source software product. Several product business models were tried, but none proved sustainable. Some of the experiences are discussed, in order to contribute to the ongoing conversation on the role of open source software in cheminformatics.

Minimizing adjuvant treatment after transoral robotic surgery through surgical margin revision and exclusion of radiographic extracapsular extension: A Prospective observational cohort study.

BACKGROUND: We investigated in a prospective cohort of patients treated with trans-oral robotic surgery (TORS) for oropharyngeal cancer (OPC), who were selected for the absence of radiographic extra-capsular extension (ECS) and surgically revised for inadequate margins, the possibility of reducing adjuvant radiation (RT)/chemo-radiation therapy (CRT) without jeopardizing tumor control and functional outcome. METHODS: We conducted a prospective observational cohort of patients treated with TORS for oropharyngeal cancer. RESULTS: Twenty-nine patients with T1/2N0 to N2B stage cancers were treated with TORS. Forty-five percent of them were treated for secondary primaries. Nine of 29 patients (31%) were revised for close/positive margins. Adjuvant RT was prescribed for 2 of 19 patients with early squamous cell carcinoma (SCCs) and CRT for 1 of 10 patients with advanced oropharyngeal SCCs. Overall survival (OS), disease-specific survival (DSS), and locoregional control at 2 years were 85%, 96%, and 93%, respectively. Posttreatment Functional Outcome Swallowing Scale (FOSS) scores worsened with prior or adjuvant RT, local recurrence, site, and revision for margins. CONCLUSION: Patients with early and moderately advanced oropharyngeal SCC selected for radiographic ECS and revised for inadequate margins have excellent tumor control and favorable functional recovery. © 2017 Wiley Periodicals, Inc. Head Neck 39: 965-973, 2017.